Number 8 August 2011

VolumeVolume 15 1 -- NumberNumber 81 MayAugust - September 2011 1997

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Scope

The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer reviewed on-line journal in open access, devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases. It presents structured review articles ("cards") on genes, leukaemias, solid tumours, cancer-prone diseases, more traditional review articles on these and also on surrounding topics ("deep insights"), case reports in hematology, and educational items in the various related topics for students in Medicine and in Sciences.

Editorial correspondance

Jean-Loup Huret Genetics, Department of Medical Information, University Hospital F-86021 Poitiers, France tel +33 5 49 44 45 46 or +33 5 49 45 47 67 [email protected] or [email protected]

Staff Mohammad Ahmad, Mélanie Arsaban, Marie-Christine Jacquemot-Perbal, Maureen Labarussias, Vanessa Le Berre, Anne Malo, Catherine Morel-Pair, Laurent Rassinoux, Alain Zasadzinski. Philippe Dessen is the Database Director, and Alain Bernheim the Chairman of the on-line version (Gustave Roussy Institute – Villejuif – France).

The Atlas of Genetics and Cytogenetics in Oncology and Haematology (ISSN 1768-3262) is published 12 times a year by ARMGHM, a non profit organisation, and by the INstitute for Scientific and Technical Information of the French National Center for Scientific Research (INIST-CNRS) since 2008.

The Atlas is hosted by INIST-CNRS (http://www.inist.fr)

http://AtlasGeneticsOncology.org

The PDF version of the Atlas of Genetics and Cytogenetics in Oncology and Haematology is a reissue of the original articles published in collaboration with the Institute for Scientific and Technical Information (INstitut de l’Information Scientifique et Technique - INIST) of the French National Center for Scientific Research (CNRS) on its electronic publishing platform I-Revues. Online and PDF versions of the Atlas of Genetics and Cytogenetics in Oncology and Haematology are hosted by INIST-CNRS.

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Editor

Jean-Loup Huret (Poitiers, France) Editorial Board

Sreeparna Banerjee (Ankara, Turkey) Solid Tumours Section Alessandro Beghini (Milan, Italy) Genes Section Anne von Bergh (Rotterdam, The Netherlands) Genes / Leukaemia Sections Judith Bovée (Leiden, The Netherlands) Solid Tumours Section Vasantha Brito-Babapulle (London, UK) Leukaemia Section Charles Buys (Groningen, The Netherlands) Deep Insights Section Anne Marie Capodano (Marseille, France) Solid Tumours Section Fei Chen (Morgantown, West Virginia) Genes / Deep Insights Sections Antonio Cuneo (Ferrara, Italy) Leukaemia Section Paola Dal Cin (Boston, Massachussetts) Genes / Solid Tumours Section Louis Dallaire (Montreal, Canada) Education Section Brigitte Debuire (Villejuif, France) Deep Insights Section François Desangles (Paris, France) Leukaemia / Solid Tumours Sections Enric Domingo-Villanueva (London, UK) Solid Tumours Section Ayse Erson (Ankara, Turkey) Solid Tumours Section Richard Gatti (Los Angeles, California) Cancer-Prone Diseases / Deep Insights Sections Ad Geurts van Kessel (Nijmegen, The Netherlands) Cancer-Prone Diseases Section Oskar Haas (Vienna, Austria) Genes / Leukaemia Sections Anne Hagemeijer (Leuven, Belgium) Deep Insights Section Nyla Heerema (Colombus, Ohio) Leukaemia Section Jim Heighway (Liverpool, UK) Genes / Deep Insights Sections Sakari Knuutila (Helsinki, Finland) Deep Insights Section Lidia Larizza (Milano, Italy) Solid Tumours Section Lisa Lee-Jones (Newcastle, UK) Solid Tumours Section Edmond Ma (Hong Kong, China) Leukaemia Section Roderick McLeod (Braunschweig, Germany) Deep Insights / Education Sections Cristina Mecucci (Perugia, Italy) Genes / Leukaemia Sections Yasmin Mehraein (Homburg, Germany) Cancer-Prone Diseases Section Fredrik Mertens (Lund, Sweden) Solid Tumours Section Konstantin Miller (Hannover, Germany) Education Section Felix Mitelman (Lund, Sweden) Deep Insights Section Hossain Mossafa (Cergy Pontoise, France) Leukaemia Section Stefan Nagel (Braunschweig, Germany) Deep Insights / Education Sections Florence Pedeutour (Nice, France) Genes / Solid Tumours Sections Elizabeth Petty (Ann Harbor, Michigan) Deep Insights Section Susana Raimondi (Memphis, Tennesse) Genes / Leukaemia Section Mariano Rocchi (Bari, Italy) Genes Section Alain Sarasin (Villejuif, France) Cancer-Prone Diseases Section Albert Schinzel (Schwerzenbach, Switzerland) Education Section Clelia Storlazzi (Bari, Italy) Genes Section Sabine Strehl (Vienna, Austria) Genes / Leukaemia Sections Nancy Uhrhammer (Clermont Ferrand, France) Genes / Cancer-Prone Diseases Sections Dan Van Dyke (Rochester, Minnesota) Education Section Roberta Vanni (Montserrato, Italy) Solid Tumours Section Franck Viguié (Paris, France) Leukaemia Section José Luis Vizmanos (Pamplona, Spain) Leukaemia Section Thomas Wan (Hong Kong, China) Genes / Leukaemia Sections

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) Atlas of Genetics and Cytogenetics in Oncology and Haematology

OPEN ACCESS JOURNAL AT INIST-CNRS

Volume 15, Number 8, August 2011

Table of contents

Gene Section

ING4 (inhibitor of growth family, member 4) 626 Angela Greco, Claudia Miranda LRIG1 (leucine-rich repeats and immunoglobulin-like domains 1) 631 Dongsheng Guo, Baofeng Wang MAPK14 (mitogen-activated protein kinase 14) 634 Almudena Porras, Carmen Guerrero RAD51L3 (RAD51-like 3 (S. cerevisiae)) 638 Mary K Taylor, Michael K Bendenbaugh, Susan M Brown, Brian D Yard, Douglas L Pittman SLC9A3R1 (solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1) 643 Wendy S McDonough, Michael E Berens USP15 (ubiquitin specific peptidase 15) 651 Monica Faronato, Sylvie Urbé, Judy M Coulson CDKN2B (cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)) 658 Joanna Fares, Linda Wolff, Juraj Bies DLX4 (distal-less homeobox 4) 664 Patricia E Berg, Saurabh Kirolikar IL17A (interleukin 17A) 668 Norimitsu Inoue, Takashi Akazawa MYBBP1A (MYB binding protein (P160) 1a) 673 Claudia Perrera, Riccardo Colombo PLCD1 (phospholipase C, delta 1) 676 Xiaotong Hu PYY (peptide YY) 680 Maria Braoudaki, Fotini Tzortzatou-Stathopoulou SIAH2 (seven in absentia homolog 2 (Drosophila)) 683 Jianfei Qi, Ze'ev Ronai TP53BP2 (tumor protein p53 binding protein, 2) 687 Kathryn Van Hook, Zhiping Wang, Charles Lopez

Leukaemia Section

8p11 myeloproliferative syndrome (EMS, eight p11 myeloproliferative syndrome) 692 Paula Aranaz, José Luis Vizmanos i(5)(p10) in acute myeloid leukemia 701 Nathalie Douet-Guilbert, Angèle Herry, Audrey Basinko, Marie-Josée Le Bris, Nadia Guéganic, Clément Bovo, Frédéric Morel, Marc De Braekeleer

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) Atlast(11;14)(q 13;q32)of Genetics in multiple myeloma and Cytogenetics Huret JL, Laï JL in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

+20 or trisomy 20 (solely) 703 Jean-Loup Huret

Deep Insight Section

TMPRSS2:ETS gene fusions in prostate cancer 705 Julia L Williams, Maisa Yoshimoto, Alexander H Boag, Jeremy A Squire, Paul C Park

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Gene Section Review

ING4 (inhibitor of growth family, member 4) Angela Greco, Claudia Miranda Dept Experimental Oncology, Molecular Mechanisms Unit, Istituto Nazionale Tumori IRCCS Foundation - via Venezian 1 - 20133 Milan Italy (AG, CM)

Published in Atlas Database: December 2010 Online updated version : http://AtlasGeneticsOncology.org/Genes/ING4ID40978ch12p13.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI ING4ID40978ch12p13.txt

homology search for expressed tag clones with a Identity PHD finger motif (Shiseki et al., 2003). ING4 gene Other names: MGC12557; my036; p29ING4 is located on chromosome 12p13.31 and consists of HGNC (Hugo): ING4 eight exons encoding a 29-kDa protein expressed in multiple human tissues. Location: 12p13.31 Transcription DNA/RNA Multiple alternatively spliced transcript variants have been observed using different splice sites in Description the coding region; transcript variants span from ING4 belongs to family of highly homologous five 1461 bp to 1313 bp. members containing PHD domain and has been Wobble splicing events have been described at exon identified through a computational sequence 4 and 5 boundary.

Figure adapted from Atlas of Genetics and Cytogenetics in Oncology and Haematology.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 626

ING4 (inhibitor of growth family, member 4) Greco A, Miranda C

Different splicing variants have been identified regulation, chromatin remodeling, and regulation of (among them -v1, -v2, -v3 and -v4/Δ4AA) gene expression. Several ING4 partners have been involving 12 bp (379-390) and resulting in in frame described. Similarly to the other ING members, deletions of one to four aminoacids in NLS (Tsai ING4 was described to interact with p53 and to and Lin, 2006). modulate p53 transcriptional activity (Shiseki et al., Several splicing variants have been described 2003). The interaction of ING4 with p53 is lacking exon 2, 3 and 6 (entirely or in part), and mediated by the bipartite ING4 nuclear localization named ING4-ΔEx2, -ΔEx3, -ΔEx6A and -ΔEx6B, signal (NLS) (Zhang et al., 2005) and drives an respectively (Raho et al., 2007). increase of p53 acetylation at lysine 382 (Shiseki et Splicing variants have been detected in all tissues al., 2003). ING4 is a critical regulator of chromatin analysed, indicating that are not tissue specific acetylation required for gene expression. In (Tsai and Lin, 2006; Raho et al., 2007). particular, ING4 associates with the HAT complex More recently five novel spliced variants of ING4- HBO1 and it is required for the majority of histone v1 and -v2 were identified, causing codon frame 4 acetylation and for normal progression through S shift and eventually deletion of NLS or PHD phase (Doyon et al., 2006; Shi et al., 2006). domains. Increased expression of these variants was Recently a critical role for specific recognition of found in gastric adenocarcinomas compared to histone H3 trimethylated at lysine 4 (H3K4me3) by normal tissue (Li M et al., 2009). the ING4 PHD finger in mediating ING4 gene expression and tumor suppressor functions has been Protein shown (Hung et al., 2009). ING4 can also function as repressor of factors Note mediating angiogenesis. It was demonstrated that 249 aminoacids, 29 kDa protein. ING4 plays an inhibitory role on NF-kappaB Description activity by interaction with p65NF-kappaB and that the lack of inhibition of the NF-kappaB pathway by ING4 protein contains several conserved regions: i) ING4 results in increased angiogenesis in a leucine zipper-like (LZL) domain, probably glioblastomas (Garkavtsev et al., 2004). More involved in protein interactions, located at the N- recently, it has been described that physiologic terminus; ii) a functional bipartite nuclear levels of ING4 govern innate immunity in mice by localization signal (NLS1); iii) a C-terminal plant regulating the levels of IkappaB and NF-kappaB homeo-domain (PHD), a Cys4-His-Cys3 zinc finger proteins and the activation of select cytokine motif spanning 50-80 residues, found in many promoters (Coles et al., 2010). nuclear proteins, such as transcription factors and ING4 was also described to repress the ability of proteins regulating chromatin structure; iv) a non hypoxia inducible factor (HIF)-1 to activate functional NLS located at the C-terminal end. transcription of its downstream target genes by Expression interacting with the HPH-2 prolyl hydroxylase. Ubiquitous. Under hypoxic conditions, ING4 may act as an adapter protein recruiting transcriptional repressors Localisation to mediate HIF activity (Ozer et al., 2005). p29ING4 is a nuclear protein. It possesses a Involvement of ING4 in regulation of apoptosis has bipartite nuclear localization signal. ING4 splicing been demonstrated in several cellular systems. Its variants have been described involving the NLS1 overexpression can induce apoptosis through the domain; most/all of them retains nuclear downregulation of Bcl-2 and the upregulation of localization. Furthermore ING4-v1 is translocated p21 and Bax expression (Shiseki et al., 2003; Yu et to the nucleolus and such subcellular localization is al., 2007; Li X et al., 2009b; Cai et al., 2009). modulated by two wobble-splicing events at the exon 4-5 boundary, causing displacement from the Homology nucleolus to the nucleus. ING4 protein shares homology with other ING family members with respect to the following Function regions: i) a leucine zipper-like (LZL) domain, ING4 was also isolated through a screening for probably involved in interaction with proteins, genes able to suppress loss of contact inhibition, located at the N-terminus of all the ING proteins thus suggesting its tumor suppressor role. except for ING1; ii) a nuclear localization signal ING4 is a nuclear protein participating to a variety (NLS); iii) a C-terminal plant homeo-domain of cellular functions, such as apoptosis, cell-cycle (PHD) involved in chromatin.

LZL: leucine zipper-like; NLS1: nuclear localization signal 1; PHD: plant homology domain; NLS2: nuclear localization signal 2.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 627

ING4 (inhibitor of growth family, member 4) Greco A, Miranda C

expression correlated significantly with tumor Mutations progression, with lower expression levels of ING4 Note observed in cases of high-grade neoplasms. A The following ING4 point mutations have been statistical significant negative correlation between found in lung adenocarcinoma and small cell lung expression of ING4 and expression of nuclear p65 carcinoma (H23 and H28, respectively) human was noticed (Klironomos et al., 2010). cancer cell lines. Hepatocellular carcinoma (HCC) N214D: it alters ING4 capability of inhibition of Prognosis proliferation, anchorage independent cell migration reducing protein stability by proteasome mediated Survival and metastasis analysis indicated that HCC degradation. patients with lower ING4 expression had poorer Y121N: it does not alter ING4 functions (Moreno et overall and disease-free survival than those with al., 2010). high expression. Multivariable Cox regression analysis revealed that the ING4 expression level Implicated in was an independent factor for prognosis (Fang et al., 2009). Breast cancer Oncogenesis Cytogenetics The ING4 mRNA and protein levels were Analysis of CGH data revealed that 10-20% of significantly lower in HCC than paracarcinomatous primary breast tumors present deletions in 12p13. liver tissue. ING4 expression level correlates with The deletions appear to affect only one copy of the prognosis and metastatic potential, suggesting that gene; no genomic mutations were found in the ING4 as a candidate prognostic marker of HCC remaining allele of ING4 (Kim et al., 2004). (Fang et al., 2009). Head and neck squamous cell Multiple myeloma (MM) carcinoma (HNSCC) Prognosis Cytogenetics MM patients with high IL-8 production and microvascular density (MVD) have significantly LOH of 12p13. lower ING4 levels compared with those with low Oncogenesis IL-8 and MVD. Loss of heterozygosity at 12p12-13 region was Oncogenesis found in 66% (33/50) of head and neck squamous ING4 suppression in MM cells up-regulated IL-8 cell carcinomas by using six highly polymorphic and OPN under hypoxic conditions, increasing the microsatellite markers. No mutations of the ING4 hypoxia inducible factor-1alpha (HIF-1alpha) gene were found. activity and its target gene NIP-3 expression. ING4 Quantitative real-time RT-PCR analysis suppression in MM cells significantly increased demonstrated decreased expression of ING4 mRNA vessel formation in vitro, blunted by blocking IL-8 in 76% of primary tumors compared to matched or OPN (Colla et al., 2007). normal samples (Gunduz et al., 2005). Glioma Lung cancer Oncogenesis Oncogenesis Reduced ING4 nuclear and cytoplasmic expression Expression of ING4 is significantly reduced in were both revealed in lung cancer and associated gliomas as compared with normal human brain with tumour grade. ING4 expression in the tissue, and the extent of reduction correlates with cytoplasm was found higher than in the nucleus in a the progression from lower to higher grades of high percentage of tumors. Nuclear ING4 inhibition tumours. ING4 regulates brain tumour angiogenesis correlated with the tumour stage and lymph node through transcriptional repression of NF-kB- metastasis, thus suggesting that ING4 is involved in responsive genes (Garkavtsev et al., 2004). the initiation and progression of lung cancers Astrocytoma (Wang et al., 2010). Prognosis Gastric cancer A potential of role of ING4 as a biomarker for the Oncogenesis prediction of the grade of astrocytic neoplasms has ING4 RNA and protein were drastically reduced in been suggested (Klironomos et al., 2010). stomach adenocarcinoma cell lines and tissues, Oncogenesis significantly less in female than male patients. Significantly reduced levels of ING4 were observed Novel spliced forms of ING4-v1 and -v2 were in human astrocytomas compared to normal brain identified in both normal and tumor tissue; tissue, suggesting that down-regulation of this increased expression of the novel spliced variants protein might be involved in the pathogenesis of was observed in tumors; however no correlation human astrocytic tumors. Decreased ING4

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 628

ING4 (inhibitor of growth family, member 4) Greco A, Miranda C

with clinical parameters was observed (Li M et al., Raho G, Miranda C, Tamborini E, Pierotti MA, Greco A. 2009). Detection of novel mRNA splice variants of human ING4 tumor suppressor gene. Oncogene. 2007 Aug References 9;26(36):5247-57 Yu X, Zhang HF, Wang JZ, Xie YF, Yang JC, Miao JC. Shiseki M, Nagashima M, Pedeux RM, Kitahama-Shiseki [Ad-ING4 inhibits K562 cell growth]. Zhonghua Xue Ye M, Miura K, Okamura S, Onogi H, Higashimoto Y, Appella Xue Za Zhi. 2007 Jun;28(6):396-400 E, Yokota J, Harris CC. p29ING4 and p28ING5 bind to p53 Li X, Cai L, Liang M, Wang Y, Yang J, Zhao Y. ING4 and p300, and enhance p53 activity. Cancer Res. 2003 induces cell growth inhibition in human lung May 15;63(10):2373-8 adenocarcinoma A549 cells by means of Wnt-1/beta- Garkavtsev I, Kozin SV, Chernova O, Xu L, Winkler F, catenin signaling pathway. Anat Rec (Hoboken). 2008 Brown E, Barnett GH, Jain RK. The candidate tumour May;291(5):593-600 suppressor protein ING4 regulates brain tumour growth Nozell S, Laver T, Moseley D, Nowoslawski L, De Vos M, and angiogenesis. Nature. 2004 Mar 18;428(6980):328-32 Atkinson GP, Harrison K, Nabors LB, Benveniste EN. The Kim S, Chin K, Gray JW, Bishop JM. A screen for genes ING4 tumor suppressor attenuates NF-kappaB activity at that suppress loss of contact inhibition: identification of the promoters of target genes. Mol Cell Biol. 2008 ING4 as a candidate tumor suppressor gene in human Nov;28(21):6632-45 cancer. Proc Natl Acad Sci U S A. 2004 Nov Palacios A, Muñoz IG, Pantoja-Uceda D, Marcaida MJ, 16;101(46):16251-6 Torres D, Martín-García JM, Luque I, Montoya G, Blanco Gunduz M, Nagatsuka H, Demircan K, Gunduz E, Cengiz FJ. Molecular basis of histone H3K4me3 recognition by B, Ouchida M, Tsujigiwa H, Yamachika E, Fukushima K, ING4. J Biol Chem. 2008 Jun 6;283(23):15956-64 Beder L, Hirohata S, Ninomiya Y, Nishizaki K, Shimizu K, Tsai KW, Tseng HC, Lin WC. Two wobble-splicing events Nagai N. Frequent deletion and down-regulation of ING4, a affect ING4 protein subnuclear localization and candidate tumor suppressor gene at 12p13, in head and degradation. Exp Cell Res. 2008 Oct 15;314(17):3130-41 neck squamous cell carcinomas. Gene. 2005 Aug 15;356:109-17 Cai L, Li X, Zheng S, Wang Y, Wang Y, Li H, Yang J, Sun J. Inhibitor of growth 4 is involved in melanomagenesis Ozer A, Bruick RK. Regulation of HIF by prolyl and induces growth suppression and apoptosis in hydroxylases: recruitment of the candidate tumor melanoma cell line M14. Melanoma Res. 2009 suppressor protein ING4. Cell Cycle. 2005 Sep;4(9):1153- Feb;19(1):1-7 6 Fang F, Luo LB, Tao YM, Wu F, Yang LY. Decreased Ozer A, Wu LC, Bruick RK. The candidate tumor expression of inhibitor of growth 4 correlated with poor suppressor ING4 represses activation of the hypoxia prognosis of hepatocellular carcinoma. Cancer Epidemiol inducible factor (HIF). Proc Natl Acad Sci U S A. 2005 May Biomarkers Prev. 2009 Feb;18(2):409-16 24;102(21):7481-6 Hung T, Binda O, Champagne KS, Kuo AJ, Johnson K, Zhang X, Wang KS, Wang ZQ, Xu LS, Wang QW, Chen F, Chang HY, Simon MD, Kutateladze TG, Gozani O. ING4 Wei DZ, Han ZG. Nuclear localization signal of ING4 plays mediates crosstalk between histone H3 K4 trimethylation a key role in its binding to p53. Biochem Biophys Res and H3 acetylation to attenuate cellular transformation. Mol Commun. 2005 Jun 17;331(4):1032-8 Cell. 2009 Jan 30;33(2):248-56 Doyon Y, Cayrou C, Ullah M, Landry AJ, Côté V, Selleck Li M, Jin Y, Sun WJ, Yu Y, Bai J, Tong DD, Qi JP, Du JR, W, Lane WS, Tan S, Yang XJ, Côté J. ING tumor Geng JS, Huang Q, Huang XY, Huang Y, Han FF, Meng suppressor proteins are critical regulators of chromatin XN, Rosales JL, Lee KY, Fu SB. Reduced expression and acetylation required for genome expression and novel splice variants of ING4 in human gastric perpetuation. Mol Cell. 2006 Jan 6;21(1):51-64 adenocarcinoma. J Pathol. 2009 Sep;219(1):87-95 Shi X, Hong T, Walter KL, Ewalt M, Michishita E, Hung T, Li X, Cai L, Chen H, Zhang Q, Zhang S, Wang Y, Dong Y, Carney D, Peña P, Lan F, Kaadige MR, Lacoste N, Cayrou Cheng H, Qi J. Inhibitor of growth 4 induces growth C, Davrazou F, Saha A, Cairns BR, Ayer DE, Kutateladze suppression and apoptosis in glioma U87MG. TG, Shi Y, Côté J, Chua KF, Gozani O. ING2 PHD domain Pathobiology. 2009a;76(4):181-92 links histone H3 lysine 4 methylation to active gene repression. Nature. 2006 Jul 6;442(7098):96-9 Li X, Zhang Q, Cai L, Wang Y, Wang Q, Huang X, Fu S, Bai J, Liu J, Zhang G, Qi J. Inhibitor of growth 4 induces Tsai KW, Lin WC. Quantitative analysis of wobble splicing apoptosis in human lung adenocarcinoma cell line A549 indicates that it is not tissue specific. Genomics. 2006 via Bcl-2 family proteins and mitochondria apoptosis Dec;88(6):855-64 pathway. J Cancer Res Clin Oncol. 2009b Jun;135(6):829- Unoki M, Shen JC, Zheng ZM, Harris CC. Novel splice 35 variants of ING4 and their possible roles in the regulation Tzouvelekis A, Aidinis V, Harokopos V, Karameris A, of cell growth and motility. J Biol Chem. 2006 Nov Zacharis G, Mikroulis D, Konstantinou F, Steiropoulos P, 10;281(45):34677-86 Sotiriou I, Froudarakis M, Pneumatikos I, Tringidou R, Colla S, Tagliaferri S, Morandi F, Lunghi P, Donofrio G, Bouros D. Down-regulation of the inhibitor of growth family Martorana D, Mancini C, Lazzaretti M, Mazzera L, member 4 (ING4) in different forms of pulmonary fibrosis. Ravanetti L, Bonomini S, Ferrari L, Miranda C, Ladetto M, Respir Res. 2009 Feb 27;10:14 Neri TM, Neri A, Greco A, Mangoni M, Bonati A, Rizzoli V, Coles AH, Gannon H, Cerny A, Kurt-Jones E, Jones SN. Giuliani N. The new tumor-suppressor gene inhibitor of Inhibitor of growth-4 promotes IkappaB promoter activation growth family member 4 (ING4) regulates the production of to suppress NF-kappaB signaling and innate immunity. proangiogenic molecules by myeloma cells and Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11423-8 suppresses hypoxia-inducible factor-1 alpha (HIF-1alpha) activity: involvement in myeloma-induced angiogenesis. Kim S, Welm AL, Bishop JM. A dominant mutant allele of Blood. 2007 Dec 15;110(13):4464-75 the ING4 tumor suppressor found in human cancer cells

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 629

ING4 (inhibitor of growth family, member 4) Greco A, Miranda C

exacerbates MYC-initiated mouse mammary recognition of H3K4me3 by the tumor suppressor ING4 tumorigenesis. Cancer Res. 2010 Jun 15;70(12):5155-62 suggests a mechanism for enhanced targeting of the HBO1 complex to chromatin. J Mol Biol. 2010 Mar Klironomos G, Bravou V, Papachristou DJ, Gatzounis G, 5;396(4):1117-27 Varakis J, Parassi E, Repanti M, Papadaki H. Loss of inhibitor of growth (ING-4) is implicated in the Wang QS, Li M, Zhang LY, Jin Y, Tong DD, Yu Y, Bai J, pathogenesis and progression of human astrocytomas. Huang Q, Liu FL, Liu A, Lee KY, Fu SB. Down-regulation Brain Pathol. 2010 Mar;20(2):490-7 of ING4 is associated with initiation and progression of lung cancer. Histopathology. 2010 Aug;57(2):271-81 Moreno A, Palacios A, Orgaz JL, Jimenez B, Blanco FJ, Palmero I. Functional impact of cancer-associated This article should be referenced as such: mutations in the tumor suppressor protein ING4. Carcinogenesis. 2010 Nov;31(11):1932-8 Greco A, Miranda C. ING4 (inhibitor of growth family, member 4). Atlas Genet Cytogenet Oncol Haematol. 2011; Palacios A, Moreno A, Oliveira BL, Rivera T, Prieto J, 15(8):626-630. García P, Fernández-Fernández MR, Bernadó P, Palmero I, Blanco FJ. The dimeric structure and the bivalent

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 630

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Gene Section Mini Review

LRIG1 (leucine-rich repeats and immunoglobulin-like domains 1) Dongsheng Guo, Baofeng Wang Dept of Neurosurgery, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, People's Republic of China (DG, BW)

Published in Atlas Database: December 2010 Online updated version : http://AtlasGeneticsOncology.org/Genes/LRIG1ID41198ch3p14.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI LRIG1ID41198ch3p14.txt

Identity Expression Other names: DKFZp586O1624; LIG-1; LIG1 LRIG1 is expressed ubiquitously in various epithelial cells, endothelial cells, heart, smooth and HGNC (Hugo): LRIG1 striated muscles, and in large neurons. Location: 3p14.1 Localisation DNA/RNA Differential subcellular distribution in a cell type- specific manner. Description Function Genomic DNA encoding LRIG1 spans a region of LRIG1 acts as a suppressor of receptor tyrosine 122.89 kilobases on chromosome 3, at 3p14. kinases, such as epidermal growth factor receptor LRIG1 gene is encoded on the reverse strand. (EGFR) family, MET (hepatocyte growth factor Transcription receptor), and RET. The interaction of the The pre-mRNA comprises 19 exons. extracellular LRR domain and immunoglobulin-like Coding sequence: 4812 bp. domains of LRIG1 with the extracellular parts of the human EGFR results in recruitment of c-Cbl to Protein the cytoplasmic domains, and induction of EGFR degradation. LRIG1 is involved in signal Description transduction, cell proliferation, cell apopotosis, cell LRIG1 is a transmembrane cell-surface protein cycle, cell migration, and cell invasion. LRIG1 as a consisting of 1093 amino acids. LRIG1 contains putative tumor suppressor gene often be down- extracellular part containing 15 leucine-rich repeats regulated in various human tumors. (LRR) and three C2-type immunoglobulin-like Soluble ectodomain of LRIG1 protein can modulate domains, a transmembrane region, and a EGFR signaling and its growth-promoting activity cytoplasmic tail. LRIG1 can be cut into soluble in a paracrine fashion. LRIG1 ectodomain by proteolytic processing, which also is a functional molecule.

LRIG1 gene. Exons are represented by red boxes (in scale). Exons 1 to 19 are from the 5' to 3' direction.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 631

LRIG1 (leucine-rich repeats and immunoglobulin-like domains Guo D, Wang B 1)

LRIG1 protein. SP: signal peptide; NF: N-terminal cysteine-rich flanking domain; LRR: leucine-rich repeat; CF: C-terminal cysteine-rich flanking domain; Ig C2: C2-type immunoglobulin-like domains; TM: transmembrane domain; Cyto: cytoplasmic domain.

Implicated in Psoriasis Note Ependymoma In psoriasis, LRIG1 is mostly absent from the cell Note surfaces in the spinous layers. Higher cytoplasmic immunoreactivity of LRIG1 correlates with older patient age and higher LRIG1 References nuclear immunoreactivity with lower WHO grade. Nilsson J, Vallbo C, Guo D, Golovleva I, Hallberg B, Prostate cancer Henriksson R, Hedman H. Cloning, characterization, and expression of human LIG1. Biochem Biophys Res Note Commun. 2001 Jun 29;284(5):1155-61 High LRIG1 expression is significantly associated Nilsson J, Starefeldt A, Henriksson R, Hedman H. LRIG1 with short overall and prostate cancer-specific protein in human cells and tissues. Cell Tissue Res. 2003 survival for 256 Swedish patients analysed. In Apr;312(1):65-71 contrast, in the U.S. series, high LRIG1 expression Thomasson M, Hedman H, Guo D, Ljungberg B, is significantly associated with longer overall Henriksson R. LRIG1 and epidermal growth factor receptor survival. in renal cell carcinoma: a quantitative RT--PCR and immunohistochemical analysis. Br J Cancer. 2003 Oct Renal cell carcinoma (RCC) 6;89(7):1285-9 Note Guo D, Holmlund C, Henriksson R, Hedman H. The LRIG LRIG1 expression is generally downregulated in gene family has three vertebrate paralogs widely expressed in human and mouse tissues and a homolog in conventional and papillary RCC but not in Ascidiacea. Genomics. 2004 Jul;84(1):157-65 chromophobic RCC. Gur G, Rubin C, Katz M, Amit I, Citri A, Nilsson J, Cutaneous squamous cell carcinoma Amariglio N, Henriksson R, Rechavi G, Hedman H, Wides R, Yarden Y. LRIG1 restricts growth factor signaling by (SCC) enhancing receptor ubiquitylation and degradation. EMBO Note J. 2004 Aug 18;23(16):3270-81 LRIG-1 expression is highest in well-differentiated Laederich MB, Funes-Duran M, Yen L, Ingalla E, Wu X, lesions of cutaneous SCC. LRIG-1 expression Carraway KL 3rd, Sweeney C. The leucine-rich repeat intensity of tumor cells is significantly correlated protein LRIG1 is a negative regulator of ErbB family receptor tyrosine kinases. J Biol Chem. 2004 Nov with histologic differentiation of SCC. The SCC 5;279(45):47050-6 patients have significant survival benefits in the high LRIG-1 expression groups compared with low Ye F, Guo DS, Niu HQ, Tao SZ, Ou YB, Lu YP, Lei T. [Molecular mechanism of LRIG1 cDNA-induced apoptosis LRIG-1 expression groups. in human glioma cell line H4]. Ai Zheng. 2004 Breast tumor Oct;23(10):1149-54 Note Tanemura A, Nagasawa T, Inui S, Itami S. LRIG-1 provides a novel prognostic predictor in squamous cell LRIG1 protein levels are significantly suppressed in carcinoma of the skin: immunohistochemical analysis for the majority of human breast tumors expressing 38 cases. Dermatol Surg. 2005 Apr;31(4):423-30 ErbB2. Guo D, Nilsson J, Haapasalo H, Raheem O, Bergenheim Cervical squamous cell carcinoma T, Hedman H, Henriksson R. Perinuclear leucine-rich repeats and immunoglobulin-like domain proteins (LRIG1- Note 3) as prognostic indicators in astrocytic tumors. Acta LRIG1 appears to be a significant prognosis Neuropathol. 2006 Mar;111(3):238-46 predictor in early-stage cervical cancer, Jensen KB, Watt FM. Single-cell expression profiling of independent of the other tumor markers. human epidermal stem and transit-amplifying cells: Lrig1 is a regulator of stem cell quiescence. Proc Natl Acad Sci U Astrocytic tumor S A. 2006 Aug 8;103(32):11958-63 Note Yang WM, Yan ZJ, Ye ZQ, Guo DS. LRIG1, a candidate Perinuclear staining of LRIG1 is associated with tumour-suppressor gene in human bladder cancer cell line low WHO grade and better survival of the patients. BIU87. BJU Int. 2006 Oct;98(4):898-902

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 632

LRIG1 (leucine-rich repeats and immunoglobulin-like domains Guo D, Wang B 1)

Goldoni S, Iozzo RA, Kay P, Campbell S, McQuillan A, Miller JK, Shattuck DL, Ingalla EQ, Yen L, Borowsky AD, Agnew C, Zhu JX, Keene DR, Reed CC, Iozzo RV. A Young LJ, Cardiff RD, Carraway KL 3rd, Sweeney C. soluble ectodomain of LRIG1 inhibits cancer cell growth by Suppression of the negative regulator LRIG1 contributes to attenuating basal and ligand-dependent EGFR activity. ErbB2 overexpression in breast cancer. Cancer Res. 2008 Oncogene. 2007 Jan 18;26(3):368-81 Oct 15;68(20):8286-94 Guo D, Han L, Shu K, Chen J, Lei T. Down-regulation of Stutz MA, Shattuck DL, Laederich MB, Carraway KL 3rd, leucine-rich repeats and immunoglobulin-like domain Sweeney C. LRIG1 negatively regulates the oncogenic proteins (LRIG1-3) in HP75 pituitary adenoma cell line. J EGF receptor mutant EGFRvIII. Oncogene. 2008 Sep Huazhong Univ Sci Technolog Med Sci. 2007 25;27(43):5741-52 Feb;27(1):91-4 Yi W, Haapasalo H, Holmlund C, Järvelä S, Raheem O, Hedman H, Henriksson R. LRIG inhibitors of growth factor Bergenheim AT, Hedman H, Henriksson R. Expression of signalling - double-edged swords in human cancer? Eur J leucine-rich repeats and immunoglobulin-like domains Cancer. 2007 Mar;43(4):676-82 (LRIG) proteins in human ependymoma relates to tumor location, WHO grade, and patient age. Clin Neuropathol. Ljuslinder I, Golovleva I, Palmqvist R, Oberg A, Stenling R, 2009 Jan-Feb;28(1):21-7 Jonsson Y, Hedman H, Henriksson R, Malmer B. LRIG1 expression in colorectal cancer. Acta Oncol. Thomasson M, Wang B, Hammarsten P, Dahlman A, 2007;46(8):1118-22 Persson JL, Josefsson A, Stattin P, Granfors T, Egevad L, Henriksson R, Bergh A, Hedman H. LRIG1 and the liar Shattuck DL, Miller JK, Laederich M, Funes M, Petersen paradox in prostate cancer: a study of the expression and H, Carraway KL 3rd, Sweeney C. LRIG1 is a novel clinical significance of LRIG1 in prostate cancer. Int J negative regulator of the Met receptor and opposes Met Cancer. 2011 Jun 15;128(12):2843-52 and Her2 synergy. Mol Cell Biol. 2007 Mar;27(5):1934-46 Yi W, Holmlund C, Nilsson J, Inui S, Lei T, Itami S, Karlsson T, Mark EB, Henriksson R, Hedman H. Henriksson R, Hedman H. Paracrine regulation of growth Redistribution of LRIG proteins in psoriasis. J Invest factor signaling by shed leucine-rich repeats and Dermatol. 2008 May;128(5):1192-5 immunoglobulin-like domains 1. Exp Cell Res. 2011 Feb Ledda F, Bieraugel O, Fard SS, Vilar M, Paratcha G. Lrig1 15;317(4):504-12 is an endogenous inhibitor of Ret receptor tyrosine kinase activation, downstream signaling, and biological responses This article should be referenced as such: to GDNF. J Neurosci. 2008 Jan 2;28(1):39-49 Guo D, Wang B. LRIG1 (leucine-rich repeats and Lindström AK, Ekman K, Stendahl U, Tot T, Henriksson R, immunoglobulin-like domains 1). Atlas Genet Cytogenet Hedman H, Hellberg D. LRIG1 and squamous epithelial Oncol Haematol. 2011; 15(8):631-633. uterine cervical cancer: correlation to prognosis, other tumor markers, sex steroid hormones, and smoking. Int J Gynecol Cancer. 2008 Mar-Apr;18(2):312-7

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 633

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Gene Section Mini Review

MAPK14 (mitogen-activated protein kinase 14) Almudena Porras, Carmen Guerrero Departamento de Bioquimica y Biologia Molecular II, Facultad de Farmacia, UCM, Ciudad Universitaria, 28040 Madrid, Spain (AP), Centro de Investigacion del Cancer, IBMCC, Universidad de Salamanca-CSIC, 37007 Salamanca, Spain (CG)

Published in Atlas Database: December 2010 Online updated version : http://AtlasGeneticsOncology.org/Genes/MAPK14ID41292ch6p21.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI MAPK14ID41292ch6p21.txt

Larger transcripts contain 12 or 13 exons. Identity (GATExplorer). Other names: CSBP1; CSBP2; CSPB1; EXIP; Transcription Mxi2; PRKM14; PRKM15; RK; SAPK2A; p38; p38ALPHA 9 types of transcripts have been described, although only 5 are protein coding transcripts. The larger HGNC (Hugo): MAPK14 4319-nucleotide transcript encodes a protein of 360 Location: 6p21.31 amino acid residues. The first and last exons are partially untranslated. DNA/RNA Pseudogene Description None described so far. The gene spans a region of 83.53 kb and the coding part is divided into 41 different exons.

Schematic representation of human chromosome 6 indicating the position of MAPK14 locus (p21.31) (red bar).

MAPK14 gene locus. Representation of the MAPK14 gene organization indicating the position of the exons (coding region) and untranslated regions.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 634

MAPK14 (mitogen-activated protein kinase 14) Porras A, Guerrero C

MAPK14 protein domains. Schematic representation of MAPK14 protein indicating the position of its functional domains. 30-54: protein kinase ATP signature, ATP-binding region; 59-162: MAPK signature; 24-308: protein kinase domain.

death, adhesion, migration, as well as the response Protein to stress and many metabolic pathways, among Description others. It does so through regulation of transcription, mRNA stability, chromatin MAPK14 is a Ser/Thr kinase composed of 90 to remodelling, protein synthesis, etc. 360 residues depending on the transcript variant. Concerning cell death, although p38alpha plays an important role as a pro-apoptotic signal, it can play a dual role, acting as either a mediator of cell survival or of cell death, depending on the cell type and the stimuli. Related with its function as a negative regulator of proliferation and a mediator of apoptosis, p38alpha acts as a tumor suppressor in the initial stages of a tumorigenic process, while at later stages it can promote metastasis.

Crystal structure of MAPK14 at 2.3 A resolution. From PDB (access number: 1WFC). Expression p38alpha MAPK is ubiquitously expressed, being the p38 most abundant isoform. Localisation p38alpha is mainly present in the cytosol, but it can translocate to the nucleus. In addition, it can be localized in the mitochondria or in other subcellular compartments. Function p38alpha is mainly activated by various environmental stresses and proinflammatory cytokines, but many other extracellular signals, Signaling through p38alphaMAPK. Signaling through including growth factors, also lead to p38alpha MAPK14 cascade and its role in the regulation of cellular activation. The canonical activation requires its functions. MAPK14 is involved in signaling pathways phosphorylation in threonine and tyrosine residues triggered by a variety of stimuli such as growth factors, oxidative stress, UV, cytokines and DNA damage. by dual-specificity MAP kinase kinases (MKKs), Depending on the stimulus, different receptors and MKK3, MKK6 and MKK4. Substrates of this intermediates (adaptors, GTPases or kinases) are activated kinase include transcription factors, such as ATF1, leading to the activation of the p38alpha MAPK cascade. ATF2, ATF6, p53, MEF2 or C/EBPbeta and protein This cascade is initiated by activation of MAPKKKs, which phosphorylate and activate MAPKKs (MKK3/6/4), which in kinases, such as MAPKAP-K2 and MAPKAP-K3 turn lead to activation of MAPK14 through dual (also known as MK-2 and MK-3), MSK-1, MNK- phosphorylation in Tyr and Thr. Once phosphorylated, 1/MNK-2 and other proteins. MAPK14 phosphorylates a number of cytosolic and nuclear p38alpha MAPK is essential for embryonic substrates, including transcription factors, which lead to the development and it regulates different cellular control of many cellular responses. functions such as proliferation, differentiation, cell

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 635

MAPK14 (mitogen-activated protein kinase 14) Porras A, Guerrero C

Additionally, the p38alpha MAPK plays a role in Mutations dopaminergic neural apoptosis through the Somatic phosphorylation of p53 and expression of the pro- apoptotic protein Bax. 4 somatic mutations according to Ensembl: COSM21366; COSM20563; COSM35409; Amyotrophic lateral sclerosis COSM12875. Disease ALS is a progressive, lethal, degenerative disorder Implicated in of motor neurons leading to paralysis of voluntary muscles. Numerous evidences point to a role of p38 Hematopoietic malignancies MAPK in the development and progression of ALS Disease induced by mutations in SOD1 (superoxide p38 MAPK, mainly the p38alpha isoform, is a key dismutase 1) gene. Mutant SOD1 provokes aberrant player in the maintenance of hematopoiesis oxyradical reactions that increase the activation of homeostasis, as it balances both proliferative and p38 MAPK in motor neurons and glial cells. This growth inhibitory signals triggered by the growth increase in active p38 MAPK may phosphorylate factors and cytokines that regulate normal cytoskeletal proteins and activate cytokines and hematopoiesis. Alterations in this p38 MAPK- nitric oxide, thus contributing to neurodegeneration controlled balance may result in either through different mechanisms including apoptosis. overproduction or depletion of myelosuppressive cytokines leading to the development of certain To be noted bone marrow failure syndromes. For example, p38alpha is responsible for the enhanced stem cell Note apoptosis characteristic of low grade See also the Deep Insight: "Role of p38alpha in myeolodysplastic syndromes (MDSs). On the other apoptosis: implication in cancer development and hand, imbalance toward the proliferative side may therapy". conduct to the development of myeloproliferative syndromes (MPSs), such as leukemia, lymphomas References and myelomas. In particular, p38alpha MAPK plays Rouse J, Cohen P, Trigon S, Morange M, Alonso- a pro-apoptotic role in chronic myeloid leukemia Llamazares A, Zamanillo D, Hunt T, Nebreda AR. A novel (CML). In fact, p38alpha MAP kinase pathway kinase cascade triggered by stress and heat shock that mediates the growth inhibitory effects of IFNalpha stimulates MAPKAP kinase-2 and phosphorylation of the small heat shock proteins. Cell. 1994 Sep 23;78(6):1027- and STI-571, two drugs used in the CML treatment, 37 which underscores the importance of this pathway Wilson KP, Fitzgibbon MJ, Caron PR, Griffith JP, Chen W, in the generation of antileukemic responses. McCaffrey PG, Chambers SP, Su MS. Crystal structure of Alzheimer's disease p38 mitogen-activated protein kinase. J Biol Chem. 1996 Nov 1;271(44):27696-700 Disease Huang Y, Yuan ZM, Ishiko T, Nakada S, Utsugisawa T, Alzheimer is an incurable, neurodegenerative Kato T, Kharbanda S, Kufe DW. Pro-apoptotic effect of the disease characterized by a progressive deterioration c-Abl tyrosine kinase in the cellular response to 1-beta-D- of the cognitive, memory and learning ability due to arabinofuranosylcytosine. Oncogene. 1997 Oct the accumulation of plaques containing 16;15(16):1947-52 amyloidogenic Abeta proteins and tangles Bulavin DV, Saito S, Hollander MC, Sakaguchi K, containing hyperphosphorylated tau protein. The Anderson CW, Appella E, Fornace AJ Jr. Phosphorylation ASK1-MKK6-p38 signaling pathway participates of human p53 by p38 kinase coordinates N-terminal phosphorylation and apoptosis in response to UV in amyeloid precursor protein (APP) and tau radiation. EMBO J. 1999 Dec 1;18(23):6845-54 phosphorylation in response to oxidative stress and Adams RH, Porras A, Alonso G, Jones M, Vintersten K, contributes to the expression of the beta-secretase Panelli S, Valladares A, Perez L, Klein R, Nebreda AR. gene and the induction of neuronal apoptosis Essential role of p38alpha MAP kinase in placental but not triggered by ROS. embryonic cardiovascular development. Mol Cell. 2000 Jul;6(1):109-16 Parkinson disease D'Amico M, Hulit J, Amanatullah DF, Zafonte BT, Albanese Disease C, Bouzahzah B, Fu M, Augenlicht LH, Donehower LA, Parkinson is a degenerative disorder of the central Takemaru K, Moon RT, Davis R, Lisanti MP, Shtutman M, nervous system characterized by muscle rigidity, Zhurinsky J, Ben-Ze'ev A, Troussard AA, Dedhar S, Pestell RG. The integrin-linked kinase regulates the cyclin tremor and loss of physical movement caused by a D1 gene through glycogen synthase kinase 3beta and progressive loss of dopaminergic neurons. cAMP-responsive element-binding protein-dependent Mutations in alpha-synuclein are one of the main pathways. J Biol Chem. 2000 Oct 20;275(42):32649-57 causes of Parkinson. alpha-synuclein activates Sanchez-Prieto R, Rojas JM, Taya Y, Gutkind JS. A role p38alpha MAPK in human microglia promoting a for the p38 mitogen-acitvated protein kinase pathway in potent inflammatory stimulation of microglial cells. the transcriptional activation of p53 on genotoxic stress by

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 636

MAPK14 (mitogen-activated protein kinase 14) Porras A, Guerrero C

chemotherapeutic agents. Cancer Res. 2000 May sclerosis: role of p38 mitogen-activated protein kinase. 1;60(9):2464-72 Neurodegener Dis. 2005;2(3-4):128-34 Park JI, Choi HS, Jeong JS, Han JY, Kim IH. Involvement Silva RM, Kuan CY, Rakic P, Burke RE. Mixed lineage of p38 kinase in hydroxyurea-induced differentiation of kinase-c-jun N-terminal kinase signaling pathway: a new K562 cells. Cell Growth Differ. 2001 Sep;12(9):481-6 therapeutic target in Parkinson's disease. Mov Disord. 2005 Jun;20(6):653-64 Platanias LC. The p38 mitogen-activated protein kinase pathway and its role in interferon signaling. Pharmacol Cuenda A, Rousseau S. p38 MAP-kinases pathway Ther. 2003 May;98(2):129-42 regulation, function and role in human diseases. Biochim Biophys Acta. 2007 Aug;1773(8):1358-75 Tamagno E, Robino G, Obbili A, Bardini P, Aragno M, Parola M, Danni O. H2O2 and 4-hydroxynonenal mediate Zhou L, Opalinska J, Verma A. p38 MAP kinase regulates amyloid beta-induced neuronal apoptosis by activating stem cell apoptosis in human hematopoietic failure. Cell JNKs and p38MAPK. Exp Neurol. 2003 Apr;180(2):144-55 Cycle. 2007 Mar 1;6(5):534-7 Tortarolo M, Veglianese P, Calvaresi N, Botturi A, Rossi C, Zuluaga S, Alvarez-Barrientos A, Gutiérrez-Uzquiza A, Giorgini A, Migheli A, Bendotti C. Persistent activation of Benito M, Nebreda AR, Porras A. Negative regulation of p38 mitogen-activated protein kinase in a mouse model of Akt activity by p38alpha MAP kinase in cardiomyocytes familial amyotrophic lateral sclerosis correlates with involves membrane localization of PP2A through disease progression. Mol Cell Neurosci. 2003 interaction with caveolin-1. Cell Signal. 2007 Jan;19(1):62- Jun;23(2):180-92 74 Mathiasen JR, McKenna BA, Saporito MS, Ghadge GD, Karunakaran S, Saeed U, Mishra M, Valli RK, Joshi SD, Roos RP, Holskin BP, Wu ZL, Trusko SP, Connors TC, Meka DP, Seth P, Ravindranath V. Selective activation of Maroney AC, Thomas BA, Thomas JC, Bozyczko-Coyne p38 mitogen-activated protein kinase in dopaminergic D. Inhibition of mixed lineage kinase 3 attenuates MPP+- neurons of substantia nigra leads to nuclear translocation induced neurotoxicity in SH-SY5Y cells. Brain Res. 2004 of p53 in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine- Apr 2;1003(1-2):86-97 treated mice. J Neurosci. 2008 Nov 19;28(47):12500-9 Porras A, Zuluaga S, Black E, Valladares A, Alvarez AM, Wagner EF, Nebreda AR. Signal integration by JNK and Ambrosino C, Benito M, Nebreda AR. P38 alpha mitogen- p38 MAPK pathways in cancer development. Nat Rev activated protein kinase sensitizes cells to apoptosis Cancer. 2009 Aug;9(8):537-49 induced by different stimuli. Mol Biol Cell. 2004 Feb;15(2):922-33 Cuadrado A, Nebreda AR. Mechanisms and functions of p38 MAPK signalling. Biochem J. 2010 Aug 1;429(3):403- Puig B, Gómez-Isla T, Ribé E, Cuadrado M, Torrejón- 17 Escribano B, Dalfó E, Ferrer I. Expression of stress- activated kinases c-Jun N-terminal kinase (SAPK/JNK-P) This article should be referenced as such: and p38 kinase (p38-P), and tau hyperphosphorylation in neurites surrounding betaA plaques in APP Tg2576 mice. Porras A, Guerrero C. MAPK14 (mitogen-activated protein Neuropathol Appl Neurobiol. 2004 Oct;30(5):491-502 kinase 14). Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8):634-637. Bendotti C, Bao Cutrona M, Cheroni C, Grignaschi G, Lo Coco D, Peviani M, Tortarolo M, Veglianese P, Zennaro E. Inter- and intracellular signaling in amyotrophic lateral

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 637

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Gene Section Review

RAD51L3 (RAD51-like 3 (S. cerevisiae)) Mary K Taylor, Michael K Bendenbaugh, Susan M Brown, Brian D Yard, Douglas L Pittman South Carolina College of Pharmacy, University of South Carolina, Coker Life Sciences Building, 715 Sumter Street, Columbia, SC 29208, USA (MKT, MKB, SMB, BDY, DLP)

Published in Atlas Database: December 2010 Online updated version : http://AtlasGeneticsOncology.org/Genes/RAD51L3ID347ch17q12.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI RAD51L3ID347ch17q12.txt

or from DNA-damaging agents, e.g., cisplatin Identity (Masson et al., 2001). Other names: HsTRAD; R51H3; RAD51D; Trad The RAD51L3 protein directly interacts with HGNC (Hugo): RAD51D RAD51L2 (RAD51C) and XRCC2. It does not directly interact with RAD51L1 (RAD51B) (Schild Location: 17q12 et al., 2000). Note Of the five RAD51 paralog proteins, four come DNA/RNA together to form the BCDX2 complex, which includes RAD51L1 (RAD51B; chromosome 14), Note RAD51L2 (RAD51C; chromosome 17), RAD51L3 The human gene is composed of 10 exons. The (RAD51D; chromosome 17), and XRCC2 study by Kawabata and Saeki (1999) describes (chromosome 14). The protein complex is involved alternative splicing of the human gene using a in homologous recombination repair of double- numbering scheme of 12 alternatively spliced stranded breaks that result during DNA replication exons. The exon alignment is illustrated below.

Human RAD51D alternative splicing. A. Exons 4 and 8 of the Kawabata and Saeki numbering scheme are considered "alternative exons" and not included in the reference sequence. B. Summary of splice variants and predicted translation products (for further details see the annexed document below).

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 638

RAD51L3 (RAD51-like 3 (S. cerevisiae)) Taylor MK, et al.

Further descriptions of mouse alternatively spliced In addition, the "linker region" located between variants are described in Gruver et al., 2009 and residues 54-77 in the amino terminus is required for Kawabata et al., 2004. proper interactions with XRCC2. Together, these Transcription interactions aid in the repair of DNA damage (Miller et al., 2004; Gruver et al., 2009). The HsTRAD transcript is the predominant variant. It is the full-length transcript and is made up of Expression 2418 base pairs. This transcript will be used as the According to the study by Kawabata and Saeki reference for the information that follows. There are (1999), RAD51L3 transcripts are expressed to multiple splice variants for the RAD51L3 gene that varying degrees in the colon, prostate, spleen, testis, translate into one of seven putative protein ovaries, thymus, small intestine and leukocytes. isoforms. Localisation Protein Located in the nucleus. Specifically, RAD51L3 localizes to the telomeres during both mitosis and Note meiosis (Tarsounas et al., 2004). There is evidence The Saccharomyces cerevisiae Rad51 protein is that RAD51L3 is found in the cytoplasm as well homologous to the RecA protein of Escherichia (Gruver et al., 2005). coli. The RecA protein is known to promote repair Function via ATP-dependent mechanisms and is responsible for pairing and strand transfer between homologous RAD51D is one of five members of the RAD51 DNA sequences. This is similar to the actions of the gene family that is known to participate in repair of RAD51 protein in repair pathways. There are 5 double stranded DNA breaks via homologous members of the RAD51 family that share similar recombination. Without repair, the DNA damage roles in recombination and DNA repair. RAD51D can result in cell death or chromosomal aberrations is one of these RecA-like genes (Pittman et al., that can ultimately lead to cancer (Thacker, 2005). 1998; Cartwright et al., 1998). Knockout studies with mice have shown a dramatic The RAD51D gene is predicted to encode seven increase in levels of chromosomal aberrations, most different protein isoforms through alternative notably, chromatid and chromosome breaks that splicing. Isoform 1 is the predominant protein and occur through unrepaired replication forks is translated from the HsTRAD transcript (Smiraldo et al., 2005; Hinz et al., 2006). Proteomic mentioned previously (Kawabata and Saeki, 1999). studies have identified an interaction between The diagram below is based on this predominant RAD51D with the SFPQ protein (Rajesh et al., form. 2011). Exposure of mouse RAD51D-deficient cells to a strong alkylating agent results in G2/M cell Description cycle arrest and ultimately apoptosis (Rajesh et al., The RAD51D protein contains regions necessary 2010). RAD51D has recently been shown to play a for interactions with other RAD51 paralogs as well diverse role in cellular processes through its as those that are required for proper function of the interaction with proteins involved in cell division, protein. RAD51D contains an ATP binding domain embryo development, protein and carbohydrate with highly conserved Walker A and B motifs metabolism, cellular trafficking, protein synthesis, (Pittman et al., 1998; Cartwright et al., 1998). modification or folding, and cellular structure Mutations targeting the conserved residues of (Rajesh et al., 2009). glycine and lysine within the Walker A motif RAD51L3 is directly associated with telomeres region resulted in a reduction in RAD51C binding prevents their dysfunction (Tarsounas et al., 2004). ability and were shown to be required for DNA In mouse studies, RAD51L3 foci were present at repair (Gruver et al., 2005). The Walker B motif telomeres in both meiosis and mitosis. Knockout contains a "GGQRE" sequence between residues studies showed that "RAD51D-deficient" mice 219-223 that is also required for DNA repair exhibited an increase in end-to-end fusion and (Wiese et al., 2006). Furthermore, RAD51D- telomere attrition (Smiraldo et al., 2005). In XRCC2 complex formation is significantly reduced addition, human studies using RAD51D-deficient with mutations targeting a highly conserved cells have shown repeated shortening of the aspartate residue within the Walker B motif (Wiese telomeric DNA, leading to chromosomal instability. et al., 2006). This suggests a role for "RAD51D" in telomere A carboxyl terminal domain spanning amino acids capping. Failure to provide this function can lead to 77-329 has been identified to be required for chromosomal aberrations (Tarsounas and West, RAD51D to interact with RAD51C. 2005).

RAD51L3 protein structure. Isoform 1 (from full-length transcript).

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 639

RAD51L3 (RAD51-like 3 (S. cerevisiae)) Taylor MK, et al.

Homology

Official gene name: Canis lupus familiaris RAD51-like 3 (S. cerevisiae) Reference material: [Dog] Genomic location: no primary references found chromosome 9 Official gene name: Pan troglodytes RAD51-like 3 (S. cerevisiae) Reference material: [Chimpanzee] Genomic location: no primary references found chromosome 17 Official gene name: Bos taurus RAD51-like 3 (S. cerevisiae) Reference material: [Cow] Genomic location: Zimin et al., 2009 chromosome 19 Official gene name: Gallus gallus RAD51-like 3 (S. cerevisiae) Reference material: [Chicken] Genomic location: no primary references found chromosome 19 Official gene name: Rattus norvegicus RAD51-like 3 (S. cerevisiae) Reference material: [Rat] Genomic location: Strausberg et al., 2002 chromosome 10

Official gene name: Reference material: Mus musculus RAD51-like 3 (S. cerevisiae) Pittman et al., 1998 [Mouse] Genomic location: Cartwright et al., 1998 chromosome 11 Official gene name: RAD51D (ARABIDOPSIS HOMOLOG OF Arabidopsis thaliana Reference material: RAD51D) [Thale cress] Durrant et al., 2007 Genomic location: chromosome 1 Official gene name: Os09g0104200 Oryza sativa Reference material: Genomic location: [Rice] no primary references found chromosome 9 **Hypothetical protein** Official gene name: Danio rerio zgc:77165 Reference material: [Zebrafish] Genomic location: no primary references found chromosome 5

** Protein alignments and protein sequences are available at the HomoloGene database.

(from the wild type GAG). This point mutation Mutations affects the 233rd amino acid as a glycine residue is Note observed in this particular mutation rather than the Single nucleotide polymorphisms have been natural glutamic acid. This particular variation in identified in RAD51L3. However, only a small amino acid sequence has been implicated as a number of the major mutations occur in coding precursor to breast cancer (see "Implicated In" regions. The majority of the other mutations are section below). Another mutation observed in the present in various locations within the introns. Of coding region is at mRNA position 188 (SNP ID: the mutations affecting the gene, only one has an rs1871892), resulting in a change in the sequence to observed clinical association. It is observed that a TCA (from the wild type CCA). This particular mutation of the mRNA position 954 (SNP ID: substitution results in the insertion of proline at the th rs28363284) results in an allele change to GGG 36 protein position rather than a serine.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 640

RAD51L3 (RAD51-like 3 (S. cerevisiae)) Taylor MK, et al.

A third mutation observed is noted to occur at favorable clinical immunohistochemical pattern mRNA positions 810 (SNP ID: rs4796033). A (Rodríguez-López et al., 2004). However, another mutation at this location results in a sequence of study found no statistically significant evidence that CAG (from the natural CGG). The effect of this this variant is associated with breast cancer risk. substitution is the insertion of a glutamine residue Yet, this study did find that it was plausible that the at the 185th amino acid position rather than the variable could lead to a small increase in the risk of arginine observed in the wild type gene. It is noted, breast cancer and that a small, yet insignificant, that this particular mutation also occurs in 2 effect was made by the variant on the risk of breast additional transcripts of the gene at the mRNA cancer (approximately 30%) (Dowty et al., 2008). th rd positions 750 and 414 affecting the 165 and 53 Prognosis amino acid residues respectively. Other mutations It has been noted that the RAD51D-E223G variant in the coding region include E237K (SNP ID: confers increased resistance to DNA damaging rs115031549), R252Q (SNP ID: rs28363283), agents such as: mitomycin C, cisplatin, ultraviolet A245T (SNP ID: rs28363282), A210T (SNP ID: light, and methyl methane sulfonate, and taxol. This rs80116829), E177D (SNP ID: rs55942401), and presents clinical implications as these are R24S (SNP ID: rs28363257). commonly utilized therapies. Furthermore, the variant has increased cellular proliferation and Implicated in telomere maintenance compared to the wild-type Cancer and exhibits reduced interaction with the binding partner RAD51C but does not affect binding to Disease XRCC2 (Nadkarni et al., 2009b). Cancer arises in part due to the accumulation of genetic damage. Furthermore, such damage has a Bloom's syndrome greater tendency to be found in significant levels Disease when genetic repair pathways such as DNA Bloom's syndrome is an autosomal recessive mismatch repair and homologous recombination disorder of rare occurrence. Characteristics include (HR) are defective. Involved in the pathway of HR short stature, immunodeficiency, fertility defects, are numerous proteins that are known as the and increased risk for the development of various RAD51 paralogs (RAD51L1, RAD51L2, types of cancer. Cells associated with this disorder RAD51L3, XRCC2 and XRCC3). It is believed that are noted for their genomic instability. They exhibit the lack of genetic stability created from the loss of an increase in sister chromatid and homologous this pathway, HR, is significant in initiation and chromosome exchanges. In normal, healthy cells, potentially the progression of cancer. In particular, BLM, a helicase of the RecQ family, interacts with defects in the HR pathway have been noted to be the RAD51L3 portion of the RAD51L3-XRCC2 associated with breast and ovarian cancer (Thacker, heteromeric complex. Upon joining with the 2005); however, it is plausible that such a defect complex, BLM disrupts synthetic 4-way junctions could potentially lead to multiple forms of cancer that resemble Holliday junctions suggesting an due to the accumulation of genetic mutations important role for the protein-protein interaction in (although it takes significant damage accumulation DNA repair. The mutated form of the gene to lead to tumor formation). A RAD51L3 variant encoding for this protein, which occurs in Bloom's does have an association with increased familial syndrome, results in the inability for BLM to bind breast cancer risk (Rodríguez-López et al., 2004). to RAD51L3. Absence of normal BLM function Breast cancer leads to the characteristic elevation in recombination events seen in Bloom's syndrome Note (Braybrooke et al., 2003). Although conflicting data exist, the RAD51D- E233G variant allele has been identified as a References potential precursor to breast cancers in women with high familial risk but do not possess a Cartwright R, Dunn AM, Simpson PJ, Tambini CE, Thacker J. Isolation of novel human and mouse genes of the BRCA1/BRCA2 mutation (Rodríguez-López et al., recA/RAD51 recombination-repair gene family. Nucleic 2004; Dowty et al., 2008). Acids Res. 1998 Apr 1;26(7):1653-9 Disease Pittman DL, Weinberg LR, Schimenti JC. Identification, In an initial study that screened for possible breast characterization, and genetic mapping of Rad51d, a new cancer alleles, it was determined that the exon 8 mouse and human RAD51/RecA-related gene. Genomics. 1998 Apr 1;49(1):103-11 mutation led to an increased frequency of breast cancer in a specific group of cases (familial cancer Kawabata M, Saeki K. Multiple alternative transcripts of the human homologue of the mouse TRAD/R51H3/RAD51D cases) versus the control group (Rodríguez-López gene, a member of the rec A/RAD51 gene family. Biochem et al., 2004). Additionally, individuals expressing Biophys Res Commun. 1999 Apr 2;257(1):156-62 the RAD51D-E233G variant have been shown to Schild D, Lio YC, Collins DW, Tsomondo T, Chen DJ. have higher proliferative indices and a less Evidence for simultaneous protein interactions between

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 641

RAD51L3 (RAD51-like 3 (S. cerevisiae)) Taylor MK, et al.

human Rad51 paralogs. J Biol Chem. 2000 Jun Tarsounas M, West SC. Recombination at mammalian 2;275(22):16443-9 telomeres: an alternative mechanism for telomere protection and elongation. Cell Cycle. 2005 May;4(5):672-4 Masson JY, Tarsounas MC, Stasiak AZ, Stasiak A, Shah R, McIlwraith MJ, Benson FE, West SC. Identification and Thacker J. The RAD51 gene family, genetic instability and purification of two distinct complexes containing the five cancer. Cancer Lett. 2005 Mar 10;219(2):125-35 RAD51 paralogs. Genes Dev. 2001 Dec 15;15(24):3296- 307 Hinz JM, Tebbs RS, Wilson PF, Nham PB, Salazar EP, Nagasawa H, Urbin SS, Bedford JS, Thompson LH. Strausberg RL, Feingold EA, Grouse LH, Derge JG, Repression of mutagenesis by Rad51D-mediated Klausner RD, Collins FS, Wagner L, Shenmen CM, homologous recombination. Nucleic Acids Res. Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer 2006;34(5):1358-68 CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Wiese C, Hinz JM, Tebbs RS, Nham PB, Urbin SS, Collins Rubin GM, Hong L, Stapleton M, Soares MB, Bonaldo MF, DW, Thompson LH, Schild D. Disparate requirements for Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, the Walker A and B ATPase motifs of human RAD51D in Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano homologous recombination. Nucleic Acids Res. NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, 2006;34(9):2833-43 McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Durrant WE, Wang S, Dong X. Arabidopsis SNI1 and Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk RAD51D regulate both gene transcription and DNA SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs recombination during the defense response. Proc Natl RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues Acad Sci U S A. 2007 Mar 6;104(10):4223-7 S, Sanchez A, Whiting M, Madan A, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman Dowty JG, Lose F, Jenkins MA, Chang JH, Chen X, JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Beesley J, Dite GS, Southey MC, Byrnes GB, Tesoriero A, Schmutz J, Myers RM, Butterfield YS, Krzywinski MI, Giles GG, Hopper JL, Spurdle AB. The RAD51D E233G Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJ, variant and breast cancer risk: population-based and clinic- Marra MA. Generation and initial analysis of more than based family studies of Australian women. Breast Cancer 15,000 full-length human and mouse cDNA sequences. Res Treat. 2008 Nov;112(1):35-9 Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903 Gruver AM, Yard BD, McInnes C, Rajesh C, Pittman DL. Braybrooke JP, Li JL, Wu L, Caple F, Benson FE, Hickson Functional characterization and identification of mouse ID. Functional interaction between the Bloom's syndrome Rad51d splice variants. BMC Mol Biol. 2009 Mar 27;10:27 helicase and the RAD51 paralog, RAD51L3 (RAD51D). J Biol Chem. 2003 Nov 28;278(48):48357-66 Nadkarni A, Furda A, Rajesh C, McInnes C, Ruch RJ, Pittman DL. Functional characterization of the RAD51D Kawabata M, Akiyama K, Kawabata T. Genomic structure E233G genetic variant. Pharmacogenet Genomics. 2009a and multiple alternative transcripts of the mouse Feb;19(2):153-60 TRAD/RAD51L3/RAD51D gene, a member of the recA/RAD51 gene family. Biochim Biophys Acta. 2004 Aug Nadkarni A, Rajesh P, Ruch RJ, Pittman DL. Cisplatin 12;1679(2):107-16 resistance conferred by the RAD51D (E233G) genetic variant is dependent upon p53 status in human breast Miller KA, Sawicka D, Barsky D, Albala JS. Domain carcinoma cell lines. Mol Carcinog. 2009b Jul;48(7):586-91 mapping of the Rad51 paralog protein complexes. Nucleic Acids Res. 2004;32(1):169-78 Rajesh C, Gruver AM, Basrur V, Pittman DL. The interaction profile of homologous recombination repair Rodríguez-López R, Osorio A, Ribas G, Pollán M, proteins RAD51C, RAD51D and XRCC2 as determined by Sánchez-Pulido L, de la Hoya M, Ruibal A, Zamora P, proteomic analysis. Proteomics. 2009 Aug;9(16):4071-86 Arias JI, Salazar R, Vega A, Martínez JI, Esteban- Cardeñosa E, Alonso C, Letón R, Urioste Azcorra M, Miner Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, C, Armengod ME, Carracedo A, González-Sarmiento R, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Caldés T, Díez O, Benítez J. The variant E233G of the Sonstegard TS, Marçais G, Roberts M, Subramanian P, RAD51D gene could be a low-penetrance allele in high- Yorke JA, Salzberg SL. A whole-genome assembly of the risk breast cancer families without BRCA1/2 mutations. Int domestic cow, Bos taurus. Genome Biol. 2009;10(4):R42 J Cancer. 2004 Jul 20;110(6):845-9 Rajesh P, Rajesh C, Wyatt MD, Pittman DL. RAD51D Sasaki MS, Takata M, Sonoda E, Tachibana A, Takeda S. protects against MLH1-dependent cytotoxic responses to Recombination repair pathway in the maintenance of O(6)-methylguanine. DNA Repair (Amst). 2010 Apr chromosomal integrity against DNA interstrand crosslinks. 4;9(4):458-67 Cytogenet Genome Res. 2004;104(1-4):28-34 Rajesh C, Baker DK, Pierce AJ, Pittman DL. The splicing- Tarsounas M, Muñoz P, Claas A, Smiraldo PG, Pittman factor related protein SFPQ/PSF interacts with RAD51D DL, Blasco MA, West SC. Telomere maintenance requires and is necessary for homology-directed repair and sister the RAD51D recombination/repair protein. Cell. 2004 Apr chromatid cohesion. Nucleic Acids Res. 2011 30;117(3):337-47 Jan;39(1):132-45 Gruver AM, Miller KA, Rajesh C, Smiraldo PG, This article should be referenced as such: Kaliyaperumal S, Balder R, Stiles KM, Albala JS, Pittman DL. The ATPase motif in RAD51D is required for Taylor MK, Bendenbaugh MK, Brown SM, Yard BD, resistance to DNA interstrand crosslinking agents and Pittman DL. RAD51L3 (RAD51-like 3 (S. cerevisiae)). Atlas interaction with RAD51C. Mutagenesis. 2005 Genet Cytogenet Oncol Haematol. 2011; 15(8):638-642. Nov;20(6):433-40 Smiraldo PG, Gruver AM, Osborn JC, Pittman DL. Extensive chromosomal instability in Rad51d-deficient mouse cells. Cancer Res. 2005 Mar 15;65(6):2089-96

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 642

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Gene Section Review

SLC9A3R1 (solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1) Wendy S McDonough, Michael E Berens The Translational Genomics Research Institute, 445 N Fifth Street, Phoenix, Arizona 85004, USA (WSM, MEB)

Published in Atlas Database: December 2010 Online updated version : http://AtlasGeneticsOncology.org/Genes/SLC9A3R1ID46023ch17q25.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI SLC9A3R1ID46023ch17q25.txt

Identity Transcription Other names: EBP50; NHERF; NHERF1; The SLC9A3R1 gene encodes a 1978 bp mRNA NPHLOP2 transcript. Reported regulatory transcription factor binding HGNC (Hugo): SLC9A3R1 sites upstream of the SLC9A3R1 promoter region Location: 17q25.1 include: NF-kappaB1, HNF-4alpha2, COUP-TF1, NF-kappaB, NRSF form 2, NRSF form 1, FOXD1, DNA/RNA PPAR-gamma2, PPAR-gamma1, GATA-1.

Description The SLC9A3R1 gene is comprised of 6 exons and spans approximately 20.7 kb of genomic DNA.

SLC9A3R1 Physical Map.

DNA size 20.71 Kb; mRNA size 1978 bp; 6 exons.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 643

SLC9A3R1 (solute carrier family 9 (sodium/hydrogen McDonough WS, Berens ME exchanger), member 3 regulator 1)

NHERF (human)-358 aminos acids.

SLC9A3R1 has been show to have binary Protein interaction with the following proteins: CFTR, Description CLCN3, MSN, NF2, RDX. The SLC9A3R1 protein is composed of 353 amino Mutations acids (389 kDa). Post-transcriptional regulation of SLC9A3R1 Note occurs via Serines S77-p, S162-p, S339-p, S340-p. SLC9A3R1 has been shown to have three natural SLC9A3R1 is also phosphroylated on T95-p. variants. SLC9A3R1 has two PDZ (DHR) domains. Natural variant 110L --> V in NPHLOP2; the SLC9A3R1 can exist as a homodimer or mutant expressed in cultured renal cells increases heterodimer with SLC9A3R2. the generation of cyclic AMP (cAMP) by Expression parathyroid hormone (PTH) and inhibits phosphate transport. SLC9A3R1 is expressed in liver, salivary glands, Natural variant 153R --> Q in NPHLOP2; the kidney, pancreas, trachea, small intestine, stomach, mutant expressed in cultured renal cells increases prostate and brain. the generation of cAMP by PTH and inhibits Localisation phosphate transport. SLC9A3R1 is a cytoplasmic protein. SLC9A3R1 Natural variant 225E --> K in NPHLOP2; the translocates from the cytoplasm to the apical cell mutant expressed in cultured renal cells increases membrane in a PODXL-dependent manner. the generation of cAMP by PTH and inhibits SLC9A3R1 colocalizes with actin in microvilli-rich phosphate transport. apical regions of the syncytiotrophoblast. SLC9A3R1 has been found in microvilli, ruffling Implicated in membrane and filopodia of HeLa cells. SLC9A3R1 Cancer progression is also been discovered in lipid rafts of T-cells. Subcellular localization is present in cells with Note apical specialized structure such as micorvili and There is growing evidence SLC9A3R1 plays an cilia. SLC9A3R1 also has a membranous important role in cancer progression. SLC9A3R1 expression in cells of non-epithelial origin functions as an adaptor protein to control cell (astrocytes) and hematopoietic stem cells and has transformation. In addition, recent evidence been found in membrane rafts in lymphocytes and suggests that SLC9A3R1 has a dual role either at the rear edge of neutrophils. acting as a tumor suppressor when it is localized as the cell membrane or as an oncogenic protein when Function it is localized in the cytoplasm (Georgescu et al., SLC9A3R1 is a scaffold protein that connects 2008). plasma membrane proteins with members of the ezrin/moesin/radixin family and thereby helps to Glioblastoma link them to the actin cytoskeleton to regulate their Note surface expression. SLC9A3R1 has been shown to The invasive nature of glioblastoma multiforme be necessary for recycling of internalized ADRB2. presents a clinical problem rendering tumors SLC9A3R1 regulates SLC9A3 as well as its incurable by conventional treatment modalities subcellular location. SLC9A3R1 is required for such as surgery, ionizing radiation, and cAMP-mediated phosphorylation and inhibition of temozolomide. SLC9A3R1. SLC9A3R1 interacts with MCC. SLC9A3R1 has been implicated to play a role in SLC9A3R1 may participate in HTR4 targeting to sustaining glioma cell migration and invasion. microvilli. SLC9A3R1 has been shown to play a SLC9A3R1 has been shown to be over-expressed in role in the WNT signaling pathway. invading glioma cells as compared to the tumor Induction: SLC9A3R1 can be induced by estrogen. core (Kislin et al., 2009).

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 644

SLC9A3R1 (solute carrier family 9 (sodium/hydrogen McDonough WS, Berens ME exchanger), member 3 regulator 1)

Breast cancer To be noted Note Increased cytoplasmic expression of SLC9A3R1 in Note breast tumors suggests a key role of its localization We acknowledge the support of Michael Northrop and compartmentalization in defining for scientific illustrations. cancerogenesis, progression, and invasion. SLC9A3R1 overexpression has been associated References with increasing tumor cytohistological grade, Cardone RA, Bellizzi A, Busco G, Weinman EJ, Dell'Aquila aggressive clinical behavior, unfavorable prognosis, ME, Casavola V, Azzariti A, Mangia A, Paradiso A, and increased tumor hypoxia. Moreover, Reshkin SJ. The NHERF1 PDZ2 domain regulates PKA- RhoA-p38-mediated NHE1 activation and invasion in SLC9A3R1 co-localizes with the oncogenic breast tumor cells. Mol Biol Cell. 2007 May;18(5):1768-80 receptor HER2/neu in HER2/neu-overexpressing carcinoma and in distant metastases (Mangia et al., Weinman EJ, Steplock D, Wang Y, Shenolikar S. Characterization of a protein cofactor that mediates protein 2009). kinase A regulation of the renal brush border membrane The switch from apical membranous to cytoplasmic Na(+)-H+ exchanger. J Clin Invest. 1995 May;95(5):2143-9 expression is compatible with a dual role for Reczek D, Berryman M, Bretscher A. Identification of NHERF1 as a tumour suppressor or tumour EBP50: A PDZ-containing phosphoprotein that associates promoter dependent on its subcellular localization with members of the ezrin-radixin-moesin family. J Cell (Georgescu et al., 2008). Biol. 1997 Oct 6;139(1):169-79 Cystic fibrosis Yun CH, Oh S, Zizak M, Steplock D, Tsao S, Tse CM, Weinman EJ, Donowitz M. cAMP-mediated inhibition of the Note epithelial brush border Na+/H+ exchanger, NHE3, requires The inherited disease cystic fibrosis is one of the an associated regulatory protein. Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):3010-5 most common chronic lung diseases in children and young adults and may lead to an early death. Hall RA, Ostedgaard LS, Premont RT, Blitzer JT, Rahman Cystic fibrosis transmembrane regulator (CFTR) N, Welsh MJ, Lefkowitz RJ. A C-terminal motif found in the beta2-adrenergic receptor, P2Y1 receptor and cystic functions as a cAMP-regulated chloride channel, fibrosis transmembrane conductance regulator determines and mutations in CFTR are contributory in cystic binding to the Na+/H+ exchanger regulatory factor family fibrosis. CFTR contains a C-terminal SLC9A3R1 of PDZ proteins. Proc Natl Acad Sci U S A. 1998 Jul consensus sequence affording the two proteins to 21;95(15):8496-501 bind with high affinity. Recent experiments have Hall RA, Premont RT, Chow CW, Blitzer JT, Pitcher JA, postulated two roles for SLC9A3R1 in CFTR Claing A, Stoffel RH, Barak LS, Shenolikar S, Weinman EJ, Grinstein S, Lefkowitz RJ. The beta2-adrenergic function. Guggino, Stanton, and coworkers have receptor interacts with the Na+/H+-exchanger regulatory proposed that NHERF functions as a membrane factor to control Na+/H+ exchange. Nature. 1998 Apr retention signal for CFTR (Moyer et al., 1999). 9;392(6676):626-30 Raghuram et al. suggest that SLC9A3R1 facilitates Murthy A, Gonzalez-Agosti C, Cordero E, Pinney D, the dimerization of CFTR leading to its full Candia C, Solomon F, Gusella J, Ramesh V. NHE-RF, a expression of chloride channel activity (Raghuram regulatory cofactor for Na(+)-H+ exchange, is a common et al., 2001). interactor for merlin and ERM (MERM) proteins. J Biol Chem. 1998 Jan 16;273(3):1273-6 Lastly, ss2-adrenoceptors have been shown to physically interact with CFTR Na+/H+ Exchanger Short DB, Trotter KW, Reczek D, Kreda SM, Bretscher A, Regulatory Factor 1 SLC9A3R1 protein. This Boucher RC, Stutts MJ, Milgram SL. An apical PDZ protein anchors the cystic fibrosis transmembrane conductance function of SLC9A3R1 could be a new therapeutic regulator to the cytoskeleton. J Biol Chem. 1998 Jul target in CF patients to facilitate the trafficking of 31;273(31):19797-801 mutated CFTR to plasma membrane (Bossard et al., Wang S, Raab RW, Schatz PJ, Guggino WB, Li M. Peptide 2011). binding consensus of the NHE-RF-PDZ1 domain matches the C-terminal sequence of cystic fibrosis transmembrane Hypophosphatemia and conductance regulator (CFTR). FEBS Lett. 1998 May nephrolithiasis 1;427(1):103-8 Note Cao TT, Deacon HW, Reczek D, Bretscher A, von Zastrow SLC9A3R1 plays an important role in tumor M. A kinase-regulated PDZ-domain interaction controls endocytic sorting of the beta2-adrenergic receptor. Nature. phosphorous transport. Inactivating missense 1999 Sep 16;401(6750):286-90 mutations in SLC9AR1 have been identified in Hall RA, Spurney RF, Premont RT, Rahman N, Blitzer JT, patients with hypercalciuria and neprolithiasis Pitcher JA, Lefkowitz RJ. G protein-coupled receptor (Karim et al., 2008). kinase 6A phosphorylates the Na(+)/H(+) exchanger regulatory factor via a PDZ domain-mediated interaction. J Biol Chem. 1999 Aug 20;274(34):24328-34

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 645

SLC9A3R1 (solute carrier family 9 (sodium/hydrogen McDonough WS, Berens ME exchanger), member 3 regulator 1)

Mohler PJ, Kreda SM, Boucher RC, Sudol M, Stutts MJ, (NHE-RF/EBP50) gene involving multiple half-estrogen Milgram SL. Yes-associated protein 65 localizes p62(c- response elements. Mol Endocrinol. 2002 Aug;16(8):1828- Yes) to the apical compartment of airway epithelia by 39 association with EBP50. J Cell Biol. 1999 Nov 15;147(4):879-90 Glynne PA, Darling KE, Picot J, Evans TJ. Epithelial inducible nitric-oxide synthase is an apical EBP50-binding Moyer BD, Denton J, Karlson KH, Reynolds D, Wang S, protein that directs vectorial nitric oxide output. J Biol Mickle JE, Milewski M, Cutting GR, Guggino WB, Li M, Chem. 2002 Sep 6;277(36):33132-8 Stanton BA. A PDZ-interacting domain in CFTR is an apical membrane polarization signal. J Clin Invest. 1999 Ingraffea J, Reczek D, Bretscher A. Distinct cell type- Nov;104(10):1353-61 specific expression of scaffolding proteins EBP50 and E3KARP: EBP50 is generally expressed with ezrin in Breton S, Wiederhold T, Marshansky V, Nsumu NN, specific epithelia, whereas E3KARP is not. Eur J Cell Biol. Ramesh V, Brown D. The B1 subunit of the H+ATPase is a 2002 Feb;81(2):61-8 PDZ domain-binding protein. Colocalization with NHE-RF in renal B-intercalated cells. J Biol Chem. 2000 Jun Karthikeyan S, Leung T, Ladias JA. Structural 16;275(24):18219-24 determinants of the Na+/H+ exchanger regulatory factor interaction with the beta 2 adrenergic and platelet-derived Maudsley S, Zamah AM, Rahman N, Blitzer JT, Luttrell growth factor receptors. J Biol Chem. 2002 May LM, Lefkowitz RJ, Hall RA. Platelet-derived growth factor 24;277(21):18973-8 receptor association with Na(+)/H(+) exchanger regulatory factor potentiates receptor activity. Mol Cell Biol. 2000 Lamprecht G, Heil A, Baisch S, Lin-Wu E, Yun CC, Nov;20(22):8352-63 Kalbacher H, Gregor M, Seidler U. The down regulated in adenoma (dra) gene product binds to the second PDZ Moyer BD, Duhaime M, Shaw C, Denton J, Reynolds D, domain of the NHE3 kinase A regulatory protein Karlson KH, Pfeiffer J, Wang S, Mickle JE, Milewski M, (E3KARP), potentially linking intestinal Cl-/HCO3- Cutting GR, Guggino WB, Li M, Stanton BA. The PDZ- exchange to Na+/H+ exchange. Biochemistry. 2002 Oct interacting domain of cystic fibrosis transmembrane 15;41(41):12336-42 conductance regulator is required for functional expression in the apical plasma membrane. J Biol Chem. 2000 Sep Li JG, Chen C, Liu-Chen LY. Ezrin-radixin-moesin-binding 1;275(35):27069-74 phosphoprotein-50/Na+/H+ exchanger regulatory factor (EBP50/NHERF) blocks U50,488H-induced down- Tang Y, Tang J, Chen Z, Trost C, Flockerzi V, Li M, regulation of the human kappa opioid receptor by Ramesh V, Zhu MX. Association of mammalian trp4 and enhancing its recycling rate. J Biol Chem. 2002 Jul phospholipase C isozymes with a PDZ domain-containing 26;277(30):27545-52 protein, NHERF. J Biol Chem. 2000 Dec 1;275(48):37559- 64 Liedtke CM, Yun CH, Kyle N, Wang D. Protein kinase C epsilon-dependent regulation of cystic fibrosis Brdicková N, Brdicka T, Andera L, Spicka J, Angelisová P, transmembrane regulator involves binding to a receptor for Milgram SL, Horejsí V. Interaction between two adapter activated C kinase (RACK1) and RACK1 binding to proteins, PAG and EBP50: a possible link between Na+/H+ exchange regulatory factor. J Biol Chem. 2002 membrane rafts and actin cytoskeleton. FEBS Lett. 2001 Jun 21;277(25):22925-33 Oct 26;507(2):133-6 Mahon MJ, Donowitz M, Yun CC, Segre GV. Na(+)/H(+ ) Gisler SM, Stagljar I, Traebert M, Bacic D, Biber J, Murer exchanger regulatory factor 2 directs parathyroid hormone H. Interaction of the type IIa Na/Pi cotransporter with PDZ 1 receptor signalling. Nature. 2002 Jun 20;417(6891):858- proteins. J Biol Chem. 2001 Mar 23;276(12):9206-13 61 He J, Lau AG, Yaffe MB, Hall RA. Phosphorylation and cell Ogura T, Furukawa T, Toyozaki T, Yamada K, Zheng YJ, cycle-dependent regulation of Na+/H+ exchanger Katayama Y, Nakaya H, Inagaki N. ClC-3B, a novel ClC-3 regulatory factor-1 by Cdc2 kinase. J Biol Chem. 2001 Nov splicing variant that interacts with EBP50 and facilitates 9;276(45):41559-65 expression of CFTR-regulated ORCC. FASEB J. 2002 Jun;16(8):863-5 Karthikeyan S, Leung T, Birrane G, Webster G, Ladias JA. Crystal structure of the PDZ1 domain of human Na(+)/H(+) Park M, Ko SB, Choi JY, Muallem G, Thomas PJ, Pushkin exchanger regulatory factor provides insights into the A, Lee MS, Kim JY, Lee MG, Muallem S, Kurtz I. The mechanism of carboxyl-terminal leucine recognition by cystic fibrosis transmembrane conductance regulator class I PDZ domains. J Mol Biol. 2001 May 18;308(5):963- interacts with and regulates the activity of the HCO3- 73 salvage transporter human Na+-HCO3- cotransport isoform 3. J Biol Chem. 2002 Dec 27;277(52):50503-9 Karthikeyan S, Leung T, Ladias JA. Structural basis of the Na+/H+ exchanger regulatory factor PDZ1 interaction with Rochdi MD, Watier V, La Madeleine C, Nakata H, Kozasa the carboxyl-terminal region of the cystic fibrosis T, Parent JL. Regulation of GTP-binding protein alpha q transmembrane conductance regulator. J Biol Chem. 2001 (Galpha q) signaling by the ezrin-radixin-moesin-binding Jun 8;276(23):19683-6 phosphoprotein-50 (EBP50). J Biol Chem. 2002 Oct 25;277(43):40751-9 Raghuram V, Mak DO, Foskett JK. Regulation of cystic fibrosis transmembrane conductance regulator single- Strausberg RL, Feingold EA, Grouse LH, Derge JG, channel gating by bivalent PDZ-domain-mediated Klausner RD, Collins FS, Wagner L, Shenmen CM, interaction. Proc Natl Acad Sci U S A. 2001 Jan Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer 30;98(3):1300-5 CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Reczek D, Bretscher A. Identification of EPI64, a Rubin GM, Hong L, Stapleton M, Soares MB, Bonaldo MF, TBC/rabGAP domain-containing microvillar protein that Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, binds to the first PDZ domain of EBP50 and E3KARP. J Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano Cell Biol. 2001 Apr 2;153(1):191-206 NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, Ediger TR, Park SE, Katzenellenbogen BS. Estrogen McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, receptor inducibility of the human Na+/H+ exchanger Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk regulatory factor/ezrin-radixin-moesin binding protein 50 SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 646

SLC9A3R1 (solute carrier family 9 (sodium/hydrogen McDonough WS, Berens ME exchanger), member 3 regulator 1)

RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues PA. Activation-independent parathyroid hormone receptor S, Sanchez A, Whiting M, Madan A, Young AC, internalization is regulated by NHERF1 (EBP50). J Biol Shevchenko Y, Bouffard GG, Blakesley RW, Touchman Chem. 2003 Oct 31;278(44):43787-96 JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Krzywinski MI, Taouil K, Hinnrasky J, Hologne C, Corlieu P, Klossek JM, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJ, Puchelle E. Stimulation of beta 2-adrenergic receptor Marra MA. Generation and initial analysis of more than increases cystic fibrosis transmembrane conductance 15,000 full-length human and mouse cDNA sequences. regulator expression in human airway epithelial cells Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903 through a cAMP/protein kinase A-independent pathway. J Biol Chem. 2003 May 9;278(19):17320-7 Benharouga M, Sharma M, So J, Haardt M, Drzymala L, Popov M, Schwapach B, Grinstein S, Du K, Lukacs GL. Terawaki S, Maesaki R, Okada K, Hakoshima T. The role of the C terminus and Na+/H+ exchanger Crystallographic characterization of the radixin FERM regulatory factor in the functional expression of cystic domain bound to the C-terminal region of the human fibrosis transmembrane conductance regulator in Na+/H+-exchanger regulatory factor (NHERF). Acta nonpolarized cells and epithelia. J Biol Chem. 2003 Jun Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):177-9 13;278(24):22079-89 Weinman EJ, Wang Y, Wang F, Greer C, Steplock D, Gentzsch M, Cui L, Mengos A, Chang XB, Chen JH, Shenolikar S. A C-terminal PDZ motif in NHE3 binds Riordan JR. The PDZ-binding chloride channel ClC-3B NHERF-1 and enhances cAMP inhibition of sodium- localizes to the Golgi and associates with cystic fibrosis hydrogen exchange. Biochemistry. 2003 Nov transmembrane conductance regulator-interacting PDZ 4;42(43):12662-8 proteins. J Biol Chem. 2003 Feb 21;278(8):6440-9 Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Gevaert K, Goethals M, Martens L, Van Damme J, Staes Villén J, Li J, Cohn MA, Cantley LC, Gygi SP. Large-scale A, Thomas GR, Vandekerckhove J. Exploring proteomes characterization of HeLa cell nuclear phosphoproteins. and analyzing protein processing by mass spectrometric Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12130-5 identification of sorted N-terminal peptides. Nat Biotechnol. Brandenberger R, Wei H, Zhang S, Lei S, Murage J, Fisk 2003 May;21(5):566-9 GJ, Li Y, Xu C, Fang R, Guegler K, Rao MS, Mandalam R, Gisler SM, Pribanic S, Bacic D, Forrer P, Gantenbein A, Lebkowski J, Stanton LW. Transcriptome characterization Sabourin LA, Tsuji A, Zhao ZS, Manser E, Biber J, Murer elucidates signaling networks that control human ES cell H. PDZK1: I. a major scaffolder in brush borders of growth and differentiation. Nat Biotechnol. 2004 proximal tubular cells. Kidney Int. 2003 Nov;64(5):1733-45 Jun;22(6):707-16 Hegedüs T, Sessler T, Scott R, Thelin W, Bakos E, Váradi Finnerty CM, Chambers D, Ingraffea J, Faber HR, Karplus A, Szabó K, Homolya L, Milgram SL, Sarkadi B. C-terminal PA, Bretscher A. The EBP50-moesin interaction involves a phosphorylation of MRP2 modulates its interaction with binding site regulated by direct masking on the FERM PDZ proteins. Biochem Biophys Res Commun. 2003 Mar domain. J Cell Sci. 2004 Mar 15;117(Pt 8):1547-52 14;302(3):454-61 Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Helms C, Cao L, Krueger JG, Wijsman EM, Chamian F, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good Gordon D, Heffernan M, Daw JA, Robarge J, Ott J, Kwok P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, PY, Menter A, Bowcock AM. A putative RUNX1 binding Jang W, Sherry S, Feolo M, Misquitta L, Lee E, site variant between SLC9A3R1 and NAT9 is associated Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, with susceptibility to psoriasis. Nat Genet. 2003 Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent Dec;35(4):349-56 M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz Hirakawa T, Galet C, Kishi M, Ascoli M. GIPC binds to the TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, human lutropin receptor (hLHR) through an unusual PDZ Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, domain binding motif, and it regulates the sorting of the Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, internalized human choriogonadotropin and the density of Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, cell surface hLHR. J Biol Chem. 2003 Dec Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan 5;278(49):49348-57 Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Lee-Kwon W, Kim JH, Choi JW, Kawano K, Cha B, Dartt Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, DA, Zoukhri D, Donowitz M. Ca2+-dependent inhibition of Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, NHE3 requires PKC alpha which binds to E3KARP to Pearson RL, Bouffard GG, Blakesly RW, Green ED, decrease surface NHE3 containing plasma membrane Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, complexes. Am J Physiol Cell Physiol. 2003 Myers RM, Butterfield YS, Griffith M, Griffith OL, Dec;285(6):C1527-36 Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Pushkin A, Abuladze N, Newman D, Muronets V, Sassani Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, P, Tatishchev S, Kurtz I. The COOH termini of NBC3 and Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, the 56-kDa H+-ATPase subunit are PDZ motifs involved in Makowski KA, Bosak S, Malek J. The status, quality, and their interaction. Am J Physiol Cell Physiol. 2003 expansion of the NIH full-length cDNA project: the Mar;284(3):C667-73 Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7 Rochdi MD, Parent JL. Galphaq-coupled receptor internalization specifically induced by Galphaq signaling. Huang P, Steplock D, Weinman EJ, Hall RA, Ding Z, Li J, Regulation by EBP50. J Biol Chem. 2003 May Wang Y, Liu-Chen LY. kappa Opioid receptor interacts 16;278(20):17827-37 with Na(+)/H(+)-exchanger regulatory factor-1/Ezrin- radixin-moesin-binding phosphoprotein-50 (NHERF- Shibata T, Chuma M, Kokubu A, Sakamoto M, Hirohashi 1/EBP50) to stimulate Na(+)/H(+) exchange independent S. EBP50, a beta-catenin-associating protein, enhances of G(i)/G(o) proteins. J Biol Chem. 2004 Jun Wnt signaling and is over-expressed in hepatocellular 11;279(24):25002-9 carcinoma. Hepatology. 2003 Jul;38(1):178-86 James MF, Beauchamp RL, Manchanda N, Kazlauskas A, Sneddon WB, Syme CA, Bisello A, Magyar CE, Rochdi Ramesh V. A NHERF binding site links the betaPDGFR to MD, Parent JL, Weinman EJ, Abou-Samra AB, Friedman

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 647

SLC9A3R1 (solute carrier family 9 (sodium/hydrogen McDonough WS, Berens ME exchanger), member 3 regulator 1)

the cytoskeleton and regulates cell spreading and anion transporter 4 function by two PDZ domain-containing migration. J Cell Sci. 2004 Jun 15;117(Pt 14):2951-61 proteins. J Am Soc Nephrol. 2005 Dec;16(12):3498-506 Kato Y, Yoshida K, Watanabe C, Sai Y, Tsuji A. Screening Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, of the interaction between xenobiotic transporters and PDZ Mortensen P, Mann M. Global, in vivo, and site-specific proteins. Pharm Res. 2004 Oct;21(10):1886-94 phosphorylation dynamics in signaling networks. Cell. 2006 Nov 3;127(3):635-48 Nawrot M, West K, Huang J, Possin DE, Bretscher A, Crabb JW, Saari JC. Cellular retinaldehyde-binding protein Pan Y, Wang L, Dai JL. Suppression of breast cancer cell interacts with ERM-binding phosphoprotein 50 in retinal growth by Na+/H+ exchanger regulatory factor 1 pigment epithelium. Invest Ophthalmol Vis Sci. 2004 (NHERF1). Breast Cancer Res. 2006;8(6):R63 Feb;45(2):393-401 Smyth DJ, Howson JM, Payne F, Maier LM, Bailey R, Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie Holland K, Lowe CE, Cooper JD, Hulme JS, Vella A, R, Wakamatsu A, Hayashi K, Sato H, Nagai K, Kimura K, Dahlman I, Lam AC, Nutland S, Walker NM, Twells RC, Makita H, Sekine M, Obayashi M, Nishi T, Shibahara T, Todd JA. Analysis of polymorphisms in 16 genes in type 1 Tanaka T, Ishii S, Yamamoto J, Saito K, Kawai Y, Isono Y, diabetes that have been associated with other immune- Nakamura Y, Nagahari K, Murakami K, Yasuda T, mediated diseases. BMC Med Genet. 2006 Mar 6;7:20 Iwayanagi T, Wagatsuma M, Shiratori A, Sudo H, Hosoiri T, Kaku Y, Kodaira H, Kondo H, Sugawara M, Takahashi Takahashi Y, Morales FC, Kreimann EL, Georgescu MM. M, Kanda K, Yokoi T, Furuya T, Kikkawa E, Omura Y, Abe PTEN tumor suppressor associates with NHERF proteins K, Kamihara K, Katsuta N, Sato K, Tanikawa M, Yamazaki to attenuate PDGF receptor signaling. EMBO J. 2006 Feb M, Ninomiya K, Ishibashi T, Yamashita H, Murakawa K, 22;25(4):910-20 Fujimori K, Tanai H, Kimata M, Watanabe M, Hiraoka S, Terawaki S, Maesaki R, Hakoshima T. Structural basis for Chiba Y, Ishida S, Ono Y, Takiguchi S, Watanabe S, NHERF recognition by ERM proteins. Structure. 2006 Yosida M, Hotuta T, Kusano J, Kanehori K, Takahashi-Fujii Apr;14(4):777-89 A, Hara H, Tanase TO, Nomura Y, Togiya S, Komai F, Hara R, Takeuchi K, Arita M, Imose N, Musashino K, Yuuki Bossard F, Robay A, Toumaniantz G, Dahimene S, Becq H, Oshima A, Sasaki N, Aotsuka S, Yoshikawa Y, F, Merot J, Gauthier C. NHE-RF1 protein rescues Matsunawa H, Ichihara T, Shiohata N, Sano S, Moriya S, DeltaF508-CFTR function. Am J Physiol Lung Cell Mol Momiyama H, Satoh N, Takami S, Terashima Y, Suzuki O, Physiol. 2007 May;292(5):L1085-94 Nakagawa S, Senoh A, Mizoguchi H, Goto Y, Shimizu F, Wakebe H, Hishigaki H, Watanabe T, Sugiyama A, Kwon SH, Pollard H, Guggino WB. Knockdown of Takemoto M, Kawakami B, Yamazaki M, Watanabe K, NHERF1 enhances degradation of temperature rescued Kumagai A, Itakura S, Fukuzumi Y, Fujimori Y, Komiyama DeltaF508 CFTR from the cell surface of human airway M, Tashiro H, Tanigami A, Fujiwara T, Ono T, Yamada K, cells. Cell Physiol Biochem. 2007;20(6):763-72 Fujii Y, Ozaki K, Hirao M, Ohmori Y, Kawabata A, Hikiji T, Li J, Poulikakos PI, Dai Z, Testa JR, Callaway DJ, Bu Z. Kobatake N, Inagaki H, Ikema Y, Okamoto S, Okitani R, Protein kinase C phosphorylation disrupts Na+/H+ Kawakami T, Noguchi S, Itoh T, Shigeta K, Senba T, exchanger regulatory factor 1 autoinhibition and promotes Matsumura K, Nakajima Y, Mizuno T, Morinaga M, Sasaki cystic fibrosis transmembrane conductance regulator M, Togashi T, Oyama M, Hata H, Watanabe M, Komatsu macromolecular assembly. J Biol Chem. 2007 Sep T, Mizushima-Sugano J, Satoh T, Shirai Y, Takahashi Y, 14;282(37):27086-99 Nakagawa K, Okumura K, Nagase T, Nomura N, Kikuchi H, Masuho Y, Yamashita R, Nakai K, Yada T, Nakamura Morales FC, Takahashi Y, Momin S, Adams H, Chen X, Y, Ohara O, Isogai T, Sugano S. Complete sequencing Georgescu MM. NHERF1/EBP50 head-to-tail and characterization of 21,243 full-length human cDNAs. intramolecular interaction masks association with PDZ Nat Genet. 2004 Jan;36(1):40-5 domain ligands. Mol Cell Biol. 2007 Apr;27(7):2527-37 Suzuki Y, Yamashita R, Shirota M, Sakakibara Y, Chiba J, Ruppelt A, Mosenden R, Grönholm M, Aandahl EM, Tobin Mizushima-Sugano J, Nakai K, Sugano S. Sequence D, Carlson CR, Abrahamsen H, Herberg FW, Carpén O, comparison of human and mouse genes reveals a Taskén K. Inhibition of T cell activation by cyclic adenosine homologous block structure in the promoter regions. 5'-monophosphate requires lipid raft targeting of protein Genome Res. 2004 Sep;14(9):1711-8 kinase A type I by the A-kinase anchoring protein ezrin. J Immunol. 2007 Oct 15;179(8):5159-68 Yoo D, Flagg TP, Olsen O, Raghuram V, Foskett JK, Welling PA. Assembly and trafficking of a multiprotein Song J, Bai J, Yang W, Gabrielson EW, Chan DW, Zhang ROMK (Kir 1.1) channel complex by PDZ interactions. J Z. Expression and clinicopathological significance of Biol Chem. 2004 Feb 20;279(8):6863-73 oestrogen-responsive ezrin-radixin-moesin-binding phosphoprotein 50 in breast cancer. Histopathology. 2007 Bomberger JM, Spielman WS, Hall CS, Weinman EJ, Jul;51(1):40-53 Parameswaran N. Receptor activity-modifying protein (RAMP) isoform-specific regulation of adrenomedullin Voltz JW, Brush M, Sikes S, Steplock D, Weinman EJ, receptor trafficking by NHERF-1. J Biol Chem. 2005 Jun Shenolikar S. Phosphorylation of PDZ1 domain attenuates 24;280(25):23926-35 NHERF-1 binding to cellular targets. J Biol Chem. 2007 Nov 16;282(46):33879-87 Kato Y, Sai Y, Yoshida K, Watanabe C, Hirata T, Tsuji A. PDZK1 directly regulates the function of organic Wang B, Bisello A, Yang Y, Romero GG, Friedman PA. cation/carnitine transporter OCTN2. Mol Pharmacol. 2005 NHERF1 regulates parathyroid hormone receptor Mar;67(3):734-43 membrane retention without affecting recycling. J Biol Chem. 2007 Dec 14;282(50):36214-22 Li J, Dai Z, Jana D, Callaway DJ, Bu Z. Ezrin controls the macromolecular complexes formed between an adapter Barbe L, Lundberg E, Oksvold P, Stenius A, Lewin E, protein Na+/H+ exchanger regulatory factor and the cystic Björling E, Asplund A, Pontén F, Brismar H, Uhlén M, fibrosis transmembrane conductance regulator. J Biol Andersson-Svahn H. Toward a confocal subcellular atlas Chem. 2005 Nov 11;280(45):37634-43 of the human proteome. Mol Cell Proteomics. 2008 Mar;7(3):499-508 Miyazaki H, Anzai N, Ekaratanawong S, Sakata T, Shin HJ, Jutabha P, Hirata T, He X, Nonoguchi H, Tomita K, Cushing PR, Fellows A, Villone D, Boisguérin P, Madden Kanai Y, Endou H. Modulation of renal apical organic DR. The relative binding affinities of PDZ partners for

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 648

SLC9A3R1 (solute carrier family 9 (sodium/hydrogen McDonough WS, Berens ME exchanger), member 3 regulator 1)

CFTR: a biochemical basis for efficient endocytic recycling. Mangia A, Chiriatti A, Bellizzi A, Malfettone A, Stea B, Zito Biochemistry. 2008 Sep 23;47(38):10084-98 FA, Reshkin SJ, Simone G, Paradiso A. Biological role of NHERF1 protein expression in breast cancer. Fanelli T, Cardone RA, Favia M, Guerra L, Zaccolo M, Histopathology. 2009 Nov;55(5):600-8 Monterisi S, De Santis T, Riccardi SM, Reshkin SJ, Casavola V. Beta-oestradiol rescues DeltaF508CFTR Martins-de-Souza D, Gattaz WF, Schmitt A, Rewerts C, functional expression in human cystic fibrosis airway Maccarrone G, Dias-Neto E, Turck CW. Prefrontal cortex CFBE41o- cells through the up-regulation of NHERF1. Biol shotgun proteome analysis reveals altered calcium Cell. 2008 Jul;100(7):399-412 homeostasis and immune system imbalance in schizophrenia. Eur Arch Psychiatry Clin Neurosci. 2009 Georgescu MM, Morales FC, Molina JR, Hayashi Y. Roles Apr;259(3):151-63 of NHERF1/EBP50 in cancer. Curr Mol Med. 2008 Sep;8(6):459-68 Martins-de-Souza D, Gattaz WF, Schmitt A, Rewerts C, Marangoni S, Novello JC, Maccarrone G, Turck CW, Dias- Karim Z, Gérard B, Bakouh N, Alili R, Leroy C, Beck L, Neto E. Alterations in oligodendrocyte proteins, calcium Silve C, Planelles G, Urena-Torres P, Grandchamp B, homeostasis and new potential markers in schizophrenia Friedlander G, Prié D. NHERF1 mutations and anterior temporal lobe are revealed by shotgun proteome responsiveness of renal parathyroid hormone. N Engl J analysis. J Neural Transm. 2009 Mar;116(3):275-89 Med. 2008 Sep 11;359(11):1128-35 Sowa ME, Bennett EJ, Gygi SP, Harper JW. Defining the Richer SL, Truong-Tran AQ, Conley DB, Carter R, human deubiquitinating enzyme interaction landscape. Vermylen D, Grammer LC, Peters AT, Chandra RK, Harris Cell. 2009 Jul 23;138(2):389-403 KE, Kern RC, Schleimer RP. Epithelial genes in chronic rhinosinusitis with and without nasal polyps. Am J Rhinol. Wang B, Yang Y, Abou-Samra AB, Friedman PA. NHERF1 2008 May-Jun;22(3):228-34 regulates parathyroid hormone receptor desensitization: interference with beta-arrestin binding. Mol Pharmacol. Zhou F, Xu W, Tanaka K, You G. Comparison of the 2009 May;75(5):1189-97 interaction of human organic anion transporter hOAT4 with PDZ proteins between kidney cells and placental cells. Amatschek S, Haller M, Oberbauer R. Renal phosphate Pharm Res. 2008 Feb;25(2):475-80 handling in human--what can we learn from hereditary hypophosphataemias? Eur J Clin Invest. 2010 Danik JS, Paré G, Chasman DI, Zee RY, Kwiatkowski DJ, Jun;40(6):552-60 Parker A, Miletich JP, Ridker PM. Novel loci, including those related to Crohn disease, psoriasis, and Bellizzi A, Malfettone A, Cardone RA, Mangia A. inflammation, identified in a genome-wide association NHERF1/EBP50 in Breast Cancer: Clinical Perspectives. study of fibrinogen in 17 686 women: the Women's Breast Care (Basel). 2010;5(2):86-90 Genome Health Study. Circ Cardiovasc Genet. 2009 Apr;2(2):134-41 Bhattacharya S, Dai Z, Li J, Baxter S, Callaway DJ, Cowburn D, Bu Z. A conformational switch in the Filer CE, Ho P, Bruce IN, Worthington J, Barton A. scaffolding protein NHERF1 controls autoinhibition and Investigation of association of genes NAT9, SLC9A3R1 complex formation. J Biol Chem. 2010 Mar and RAPTOR on chromosome 17q25 with psoriatic 26;285(13):9981-94 arthritis. Ann Rheum Dis. 2009 Feb;68(2):292-3 Cuello-Carrión FD, Troncoso M, Guiñazu E, Valdez SR, Fouassier L, Rosenberg P, Mergey M, Saubaméa B, Fanelli MA, Ciocca DR, Kreimann EL. Estrogens regulate Clapéron A, Kinnman N, Chignard N, Jacobsson-Ekman the expression of NHERF1 in normal colon during the G, Strandvik B, Rey C, Barbu V, Hultcrantz R, Housset C. reproductive cycle of Wistar rats. Histochem Cell Biol. Ezrin-radixin-moesin-binding phosphoprotein (EBP50), an 2010 Dec;134(6):623-30 estrogen-inducible scaffold protein, contributes to biliary epithelial cell proliferation. Am J Pathol. 2009 Donowitz M, Singh S, Singh P, Salahuddin FF, Chen Y, Mar;174(3):869-80 Chakraborty M, Murtazina R, Gucek M, Cole RN, Zachos NC, Kovbasnjuk O, Broere N, Smalley-Freed WG, Hoque MT, Conseil G, Cole SP. Involvement of NHERF1 Reynolds AB, Hubbard AL, Seidler U, Weinman E, de in apical membrane localization of MRP4 in polarized Jonge HR, Hogema BM, Li X. Alterations in the proteome kidney cells. Biochem Biophys Res Commun. 2009 Jan of the NHERF1 knockout mouse jejunal brush border 30;379(1):60-4 membrane vesicles. Physiol Genomics. 2010 Nov 15;42A(3):200-10 Huang FD, Kung FL, Tseng YC, Chen MR, Chan HS, Lin CJ. Regulation of protein expression and function of octn2 Flynt AS, Patton JG. Crosstalk between planar cell polarity in forskolin-induced syncytialization in BeWo Cells. signaling and miR-8 control of NHERF1-mediated actin Placenta. 2009 Feb;30(2):187-94 reorganization. Cell Cycle. 2010 Jan 15;9(2):235-7 Kislin KL, McDonough WS, Eschbacher JM, Armstrong Garbett D, LaLonde DP, Bretscher A. The scaffolding BA, Berens ME. NHERF-1: modulator of glioblastoma cell protein EBP50 regulates microvillar assembly in a migration and invasion. Neoplasia. 2009 Apr;11(4):377-87 phosphorylation-dependent manner. J Cell Biol. 2010 Oct 18;191(2):397-413 Kunkel MT, Garcia EL, Kajimoto T, Hall RA, Newton AC. The protein scaffold NHERF-1 controls the amplitude and Hughes SC, Formstecher E, Fehon RG. Sip1, the duration of localized protein kinase D activity. J Biol Chem. Drosophila orthologue of EBP50/NHERF1, functions with 2009 Sep 4;284(36):24653-61 the sterile 20 family kinase Slik to regulate Moesin activity. J Cell Sci. 2010 Apr 1;123(Pt 7):1099-107 LaLonde DP, Bretscher A. The scaffold protein PDZK1 undergoes a head-to-tail intramolecular association that Klenk C, Vetter T, Zürn A, Vilardaga JP, Friedman PA, negatively regulates its interaction with EBP50. Wang B, Lohse MJ. Formation of a ternary complex Biochemistry. 2009 Mar 17;48(10):2261-71 among NHERF1, beta-arrestin, and parathyroid hormone receptor. J Biol Chem. 2010 Sep 24;285(39):30355-62 Li J, Callaway DJ, Bu Z. Ezrin induces long-range interdomain allostery in the scaffolding protein NHERF1. J Molina JR, Morales FC, Hayashi Y, Aldape KD, Georgescu Mol Biol. 2009 Sep 11;392(1):166-80 MM. Loss of PTEN binding adapter protein NHERF1 from

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 649

SLC9A3R1 (solute carrier family 9 (sodium/hydrogen McDonough WS, Berens ME exchanger), member 3 regulator 1)

plasma membrane in glioblastoma contributes to PTEN Bossard F, Silantieff E, Lavazais-Blancou E, Robay A, inactivation. Cancer Res. 2010 Sep 1;70(17):6697-703 Sagan C, Rozec B, Gauthier C. β1, β2, and β3 adrenoceptors and Na+/H+ exchanger regulatory factor 1 Wang B, Ardura JA, Romero G, Yang Y, Hall RA, expression in human bronchi and their modifications in Friedman PA. Na/H exchanger regulatory factors control cystic fibrosis. Am J Respir Cell Mol Biol. 2011 parathyroid hormone receptor signaling by facilitating Jan;44(1):91-8 differential activation of G(alpha) protein subunits. J Biol Chem. 2010 Aug 27;285(35):26976-86 Wheeler DS, Barrick SR, Grubisha MJ, Brufsky AM, Friedman PA, Romero G. Direct interaction between Xing W, Kim J, Wergedal J, Chen ST, Mohan S. Ephrin B1 NHERF1 and Frizzled regulates β-catenin signaling. regulates bone marrow stromal cell differentiation and Oncogene. 2011 Jan 6;30(1):32-42 bone formation by influencing TAZ transactivation via complex formation with NHERF1. Mol Cell Biol. 2010 This article should be referenced as such: Feb;30(3):711-21 McDonough WS, Berens ME. SLC9A3R1 (solute carrier Zhang Q, Pan Z, You G. Regulation of human organic family 9 (sodium/hydrogen exchanger), member 3 anion transporter 4 by protein kinase C and NHERF-1: regulator 1). Atlas Genet Cytogenet Oncol Haematol. altering the endocytosis of the transporter. Pharm Res. 2011; 15(8):643-650. 2010 Apr;27(4):589-96

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 650

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Gene Section Review

USP15 (ubiquitin specific peptidase 15) Monica Faronato, Sylvie Urbé, Judy M Coulson Physiology Department, School of Biomedical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool, L69 3BX, UK (MF, SU, JMC)

Published in Atlas Database: December 2010 Online updated version : http://AtlasGeneticsOncology.org/Genes/USP15ID44585ch12q14.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI USP15ID44585ch12q14.txt

Identity Transcription Other names: KIAA0529; UNPH4; Unph-2 Four transcripts of the human USP15 gene are described by Ensembl and are summarized in the HGNC (Hugo): USP15 accompanying diagram and table. According to Location: 12q14.1 Entrezgene, USP15 encodes a single reference sequence mRNA of 4611bp (NM_006313.1) DNA/RNA composed of 21 exons, which corresponds to USP15-203. However, three other USP15 splice Note variants utilise several alternative-splicing sites USP15 is a member of the ubiquitin-specific between exon 5 and exon 7 of this reference protease (USP) family; these cysteine proteases sequence. USP15-201, a 4698 bp mRNA comprised comprise the largest sub-group of deubiquitinase of 22 exons, is expressed at similar levels to the enzymes (DUBs). USP15 cleaves the isopeptide reference sequence (Angelats et al., 2003). bonds of polyubiquitin chains, and can cleave linear Expression of the remaining variants, USP15-204 ubiquitin fusion proteins (Baker et al., 1999). and the truncated USP15-202, is less well studied. Description The USP15 gene spans 145 kb of genomic DNA.

Schematic illustrating four human USP15 transcripts. The USP15 reference sequence mRNA (USP15-203) and three alternative splice variants are illustrated. The approximate position and size of exons within the USP15 gene, according to Ensembl, is shown for each splice variant.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 651

USP15 (ubiquitin specific peptidase 15) Faronato M, et al.

Summary table of USP15 transcripts.

Name Ensembl Entrez Aceview Size (bp) Exons

USP15-203 ENST00000353364 NM_006313.1 Variant b 4611 21

USP15-201 ENST00000280377 Variant a 4698 22

USP15-204 ENST00000393654 4626 23

USP15-202 ENST00000312635 Variant e 717 7

Schematic illustrating four human USP15 isoforms. The domain structure is shown for the reference sequence protein (USP15-203) and three alternative isoforms according to Ensembl. DUSP, domain present in ubiquitin-specific proteases; UBL, ubiquitin-like fold; UCH, ubiquitin carboxyl-terminal hydrolase. The cysteine motifs that form the zinc-binding site are shown in purple and the amino acids comprising the catalytic triad are shown in red. The approximate location of nuclear export sequences (triangles) and a putative nuclear localisation signal (inverted triangle) are shown above isoform USP15-203. Differences in amino acid sequence between isoforms are shown in light blue. The UCH is absent in isoform USP15-202, but USP15-201, USP15-203 and USP15-204 are predicted to be catalytically active.

Summary table of USP15 protein isoforms.

Name Ensembl Entrez Size (aa) MW (kDa)

USP15-203 ENSP00000258123 NP_006304.1 952 109

USP15-201 ENSP00000280377 981 112

USP15-204 ENSP00000377264 957 109

USP15-202 ENSP00000309240 235 40

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 652

USP15 (ubiquitin specific peptidase 15) Faronato M, et al.

cytoplasm and the nuclear compartment, with the Protein latter dependent on a C-terminal NLS (Park et al., Description 2000) that is conserved across species. Using an Usp15/USP15-specific polyclonal antibody, All USP15 isoforms encompass a single N-terminal Soboleva et al. demonstrated that in HeLa (human DUSP (domain in USPs) characterised by a novel cervical cancer cells) endogenous USP15 localised tripod-like fold with a conserved hydrophobic to the cytoplasm and nucleolus, but was largely surface patch that is predicted to participate in excluded from the nucleoplasm; whilst in NIH3T3 protein-protein interaction (de Jong et al., 2006). (mouse fibroblast cells), Usp15 localised in the The ubiquitin carboxyl-terminal hydrolase (UCH) cytoplasm and was enriched proximal to the plasma catalytic core of the USPs is typically around 350 membrane (Soboleva et al., 2005). Interestingly, amino acids, but consists of six conserved boxes, GFP-tagged USP15 (isoform USP15-203) adopts a interspersed by insertion sites for additional largely cytoplasmic distribution in human cancer sequence that can confer diversity (Ye et al., 2009). cell lines (Urbé, unpublished observation). The major insertion in USP15 is between boxes 3/4, and embeds an ubiquitin-like fold (UBL) domain Function within the catalytic domain. UBLs are commonly Human USP15 was cloned and characterized in found in the USPs and in certain other DUB 1999 (Baker et al., 1999) and belongs to the largest families (Zhu et al., 2007; Komander et al., 2009a). ubiquitin specific protease (USP) group of They exhibit low sequence conservation, but have deubiquitinating enzymes (DUBs). Protein high structural similarity with ubiquitin and have ubiquitination occurs at lysine residues through the been proposed to play important roles in regulating concerted action of E1 activating, E2 conjugating DUB catalytic function or interactions (Zhu et al., and E3 ligase enzymes. Ubiquitin contains seven 2007; Ye et al., 2009). The intercalation of a UBL lysine residues (K6, K11, K27, K29, K33, K48 and between boxes 3 and 4 of the catalytic domain K63), which allow poly-ubiquitin chains to increases the spacing between two sets of zinc- assemble through alternative isopeptide bond coordinating cysteine motifs, which form a linkages. In addition, linear ubiquitin chains may be functional zinc finger that is required for activity assembled through the amino-terminus and (Hetfeld et al., 2005). In the case of USP15, a substrate proteins may also be mono-ubiquitinated. second UBL is located directly adjacent to the Consequently, in addition to the classical K48-poly- DUSP (Zhu et al., 2007; Ye et al., 2009). ubiquitin tag that targets substrates for proteasome- The four USP15 splice variants encode four distinct mediated degradation, ubiquitination has multiple protein isoforms, which are illustrated in the cellular functions including regulation of protein diagram and summarised in the accompanying localisation and activity (Pickart and Eddins, 2004). table. As a consequence of alternative splicing, The general role of the DUBs, in addition to isoform USP15-201 has a 29 amino acid insert processing inactive ubiquitin precursors and within the unstructured region between the first keeping the 26S proteasome free of inhibitory UBL domain and the start of the UCH domain, ubiquitin chains, is to reverse the ubiquitination of whereas USP15-204 has a substitution of 3 amino substrate proteins (Amerik and Hochstrasser, 2004). acids for 8 residues within the first UBL. Otherwise There are approximately 80 active human DUBs the three isoforms that retain the catalytic domain that are divided into five families (Komander et al., are identical. They also retain predicted nuclear 2009a). These DUBs are steadily being assigned to export signals (NES) (Soboleva et al., 2005) and, specific substrates (Ventii and Wilkinson, 2008), by homology with rat, a functional nuclear which is increasingly revealing associations with localisation signal (NLS) (Park et al., 2000). signalling pathways in cancer (Sacco et al., 2010). Expression USP15 has activity against both mono- ubiquitinated and poly-ubiquitinated substrates; the USP15 messenger RNA (mRNA) expression is zinc-binding domain is necessary for USP15 to prevalent throughout the tissues of the body, process poly-ubiquitin chains, but is not required although its levels vary. Human USP15 is least for USP15 to remove ubiquitin from linear abundant in brain, lung and kidney, consistent with ubiquitin-GFP fusion proteins (Hetfeld et al., 2005). observations for mouse Usp15 and the rat ortholog Although USP15 is relatively promiscuous in UBP109 (Park et al., 2000; Angelats et al., 2003). showing little specificity between K48- and K63- In each species, USP15 is most abundant in testes, linked poly-ubiquitin chains, or between K63 and and is variously enriched in spleen, heart, skeletal K11 di-ubiquitin linkages, it has limited activity muscle or peripheral blood leukocytes. against K11-linked poly-ubiquitin chains or linear Localisation ubiquitin (Komander et al., 2009b; Bremm et al., As USP15 harbours both putative NES and NLS, its 2010). sub-cellular distribution may in part depend on the A recent endeavour to map protein partners of the cellular context. Rat UBP109 localises to both the DUBs by mass spectroscopy reported that, in common with USP4 and USP39, USP15 interacts

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 653

USP15 (ubiquitin specific peptidase 15) Faronato M, et al.

with several proteins involved in mRNA processing proteasomal degradation, allowing NF-kB to enter and so may play a role in ubiquitin-dependent the nucleus and activate transcription (Karin and control of splicing or mRNA decay (Sowa et al., Ben-Neriah, 2000). In response to TNFalpha, IkBa 2009). In addition, various cancer-signalling has been reported to interact with the CSN leading pathways have been associated with USP15. For to its deubiquitination and stabilisation by CSN- example, USP15 was one of twelve DUBs associated USP15 (Schweitzer et al., 2007). identified from an siRNA screen that impact on the The adenomatous polyposis coli (APC) tumour hepatocyte growth factor (HGF)-dependent cell suppressor and the beta-catenin oncogene are scattering response in non-small cell lung cancer frequently mutated in cancers, particularly of the and pancreatic cancer cells (Buus et al., 2009). A intestine, leading to constitutive wingless and Int-1 number of specific USP15 substrates have also (Wnt) signalling (Clevers, 2006). The CSN is been described, including the human papilloma proposed to control the balance of beta-catenin and virus (HPV) E6 oncoprotein (Vos et al., 2009), the APC through formation of a regulatory super- RING-box protein Rbx1 (Hetfeld et al., 2005), the complex. Deneddylation by the CSN promotes adenomatous polyposis coli (APC) tumour assembly of the beta-catenin destruction complex, suppressor (Huang et al., 2009), and the NF-kB whilst CSN-associated USP15 stabilises APC inhibitor IkBa (Schweitzer et al., 2007). (Huang et al., 2009). The APC also plays a role in The latter three examples are all connected with the mitotic fidelity through interaction with the plus COP9-signalosome (CSN), a conserved multi- end-binding protein EB1 that controls microtubule protein complex that regulates the cullin-RING growth and dynamics. In contrast to APC, EB1 is ligase (CRL) superfamily of ubiquitin E3 ligases destabilised by USP15, suggesting that this is not a (Wei et al., 2008). CRLs have a core complex direct substrate, but rather that USP15 stabilises a comprised of a cullin scaffold and the RING-box CRL that accelerates ubiquitination and degradation protein Rbx1 that recruit alternative adapter and of EB1 (Peth et al., 2007). It is interesting to substrate recognition proteins to form diverse E3 speculate that such links with microtubule complexes with different substrate specificities. The regulation may underpin recent reports that USP15 primary function of the CSN is to remove the levels can influence the taxol sensitivity of cancer ubiquitin-like modifier Nedd8 from the cullin cells (Xu et al., 2009; Xie et al., 2010). component. This both terminates E3 activity and is VCP/p97 is a large AAA+-type ATPase that acts as required for the reassembly of new CRLs (Wei et a chaperone in many cellular processes. Its basic al., 2008). The CSN plays a role in many cancer- function is to segregate ubiquitinated proteins from associated pathways including the cell cycle and macromolecular complexes, and VCP plays an DNA damage repair, and both CSN and CRL important role in recognizing and handling components may be dysregulated in tumours misfolded proteins, which are then either handed (Richardson and Zundel, 2005). Ubp12p, an S. over for degradation or recycled. The CSN directly pombe ortholog of human USP15, was shown interacts with VCP and USP15 can process VCP- through a systematic mass spectrometry screen to bound poly-ubiquitinated substrates, which bind the CSN (Zhou et al., 2003). This targets accumulate following USP15 depletion (Cayli et Ubp12p to nuclear cullins, where it is proposed to al., 2009). VCP is implicated in human protect against auto-ubiquitination and degradation neurodegenerative disorders where it co-localises of CRL components, in particular the substrate- with poly-glutamine aggregates and is proposed to specific adaptors. (Zhou et al., 2003; Wee et al., act as both an aggregate-formase and an unfoldase 2005). (Kakizuka, 2008). Another established VCP- Human USP15 also co-purifies with the CSN associated cofactor, the DUB Ataxin-3, is subject to complex and was reported to stabilise the CRL core polyglutamine repeat expansion, which causes component Rbx1 (Hetfeld et al., 2005), thereby Machado-Joseph disease (Madsen et al., 2009). acting as a positive regulator of these E3 ligase Although the mechanism is as yet unclear, USP15 complexes. In contrast, other studies suggest was recently associated with this same disorder USP15 may directly oppose CRL E3 ligase activity (Menzies et al., 2010). by deubiquitinating specific substrates. For Homology example, the CSN is involved in ubiquitin- dependent turnover of the IkBa inhibitor that retains USP15 belongs to the peptidase C19 family. The NF-kB in the cytosol (Schweitzer et al., 2007). closest paralogs based on sequence homology are Phosphorylation of IkBa triggers CRL-mediated USP4 and USP11. poly-ubiquitination of IkBa and subsequent

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 654

USP15 (ubiquitin specific peptidase 15) Faronato M, et al.

USP15 and the paralogs USP4 and USP11.The highly similar domain structure is illustrated for USP15 (NP_006304.1), USP4 (NP_003354.2) and USP11 (NP_004642.2). The degree of identity (Id) or similarity (Sim) was derived using ClustalW (EMBL- EBI); note that the indicated UCH homology includes the internal UBL domain. Overall, USP15 shares 56.9% identity (71.2% similarity) with USP4, and 42.4% identity (60.2% similarity) with USP11.

Mutations Ovarian cancer Somatic Note USP15 was identified from a genome-wide siRNA No mutations have yet been reported for USP15 screen for Paclitaxel-resistance in the cervical according to the COSMIC database, which includes cancer cell line HeLa and, in ovarian cancer data from four studies of 595 renal carcinoma, samples, Paclitaxel-resistant cases (n=3) showed glioblastoma, breast and colon cancers. lower expression of USP15 mRNA than drug- sensitive cases (n=6) (Xu et al., 2009). Moreover, Implicated in USP15 appeared to stabilise caspase-3, suggesting that reduced levels of USP15 may promote cell Cervical cancer survival rather than apoptosis in response to drug Note treatment. USP15 plays an oncogenic role in cervical cancer. Gastro-intestinal cancers Specific HPV strains are associated with cervical carcinoma and two HPV oncoproteins, E6 and E7, Note are expressed in these cancers. E6 hijacks a cellular USP15 was also amongst four genes, identified by E3 ubiquitin ligase and forms a complex with p53, expression profiling of Docetaxel-sensitive versus whilst E7 binds the retinoblastoma (Rb) protein; in resistant cells, which correlated with drug- each case the viral oncoproteins facilitate sensitivity in a panel of gastric cell lines. However, degradation of the cellular tumour suppressor. It no statistical correlation was established between was recently found that USP15 interacts with the elevated USP15 transcript levels and Docetaxel- oncogenic HPV16 E6 protein (Vos et al., 2009). sensitivity in 25 gastric cancer tissues (Xie et al., siRNA mediated depletion of USP15 led to a 2010). decrease in E6 protein, whilst overexpression of Germline mutations in APC lead to inherited colon wild-type but not catalytically inactive USP15 cancer and sporadic tumours are associated with promoted the stabilisation of E6. Interesting, beta-catenin stabilisation. Huang et al. show a role another group has shown that E7 is regulated in a for USP15 in stabilizing APC levels through the similar fashion by USP11 (Lin et al., 2008). action of the CSN (Huang et al., 2009). Intriguingly, USP4 also has functional Rb binding Machado-Joseph disease motifs (Blanchette et al., 2001; DeSalle et al., 2001) that are conserved in USP11 and USP15 (Baker et Note al., 1999). USP15 was identified from microarray analysis of a mouse model of spinocerebellar ataxia type 3. In

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 655

USP15 (ubiquitin specific peptidase 15) Faronato M, et al.

this study, USP15 transcript and protein levels were de Jong RN, Ab E, Diercks T, Truffault V, Daniëls M, decreased in both the ataxin-3 model, and in a Kaptein R, Folkers GE. Solution structure of the human ubiquitin-specific protease 15 DUSP domain. J Biol Chem. second huntingtin transgenic model of a 2006 Feb 24;281(8):5026-31 polyglutamine disorder; although overexpression of Peth A, Boettcher JP, Dubiel W. Ubiquitin-dependent USP15 promoted the accumulation of protein proteolysis of the microtubule end-binding protein 1, EB1, aggregates, this was independent of its activity on is controlled by the COP9 signalosome: possible poly-ubiquitin chains (Menzies et al., 2010). consequences for microtubule filament stability. J Mol Biol. 2007 Apr 27;368(2):550-63 References Schweitzer K, Bozko PM, Dubiel W, Naumann M. CSN controls NF-kappaB by deubiquitinylation of IkappaBalpha. Baker RT, Wang XW, Woollatt E, White JA, Sutherland EMBO J. 2007 Mar 21;26(6):1532-41 GR. Identification, functional characterization, and chromosomal localization of USP15, a novel human Zhu X, Ménard R, Sulea T. High incidence of ubiquitin-like ubiquitin-specific protease related to the UNP oncoprotein, domains in human ubiquitin-specific proteases. Proteins. and a systematic nomenclature for human ubiquitin- 2007 Oct 1;69(1):1-7 specific proteases. Genomics. 1999 Aug 1;59(3):264-74 Kakizuka A. Roles of VCP in human neurodegenerative Karin M, Ben-Neriah Y. Phosphorylation meets disorders. Biochem Soc Trans. 2008 Feb;36(Pt 1):105-8 ubiquitination: the control of NF-[kappa]B activity. Annu Lin CH, Chang HS, Yu WC. USP11 stabilizes HPV-16E7 Rev Immunol. 2000;18:621-63 and further modulates the E7 biological activity. J Biol Park KC, Choi EJ, Min SW, Chung SS, Kim H, Suzuki T, Chem. 2008 Jun 6;283(23):15681-8 Tanaka K, Chung CH. Tissue-specificity, functional Ventii KH, Wilkinson KD. Protein partners of characterization and subcellular localization of a rat deubiquitinating enzymes. Biochem J. 2008 Sep ubiquitin-specific processing protease, UBP109, whose 1;414(2):161-75 mRNA expression is developmentally regulated. Biochem J. 2000 Jul 15;349(Pt 2):443-53 Wei N, Serino G, Deng XW. The COP9 signalosome: more than a protease. Trends Biochem Sci. 2008 Blanchette P, Gilchrist CA, Baker RT, Gray DA. Dec;33(12):592-600 Association of UNP, a ubiquitin-specific protease, with the pocket proteins pRb, p107 and p130. Oncogene. 2001 Sep Buus R, Faronato M, Hammond DE, Urbé S, Clague MJ. 6;20(39):5533-7 Deubiquitinase activities required for hepatocyte growth factor-induced scattering of epithelial cells. Curr Biol. 2009 DeSalle LM, Latres E, Lin D, Graner E, Montagnoli A, Sep 15;19(17):1463-6 Baker RT, Pagano M, Loda M. The de-ubiquitinating enzyme Unp interacts with the retinoblastoma protein. Cayli S, Klug J, Chapiro J, Fröhlich S, Krasteva G, Orel L, Oncogene. 2001 Sep 6;20(39):5538-42 Meinhardt A. COP9 signalosome interacts ATP- dependently with p97/valosin-containing protein (VCP) and Angelats C, Wang XW, Jermiin LS, Copeland NG, Jenkins controls the ubiquitination status of proteins bound to NA, Baker RT. Isolation and characterization of the mouse p97/VCP. J Biol Chem. 2009 Dec 11;284(50):34944-53 ubiquitin-specific protease Usp15. Mamm Genome. 2003 Jan;14(1):31-46 Huang X, Langelotz C, Hetfeld-Pechoc BK, Schwenk W, Dubiel W. The COP9 signalosome mediates beta-catenin Zhou C, Wee S, Rhee E, Naumann M, Dubiel W, Wolf DA. degradation by deneddylation and blocks adenomatous Fission yeast COP9/signalosome suppresses cullin activity polyposis coli destruction via USP15. J Mol Biol. 2009 Aug through recruitment of the deubiquitylating enzyme 28;391(4):691-702 Ubp12p. Mol Cell. 2003 Apr;11(4):927-38 Komander D, Clague MJ, Urbé S. Breaking the chains: Amerik AY, Hochstrasser M. Mechanism and function of structure and function of the deubiquitinases. Nat Rev Mol deubiquitinating enzymes. Biochim Biophys Acta. 2004 Cell Biol. 2009 Aug;10(8):550-63 Nov 29;1695(1-3):189-207 Komander D, Reyes-Turcu F, Licchesi JD, Odenwaelder Pickart CM, Eddins MJ. Ubiquitin: structures, functions, P, Wilkinson KD, Barford D. Molecular discrimination of mechanisms. Biochim Biophys Acta. 2004 Nov 29;1695(1- structurally equivalent Lys 63-linked and linear 3):55-72 polyubiquitin chains. EMBO Rep. 2009 May;10(5):466-73 Hetfeld BK, Helfrich A, Kapelari B, Scheel H, Hofmann K, Madsen L, Seeger M, Semple CA, Hartmann-Petersen R. Guterman A, Glickman M, Schade R, Kloetzel PM, Dubiel New ATPase regulators--p97 goes to the PUB. Int J W. The zinc finger of the CSN-associated deubiquitinating Biochem Cell Biol. 2009 Dec;41(12):2380-8 enzyme USP15 is essential to rescue the E3 ligase Rbx1. Curr Biol. 2005 Jul 12;15(13):1217-21 Sowa ME, Bennett EJ, Gygi SP, Harper JW. Defining the human deubiquitinating enzyme interaction landscape. Richardson KS, Zundel W. The emerging role of the COP9 Cell. 2009 Jul 23;138(2):389-403 signalosome in cancer. Mol Cancer Res. 2005 Dec;3(12):645-53 Vos RM, Altreuter J, White EA, Howley PM. The ubiquitin- specific peptidase USP15 regulates human papillomavirus Soboleva TA, Jans DA, Johnson-Saliba M, Baker RT. type 16 E6 protein stability. J Virol. 2009 Sep;83(17):8885- Nuclear-cytoplasmic shuttling of the oncogenic mouse 92 UNP/USP4 deubiquitylating enzyme. J Biol Chem. 2005 Jan 7;280(1):745-52 Xu M, Takanashi M, Oikawa K, Tanaka M, Nishi H, Isaka K, Kudo M, Kuroda M. USP15 plays an essential role for Wee S, Geyer RK, Toda T, Wolf DA. CSN facilitates Cullin- caspase-3 activation during Paclitaxel-induced apoptosis. RING ubiquitin ligase function by counteracting Biochem Biophys Res Commun. 2009 Oct 16;388(2):366- autocatalytic adapter instability. Nat Cell Biol. 2005 71 Apr;7(4):387-91 Ye Y, Scheel H, Hofmann K, Komander D. Dissection of Clevers H. Wnt/beta-catenin signaling in development and USP catalytic domains reveals five common insertion disease. Cell. 2006 Nov 3;127(3):469-80 points. Mol Biosyst. 2009 Dec;5(12):1797-808

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 656

USP15 (ubiquitin specific peptidase 15) Faronato M, et al.

Bremm A, Freund SM, Komander D. Lys11-linked ubiquitin Xie L, Wei J, Qian X, Chen G, Yu L, Ding Y, Liu B. chains adopt compact conformations and are preferentially CXCR4, a potential predictive marker for docetaxel hydrolyzed by the deubiquitinase Cezanne. Nat Struct Mol sensitivity in gastric cancer. Anticancer Res. 2010 Biol. 2010 Aug;17(8):939-47 Jun;30(6):2209-16

Menzies FM, Huebener J, Renna M, Bonin M, Riess O, This article should be referenced as such: Rubinsztein DC. Autophagy induction reduces mutant ataxin-3 levels and toxicity in a mouse model of Faronato M, Urbé S, Coulson JM. USP15 (ubiquitin spinocerebellar ataxia type 3. Brain. 2010 Jan;133(Pt specific peptidase 15). Atlas Genet Cytogenet Oncol 1):93-104 Haematol. 2011; 15(8):651-657. Sacco JJ, Coulson JM, Clague MJ, Urbé S. Emerging roles of deubiquitinases in cancer-associated pathways. IUBMB Life. 2010 Feb;62(2):140-57

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 657

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Gene Section Review

CDKN2B (cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)) Joanna Fares, Linda Wolff, Juraj Bies Lab Cell Oncology, National Cancer Institute NIH, 37 Convent Dr, Bethesda MD 20892, USA (JF, LW, JB); Biochemistry and Molecular Biology Department, Georgetown University, Washington DC 20037, USA (JF)

Published in Atlas Database: January 2011 Online updated version : http://AtlasGeneticsOncology.org/Genes/CDKN2BID187ch9p21.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI CDKN2BID187ch9p21.txt

1 (PRC1) are strongly expressed and are found to Identity localize to the INK4/ARF RD. BMI1 has been Other names: CDK4I; INK4B; MTS2; P15; TP15; shown to interact specifically with CDC6. These p15INK4b polycomb group (PcG) complexes repress the locus HGNC (Hugo): CDKN2B activity through the establishment of repressive chromatin modifications such as H3K27 Location: 9p21.3 trimethylation. During senescence, binding of these complexes to RD is lost and correlates with DNA/RNA increased expression of the INK4/ARF genes Description (Figure 1). The p15INK4B gene is also silenced by a long non The p15INK4B gene encompasses 6.41 Kb of DNA coding RNA, called antisense non-coding RNA in and has 2 coding exons. It is tandemly linked to the INK4 locus (ANRIL), whose expression was p16INK4A and p14ARF within 42 Kb of genomic found to be inversed to the expression of locus located on chromosome 9p21. The locus is p15INK4B in leukemia cell lines. It was shown that commonly referred to as INK4/ARF locus. ANRIL induces the silencing of p15INK4B in cis Transcription and trans by triggering heterochromatin formation in a Dicer-independent manner. PcG complexes are CDKN2B gene encodes 2 distinct transcript recruited to the INK4/ARF locus by ANRIL and variants: p15 and p10. p10 arises from an modulate its repression (Figure 1). Additionally, a alternative 5' splice donor site within intron 1 of: naturally occurring antisense circular ANRIL - p15. RNAs (cANRIL) has also been described. Different - p15: 3.82 Kb of mRNA. forms of cANRIL are produced in most INK4/ARF - p10: 0.86 Kb of mRNA. expressing cells, suggesting that alternative splicing Regulation: A conserved DNA element with the events leading to different ANRIL structures can ability to regulate the entire INK4/ARF locus has contribute to changes in PcG-mediated INK4/ARF been identified in close proximity of the locus and repression. named regulatory domain (RD). It appears to Specific transcription regulators of p15INK4B have promote transcriptional repression of all three genes also been reported (see Figure 2). These include encoded by the locus, in a manner dependent on TGF-b, MIZ-1, SMAD3/SMAD4 complex, SP1, c- CDC6. In proliferating embryonic fibroblasts MYC, IRF8, PU.1, SNAIL and EGR1 factors (MEFs), EZH2 a member of the polycomb among others. repressive complex 2 (PRC2) as well as BMI1 and M33 members of the polycomb repressive complex

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 658

CDKN2B (cyclin-dependent kinase inhibitor 2B (p15, inhibits Fares J, et al. CDK4))

Figure 1. p15INK4B expression is dramatically induced by its ability to trigger the p15INK4b promoter TGF-b, suggesting that it is a potent downstream activation upon TPA treatment. effector of TGF-b mediated growth arrest. In murine myeloid cells specifically, the interferon MIZ-1 is a transcription factor that has been shown consensus sequence-binding protein/interferon to bind the initiator element (Inr) in the promoter regulatory factor 8 (ICSBP/IRF-8) in combination region and induce the transcription of p15INK4B in with PU.1 were shown to bind p15Ink4b promoter epithelial cells. However it can also recruit and activate the transcription of the gene in transcriptional co-repressors such as c-MYC and response to IFN-b treatment. GFI-1 to the promoter region by binding to them In AML patients with inv(16), p15INK4B silencing and forming inhibitory complexes. TGF-b has been was found to be caused by inv(16)-encoded core reported to re-activate the core promoter through binding factor beta-smooth muscle myosin heavy downregulation of C-MYC and GFI-1, thereby chain (CBFb-SMMHC). CBFb-SMMHC was releasing endogenous MIZ-1 from inhibition. shown to displace RUNX1 from a newly The SMAD3/4 complex readily forms following determined CBF site in the promoter of p15INK4B. TGF-b treatment and physical interaction between this complex, MIZ-1 and promoter-bound SP1 Protein protein has been described. These interactions have been proposed to constitute a platform for the Description recruitment of co-activators, and do not seem to be p15INK4B transcript encodes two protein isoforms affected by the suppressor activity of c-MYC. The p15 and p15.5 that are functionally inhibitory function of c-MYC seems to be cell-type indistinguishable. p15.5 is an N-terminally dependent, as it was confirmed in epithelial cells extended variant of p15 initiated from an upstream but not in the hematopoietic lineage. In myeloid alternative in frame initiation codon. p15 protein is cells, the transcription factor c-MYB was shown to 138 aa long and its mass is 14.72 KDa. prevent the transcription and the upregulation of p10 transcript encodes the shorter variant. The p15INK4B which is normally associated with the protein consists of 78 aa only and its mass is 10 differentiation process. The mechanism by which KDa. It shares a similar NH2 terminus to p15 but C-MYB does this is unclear but it is not through contains a different basic COOH terminus that is upregulation of c-MYC, a known target of c-MYB. translated from the p15Ink4b intronic region A tri-component transcriptional complex consisting (Figure 2). of SNAIL, SP1 and EGR-1 was also described for

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 659

CDKN2B (cyclin-dependent kinase inhibitor 2B (p15, inhibits Fares J, et al. CDK4))

Figure 2.

Expression II- Function during hematopoietic cell differentiation. p15INK4B is expressed at very low levels under Another role for p15INK4B during differentiation normal physiological conditions. Its expression of early hematopoietic progenitors has also been seems to be lineage restricted. In bone marrow cells described. In knockout mice, loss of p15INK4B the highest level of p15INK4B is mainly detected in was shown to favor the differentiation of common maturing monocytes/macrophages and myeloid progenitors (CMP) into granulocyte lymphocytes. The gene expression has also been macrophage progenitors (GMP) resulting in an reported to be normally up-regulated during imbalance between the myeloid and the erythroid megakaryocytic differentiation. Increased compartments. expression of p15INK4B is also detected during III- Function during cellular senescence. stress and senescence of cells. Cellular senescence is accompanied by hallmark Localisation features that include the up-regulation of cell cycle Nucleus and cytoplasm. inhibitors like p15INK4B, p16INK4A and p21CIP. When overexpressed, p15INK4B engages the RB Function pathway to promote a stable senescent state which I- Function in the cell cycle. has been shown to occur in part through a process p15INK4B belongs to the INK4 family of protein that involves alterations in heterochromatin and the kinase inhibitors named for their high and exclusive stable silencing of E2F target genes. specificity towards the catalytic activity of cyclin Another mechanism that has been described is the dependent kinases 4 (CDK4) or 6 (CDK6). inactivation of c-MYC which results in the Structural studies have demonstrated that the induction of p15INK4B expression and correlates protein performs its inhibitory activity by allosteric with the global changes in heterochromatin competition with the D-type cyclins to bind structure known to be associated with cellular CDK4/6 kinases and prevents the formation of senescence. active CDK4/6-cyclin-Ds complexes. This keeps the retinoblastoma protein (RB), which is Homology downstream of this pathway, in its p15INK4B is highly conserved. Its sequence in hypophosphorylated state. Hypophosporylated RB homo sapiens is > 85% similar to bos taurus, mus binds and inactivates the E2F transcription factors musculus and rattus norvegicus; and > 70% similar required for the transcriptional activation of genes to gallus gallus. necessary for entry into the S phase of the cell cycle and DNA synthesis. Mutations Three other members of the INK4 family of CDK Note inhibitors: p16INK4A, p18INK4C and p19INK4D Intragenic p15INK4B mutations are highly are encoded by unique genes and share roughly infrequent. 40% homology. They have similar protein structure characterized by the presence of four ankyrin-like motif tandem repeats that are predicted to be engaged in protein-protein interactions.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 660

CDKN2B (cyclin-dependent kinase inhibitor 2B (p15, inhibits Fares J, et al. CDK4))

Implicated in Prognosis Hypermethylation is found in up to 60% of CMML Various hematological disorders and cases and correlates with a more aggressive form of malignancies disease. Experimentally, a LysMCre mouse model was developed in which p15INK4B gene is deleted Note specifically in cells of the myeloid lineage, to better p15INK4B is frequently epigenetically silenced in mimic the loss of the gene expression the way it is leukemias, myelodysplastic syndromes and observed in humans. The mice develop non-reactive myeloproliferative diseases by mechanisms monocytosis of the peripheral blood as well as involving aberrant DNA methylation and/or histone increased myeloid blast progenitors in the bone modifications. These diseases are subcategorized by marrow. In this way the mice develop symptoms the French-American-British (FAB) co-operative that closely resemble CMML in human patients. group, based on the percentage of blast cells in bone marrow and peripheral blood, degree of Acute myeloid leukemia (AML) cytopenia, and in accordance to the direction of Disease differentiation along the myeloid or lymphoid AML is the most common type of leukemia among lineages as well as the degree of maturation of the adults with 14000 new cases diagnosed each year, hematopoietic cells. and with 9000 deaths per year in the United States. Myelodysplastic syndromes (MDS) AML classification into ten different subtypes was originally defined by the FAB cooperative group Disease according to the direction of differentiation along Myelodysplastic syndromes are heterogeneous the different myeloid lineages as well as the degree clonal hematologic disorders characterized by of maturation of the cells. However, AML dysplasia of the myeloid bone marrow cells exemplifies a genetically heterogeneous cancer with accompanied with peripheral blood cytopenia and more than a hundred genetic aberrations implicated increased risk of transformation to acute myeloid in the disease. leukemia (AML). MDS transforms into AML once Prognosis the percentage of blasts in the bone marrow has Despite the great genetic and phenotypic exceeded 30% (FAB). MDS can arise in patients de heterogeneity of AML, hypermethylation of the novo (primary MDS), or following chemotherapy or exposure to toxins (secondary MDS). According p15INK4B promoter region (CpG island) is found to the Leukemia and Lymphoma Society reports, to occur in up to 80% of AML cases across all FAB subtypes. It correlates with a loss of p15INK4B MDS most commonly affects males aged 70 and expression, poor prognosis and shorter survival above, and is considered to be a disease of the time in patients. The p15INK4B methylation status elderly. About 11000 new cases are diagnosed each year, resulting in an incidence rate of 4 cases per in AML patients in clinical remission is now 100000 population for both genders. monitored and used as a reliable prognostic marker for relapse. These findings were further Prognosis experimentally confirmed in a conditional knockout p15INK4B is silenced by promoter mouse model where myeloid-specific gene hypermethylation in > 50% of MDS cases. Levels inactivation resulted in an increased susceptibility of p15INK4B methylation increase as the disease to retrovirus-induced myeloid leukemia. progresses and provide a marker that can predict occurrence of AML. Acute lymphoblastic leukemia (ALL) Chronic myelomonocytic leukemia Disease There are about 4000 new cases of ALL in the (CMML) United States each year. It appears most often in Disease children younger than age 10. ALL is the most The defining features of CMML are an absolute common leukemia in children. However, it can monocytosis in peripheral blood (> 1x109/L), appear in people of any age. About one-third of increased numbers of monocytes in bone marrow, a cases are adults. variable degree of dysplasia and less than 5% and Prognosis 20% of blasts in peripheral blood and bone marrow, In B and T acute lymphoblastic leukemia the respectively. There are two types of CMML: p15INK4B promoter methylation as well as proliferative and dysplastic. Roughly half of deletion of the entire locus has been reported. CMML diagnosed patients have an elevated white blood cell count commonly associated with Chronic leukemia hepatomegaly and splenomegaly Disease (myeloproliferative form of the disease). Patients Chronic leukemia can be subdivided into two lacking these features are generally considered to subtypes, chronic myelogenous leukemia (CML) have the myelodysplastic form of the disease. and chronic lymphocytic leukemia (CLL). CLL is

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 661

CDKN2B (cyclin-dependent kinase inhibitor 2B (p15, inhibits Fares J, et al. CDK4)) primarily an adult disease; it is very rare in children and young adults. The median age of diagnosis is References 72 years, and about 60% of patients are male. In the Jen J, Harper JW, Bigner SH, Bigner DD, Papadopoulos United States, about 15000 people are diagnosed N, Markowitz S, Willson JK, Kinzler KW, Vogelstein B. Deletion of p16 and p15 genes in brain tumors. Cancer with CLL each year. Res. 1994 Dec 15;54(24):6353-8 This disease is also commonly referred to as B-cell chronic lymphocytic leukemia (B-CLL). Tsubari M, Tiihonen E, Laiho M. Cloning and characterization of p10, an alternatively spliced form of p15 Prognosis cyclin-dependent kinase inhibitor. Cancer Res. 1997 Jul Promoter hypermethylation has been reported in a 15;57(14):2966-73 small subset of B-CLL (11%) at all stages of the Drexler HG. Review of alterations of the cyclin-dependent disease. In CML, silencing of p15INK4B either by kinase inhibitor INK4 family genes p15, p16, p18 and p19 deletion or hypermethylation of its promoter was in human leukemia-lymphoma cells. Leukemia. 1998 Jun;12(6):845-59 not found to be a very frequent event. Aoki E, Uchida T, Ohashi H, Nagai H, Murase T, Ichikawa Glioblastoma multiforme (GBM) A, Yamao K, Hotta T, Kinoshita T, Saito H, Murate T. Disease Methylation status of the p15INK4B gene in hematopoietic progenitors and peripheral blood cells in myelodysplastic GBM is the most common and very aggressive syndromes. Leukemia. 2000 Apr;14(4):586-93 brain tumor in adults. It involves glial cells and Fuxe J, Raschperger E, Pettersson RF. Translation of accounts for more than 50% of parenchymal brain p15.5INK4B, an N-terminally extended and fully active tumors approximately 20% of all intracranial form of p15INK4B, is initiated from an upstream GUG tumors. Glioblastoma growth is characterized by a codon. Oncogene. 2000 Mar 23;19(13):1724-8 high motility of tumor cells that display broad Jeffrey PD, Tong L, Pavletich NP. Structural basis of chemoresistance leading to frequent post-surgical inhibition of CDK-cyclin complexes by INK4 inhibitors. tumor recurrence. It is one of the most dreaded Genes Dev. 2000 Dec 15;14(24):3115-25 cancer diagnoses due to its poor prognosis and the Latres E, Malumbres M, Sotillo R, Martín J, Ortega S, limited treatment options, with the median survival Martín-Caballero J, Flores JM, Cordón-Cardo C, Barbacid duration after diagnosis varying from 6 months to 2 M. Limited overlapping roles of P15(INK4b) and P18(INK4c) cell cycle inhibitors in proliferation and years. tumorigenesis. EMBO J. 2000 Jul 3;19(13):3496-506 Prognosis Malumbres M, Ortega S, Barbacid M. Genetic analysis of Homozygous deletion of the mammalian cyclin-dependent kinases and their inhibitors. p15INK4B/p14ARF/p16INK4A locus on Biol Chem. 2000 Sep-Oct;381(9-10):827-38 chromosome 9p21.3 is a signature genetic event Teofili L, Morosetti R, Martini M, Urbano R, Putzulu R, that drives the pathogenesis of GBM. The deletion Rutella S, Pierelli L, Leone G, Larocca LM. Expression of of this locus is the most common homozygous cyclin-dependent kinase inhibitor p15(INK4B) during deletion present in GBM (> 75% of samples). normal and leukemic myeloid differentiation. Exp Hematol. 2000 May;28(5):519-26 Specific p15INK4B promoter methylation was also detected in 37% of patients diagnosed with Amati B. Integrating Myc and TGF-beta signalling in cell- glioblastoma and it correlated with shorter survival. cycle control. Nat Cell Biol. 2001 May;3(5):E112-3 Schmidt M, Koller R, Haviernik P, Bies J, Maciag K, Wolff Hepatocellular carcinoma (HCC) L. Deregulated c-Myb expression in murine myeloid Disease leukemias prevents the up-regulation of p15(INK4b) normally associated with differentiation. Oncogene. 2001 HCC is a primary malignancy of the liver that Sep 27;20(43):6205-14 mostly arises secondary to hepatitis B or C viral infections. Outcome of the disease is poor, because Seoane J, Pouponnot C, Staller P, Schader M, Eilers M, Massagué J. TGFbeta influences Myc, Miz-1 and Smad to only 10 - 20% of hepatocellular carcinomas can be control the CDK inhibitor p15INK4b. Nat Cell Biol. 2001 removed completely using surgery, and the cancer Apr;3(4):400-8 is usually deadly within 3 to 6 months. Staller P, Peukert K, Kiermaier A, Seoane J, Lukas J, Prognosis Karsunky H, Möröy T, Bartek J, Massagué J, Hänel F, Eilers M. Repression of p15INK4b expression by Myc The suppression of the C-MYC oncogene induces through association with Miz-1. Nat Cell Biol. 2001 cellular senescence in diverse tumor types including Apr;3(4):392-9 hepatocellular carcinoma and correlates with Teofili L, Martini M, Di Mario A, Rutella S, Urbano R, increased p15INK4b expression. In primary HCC, Luongo M, Leone G, Larocca LM. Expression of p15INK4B promoter is hypermethylated in about p15(ink4b) gene during megakaryocytic differentiation of 50% of the cases, and homozygous deletions of normal and myelodysplastic hematopoietic progenitors. both p16INK4A and p15INK4B have been reported Blood. 2001 Jul 15;98(2):495-7 in 30% HCC patients and cell lines. This suggests Wolff L, Schmidt M, Koller R, Haviernik P, Watson R, Bies that p15INK4B might be contributing to human J, Maciag K. Three genes with different functions in hepatocarcinogenesis through a pathway associated transformation are regulated by c-Myb in myeloid cells. Blood Cells Mol Dis. 2001 Mar-Apr;27(2):483-8 with cellular senescence.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 662

CDKN2B (cyclin-dependent kinase inhibitor 2B (p15, inhibits Fares J, et al. CDK4))

Narita M, Nũnez S, Heard E, Narita M, Lin AW, Hearn SA, Peters G. An INKlination for epigenetic control of Spector DL, Hannon GJ, Lowe SW. Rb-mediated senescence. Nat Struct Mol Biol. 2008 Nov;15(11):1133-4 heterochromatin formation and silencing of E2F target genes during cellular senescence. Cell. 2003 Jun Solomon DA, Kim JS, Jean W, Waldman T. Conspirators 13;113(6):703-16 in a capital crime: co-deletion of p18INK4c and p16INK4a/p14ARF/p15INK4b in glioblastoma multiforme. Tessema M, Länger F, Dingemann J, Ganser A, Kreipe H, Cancer Res. 2008 Nov 1;68(21):8657-60 Lehmann U. Aberrant methylation and impaired expression of the p15(INK4b) cell cycle regulatory gene in chronic Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, myelomonocytic leukemia (CMML). Leukemia. 2003 Feinberg AP, Cui H. Epigenetic silencing of tumour May;17(5):910-8 suppressor gene p15 by its antisense RNA. Nature. 2008 Jan 10;451(7175):202-6 Qin Y, Liu JY, Li B, Sun ZL, Sun ZF. Association of low p16INK4a and p15INK4b mRNAs expression with their Basu S, Liu Q, Qiu Y, Dong F. Gfi-1 represses CDKN2B CpG islands methylation with human hepatocellular encoding p15INK4B through interaction with Miz-1. Proc carcinogenesis. World J Gastroenterol. 2004 May Natl Acad Sci U S A. 2009 Feb 3;106(5):1433-8 1;10(9):1276-80 Bies J, Sramko M, Fares J, Rosu-Myles M, Zhang S, Koller Schmidt M, Bies J, Tamura T, Ozato K, Wolff L. The R, Wolff L. Myeloid-specific inactivation of p15Ink4b results interferon regulatory factor ICSBP/IRF-8 in combination in monocytosis and predisposition to myeloid leukemia. with PU.1 up-regulates expression of tumor suppressor Blood. 2010 Aug 12;116(6):979-87 p15(Ink4b) in murine myeloid cells. Blood. 2004 Jun Burd CE, Jeck WR, Liu Y, Sanoff HK, Wang Z, Sharpless 1;103(11):4142-9 NE. Expression of linear and novel circular forms of an Aggerholm A, Holm MS, Guldberg P, Olesen LH, Hokland INK4/ARF-associated non-coding RNA correlates with P. Promoter hypermethylation of p15INK4B, HIC1, CDH1, atherosclerosis risk. PLoS Genet. 2010 Dec and ER is frequent in myelodysplastic syndrome and 2;6(12):e1001233 predicts poor prognosis in early-stage patients. Eur J Hu CT, Chang TY, Cheng CC, Liu CS, Wu JR, Li MC, Wu Haematol. 2006 Jan;76(1):23-32 WS. Snail associates with EGR-1 and SP-1 to upregulate Markus J, Garin MT, Bies J, Galili N, Raza A, Thirman MJ, transcriptional activation of p15INK4b. FEBS J. 2010 Le Beau MM, Rowley JD, Liu PP, Wolff L. Methylation- Mar;277(5):1202-18 independent silencing of the tumor suppressor INK4b Kotake Y, Nakagawa T, Kitagawa K, Suzuki S, Liu N, (p15) by CBFbeta-SMMHC in acute myelogenous Kitagawa M, Xiong Y. Long non-coding RNA ANRIL is leukemia with inv(16). Cancer Res. 2007 Feb 1;67(3):992- required for the PRC2 recruitment to and silencing of 1000 p15(INK4B) tumor suppressor gene. Oncogene. 2011 Apr Papageorgiou SG, Lambropoulos S, Pappa V, 21;30(16):1956-62 Economopoulou C, Kontsioti F, Papageorgiou E, Tsirigotis P, Dervenoulas J, Economopoulos T. Hypermethylation of This article should be referenced as such: the p15INK4B gene promoter in B-chronic lymphocytic Fares J, Wolff L, Bies J. CDKN2B (cyclin-dependent leukemia. Am J Hematol. 2007 Sep;82(9):824-5 kinase inhibitor 2B (p15, inhibits CDK4)). Atlas Genet Wu CH, van Riggelen J, Yetil A, Fan AC, Bachireddy P, Cytogenet Oncol Haematol. 2011; 15(8):658-663. Felsher DW. Cellular senescence is an important mechanism of tumor regression upon c-Myc inactivation. Proc Natl Acad Sci U S A. 2007 Aug 7;104(32):13028-33

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 663

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Gene Section Review

DLX4 (distal-less homeobox 4) Patricia E Berg, Saurabh Kirolikar The George Washington University Medical Center, Washington DC 20037, USA (PEB), The George Washington University, Department of Biochemistry and Molecular Biology, Washington DC 20037, USA (SK)

Published in Atlas Database: January 2011 Online updated version : http://AtlasGeneticsOncology.org/Genes/DLX4ID49827ch17q21.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI DLX4ID49827ch17q21.txt

mapped to 17q21-22 (Nakamura et al., 1996). We Identity then mapped BP1, which also mapped to the same Other names: BP1; DLX7; DLX8; DLX9 chromosomal region (Fu et al., 2001). In fact, our HGNC (Hugo): DLX4 BAC included sequences from both BP1 and DLX7. When we published the paper showing that Location: 17q21.33 BP1 is a repressor of the beta-globin gene and identifying BP1, DLX4 and DLX7 as isoforms, to DNA/RNA prevent confusion in the literature we gave the gene Note a single name, DLX4, based on the fact that the BP1, DLX4 and DLX7 are not interchangeable DLX4 DNA sequence was published first (Chase et names for the same gene, as sometimes claimed. al., 2002). Thus, the DLX4 gene encodes at least We cloned a cDNA encoding BP1 from a library three different proteins with presumably different made from K562 erythroleukemia cells, often used functions, DLX4, BP1 and DLX7. The NCBI as a model for hemoglobin switching. After it was Database is somewhat confusing in this regard - the sequenced it was apparent that part of the BP1 gene is called DLX4, but BP1 is named DLX4 sequence was identical to that of two other variant 1 and DLX7 is called DLX4 variant 2. published "genes", DLX4 and DLX7; upstream of Description nucleotide 565 of BP1, all three had entirely The DLX4 gene is located at 17q21.33 and is about different sequences, while downstream of that site 5761 bp in length (chr17:48,046,562-48,052,322). the sequences were identical (Fu et al., 2001; Chase et al., 2002). This suggested that the three might be Transcription isoforms of one gene, differing only in the first Three different mRNAs are expressed by DLX4, exon; this can occur by alternative splicing or by BP1 and DLX7. BP1 mRNA is about 2012 bp. use of alternative promoters. DLX7 had been

The red lines indicate the predicted ORFs. Number 565 indicates the nucleotide of BP1 where divergence occurs among BP1, DLX4, and DLX7. HB is the homeobox region. The regions between the two vertical lines indicate the regions of DNA identity. The complete ORF is not available for DLX4.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 664

DLX4 (distal-less homeobox 4) Berg PE, Kirolikar S

Amino acid sequence alignment between BP1 (Q92988-1), DLX7 (Q92988-2) and an unidentified isoform of DLX4 (Q92988-3). The sequences were obtained from the UniProt database which has incorrectly identified the BP1 sequence as DLX4.

expression can lead to decreased cell death and, as Protein shown below, increased proliferation. Description BP1 appears to be a repressor of BRCA1. Three breast cancer cell lines engineered to overexpress The BP1 protein is an alternatively spliced isoform BP1 show decreased BRCA1 RNA and protein, derived from the DLX4 gene. The protein is about while cells in which BP1 is knocked down by 240 aa in length with the calculated molecular siRNA treatment show increased BRCA1 weight of 26 kDa. The observed weight of the expression, suggesting that BP1 activity may protein is about 36 kDa on Western blots using contribute to reduced BRCA1 in some breast lysates from breast cancer and prostate cancer cell cancers (Kluk et al., 2010). lines. This difference may be due to post- translational modifications of BP1 protein. BP1 Implicated in protein has a 116 aa N-terminal region, 60 aa homeobox domain and a 64 aa C-terminal domain, Breast cancer while DLX7 is 168 aa. Note Expression BP1 is activated in about 80% of invasive ductal In normal tissue: BP1 protein is expressed in adult breast (IDC) tumors. Aberrant expression of BP1 kidney and placenta and in low levels in normal was shown by semi-quantitative RT-PCR, where breast and fetal liver (Chase et al., 2002). 80% of tumors were BP1 positive, and by immunostaining, where 81% of tumors were BP1 Localisation positive, a remarkable agreement between mRNA Both nuclear and cytoplasmic immunostaining are and protein expression (Fu et al., 2003; Man et al., seen in BP1 positive breast tumors and prostate 2005). Surprisingly, 89% of the tumors of African tumors (Man et al., 2005; Schwartz et al., 2009). American women (AAW) were BP1 positive, Function compared with 57% of the tumors of Caucasian women (p=0.04). In addition, 100% of ER negative Functionally, we demonstrated that BP1 is a tumors were BP1 positive, compared with 73% of repressor of the beta-globin gene, while DLX7 ER positive (p=0.03). Both tumors of AAW and ER binds to the same DNA sequence upstream of the negative tumors are associated with aggressiveness. beta-globin gene but lacks the ability to repress it A group in China quantitated BP1 mRNA in the (Fu et al., 2001; Chase et al., 2002). Thus, the tumors of 142 Chinese women, discovering that functions of BP1 and DLX7 are clearly different in 65% of their tumors were BP1 positive, and this context. BP1 acts to repress embryonic and confirming an association between high BP1 fetal globin genes during early development but is mRNA expression and ER negative tumors (Yu et itself repressed during normal adult erythropoiesis. al., 2008b). Inflammatory breast cancer (IBC) is an BP1 overexpression induces increased Bcl-2 extremely aggressive breast cancer, with expression and decreased apoptosis. pBP1 binds to approximately half the survival seen in IDC; 100% the regulatory region of the bcl-2 gene, an anti- of the forty-six cases of IBC we examined were apoptotic gene, resulting in elevated expression of highly BP1 immunoreactive, suggesting an Bcl-2 protein and resistance to TNF-alpha in MCF- association between aggressiveness, frequency of 7 breast cancer cells (Stevenson et al., 2007). BP1 positivity, and BP1 protein (pBP1) staining Increased BP1 is associated with decreased intensity (Man et al., 2009). cleavage of caspase-7, caspase-8 and caspase-9, and pBP1 expression correlates with breast cancer increased expression of PARP. Thus, high BP1 progression. The frequency of pBP1 positivity,

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 665

DLX4 (distal-less homeobox 4) Berg PE, Kirolikar S

distribution and intensity of BP1 expression all Interestingly, the three isoforms were frequently co- increased with the progression of tumor expressed in the same cases. development from 0% (normal) to 21% in Next we compared the growth-inhibitory and cyto- hyperplasia, 46% in ductal carcinoma in situ, and differentiating activities of all-trans retinoic acid 81% in IDC (p <0.0001) (Man et al., 2005). This (ATRA) in two acute promyelocytic leukemia suggests BP1 expression may be an important (APL) cells lines, NB4 (ATRA-responsive) and R4 upstream factor in an oncogenic pathway and may (ATRA-resistant) cells relative to BP1 levels contribute to tumor progression. (Awwad et al., 2008). NB4 cells and R4 cells both Expression of BP1 is associated with larger expressed BP1; BP1 was repressed after ATRA tumor size. We have recently shown a correlation treatment of NB4 cells but not R4 cells. In NB4 between BP1 mRNA or protein expression and cells engineered to overexpress BP1, proliferation tumor size in women with invasive ductal breast was no longer inhibited and differentiation was cancer. This correlation is also true in a mouse reduced two- to three-fold. In patients, BP1 levels model (submitted). were increased in all pre-treatment APL patients BP1 positivity correlates with increased tested, while BP1 expression was decreased in 91% proliferation. BP1 positive cells were significantly of patients after combined ATRA and more frequently positive for Ki67, a proliferation chemotherapy treatment. Two patients underwent marker, when 5000 BP1 positive tumor cells were disease relapse during follow up; one patient compared with 5000 BP1 negative tumor cells exhibited a 42-fold increase in BP1 expression, (Man et al., 2005). while the other showed no change. This suggests BP1 appears to be associated with metastasis. BP1 may be part of a pathway involved in Among the IBC cases, nine had metastasized. The resistance to therapy. lymph nodes corresponding to these cases were all Prostate cancer BP1 positive, providing evidence that BP1 is expressed in metastasis (Man et al., 2009). Note Moreover, BP1 positive cells were observed in Prostate cancer, another hormone dependent solid lymphatic ducts of patients with metastatic IBC. A tumor, was examined for activation of BP1 correlation between high BP1 mRNA levels and (Schwartz et al., 2008). Significant BP1 metastasis in invasive ductal breast cancer was immunoreactivity was identified in 70% of prostatic observed by Yu et al. (2008b). tumors, whether the analysis was performed on BP1 mRNA levels are associated with survival. tissue sections (50 cases) or tissue microarray Kaplan-Meier curves revealed that patients with platforms (123 cases). We also observed low BP1 grade III tumors expressing high BP1 mRNA levels immunostaining in 42% of hyperplastic cells, showed decreased survival compared with patients similar to the 46% BP1 positivity in hyperplastic whose grade III tumors contained lower BP1 breast cells. Compared to normal and hyperplastic mRNA levels (Yu et al., 2008b). tissues, the malignant tissues consistently showed BP1 is activated by DNA amplification. It is the highest number of BP1 positive cells and the important to determine the factors that activate highest intensity of BP1 immunostaining, similar to BP1. Approximately 33% of the tumors we our observations in breast. In tissue sections, twelve examined from women with metastatic breast cases with paired carcinoma and prostatic cancer exhibited DNA amplification of BP1. intraepithelial neoplasia (PIN) showed agreement, Amplification was associated with BP1 positivity both components exhibiting strong by immunostaining in all cases (Cavalli et al., immunoreactivity. Tumor proliferation, assayed 2008). with Ki67 immunostaining, was higher in cancer Overall, the data strongly suggest that BP1 may be cells that were BP1 positive relative to those that a useful new biomarker in early detection of breast were BP1 negative, in agreement with the data in cancer and a potential therapeutic target. breast cancer cells. These findings suggest that BP1 is an important upstream factor in the carcinogenic Leukemia pathway of prostate cancer and that the expression Note of BP1 may reflect or directly contribute to tumor We examined BP1 in the bone marrow of leukemia progression and/or invasion. patients by semi-quantitative RT-PCR, finding that Non-small cell lung cancer (NSCLC) BP1 was activated in 63% of acute myeloid leukemias (AML), including 81% of pediatric and Note 47% of adult patients with AML, in 32% of T-cell An interesting study by Yu et al. (2008a) acute lymphocytic leukemias (ALL) but not in the demonstrated that high BP1 mRNA levels occur in pre-B ALL cases (Haga et al., 2000). Expression of NSCLC tumors, compared with adjacent normal BP1 occurred in primitive leukemia cells and in cells or normal lung samples. High mRNA levels CD34 positive progenitors. In the same study we are associated with stage III tumors, lower disease examined expression of DLX4 and DLX7 by free survival (DFS) and lower overall survival. In designing primers specific for each isoform.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 666

DLX4 (distal-less homeobox 4) Berg PE, Kirolikar S

fact, high BP1 mRNA is an independent predictor Awwad RT, Do K, Stevenson H, Fu SW, Lo-Coco F, of DFS. Costello M, Campbell CL, Berg PE. Overexpression of BP1, a homeobox gene, is associated with resistance to all-trans retinoic acid in acute promyelocytic leukemia References cells. Ann Hematol. 2008 Mar;87(3):195-203 Nakamura S, Stock DW, Wydner KL, Bollekens JA, Cavalli LR, Man YG, Schwartz AM, Rone JD, Zhang Y, Takeshita K, Nagai BM, Chiba S, Kitamura T, Freeland Urban CA, Lima RS, Haddad BR, Berg PE. Amplification of TM, Zhao Z, Minowada J, Lawrence JB, Weiss KM, the BP1 homeobox gene in breast cancer. Cancer Genet Ruddle FH. Genomic analysis of a new mammalian distal- Cytogenet. 2008 Nov;187(1):19-24 less gene: Dlx7. Genomics. 1996 Dec 15;38(3):314-24 Yu M, Wan Y, Zou Q. Prognostic significance of BP1 Haga SB, Fu S, Karp JE, Ross DD, Williams DM, Hankins mRNA expression level in patients with non-small cell lung WD, Behm F, Ruscetti FW, Chang M, Smith BD, Becton D, cancer. Clin Biochem. 2008a Jul;41(10-11):824-30 Raimondi SC, Berg PE. BP1, a new homeobox gene, is Yu M, Yang Y, Shi Y, Wang D, Wei X, Zhang N, Niu R. frequently expressed in acute leukemias. Leukemia. 2000 Expression level of beta protein 1 mRNA in Chinese breast Nov;14(11):1867-75 cancer patients: a potential molecular marker for poor Fu S, Stevenson H, Strovel JW, Haga SB, Stamberg J, Do prognosis. Cancer Sci. 2008b Jan;99(1):173-8 K, Berg PE. Distinct functions of two isoforms of a Man YG, Schwartz A, Levine PH, Teal C, Berg PE. BP1, a homeobox gene, BP1 and DLX7, in the regulation of the putative signature marker for inflammatory breast cancer beta-globin gene. Gene. 2001 Oct 31;278(1-2):131-9 and tumor aggressiveness. Cancer Biomark. 2009;5(1):9- Chase MB, Fu S, Haga SB, Davenport G, Stevenson H, 17 Do K, Morgan D, Mah AL, Berg PE. BP1, a homeodomain- Schwartz AM, Man YG, Rezaei MK, Simmens SJ, Berg containing isoform of DLX4, represses the beta-globin PE. BP1, a homeoprotein, is significantly expressed in gene. Mol Cell Biol. 2002 Apr;22(8):2505-14 prostate adenocarcinoma and is concordant with prostatic Fu SW, Schwartz A, Stevenson H, Pinzone JJ, Davenport intraepithelial neoplasia. Mod Pathol. 2009 Jan;22(1):1-6 GJ, Orenstein JM, Gutierrez P, Simmens SJ, Abraham J, Kluk BJ, Fu Y, Formolo TA, Zhang L, Hindle AK, Man YG, Poola I, Stephan DA, Berg PE. Correlation of expression of Siegel RS, Berg PE, Deng C, McCaffrey TA, Fu SW. BP1, BP1, a homeobox gene, with estrogen receptor status in an isoform of DLX4 homeoprotein, negatively regulates breast cancer. Breast Cancer Res. 2003;5(4):R82-7 BRCA1 in sporadic breast cancer. Int J Biol Sci. 2010 Sep Man YG, Fu SW, Schwartz A, Pinzone JJ, Simmens SJ, 10;6(5):513-24 Berg PE. Expression of BP1, a novel homeobox gene, correlates with breast cancer progression and invasion. This article should be referenced as such: Breast Cancer Res Treat. 2005 Apr;90(3):241-7 Berg PE, Kirolikar S. DLX4 (distal-less homeobox 4). Atlas Stevenson HS, Fu SW, Pinzone JJ, Rheey J, Simmens SJ, Genet Cytogenet Oncol Haematol. 2011; 15(8):664-667. Berg PE. BP1 transcriptionally activates bcl-2 and inhibits TNFalpha-induced cell death in MCF7 breast cancer cells. Breast Cancer Res. 2007;9(5):R60

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 667

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Gene Section Review

IL17A (interleukin 17A) Norimitsu Inoue, Takashi Akazawa Department of Molecular Genetics, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Osaka 537-8511, Japan (NI, TA)

Published in Atlas Database: January 2011 Online updated version : http://AtlasGeneticsOncology.org/Genes/IL17AID40945ch6p12.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI IL17AID40945ch6p12.txt

Identity Pseudogene Other names: CTLA8; IL-17; IL-17A; IL17 No pseudogene. HGNC (Hugo): IL17A Protein Location: 6p12.2 Note Local order: Centromere-PKHD1 (polycystic The IL17A protein is a disulfide-linked kidney and hepatic diseases 1)-MIR206 homodimeric glycoprotein. Members of the IL17 (microRNA 206)-MIR133B (microRNA 133b)- protein family (IL17A to F) have four highly IL17A-IL17F (interleukin 17F)-SLC25A20P1 conserved cysteine residues on each of the (solute carrier family 25, member 20 pseudogene monomeric peptides (Moseley et al., 2003; Kolls et 1)-MCM3 (minichromosome maintenance complex al., 2004; Korn et al., 2009). Structural analysis of component 3)-Telomere. the IL17F protein indicates that these four cysteines participate in the characteristic cysteine-knot DNA/RNA formation found in certain other growth factors Description such as nerve growth factor (NGF), bone morphogenetic proteins (BMPs), and transforming 3 exons. growth factor-beta1 (TGFbeta1) (Hymowitz et al., Transcription 2001). Two additional cysteine residues participate The transcript is 1859 bp and has a 45 bp 5' UTR, a in homodimer formation via inter-chain disulfide- 468 bp coding sequence, and a 1346 bp 3' UTR. bonds. The IL17F peptide can also form a functional heterodimer with IL17A.

IL17A gene. The IL17A gene spans a region of 4252 bp composed of three exons (untranslated region (UTR), light blue; coding region, blue) and two introns (brown). Exons 1, 2, and 3 are 72 bp (45 bp 5' UTR plus 27 bp coding region), 203 bp (all coding region), and 1584 bp (238 bp coding region plus 1346 bp 3' UTR) in length, respectively. The two introns are 1144 bp and 1249 bp in length, respectively.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 668

IL17A (interleukin 17A) Inoue N, Akazawa T

IL-17A protein. IL17A protein (155 amino acids) is composed of a signal peptide (light green, 23 amino acids) and a mature peptide (green, 132 amino acids). The four conserved cysteines (Cys) form the intra-chain disulfide bonds indicated by black lines (Cys94/Cys144 and Cys99/Cys146) (Hymowitz et al., 2001). The two cysteines indicated by asterisks (Cys33 and Cys129) participate in homodimer formation via inter-chain disulfide bonds. Asparagine 68 (Asn68, black circle) is predicted to be glycosylated.

Description factor 4 (IRF4), runt-related transcriptional factor 1 (RUNX1), and aryl hydrocarbon receptor (AHR, a Each IL17A monomer is a 19.9-kD peptide that nuclear receptor for a number of low-molecular consists of 155 amino acids. The IL17A peptide weight chemicals such as the tryptophan comprises a 23-amino acid signal peptide and a photoproduct 6-formylindolo[3,2-b]carbazole 132-amino acid mature peptide (IL17A homodimer, (FICZ)) all positively regulate Th17 cell 35 kD). differentiation (Korn et al., 2009; Hirahara et al., Expression 2010). Moreover, prostaglandin E2, ATP, and C- IL17A is secreted by CD4-positive T cells (Th17 type lectin ligands act on antigen-presenting cells to cells), which also produce IL17F, IL21, and IL22 facilitate Th17 cell differentiation. In contrast, IL4, (Korn et al., 2009; Eyerich et al., 2010). CD8- Interferon-gamma (IFNgamma), IL27, suppressor positive T cells, gamma delta T cells, natural killer of cytokine signaling 3 (SOCS3), and STAT5 (NK) cells, NKT cells, and lymphoid tissue inducer suppress Th17 cell differentiation. Finally, high (LTi) cells also secret IL17A. These leukocytes all levels of lactic acid secreted from tumors via the express the retinoic acid receptor-related orphan Warburg effect act on macrophages to mediate nuclear receptor C (RORC, the human analogue of increased IL17A production but not Th17 cell mouse RORgammat that is a splice variant of the differentiation (Shime et al., 2008; Yabu et al., Rorc gene). RORC is essential for IL17A 2011). production. Th17 cells in both the mouse and the human have Th17 cells are the third subset of helper T cells, recently been shown to differentiate from naïve with effector functions distinct from Th1 and Th2 CD4 T cells independently of TGFbeta1 signaling. cells. Th17 cells are differentiated from naïve T These TGFbeta1-independent Th17 cells instead cells in the presence of IL6 plus TGFbeta1 (Bettelli differentiate in the presence of IL6, IL23 and et al., 2007; McGeachy et al., 2008; Awasthi et al., IL1beta (Hirahara et al., 2010; Ghoreschi et al., 2009). In the presence of TGFbeta1 alone, naïve T 2010). TGFbeta1-independent Th17 cells co- cells express the transcriptional factor forkhead box express RORgammat and T-bet (TBX21, T-box P3 (FOXP3) and differentiate into induced protein 21) and exhibit more pathogenic potential regulatory T cells (iTreg cells). In the presence of than TGFbeta1-dependent Th17 cells in the IL6 alone, the cells express the transcriptional development of experimental allergic factor BCL6 and differentiate into T follicular encephalomyelitis (EAE). helper cells (Tfh cells) (Nurieva et al., 2009). Function Interleukin 21 is secreted from Th17 cells and Interleukin 17A is a pro-inflammatory cytokine and amplifies Th17 cell generation by an autocrine act on a variety of cells (e.g., fibroblasts, epithelial mechanism. Interleukin 21 also induces the cells, and monocytes) to induce the production of expression of the IL23 receptor in the Th17 cells cytokines (IL6, tumor necrosis factor-alpha (Bettelli et al., 2007; McGeachy and Cua, 2008; TNFalpha, granulocyte-macrophage colony- Awasthi and Kuchroo, 2009). Interleukin 23 is stimulating-factor (GMCSF), granulocyte colony- secreted from dendritic cells and macrophages stimulating-factor (GCSF)), chemokines following stimulation by Toll-like receptor ligands. (chemokine (C-X-C motif) ligand 1 (CXCL1), IL23 in turn mediates the stabilization and CXCL2, CXCL5, CXCL8) and matrix maintenance of the Th17 cell phenotype, inducing metalloproteinases (MMP2, MMP13) to mediate IL17A production by Th17 cells (Stritesky et al., the recruitment, activation and migration of 2008; McGeachy et al., 2009). Interleukin 1beta is neutrophils and myeloid cells (Kolls and Linden, also involved in the induction of IL17A secretion 2004; Eyerich et al., 2010). and the promotion of Th17 differentiation (Chung IL17A, IL17F, and the IL17A-IL17F heterodimer et al., 2009). bind to a heteromeric receptor complex composed In addition to RORC and the aforementioned of IL17 receptor A (IL17RA) and IL17 receptor C cytokines, signal transducer and activator of (IL17RC). IL17RA is expressed at high levels in transcription 3 (STAT3), interferon regulatory

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 669

IL17A (interleukin 17A) Inoue N, Akazawa T

hematopoietic cells and at low levels in epithelial 2009a). An increased population of Th17 cells is cells, fibroblasts and endothelial cells (Gaffen, also associated with lower grading stages of 2009). On the other hand, IL17RC is expressed at prostate cancer (Sfanos et al., 2008). In addition, low levels in hematopoietic cells and at high levels Immunotherapy is more effective in patients with in the adrenal gland, prostate, liver, and thyroid. prostate cancer that have a higher number of Th17 Although cytokines secreted by most activated cells. helper T cells generally stimulate the Janus kinase In the mouse system, the overexpression of IL17A (JAK)/STAT pathway, the IL17 family cytokines in tumor cells suppresses tumor growth in a stimulate signal pathways that are common in the cytotoxic T lymphocyte-dependent manner innate immune system, such as the Toll-like (Benchetrit et al., 2002). The transfer of tumor receptor signaling pathway. antigen-specific T cells polarized to the IL17- IL17 receptors have a conserved domain termed the producing phenotype also induces the eradication of "similar expression to fibroblast growth factor/IL- tumor cells by inducing strong CD8-positive T cell 17R (SEFIR)" domain in the cytoplasmic region. activation (Martin-Orozco et al., 2009). This domain is similar to the Toll-/IL-1R (TIR) Furthermore, the deficiency of IL17A in mice domain (Gaffen, 2009). When the IL17 receptor is promotes the growth and metastasis of tumors activated, the adaptor molecule actin related gene 1 (Martin-Orozco et al., 2009; Kryczek et al., 2009b). (Act1, a U-box E3 ubiquitin ligase) is recruited to Interleukin 17A-producing T cells are predicted to the SEFIR domain and mediates the lysine63-linked induce the recruitment of other effector cells (e.g., ubiquitination of tumor necrosis factor receptor- cytotoxic CD8-positive T cells and NK cells) to the associated factor 6 (TRAF6). Ubiquitinated TRAF6 tumors by inducing the expression of CXCL9 and then activates the transcriptional factor nuclear CXCL10 by tumors (Kryczek et al., 2009a). factor-kappaB (NFkappaB), various mitogen- Moreover, Th17 cells induce the expression of activated protein (MAP) kinases including Erk and chemokine (C-C motif) ligand 20 (CCL20, a ligand p38, and CCAAT/enhancer-binding proteins for chemokine (C-C motif) receptor 6 (CCR6)) in (C/EBP beta and C/EBP gamma). tumor tissues. Chemokine (C-C motif) ligand 20 Homology recruits dendritic cells to mediate anti-tumor effects in a CCL20/CCR6-depedent manner (Martin- IL17A is a prototypical member of the IL17 family. Orozco et al., 2009). This family includes six proteins, termed IL17A, Pro-tumor effects. IL17B, IL17C, IL17D, IL17E (also called IL25), The proportion of Th17 cells in the peripheral blood and IL17F. Interleukin 17A to F are not is increased in patients with advanced stage gastric homologous to any other known proteins. IL17A cancer compared with patients with early stage shows the highest homology with IL17F (55%). It diseases (Zhang et al., 2008). In patients with is less similar to the other IL17 family members hepatocellular carcinoma, increased intratumoral (IL17B, 29%; IL17C, 23%; IL17D, 25%; and accumulation of IL17A-producing cells is IL17E, 17%) (Kolls and Linden, 2004). significantly associated with a poor prognosis (Zhang et al., 2009). Implicated in In the mouse system, the overexpression of IL17A in tumors facilitates tumor growth via the induction Various cancers of angiogenesis in the tumor microenvironment Note (Numasaki et al., 2003; Numasaki et al., 2005). Infiltration of IL17A-producing T cells in tumors. Furthermore, IL17A-deficient or IL17RA-deficient IL17A-producing T cells and/or IL17A expression mouse models were used to show that IL17A was are detected in many human tumor tissues, involved in the promotion of tumor growth via including ovarian, pancreatic, renal cell, prostate, induction of myeloid derived suppressor cells gastric, and hepatocellular cancers (Zou et al., (MDSC) (He et al., 2010), activation of IL6-STAT3 2010; Maniati et al., 2010). Although IL17A- pathway (Wang et al., 2009), and production of producing cells are not the dominant T cell subset IL17A by tumor-infiltrating gamma delta T cells in the tumor microenvironment, they are increased (Wakita et al., 2010). to greater extent in the tumor site than in the The discrepancies between anti-tumor and pro- peripheral blood of the patients (Kryczek et al., tumor effects may be due to distinct roles of IL17A 2009a). and IL17A-producing cells in different tumors. Anti-tumor effects. Gastric cancer In some human tumors, such as ovarian and prostate cancer, IL17A and IL17A-producing cells Note are associated with antitumorigenic actions. The single nucleotide polymorphism (SNP) in the Increased IL17A levels in ascites are well- IL17A gene promoter region, which is located at a correlated with better patient survival and lower position -197 from the start codon (rs2275913, G/A grading stages of ovarian cancer (Kryczek et al., SNPs, a position at 52051033 bp from pter), has been examined in Japanese gastric cancer patients

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 670

IL17A (interleukin 17A) Inoue N, Akazawa T

(Shibata et al., 2009). The frequency of the A-allele Bettelli E, Korn T, Kuchroo VK. Th17: the third member of (odds ratio, 1.42) and the A/A homozygote (odds the effector T cell trilogy. Curr Opin Immunol. 2007 Dec;19(6):652-7 ratio, 3.02) is significantly increased in gastric cancer patients compared with healthy controls. McGeachy MJ, Cua DJ. Th17 cell differentiation: the long and winding road. Immunity. 2008 Apr;28(4):445-53 Autoimmune and inflammatory Roark CL, Simonian PL, Fontenot AP, Born WK, O'Brien diseases RL. gammadelta T cells: an important source of IL-17. Curr Note Opin Immunol. 2008 Jun;20(3):353-7 Interleukin 17A and IL17-producing cells are Sfanos KS, Bruno TC, Maris CH, Xu L, Thoburn CJ, associated with the pathogenesis of many DeMarzo AM, Meeker AK, Isaacs WB, Drake CG. Phenotypic analysis of prostate-infiltrating lymphocytes autoimmune and inflammatory diseases such as reveals TH17 and Treg skewing. Clin Cancer Res. 2008 EAE/multiple sclerosis, inflammatory skin Jun 1;14(11):3254-61 diseases/psoriasis, inflammatory bowel diseases, Shime H, Yabu M, Akazawa T, Kodama K, Matsumoto M, and experimental arthritis/rheumatoid arthritis in Seya T, Inoue N. Tumor-secreted lactic acid promotes IL- humans as well as mice (Korn et al., 2009; Awasthi 23/IL-17 proinflammatory pathway. J Immunol. 2008 Jun and Kuchroo, 2009). 1;180(11):7175-83 Stritesky GL, Yeh N, Kaplan MH. IL-23 promotes Infections maintenance but not commitment to the Th17 lineage. J Note Immunol. 2008 Nov 1;181(9):5948-55 Both IL17A and IL17F are preferentially produced Zhang B, Rong G, Wei H, Zhang M, Bi J, Ma L, Xue X, Wei during infections with the Gram-negative bacteria G, Liu X, Fang G. The prevalence of Th17 cells in patients Klebsiella pneumonia, Borrelia burgdorferi, and with gastric cancer. Biochem Biophys Res Commun. 2008 Salmonella enterica enteritidis; the Gram-positive Sep 26;374(3):533-7 bacterium Listeria monocytogenes; the acid-fast Awasthi A, Kuchroo VK. Th17 cells: from precursors to bacterium Mycobacterium tuberculosis; and the players in inflammation and infection. Int Immunol. 2009 May;21(5):489-98 yeast-like fungi Pneumocystis jirovecii and Candida albicans (Korn et al., 2009; O'Connor et Chung Y, Chang SH, Martinez GJ, Yang XO, Nurieva R, al., 2010). In an early response to the infection, Kang HS, Ma L, Watowich SS, Jetten AM, Tian Q, Dong C. Critical regulation of early Th17 cell differentiation by IL17A is predominantly secreted by gamma delta T interleukin-1 signaling. Immunity. 2009 Apr 17;30(4):576- cells (Roark et al., 2008; Cua et al., 2010). This 87 results in the rapid recruitment of neutrophils to Gaffen SL. Structure and signalling in the IL-17 receptor sites of infection for efficient pathogen clearance. family. Nat Rev Immunol. 2009 Aug;9(8):556-67 Later, antigen-specific alphabetaTh17 cells Korn T, Bettelli E, Oukka M, Kuchroo VK. IL-17 and Th17 contribute to the response. Cells. Annu Rev Immunol. 2009;27:485-517 Kryczek I, Banerjee M, Cheng P, Vatan L, Szeliga W, Wei References S, Huang E, Finlayson E, Simeone D, Welling TH, Chang Hymowitz SG, Filvaroff EH, Yin JP, Lee J, Cai L, Risser P, A, Coukos G, Liu R, Zou W. Phenotype, distribution, Maruoka M, Mao W, Foster J, Kelley RF, Pan G, Gurney generation, and functional and clinical relevance of Th17 AL, de Vos AM, Starovasnik MA. IL-17s adopt a cystine cells in the human tumor environments. Blood. 2009a Aug knot fold: structure and activity of a novel cytokine, IL-17F, 6;114(6):1141-9 and implications for receptor binding. EMBO J. 2001 Oct Kryczek I, Wei S, Szeliga W, Vatan L, Zou W. Endogenous 1;20(19):5332-41 IL-17 contributes to reduced tumor growth and metastasis. Benchetrit F, Ciree A, Vives V, Warnier G, Gey A, Sautès- Blood. 2009b Jul 9;114(2):357-9 Fridman C, Fossiez F, Haicheur N, Fridman WH, Tartour Martin-Orozco N, Muranski P, Chung Y, Yang XO, E. Interleukin-17 inhibits tumor cell growth by means of a Yamazaki T, Lu S, Hwu P, Restifo NP, Overwijk WW, T-cell-dependent mechanism. Blood. 2002 Mar Dong C. T helper 17 cells promote cytotoxic T cell 15;99(6):2114-21 activation in tumor immunity. Immunity. 2009 Nov Moseley TA, Haudenschild DR, Rose L, Reddi AH. 20;31(5):787-98 Interleukin-17 family and IL-17 receptors. Cytokine Growth McGeachy MJ, Chen Y, Tato CM, Laurence A, Joyce- Factor Rev. 2003 Apr;14(2):155-74 Shaikh B, Blumenschein WM, McClanahan TK, O'Shea JJ, Numasaki M, Fukushi J, Ono M, Narula SK, Zavodny PJ, Cua DJ. The interleukin 23 receptor is essential for the Kudo T, Robbins PD, Tahara H, Lotze MT. Interleukin-17 terminal differentiation of interleukin 17-producing effector promotes angiogenesis and tumor growth. Blood. 2003 Apr T helper cells in vivo. Nat Immunol. 2009 Mar;10(3):314-24 1;101(7):2620-7 Nurieva RI, Chung Y, Martinez GJ, Yang XO, Tanaka S, Kolls JK, Lindén A. Interleukin-17 family members and Matskevitch TD, Wang YH, Dong C. Bcl6 mediates the inflammation. Immunity. 2004 Oct;21(4):467-76 development of T follicular helper cells. Science. 2009 Aug 21;325(5943):1001-5 Numasaki M, Watanabe M, Suzuki T, Takahashi H, Nakamura A, McAllister F, Hishinuma T, Goto J, Lotze MT, Shibata T, Tahara T, Hirata I, Arisawa T. Genetic Kolls JK, Sasaki H. IL-17 enhances the net angiogenic polymorphism of interleukin-17A and -17F genes in gastric activity and in vivo growth of human non-small cell lung carcinogenesis. Hum Immunol. 2009 Jul;70(7):547-51 cancer in SCID mice through promoting CXCR-2- Wang L, Yi T, Kortylewski M, Pardoll DM, Zeng D, Yu H. dependent angiogenesis. J Immunol. 2005 Nov IL-17 can promote tumor growth through an IL-6-Stat3 1;175(9):6177-89 signaling pathway. J Exp Med. 2009 Jul 6;206(7):1457-64

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 671

IL17A (interleukin 17A) Inoue N, Akazawa T

Zhang JP, Yan J, Xu J, Pang XH, Chen MS, Li L, Wu C, Li transcriptional regulation in Th17 cell differentiation. SP, Zheng L. Increased intratumoral IL-17-producing cells Cytokine Growth Factor Rev. 2010 Dec;21(6):425-34 correlate with poor survival in hepatocellular carcinoma patients. J Hepatol. 2009 May;50(5):980-9 Maniati E, Soper R, Hagemann T. Up for Mischief? IL- 17/Th17 in the tumour microenvironment. Oncogene. 2010 Cua DJ, Tato CM. Innate IL-17-producing cells: the Oct 21;29(42):5653-62 sentinels of the immune system. Nat Rev Immunol. 2010 Jul;10(7):479-89 O'Connor W Jr, Zenewicz LA, Flavell RA. The dual nature of T(H)17 cells: shifting the focus to function. Nat Immunol. Eyerich S, Eyerich K, Cavani A, Schmidt-Weber C. IL-17 2010 Jun;11(6):471-6 and IL-22: siblings, not twins. Trends Immunol. 2010 Sep;31(9):354-61 Wakita D, Sumida K, Iwakura Y, Nishikawa H, Ohkuri T, Chamoto K, Kitamura H, Nishimura T. Tumor-infiltrating IL- Ghoreschi K, Laurence A, Yang XP, Tato CM, McGeachy 17-producing gammadelta T cells support the progression MJ, Konkel JE, Ramos HL, Wei L, Davidson TS, of tumor by promoting angiogenesis. Eur J Immunol. 2010 Bouladoux N, Grainger JR, Chen Q, Kanno Y, Watford Jul;40(7):1927-37 WT, Sun HW, Eberl G, Shevach EM, Belkaid Y, Cua DJ, Chen W, O'Shea JJ. Generation of pathogenic T(H)17 Zou W, Restifo NP. T(H)17 cells in tumour immunity and cells in the absence of TGF-β signalling. Nature. 2010 Oct immunotherapy. Nat Rev Immunol. 2010 Apr;10(4):248-56 21;467(7318):967-71 Yabu M, Shime H, Hara H, Saito T, Matsumoto M, Seya T, He D, Li H, Yusuf N, Elmets CA, Li J, Mountz JD, Xu H. IL- Akazawa T, Inoue N. IL-23-dependent and -independent 17 promotes tumor development through the induction of enhancement pathways of IL-17A production by lactic acid. tumor promoting microenvironments at tumor sites and Int Immunol. 2011 Jan;23(1):29-41 myeloid-derived suppressor cells. J Immunol. 2010 Mar 1;184(5):2281-8 This article should be referenced as such: Hirahara K, Ghoreschi K, Laurence A, Yang XP, Kanno Y, Inoue N, Akazawa T. IL17A (interleukin 17A). Atlas Genet O'Shea JJ. Signal transduction pathways and Cytogenet Oncol Haematol. 2011; 15(8):668-672.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 672

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Gene Section Mini Review

MYBBP1A (MYB binding protein (P160) 1a) Claudia Perrera, Riccardo Colombo Department of Cell Biology-Oncology, Nerviano Medical Sciences, Viale Pasteur 10, Nerviano 20014, Italy (CP, RC)

Published in Atlas Database: January 2011 Online updated version : http://AtlasGeneticsOncology.org/Genes/MYBBP1AID41467ch17p13.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI MYBBP1AID41467ch17p13.txt

Identity Protein Other names: FLJ37886; P160; PAP2 Description HGNC (Hugo): MYBBP1A Human MYBBP1A is a 1328 aa long protein. Location: 17p13.2 Murine MYBBP1A was originally identified as a protein interacting with the leucine zipper of c-Myb DNA/RNA (Favier et al., 1994). Subsequently, in 1998, the human gene homologue of MYBBP1A was cloned Note and its chromosomal location mapped to 17p13.3 Total gene length 16491 bp, mRNA length 4122 bp, (Keough et al., 1999). telomeric to SPNS2 and centromeric to GGT6. Two variants described. MYBBP1A gene is composed Expression by 26 exones and 28 introns. MYBBP1A is ubiquitously expressed (Tavner et Description al., 1998). The human MYBBP1A gene is located on Localisation chromosome 17p13.3 (Keough et al., 1999). MYBBP1A is a nuclear protein, predominantly Transcription localized in the nucleolus (Keough et al., 2003). MYBBP1A has been confirmed as a resident The complete MYBBP1A cDNA is 4518 bp, protein of the nucleolus by three large-scale including 25 bp of 5' UTR and 506 bp of 3' UTR up proteomic studies that have established a protein to the polyA tail. inventory of this sub-nuclear compartment

Schematic representation of Mybbp1A protein. aa 1-582 is the domain reported to interact in vitro with Myb. NLS: Nuclear and nucleolar localisation signal. The indicated S, T and Y are phosphorylated residues identified in several phospho-proteomic studies.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 673

MYBBP1A (MYB binding protein (P160) 1a) Perrera C, Colombo R

(Andersen et al., 2002; Scherl et al., 2002; studies (18 out of a total of 21) reside within the Andersen et al., 2005). The nuclear/nucleolar ~200 amino-acid long C-terminal portion of the localization signals are present in the C-terminal tail protein, which has been shown to be relevant for its of MYBBP1A. nuclear and nucleolar localization (Keough et al., Function 2003). Notably, MYBBP1A was also found to be also a component of the proteome as well as the MYBBP1A functions have not yet been completely phospho-proteome of the human mitotic spindle. clarified. It was originally identified as a protein MYBBP1A contains several consensus motifs for able to interact with the negative regulatory domain several kinases, but until now, only Ser1303 has (NRD) of c-Myb; however, it was later shown to been proven in vitro and in HeLa cells to be indeed lack any significant effect in a Myb-dependent phosphorylated by Aurora B kinase (Perrera et al., transcription reporter assay (Favier et al., 1994). 2010). In this work, it has been shown that MYBBP1A has been found to interact with and MYBBP1A depletion by RNAi causes a delay in regulate several transcription factors: it binds and progression through mitosis and defects in mitotic represses both Prep1-Pbx1, involved in spindle assembly and stability, indicating that, like development and organogenesis, and also PGC-1a, other nucleolar proteins, MYBBP1A may have a a key regulator of metabolic processes such as role in insuring correct mitotic progression (Perrera mitochondrial biogenesis and respiration and et al., 2010). gluconeogenesis in liver (Fan et al., 2004; Diaz et MYBBP1A has been reported to be also al., 2007). MYBBP1A acts as a co-repressor for sumoylated upon MG132 treatment (Matafora et RelA/p65, a member of the NFkB family, by al., 2009). competing with the co-activator p300 histone acetyltrasferase for interaction with the Homology transcription activation domain (TAD) of Orthologous genes for MYBBP1A sharing a high RelA/p65. It is also a co-repressor on the Period2 degree of similarity are present in rat and mice. promoter, repressing the expression of Per2, an Protein homologues have also been recognized in essential gene in the regulation of the circadian dog, bovine, and chicken and a MYBBP1A-like clock (Owen et al., 2007; Hara et al., 2009). protein spanning 1269 residues and showing a 60% Conversely, MYBBP1A is a positive regulator of similarity to the human protein has been identified the aromatic hydrocarbon receptor (AhR) which in zebrafish, suggesting that MYBBP1A is mediates transcriptional responses to certain significantly conserved across vertebrate species hydrophobic ligands, such as dioxin, by enhancing (Amsterdam et al., 2004). MYBBP1A shares some the ability of AhR to activate transcription (Jones et homology to a yeast protein called POL5, reported al., 2002). to be an essential DNA polymerase in MYBBP1A has also been reported to be a Saccharomyces cerevisiae (Yang et al., 2003). component of macromolecular complexes such as the B-WICH complex, a 3 MDa assembly made of Implicated in proteins and RNAs, formed during active transcription (Cavellan et al., 2006) or part of large Various cancers interactomes such as the SMN interactome (Fuller Disease et al., 2010). MYBBP1A maps at 17p13.3, a region frequently MYBBP1A can be post-translationally processed in lost in many solid and haematological tumors, such some type of cells to generate an amino-terminal as breast and ovarian cancer, medulloblastoma, fragments of 67 kDa (p67). Ribosomal stress astrocytoma, leukemias, etc. This indicates that this induced by Actinomycin D (an inhibitor of chromosomal band contains one or more tumor ribosome biogenesis) treatment causes MYBBP1A suppressor genes. However, MYBBP1A is unlikely processing and translocation from the nucleolus to a candidate for being a tumor suppressor gene, as it the nucloplasm (Diaz et al., 2007; Yamauchi et al., lies centromeric to the regions of LOH described 2008), indicating a possible MYBBP1A role in (Keough et al., 1999). ribosome biogenesis. Several post-translational modifications have been References described for MYBBP1A, even if their biological significance is not yet clarified. MYBBP1A is Favier D, Gonda TJ. Detection of proteins that bind to the leucine zipper motif of c-Myb. Oncogene. 1994 reported to be a heavily phosphorylated protein in Jan;9(1):305-11 cells, according to several large-scale mass spectrometry-based phosphoproteomic studies Tavner FJ, Simpson R, Tashiro S, Favier D, Jenkins NA, Gilbert DJ, Copeland NG, Macmillan EM, Lutwyche J, (Beausoleil et al., 2004; Beausoleil et al., 2006; Keough RA, Ishii S, Gonda TJ. Molecular cloning reveals Nousiainen et al., 2006; Olsen et al., 2006; Cantin that the p160 Myb-binding protein is a novel, et al., 2008; Daub et al., 2008; Dephoure et al., predominantly nucleolar protein which may play a role in 2008; Imami et al., 2008). The majority of the transactivation by Myb. Mol Cell Biol. 1998 Feb;18(2):989- 1002 phosphosites mapped in MYBBP1A in these

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 674

MYBBP1A (MYB binding protein (P160) 1a) Perrera C, Colombo R

Keough R, Woollatt E, Crawford J, Sutherland GR, phosphorylation dynamics in signaling networks. Cell. Plummer S, Casey G, Gonda TJ. Molecular cloning and 2006 Nov 3;127(3):635-48 chromosomal mapping of the human homologue of MYB binding protein (P160) 1A (MYBBP1A) to 17p13.3. Díaz VM, Mori S, Longobardi E, Menendez G, Ferrai C, Genomics. 1999 Dec 15;62(3):483-9 Keough RA, Bachi A, Blasi F. p160 Myb-binding protein interacts with Prep1 and inhibits its transcriptional activity. Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Mol Cell Biol. 2007 Nov;27(22):7981-90 Steen H, Mann M, Lamond AI. Directed proteomic analysis of the human nucleolus. Curr Biol. 2002 Jan 8;12(1):1-11 Owen HR, Elser M, Cheung E, Gersbach M, Kraus WL, Hottiger MO. MYBBP1a is a novel repressor of NF- Jones LC, Okino ST, Gonda TJ, Whitlock JP Jr. Myb- kappaB. J Mol Biol. 2007 Feb 23;366(3):725-36 binding protein 1a augments AhR-dependent gene expression. J Biol Chem. 2002 Jun 21;277(25):22515-9 Cantin GT, Yi W, Lu B, Park SK, Xu T, Lee JD, Yates JR 3rd. Combining protein-based IMAC, peptide-based IMAC, Scherl A, Couté Y, Déon C, Callé A, Kindbeiter K, Sanchez and MudPIT for efficient phosphoproteomic analysis. J JC, Greco A, Hochstrasser D, Diaz JJ. Functional Proteome Res. 2008 Mar;7(3):1346-51 proteomic analysis of human nucleolus. Mol Biol Cell. 2002 Nov;13(11):4100-9 Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Körner R, Greff Z, Kéri G, Stemmann O, Mann M. Kinase- Keough RA, Macmillan EM, Lutwyche JK, Gardner JM, selective enrichment enables quantitative Tavner FJ, Jans DA, Henderson BR, Gonda TJ. Myb- phosphoproteomics of the kinome across the cell cycle. binding protein 1a is a nucleocytoplasmic shuttling protein Mol Cell. 2008 Aug 8;31(3):438-48 that utilizes CRM1-dependent and independent nuclear export pathways. Exp Cell Res. 2003 Sep 10;289(1):108- Dephoure N, Zhou C, Villén J, Beausoleil SA, Bakalarski 23 CE, Elledge SJ, Gygi SP. A quantitative atlas of mitotic phosphorylation. Proc Natl Acad Sci U S A. 2008 Aug Yang W, Rogozin IB, Koonin EV. Yeast POL5 is an 5;105(31):10762-7 evolutionarily conserved regulator of rDNA transcription unrelated to any known DNA polymerases. Cell Cycle. Imami K, Sugiyama N, Kyono Y, Tomita M, Ishihama Y. 2003 Mar-Apr;2(2):120-2 Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined Amsterdam A, Nissen RM, Sun Z, Swindell EC, Farrington titania/C18 biphasic column. Anal Sci. 2008 Jan;24(1):161- S, Hopkins N. Identification of 315 genes essential for 6 early zebrafish development. Proc Natl Acad Sci U S A. 2004 Aug 31;101(35):12792-7 Yamauchi T, Keough RA, Gonda TJ, Ishii S. Ribosomal stress induces processing of Mybbp1a and its Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, translocation from the nucleolus to the nucleoplasm. Villén J, Li J, Cohn MA, Cantley LC, Gygi SP. Large-scale Genes Cells. 2008 Jan;13(1):27-39 characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12130-5 Hara Y, Onishi Y, Oishi K, Miyazaki K, Fukamizu A, Ishida N. Molecular characterization of Mybbp1a as a co- Fan M, Rhee J, St-Pierre J, Handschin C, Puigserver P, repressor on the Period2 promoter. Nucleic Acids Res. Lin J, Jäeger S, Erdjument-Bromage H, Tempst P, 2009 Mar;37(4):1115-26 Spiegelman BM. Suppression of mitochondrial respiration through recruitment of p160 myb binding protein to PGC- Matafora V, D'Amato A, Mori S, Blasi F, Bachi A. 1alpha: modulation by p38 MAPK. Genes Dev. 2004 Feb Proteomics analysis of nucleolar SUMO-1 target proteins 1;18(3):278-89 upon proteasome inhibition. Mol Cell Proteomics. 2009 Oct;8(10):2243-55 Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M. Nucleolar proteome dynamics. Fuller HR, Man NT, Lam le T, Thanh le T, Keough RA, Nature. 2005 Jan 6;433(7021):77-83 Asperger A, Gonda TJ, Morris GE. The SMN interactome includes Myb-binding protein 1a. J Proteome Res. 2010 Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP. A Jan;9(1):556-63 probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Perrera C, Colombo R, Valsasina B, Carpinelli P, Troiani Biotechnol. 2006 Oct;24(10):1285-92 S, Modugno M, Gianellini L, Cappella P, Isacchi A, Moll J, Rusconi L. Identification of Myb-binding protein 1A Cavellán E, Asp P, Percipalle P, Farrants AK. The WSTF- (MYBBP1A) as a novel substrate for aurora B kinase. J SNF2h chromatin remodeling complex interacts with Biol Chem. 2010 Apr 16;285(16):11775-85 several nuclear proteins in transcription. J Biol Chem. 2006 Jun 16;281(24):16264-71 This article should be referenced as such: Nousiainen M, Silljé HH, Sauer G, Nigg EA, Körner R. Perrera C, Colombo R. MYBBP1A (MYB binding protein Phosphoproteome analysis of the human mitotic spindle. (P160) 1a). Atlas Genet Cytogenet Oncol Haematol. 2011; Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5391-6 15(8):673-675. Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M. Global, in vivo, and site-specific

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 675

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Gene Section Mini Review

PLCD1 (phospholipase C, delta 1) Xiaotong Hu Biomedical Research Center, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China (XH)

Published in Atlas Database: January 2011 Online updated version : http://AtlasGeneticsOncology.org/Genes/PLCD1ID43927ch3p22.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI PLCD1ID43927ch3p22.txt

resulting in a shorter isoform 2 (NP_006216) with a Identity different N-terminus compared to isoform 1. HGNC (Hugo): PLCD1 Location: 3p22.2 Protein Local order: The PLCD1 gene is located between Description the VILL gene and the DLEC1 gene. The deduced 777-amino acid isoform 1 (NM_001130964) and 756-amino acid isoform 2 DNA/RNA (NP_006216) shares 95% sequence homology with Description the rat protein. They contain a N-terminal PH domain, 2 EF-hand1 domains, PI-PLC X-box, PI- The PLCD1 gene is a functioning gene and contains PLC Y-box and C2 region. 15 exons and spans 22.17 kb. Expression Transcription Expressed high or medium in CNS (brain), The variant 1 (NM_001130964) encodes the longer hematopoietic (blood), liver and pancreas, digestive isoform 1 (NP_001124436). The variant 2 (GI-tract), respiratory (lung), male and female (NM_006225.3) contains an alternate 5' terminal tissues, placenta, urinary tract (kidney) skin and exon compared to transcript variant 1, and initiates soft tissues but no expression in cardio vascular and translation from an in-frame upstream AUG, endocrine tissues.

PLCD1 starts at 38048987 bp and ends at 38071253 bp from pter on Chr3p22-p21.3 and located between VILL and DLEC1 gene.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 676

PLCD1 (phospholipase C, delta 1) Hu X

Closed and opened boxes represent coding and non-coding sequences of PLCD1 gene, respectively.

Protein domain organization of the mammalian PLCD1.

Localisation mediated by its Ca2+-dependent interaction with importin beta 1. Playing an important suppressive Intracellular: cytoplasm and nucleus. role in the development and progression of cancers Function such as esophageal squamous cell carcinoma Catalyzing the hydrolysis of phosphatidylinositol (ESCC) and gastric cancer (GC). 4,5 biphosphate to generate diacylglycerol and Homology inositol 1,4,5 triphosphate. Mediating a wide The PLCD1 gene is conserved in dog, cow, mouse, variety of cellular stimuli. Shuttling between the rat, chicken, zebrafish, and A. thaliana. nucleus and the cytoplasm, and nuclear import is Mutations

The mutation location is highlighted in red and this mutation occured in 17% (1/6) skin samples. AA Mutation: p.E226K (Substitution - Missense). CDS Mutation: c.676G>A (Substitution).

Implicated in Esophageal squamous cell potential TSGs may contribute to the pathogenesis carcinoma of esophageal cancer. Secondly, absent expression of PLC delta 1 was Prognosis detected in 26 of 50 (52%) primary ESCCs and 4 of Firstly, four commonly deleted regions (CDRs) at 9 (44.4%) ESCC cell lines, which was significantly 3p26.3, 3p22, 3p21.3 and 3p14.2 were identified. associated with DNA copy number loss and Absent and down-regulated expression of several promoter hypermethylation (P < 0.05). Functional candidate TSGs, including CHL1, PCAF, RBMS3, studies showed that PLC delta 1 was able to PLCD1 and CACNA2D3, were detected in primary suppress both in vitro and in vivo tumorigenic ESCC tumors and ESCC cell lines. These results ability of ESCC cells, including foci formation, provided evidence that minimal deleted regions at colony formation in soft agar, and tumor formation 3p26.3, 3p22, 3p21.3 and 3p14.2 containing in nude mice. The tumor-suppressive mechanism of

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 677

PLCD1 (phospholipase C, delta 1) Hu X

PLC delta 1 was associated with its role in the cell expression and hampering the reorganization of cycle arrest at the G(1)-S checkpoint by up- cytoskeleton through cofilin inactivation by regulation of p21 and down-regulation of phosphorylation. Thus, epigenetic inactivation of phosphorylated Akt (Ser(473)). In addition, down- PLCD1 is common and tumor-specific in gastric regulation of PLC delta 1 protein was significantly cancer, and PLCD1 acts as a functional tumor correlated with ESCC metastasis (P = 0.014), which suppressor involved in gastric carcinogenesis. was associated with its function in increasing cell Colon carcinomas adhesion and inhibiting cell mobility. These results suggest that PLC delta 1 plays an important Prognosis suppressive role in the development and Decreased levels of the PLC delta 1 protein were progression of ESCC. seen in most colon carcinomas (12 of 13 paired samples) and PLC delta 1 protein was not detected Breast carcinoma in any of the carcinoma cell lines. Prognosis Rat colon neoplasms PLCD1 are more highly expressed in the transformed cell lines compared to MCF-10A. To Prognosis test whether PLCd1 or PLCd3 played any role in The expression of PLC-delta expression in rat colon tumor cell proliferation or cell migration. RNAi neoplasms induced by methylazoxymethanol mediated knockdown of PLCD1 reduced (MAM) acetate was examined. Large-bowel proliferation of the MDA-MB-231 cells. neoplasms were observed in five of 10 rats given Morphological changes including cell rounding, MAM acetate 40 weeks after treatment. PLC-delta and surface blebbing and nuclear fragmentation expression in the neoplasms was not detected by were observed. These changes were accompanied northern blot analysis, and a low level of expression by reductions in cell migration activities. On the was detected by immunoblot analysis, although other hand, PLCD1 knockdown failed to cause PLC-delta expression was apparent in the non- comparable morphological changes in the normal neoplastic colon mucosae of MAM acetate-treated MCF-10A line, but did reduce cell proliferation and rats as well as in the colon mucosae of control rats. migration. Taken together, these data are consistent Insulinoma with the idea that PLCD1 support the growth and Note migration of normal and neoplastic mammary epithelial cells in vitro. Insulinoma MIN6 cells. However there is contrasted results published in Prognosis another paper. Their results suggested that PLCD1 To study the effects of enhanced phosphoinositide is a functional tumor suppressor inducing G(2)/M hydrolysis on insulin secretion, phosphoinositide- arrest and frequently methylated in breast cancer. specific phospholipase Cbeta1 (PLCbeta1) or Gastric cancer PLCdelta1 was overexpressed in insulinoma MIN6 cells via adenoviral vectors. Inositol phosphate Prognosis production stimulated by KCl or glucose in both Located at the important tumor suppressor locus, PLCbeta1- and PLCdelta1-overexpressing cells 3p22, PLCD1 encodes an enzyme that mediates were greater than that in control cells, reduced regulatory signaling of energy metabolism, calcium phosphatidylinositol-4,5-bisphosphate levels were homeostasis and intracellular movements. We observed in these cells stimulated by NaF or KCl. identified PLCD1 as a downregulated gene in These data suggest that excessive phosphoinositide aerodigestive carcinomas through expression hydrolysis inhibits secretagogue-induced insulin profiling and epigenetic characterization. We found release in MIN6 cells. that PLCD1 was expressed in all normal adult tissues but low or silenced in 84% (16/19) gastric Pheochromocytoma cancer cell lines, well correlated with its CpG island Note (CGI) methylation status. Methylation was further Pheochromocytoma PC12 cells. detected in 62% (61/98) gastric primary tumors, but Prognosis none of normal gastric mucosa tissues. PLCD1 PLCD1 is recruited from the cytoplasm to lipid methylation was significantly correlated with tumor rafts after CCH-induced Ca2+ mobilization high stage. Detailed methylation analysis of 37 following the activation of PLCbeta by GPCR and CpG sites at the PLCD1 CGI by bisulfite genomic PLCD1 is activated only in lipid rafts by localized sequencing confirmed its methylation. PLCD1 capacitative entry of extracellular Ca2+. PLCD1, silencing could be reversed by pharmacological p122RhoGAP and RhoA in combination could demethylation with 5-aza-2'-deoxycytidine, constitute a unique functional unit for the regulation indicating a direct epigenetic silencing. Ectopic of both phosphoinositide/Ca2+ signaling and the expression of PLCD1 in silenced gastric tumor cells actin cytoskeleton in the periphery of specified dramatically inhibited their clonogenicity and membrane domains. This would provide further migration, possibly through downregulating MMP7

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 678

PLCD1 (phospholipase C, delta 1) Hu X

insights into the molecular mechanisms of cancer Qin YR, Fu L, Sham PC, Kwong DL, Zhu CL, Chu KK, Li development. Y, Guan XY. Single-nucleotide polymorphism-mass array reveals commonly deleted regions at 3p22 and 3p14.2 associate with poor clinical outcome in esophageal References squamous cell carcinoma. Int J Cancer. 2008 Aug 15;123(4):826-30 Yoshimi N, Wang A, Makita H, Suzui M, Mori H, Okano Y, Banno Y, Nozawa Y. Reduced expression of Yamaga M, Kawai K, Kiyota M, Homma Y, Yagisawa H. phospholipase C-delta, a signal-transducing enzyme, in rat Recruitment and activation of phospholipase C (PLC)- colon neoplasms induced by methylazoxymethanol delta1 in lipid rafts by muscarinic stimulation of PC12 cells: acetate. Mol Carcinog. 1994 Dec;11(4):192-6 contribution of p122RhoGAP/DLC1, a tumor-suppressing PLCdelta1 binding protein. Adv Enzyme Regul. Nomoto K, Tomita N, Miyake M, Xhu DB, LoGerfo PR, 2008;48:41-54 Weinstein IB. Expression of phospholipases gamma 1, beta 1, and delta 1 in primary human colon carcinomas Hu XT, Zhang FB, Fan YC, Shu XS, Wong AH, Zhou W, and colon carcinoma cell lines. Mol Carcinog. 1995 Shi QL, Tang HM, Fu L, Guan XY, Rha SY, Tao Q, He C. Mar;12(3):146-52 Phospholipase C delta 1 is a novel 3p22.3 tumor suppressor involved in cytoskeleton organization, with its Ishikawa S, Takahashi T, Ogawa M, Nakamura Y. epigenetic silencing correlated with high-stage gastric Genomic structure of the human PLCD1 (phospholipase C cancer. Oncogene. 2009 Jul 2;28(26):2466-75 delta 1) locus on 3p22-->p21.3. Cytogenet Cell Genet. 1997;78(1):58-60 Rebecchi MJ, Raghubir A, Scarlata S, Hartenstine MJ, Brown T, Stallings JD. Expression and function of Ishihara H, Wada T, Kizuki N, Asano T, Yazaki Y, Kikuchi phospholipase C in breast carcinoma. Adv Enzyme Regul. M, Oka Y. Enhanced phosphoinositide hydrolysis via 2009;49(1):59-73 overexpression of phospholipase C beta1 or delta1 inhibits stimulus-induced insulin release in insulinoma MIN6 cells. Xiang T, Li L, Fan Y, Jiang Y, Ying Y, Putti TC, Tao Q, Ren Biochem Biophys Res Commun. 1999 Jan 8;254(1):77-82 G. PLCD1 is a functional tumor suppressor inducing G(2)/M arrest and frequently methylated in breast cancer. Fu L, Qin YR, Xie D, Hu L, Kwong DL, Srivastava G, Tsao Cancer Biol Ther. 2010 Sep;10(5):520-7 SW, Guan XY. Characterization of a novel tumor- suppressor gene PLC delta 1 at 3p22 in esophageal This article should be referenced as such: squamous cell carcinoma. Cancer Res. 2007 Nov 15;67(22):10720-6 Hu X. PLCD1 (phospholipase C, delta 1). Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8):676-679.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 679

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Gene Section Mini Review

PYY (peptide YY) Maria Braoudaki, Fotini Tzortzatou-Stathopoulou University Research Institute for the Study and Treatment of Childhood Genetic and Malignant Diseases, University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece (MB), Hematology/Oncology Unit, First Department of Pediatrics, University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece (FTS)

Published in Atlas Database: January 2011 Online updated version : http://AtlasGeneticsOncology.org/Genes/PYYID46182ch17q21.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI PYYID46182ch17q21.txt

Identity Expression Other names: PYY1 PYY is expressed predominantly in endocrine L- cells that line the distal small bowel and colon. HGNC (Hugo): PYY Localisation Location: 17q21.31 Extracellular, subcellular location: secreted DNA/RNA granules. Co-localized with proglucagon products, glicentin and glucagon-like peptide-1 (GLP-1) and Description GLP-2. PYY is a gastrointestinal track-derived PYY gene is composed of 4 exons and 3 introns hormone synthesized by endocrine cells of terminal that span approximately 51732 bases (start ileum and colon, involved in the regulation of food 42030106 bp to end 42081837 bp from pter) intake. oriented at the minus strand. Function Transcription Enteroendocrine L-cells release two circulating Two transcript variants (1048 bp and 1048 bp in forms of PYY in the distal gut: PYY1-36 and length). PYY3-36. The latter form is considered the predominant form in both fasted and fed states and Protein is produced by the cleavage of the N-terminal Tyr- Pro residues from PYY1-36 by dipeptidyl-peptidase Description IV (DPPIV). Size: 97 amino acids; 11046 Da.

Human peptide YY (PYY). Adapted from Shih et al., 2009.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 680

PYY (peptide YY) Braoudaki M, Tzortzatou-Stathopoulou F

PYY exerts its inhibitory actions via various Y Breast cancer receptors, including Y1 receptor-mediated epithelial Note responses and Y2 receptor-mediated neuronal PYY inhibits in vitro growth of breast cancer cells, effects. It inhibits food intake via NPY-2 receptors however the exact mechanism of antitumor activity expressed by neurons of the arcuate nucleus of the remains unknown. Previous studies have proposed hypothalamus. Generally, it is considered to act in that PYY reduces intracellular levels of cAMP in the hypothalamus as a signal of satiety. Other breast carcinoma cells. Moreover, it has been inhibitory actions include slowing gastric emptying; reported that combination of PYY with vitamin E increasing nutrient absorption, inducing intestinal results in a significant additive inhibition of breast anion and electrolytic secretion as well as slowing carcinoma cells. small intestine motility. In addition, it has been shown to decrease exocrine pancreatic secretion Cancer cachexia and act as an appetite suppressant in the fasting Note state at physiological concentrations. Cancer cachexia is generally characterized by Homology decreased protein synthesis and loss in the small PPY or PNP or PP and NPY. bowel. PYY has been shown to increase small bowel weight and protein content. However, the Mutations exact role of PYY on cancer cachexia has not yet been clarified. Note Body weight Common polymorphisms: Arg72Thr, which has been associated with type-2 diabetes and in some Note cases with enhanced body mass. Other variants: PYY-36 plays a role in long-term body weight Gln62Pro and Leu73Pro associated with body mass regulation, due to the negative correlation between and obesity, respectively as well as A-23G,C888T PYY concentrations and adiposity markers in and 3' UTR variant C+1134A. The latter has been humans, such that PYY levels increase with weight related to enhanced body mass. loss and when leptin levels are low. Obesity and type II diabetes Implicated in Note Colon cancer Low endogenous PYY levels in obese individuals, have previously suggested that PYY deficiency Note may contribute to hyperinsulinemia and insulin Loss of PYY expression has been implicated in the resistance and predispose obesity and type II development and progression to colon diabetes. adenocarcinoma. PYY expression has been associated with elevated differentiation, whilst PYY References treatment of colon cancers resulted in selected overexpression of enzymes frequently identified in Conn MP, Melmed S.. Endocrinology: Basic and clinical the normal colonocytic phenotype. The colon principles. Humana Press. 1997. cancer growth regulatory effects of PYY might be Grise KR, Rongione AJ, Laird EC, McFadden DW.. dose dependent. Peptide YY inhibits growth of human breast cancer in vitro and in vivo. J Surg Res. 1999 Apr;82(2):151-5. Pancreatic cancer and pancreatitis Heisler T, Towfigh S, Simon N, Liu C, McFadden DW.. Note Peptide YY augments gross inhibition by vitamin E PYY suppresses growth and levels of intracellular succinate of human pancreatic cancer cell growth. J Surg Res. 2000a Jan;88(1):23-5. cyclic adenosine monophosphate (cAMP) in pancreatic adenocarcinoma. It is considered to have Heisler T, Towfigh S, Simon N, McFadden DW.. Peptide YY and vitamin E inhibit hormone-sensitive and - a therapeutic value for pancreatic cancer and insensitive breast cancer cells. J Surg Res. 2000b Jun pancreatitis, since it exerts its immune function by 1;91(1):9-14. altering transcription factors vital for cell signaling Tseng WW, Liu CD.. Peptide YY and cancer: current pathways. In addition, administration of PYY has findings and potential clinical applications. Peptides. 2002 been shown to improve amylase and cytokine Feb;23(2):389-95. (REVIEW) release in pancreatitis cases. It has also been Vona-Davis L, Yu A, Magabo K, Evans T, Jackson B, suggested that PYY in combination with vitamin E Riggs D, McFadden D.. Peptide YY attenuates exhibit a significantly increased inhibitory effect on transcription factor activity in tumor necrosis factor-alpha- pancreatic cancer in vitro. induced pancreatitis. J Am Coll Surg. 2004 Jul;199(1):87- 95.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 681

PYY (peptide YY) Braoudaki M, Tzortzatou-Stathopoulou F

Torekov SS, Larsen LH, Glumer C, Borch-Johnsen K, ghrelin during chemotherapy in children with acute Jorgensen T, Holst JJ, Madsen OD, Hansen T, Pedersen lymphoblastic leukemia. J Pediatr Hematol Oncol. 2008 O.. Evidence of an association between the Arg72 allele of Oct;30(10):733-7. the peptide YY and increased risk of type 2 diabetes. Diabetes. 2005 Jul;54(7):2261-5. Lomenick JP, Melguizo MS, Mitchell SL, Summar ML, Anderson JW.. Effects of meals high in carbohydrate, Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, protein, and fat on ghrelin and peptide YY secretion in Collier JM, Hebert S, Doelle H, Dent R, Pennacchio LA, prepubertal children. J Clin Endocrinol Metab. 2009 McPherson R.. A PYY Q62P variant linked to human Nov;94(11):4463-71. Epub 2009 Oct 9. obesity. Hum Mol Genet. 2006 Feb 1;15(3):387-91. Epub 2005 Dec 20. Shih PA, Wang L, Chiron S, Wen G, Nievergelt C, Mahata M, Khandrika S, Rao F, Fung MM, Mahata SK, Hamilton Boey D, Heilbronn L, Sainsbury A, Laybutt R, Kriketos A, BA, O'Connor DT.. Peptide YY (PYY) gene polymorphisms Herzog H, Campbell LV.. Low serum PYY is linked to in the 3'-untranslated and proximal promoter regions insulin resistance in first-degree relatives of subjects with regulate cellular gene expression and PYY secretion and type 2 diabetes. Neuropeptides. 2006 Oct;40(5):317-24. metabolic syndrome traits in vivo. J Clin Endocrinol Metab. Epub 2006 Oct 12. 2009 Nov;94(11):4557-66. Epub 2009 Oct 9. Pfluger PT, Kampe J, Castaneda TR, Vahl T, D'Alessio Cox HM, Tough IR, Woolston AM, Zhang L, Nguyen AD, DA, Kruthaupt T, Benoit SC, Cuntz U, Rochlitz HJ, Moehlig Sainsbury A, Herzog H.. Peptide YY is critical for M, Pfeiffer AF, Koebnick C, Weickert MO, Otto B, acylethanolamine receptor Gpr119-induced activation of Spranger J, Tschop MH.. Effect of human body weight gastrointestinal mucosal responses. Cell Metab. 2010 Jun changes on circulating levels of peptide YY and peptide 9;11(6):532-42. YY3-36. J Clin Endocrinol Metab. 2007 Feb;92(2):583-8. Epub 2006 Nov 21. Kirchner H, Tong J, Tschop MH, Pfluger PT.. Ghrelin and PYY in the regulation of energy balance and metabolism: Vona-Davis L, McFadden DW.. PYY and the pancreas: lessons from mouse mutants. Am J Physiol Endocrinol inhibition of tumor growth and inflammation. Peptides. Metab. 2010 May;298(5):E909-19. Epub 2010 Feb 23. 2007 Feb;28(2):334-8. Epub 2006 Dec 27. (REVIEW) (REVIEW)

Cox HM.. Endogenous PYY and NPY mediate tonic Y1- This article should be referenced as such: and Y2-mediated absorption in human and mouse colon. Nutrition. 2008 Sep;24(9):900-6. Epub 2008 Jul 26. Braoudaki M, Tzortzatou-Stathopoulou F. PYY (peptide YY). Atlas Genet Cytogenet Oncol Haematol. 2011; Moschovi M, Trimis G, Vounatsou M, Katsibardi K, Margeli 15(8):680-682. A, Dimitriadi F, Papassotiriou I, Chrousos G, Tzortzatou- Stathopoulou F.. Serial plasma concentrations of PYY and

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 682

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Gene Section Review

SIAH2 (seven in absentia homolog 2 (Drosophila)) Jianfei Qi, Ze'ev Ronai Signal Transduction Program, Sanford-Burnham Medical Research Institute, La Jolla, CA, 92037, USA (JQ, ZR)

Published in Atlas Database: January 2011 Online updated version : http://AtlasGeneticsOncology.org/Genes/SIAH2ID46199ch3q25.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI SIAH2ID46199ch3q25.txt

two zinc finger motifs, and a C-terminal substrate Identity binding domain (SBD). The ring domain is the Other names: hSiah2 catalytic domain that recruits E2 ubiquitin- HGNC (Hugo): SIAH2 conjugating enzymes, while the SBD mediates the binding of adaptor proteins or some Siah substrate Location: 3q25.1 proteins. The structure of murine Siah1a SBD has been solved. The structure reveals that Siah is a DNA/RNA dimeric protein, and the SBD adopts an eight- Description stranded beta-sandwich fold (Polekhina et al., 2001). The substrate binding groove is formed by The human Siah2 gene is composed of 2 exons the beta-sandwich fold and the beta-strand that spanning a genomic region of about 22.4 kb. connects to the second zinc finger domain (House Transcription et al., 2005). The transcript length of human Siah2 is 2632 bp. Expression The open reading frame of the coding region is 975 Siah2 mRNA is widely expressed in the embryonic bp. and adult mouse tissues. It is expressed at a higher Pseudogene level in the olfactory epithelium, retina, forebrain and proliferating cartilage of developing bone No pseudogene of Siah2 has been reported. (Della et al., 1993). Siah2 mRNA is also expressed Protein in most human tissues (Hu et al., 1997). Localisation Description Siah protein can be localized in both cytoplasm and Human Siah2 protein consists of 324 amino acids, nucleus. with a molecular weight of 36 kDa. Siah protein consists of an N-terminal ring domain, followed by

Genomic organization of human Siah2. The line indicates intron and boxes indicate coding regions (exon 1-2) of the gene. Exon and intron lengths, the ATG transcription start site and the TGA stop codon are indicated.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 683

SIAH2 (seven in absentia homolog 2 (Drosophila)) Qi J, Ronai Z

Domains of human Siah2 protein.

Function Homology Siah2 is the mammalian homolog of Drosophila Homologs: Human has two Siah genes (Siah1 and SINA (seven in absentia), which interacts with Siah2) (Hu et al., 1997), while mouse has three Siah transcriptional repressor Tramtrack via adaptor genes (Siah2, Siah1a, Siah1b) (Della et al., 1993). protein PHYL (Phyllopod) and induces the Human Siah2 shares 77% identity with human proteasomal degradation of Tramtrack, thereby Siah1 (Hu et al., 1997). determining R7 cell fate (Li et al., 1997; Tang et al., Orthologs: Highly conserved Siah2 orthologs have 1997). As a ring-finger E3 ubiquitin ligase, Siah been identified in all multicellular organisms targets the degradation of diverse substrates via examined (Nakayama et al., 2009). ubiquitin-proteasome pathway, and affects multiple signaling pathways such as HIF (Nakayama et al., Mutations 2004), Ras (Nadeau et al., 2007; Schmidt et al., 2007), NF-kB (Polekhina et al., 2002; Habelhah et Note al., 2002), and beta-catenin (Liu et al., 2001; No SIAH2 mutations have been reported. Matsuzawa and Reed, 2001). Siah2 transcription is upregulated by hypoxia (Nakayama et al., 2004); Implicated in p38-mediated phosphorylation of mouse Siah2 on Thr24 and Ser29 alters its subcellular localization Lung cancer (Khurana et al., 2006); HIPK2-mediated Note phosphorylation of human Siah2 on Thr 26, Ser 28 Ahmed et al. showed that Siah2 knockdown in and Ser 68 decreases the stability of Siah2 and human lung cancer cell lines (BZR, A549, H727, impairs its interaction with HIPK2 (Calzado et al., and UMC11) inhibited MAPK-ERK signaling, 2009). reduced cell proliferation and increased apoptosis; Over 20 Siah substrates have been reported Siah2 knockdown also reduced anchorage- (Nakayama et al., 2009) and some of them can be independent growth of A549 cells in soft agar, and degradated by Siah2, Siah1 or both of them. In blocked the growth of A549 xenograft tumors in contrast to Siah1a knockout mice which exibit nude mice (Ahmed et al., 2007). growth retardation and spermatogenesis defect, Siah2 knockout mice display no apparent Melanoma phenotype, whereas Siah2 and Siah1a double Note knockout mice are embryonic or neonatal lethal, Qi et al. showed that inhibition of Siah2 activity suggesting that the two Siah homologs have both using different inhibitory proteins blocked tumor overlapping and distinct functions in vivo (Frew et formation or metastasis of SW1 melanoma cells in al., 2003). Despite the diverse substrates of Siah a syngeneic mouse model due to the inhibition of identified in vitro, loss of Siah2 (or both Siah2 and Ras and HIF pathways, respectively (Qi et al., Siah1a) in vivo largely has no effect on the levels of 2008). Similary, Shah et al. showed that a putative many Siah substrates and the physiological chemical inhibitor of Siah2, menadione, decreased processes associated with these substrates (Frew et the levels of HIF-1alpha and phospho-ERK in al., 2002; Frew et al., 2003). human melanoma cell line UACC903 and abolished Siah2 is implicated in the regulation of hypoxia the growth of xenograft tumor in nude mice (Shah response through its effect on HIF prolyl et al., 2009). hydroxylases or HIPK2 (Nakayama et al., 2004; Breast cancer Calzado et al., 2009). Siah2 knockout mice subject to hypoxia showed impaired respiratory response Note and defect to adjust levels of red blood cells Möller et al. showed that inhibition of Siah in a (Nakayama et al., 2004). Siah2 has been shown to mouse breast cancer cell line reduced the xenograft be required for development and progression of tumor growth and prolonged the survival of mice several types of cancers via its regulation of HIF or due to inhibition of HIF pathway (Möller et al., Ras pathways (House et al., 2009). Siah2- 2009). Behling et al. examined the SIAH staining in dependent degradation of Pard3A is found to 65 patients of ductal carcinoma in situ (DCIS). control germinal zone exit of neuronal progenitors Higher level of Siah staining was observed in or immature neurons in mice (Famulski et al., tumors compared with the normal adjacent tissues, 2010). and in tumors with more aggressive features.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 684

SIAH2 (seven in absentia homolog 2 (Drosophila)) Qi J, Ronai Z

There was also higher Siah staining in specimens Habelhah H, Frew IJ, Laine A, Janes PW, Relaix F, from patients with recurrence as compared to Sassoon D, Bowtell DD, Ronai Z. Stress-induced decrease in TRAF2 stability is mediated by Siah2. EMBO J. 2002 patients without recurrence. This study stuggests Nov 1;21(21):5756-65 that Siah may serve as a prognostic biomarker that Polekhina G, House CM, Traficante N, Mackay JP, Relaix predicts DCIS progression to invasive breast cancer F, Sassoon DA, Parker MW, Bowtell DD. Siah ubiquitin (Behling et al., 2010). ligase is structurally related to TRAF and modulates TNF- Pancreatic cancer alpha signaling. Nat Struct Biol. 2002 Jan;9(1):68-75 Frew IJ, Hammond VE, Dickins RA, Quinn JM, Walkley Note CR, Sims NA, Schnall R, Della NG, Holloway AJ, Digby Schmidt et al. showed that inhibition of Siah MR, Janes PW, Tarlinton DM, Purton LE, Gillespie MT, activity attenuated MAPK-ERK signaling, blocked Bowtell DD. Generation and analysis of Siah2 mutant RAS-induced focus formation in fibroblasts, mice. Mol Cell Biol. 2003 Dec;23(24):9150-61 abolished anchorage-independent growth of human Nakayama K, Frew IJ, Hagensen M, Skals M, Habelhah H, pancreatic cancer cells in soft agar and xenograft Bhoumik A, Kadoya T, Erdjument-Bromage H, Tempst P, tumor growth in nude mice (Schmidt et al., 2008). Frappell PB, Bowtell DD, Ronai Z. Siah2 regulates stability of prolyl-hydroxylases, controls HIF1alpha abundance, and Prostate cancer modulates physiological responses to hypoxia. Cell. 2004 Jun 25;117(7):941-52 Note House CM, Hancock NC, Möller A, Cromer BA, Fedorov V, Qi et al. showed that knockout of Siah2 in the Bowtell DD, Parker MW, Polekhina G. Elucidation of the TRAMP model abolished the formation of prostate substrate binding site of Siah ubiquitin ligase. Structure. neuroendocrine tumor, inhibition of Siah2 activity 2006 Apr;14(4):695-701 blocked hypoxia-induced neuroendocrine Khurana A, Nakayama K, Williams S, Davis RJ, Mustelin differentiation (NED) in prostate cancer cells or in T, Ronai Z. Regulation of the ring finger E3 ligase Siah2 by the xenogaft tumors, and Siah2 protein levels were p38 MAPK. J Biol Chem. 2006 Nov 17;281(46):35316-26 higher in high-grade PCa that expresss NE markers. Nadeau RJ, Toher JL, Yang X, Kovalenko D, Friesel R. This study suggests that Siah2 plays a key role in Regulation of Sprouty2 stability by mammalian Seven-in- development of prostate NE tumor and NED of Absentia homolog 2. J Cell Biochem. 2007 Jan human PCa by controling a cooperation between 1;100(1):151-60 HIF and NE-specific transcription factor FoxA2 (Qi Schmidt RL, Park CH, Ahmed AU, Gundelach JH, Reed et al., 2010). NR, Cheng S, Knudsen BE, Tang AH. Inhibition of RAS- mediated transformation and tumorigenesis by targeting the downstream E3 ubiquitin ligase seven in absentia Breakpoints homologue. Cancer Res. 2007 Dec 15;67(24):11798-810 Note Ahmed AU, Schmidt RL, Park CH, Reed NR, Hesse SE, Thomas CF, Molina JR, Deschamps C, Yang P, Aubry There is no breakpoint reported. MC, Tang AH. Effect of disrupting seven-in-absentia homolog 2 function on lung cancer cell growth. J Natl References Cancer Inst. 2008 Nov 19;100(22):1606-29 Hu G, Chung YL, Glover T, Valentine V, Look AT, Fearon Qi J, Nakayama K, Gaitonde S, Goydos JS, Krajewski S, ER. Characterization of human homologs of the Drosophila Eroshkin A, Bar-Sagi D, Bowtell D, Ronai Z. The ubiquitin seven in absentia (sina) gene. Genomics. 1997 Nov ligase Siah2 regulates tumorigenesis and metastasis by 15;46(1):103-11 HIF-dependent and -independent pathways. Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16713-8 Li S, Li Y, Carthew RW, Lai ZC. Photoreceptor cell differentiation requires regulated proteolysis of the House CM, Möller A, Bowtell DD. Siah proteins: novel drug transcriptional repressor Tramtrack. Cell. 1997 Aug targets in the Ras and hypoxia pathways. Cancer Res. 8;90(3):469-78 2009 Dec 1;69(23):8835-8 Tang AH, Neufeld TP, Kwan E, Rubin GM. PHYL acts to Calzado MA, de la Vega L, Möller A, Bowtell DD, Schmitz down-regulate TTK88, a transcriptional repressor of ML. An inducible autoregulatory loop between HIPK2 and neuronal cell fates, by a SINA-dependent mechanism. Siah2 at the apex of the hypoxic response. Nat Cell Biol. Cell. 1997 Aug 8;90(3):459-67 2009 Jan;11(1):85-91 Liu J, Stevens J, Rote CA, Yost HJ, Hu Y, Neufeld KL, Möller A, House CM, Wong CS, Scanlon DB, Liu MC, White RL, Matsunami N. Siah-1 mediates a novel beta- Ronai Z, Bowtell DD. Inhibition of Siah ubiquitin ligase catenin degradation pathway linking p53 to the function. Oncogene. 2009 Jan 15;28(2):289-96 adenomatous polyposis coli protein. Mol Cell. 2001 Nakayama K, Qi J, Ronai Z. The ubiquitin ligase Siah2 and May;7(5):927-36 the hypoxia response. Mol Cancer Res. 2009 Matsuzawa SI, Reed JC. Siah-1, SIP, and Ebi collaborate Apr;7(4):443-51 in a novel pathway for beta-catenin degradation linked to Shah M, Stebbins JL, Dewing A, Qi J, Pellecchia M, Ronai p53 responses. Mol Cell. 2001 May;7(5):915-26 ZA. Inhibition of Siah2 ubiquitin ligase by vitamin K3 Frew IJ, Dickins RA, Cuddihy AR, Del Rosario M, Reinhard (menadione) attenuates hypoxia and MAPK signaling and C, O'Connell MJ, Bowtell DD. Normal p53 function in blocks melanoma tumorigenesis. Pigment Cell Melanoma primary cells deficient for Siah genes. Mol Cell Biol. 2002 Res. 2009 Dec;22(6):799-808 Dec;22(23):8155-64 Behling KC, Tang A, Freydin B, Chervoneva I, Kadakia S, Schwartz GF, Rui H, Witkiewicz AK. Increased SIAH expression predicts ductal carcinoma in situ (DCIS)

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 685

SIAH2 (seven in absentia homolog 2 (Drosophila)) Qi J, Ronai Z

progression to invasive carcinoma. Breast Cancer Res Della NG, Senior PV, Bowtell DD. Isolation and Treat. 2010 Nov 19; characterisation of murine homologues of the Drosophila seven in absentia gene (sina). Development. 1993 Famulski JK, Trivedi N, Howell D, Yang Y, Tong Y, Apr;117(4):1333-43 Gilbertson R, Solecki DJ. Siah regulation of Pard3A controls neuronal cell adhesion during germinal zone exit. This article should be referenced as such: Science. 2010 Dec 24;330(6012):1834-8 Qi J, Ronai Z. SIAH2 (seven in absentia homolog 2 Qi J, Nakayama K, Cardiff RD, Borowsky AD, Kaul K, (Drosophila)). Atlas Genet Cytogenet Oncol Haematol. Williams R, Krajewski S, Mercola D, Carpenter PM, 2011; 15(8):683-686. Bowtell D, Ronai ZA. Siah2-dependent concerted activity of HIF and FoxA2 regulates formation of neuroendocrine phenotype and neuroendocrine prostate tumors. Cancer Cell. 2010 Jul 13;18(1):23-38

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 686

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Gene Section Review

TP53BP2 (tumor protein p53 binding protein, 2) Kathryn Van Hook, Zhiping Wang, Charles Lopez Department of Medicine, Division of Hematology and Medical Oncology, Oregon Health and Science University, Portland, OR, USA (KV, ZW, CL)

Published in Atlas Database: January 2011 Online updated version : http://AtlasGeneticsOncology.org/Genes/TP53BP2ID42667ch1q42.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI TP53BP2ID42667ch1q42.txt

Identity Pseudogene Other names: 53BP2; ASPP2; BBP; P53BP2; Not known. PPP1R13A Protein HGNC (Hugo): TP53BP2 Location: 1q41 Description ASPP2 is a pro-apoptotic protein with a predicted DNA/RNA size of approximately 135 kDa. It is the founding member of a family of ASPP proteins that all share Description the common motifs of four Ankyrin-repeats, a Src- The TP53BP2 gene spans about 66 kb on homology 3 (SH3) domain, and a Polyproline chromosome 1q42.1 on the minus strand (Yang et domain in their C-terminus (Iwabuchi et al., 1994). al., 1997). There are two transcripts as a result of The N-terminus of ASPP2 is thought to be alternative splicing (Takahashi et al., 2004). The important for regulating its apoptotic function and transcript variant 1, which is shorter (4670 bp), contains a putative Ras-association domain as well does not contain exon 3 and gives rise to a longer as a ubiquitin-like fold (Tidow et al., 2007). ASPP2 form of the protein named TP53BPL (long) or has been most widely studied for its ability to ASPP2. The transcript variant 2, which is longer interact with and stimulate the apoptotic function of (4802 bp), contains exon 3 which harbors a stop the tumor suppressor p53 (and p63/p73) but several codon. As a result, the transcription initiates at exon studies have also demonstrated p53-independent as 6 giving rise to a shorter form of the protein named well as apoptosis-independent functions for ASPP2 TP53BPS (short) or BBP. as well (Kampa et al., 2009a). Transcription ASPP2 was originally pulled out of a yeast two- hybrid screen using the p53-binding domain as bait ASPP2 is a serum inducible protein and subject to as a partial C-terminal clone named 53BP2 transcriptional regulation by E2F and its family (Iwabuchi et al., 1994). members (Chen et al., 2005; Fogal et al., 2005).

TSS=transcription start site.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 687

TP53BP2 (tumor protein p53 binding protein, 2) Van Hook K, et al.

ASPP2 protein domains. RA=Ras-association domain; PP=polyproline domain; AR=ankyrin repeats.

In 1996, Naumovski and Cleary determined that mitochondrial-mediated apoptosis (Kobayashi et 53BP2 was a partial clone of a longer transcript al., 2005). they named Bcl-2 binding protein (Bbp or Tumor suppressor. Several clinical studies Bbp/53BP2) for its ability to bind the anti-apoptotic demonstrate low ASPP2 expression in a variety of protein Bcl-2. It was later determined that Bbp is a human tumors (breast, lung, lymphoma) and this splice isoform of the full length gene product from low expression often correlates with poor clinical this locus, ASPP2 (Samuels-Lev et al., 2001). outcome, suggesting that ASPP2 may function as a Expression tumor suppressor (Mori et al., 2000; Samuels-Lev et al., 2001; Lossos et al., 2002; Cobleigh et al., Northern blot analysis, using a C-terminal probe, 2005). In support of this concept, Iwabuchi et al. shows elevated levels of ASPP2 mRNA in several demonstrated in 1998 that transfection of 53BP2 human tissues including heart, testis, and peripheral inhibits Ras/E1A-mediated transformation in rat blood leukocytes (Yang et al., 1999). ASPP2 embryonic fibroblasts. Since then two separate protein levels are controlled by proteasomal mouse models targeting the ASPP2 locus via degradation (Zhu et al., 2005). homologous recombination have demonstrated that Localisation loss of only one copy of ASPP2 increases spontaneous and irradiation-induced tumor ASPP2 contains a nuclear localization signal within formation in vivo (Vives et al., 2006; Kampa et al., its ankyrin repeat domain (amino acid residues 795- 2009b). Taken together these data strongly suggest 894) that when expressed alone or as a fusion with that ASPP2 is a haplo-insufficient tumor other proteins localizes in the nucleus of cells suppressor. (Sachdev et al., 1998; Yang et al., 1999). Despite Cell cycle. Bbp, a splice isoform of ASPP2, can this signal however, full length ASPP2 is induce accumulation of cells in G /M and thus predominantly located in the cytoplasm and often 2 impede cell cycle progression (Naumovski and seen near the cell periphery (Naumovski and Cleary, 1996). Additionally, ASPP2 appears to play Cleary, 1996; Iwabuchi et al., 1998; Yang et al., a role in the G /G cell cycle checkpoint in response 1999). 0 1 to gamma-irradiation as murine thymocytes that Function lack one copy of the ASPP2 locus did not arrest at Apoptosis. Before ASPP2 was known to be the full G0/G1 as efficiently as wild type thymocytes length gene product from the TP53BP2 locus, Yang (Kampa et al., 2009b). and colleagues showed that overexpression of Cell polarity. ASPP2 is often seen near the cell Bbp/53BP2 in cells induces apoptosis (Yang et al., periphery and has been shown to co-localize with 1999). In 2000, Lopez et al. demonstrated that and bind to the tight junction protein PAR-3. Bbp/53BP2 was UV-damage inducible and that loss Furthermore, loss of ASPP2 expression correlates of this endogenous protein promotes cell survival in with a loss of tight junction integrity and an response to damage, thus implicating a function in impaired ability to maintain apical domains in the damage response pathway. In 2001, Samuels- polarized cells in culture (Cong et al., 2010). Lev et al. provided evidence that not only does full Interestingly these findings hold true in vivo as length ASPP2 promote apoptosis but that it does so, well. ASPP2 co-localizes with the PAR-3 complex at least in part, through a p53-mediated mechanism and apical junctions in the brain and is necessary that may involve preferential binding of p53 to its for tight junction integrity. Targeted deletion of apoptotic target genes. ASPP2 has also been shown ASPP2 in the mouse leads to defects associated to modulate the apoptotic activity of the p53 family with a loss of structural organization in the brain members, p63/p73 (Bergamaschi et al., 2004), and and retina (Sottocornola et al., 2010). is known to bind other proteins involved in Senescence. Senescence, a type of irreversible cell apoptosis such as Bcl-2 and NF-kappaB cycle arrest, is considered an intrinsic protective (Naumovski and Cleary, 1996; Yang et al., 1999). response against malignant transformation. Wang et However, the functional ramifications of these al. recently identified ASPP2 as a mediator of Ras- interactions remain unclear. Additionally, there is induced senescence by demonstrating that mouse evidence to indicate ASPP2 as a player in embryonic fibroblasts with a targeted deletion of

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 688

TP53BP2 (tumor protein p53 binding protein, 2) Van Hook K, et al.

Potential functions and putative interacting partners of ASPP2. Modified from Kampa et al., 2009a. exon 3 of the ASPP2 gene (TP53BP2) are less polymorphisms in TP53BP2 have been found prone to senescence in the presence of activated associated with gastric cancer susceptibility (Ju et Ras as compared to wild type fibroblasts (as al., 2005) and epigenetic silencing of the promoter measured by beta-galactosidase staining). Data also by methylation is frequently observed (Sarraf and suggests that Ras-induced senescence may be Stancheva, 2004; Liu et al., 2005; Zhao et al., mediated by ASPP2 through its ability to inhibit 2010). Ras from inducing accumulation of cyclin D1 in the nucleus (Wang et al., 2011). Implicated in Homology Breast cancer ASPP2 is a member of the ASPP family of proteins Note that share a significant amount of homology in their ASPP2 mRNA expression is frequently C-terminal domains. ASPP1, ASPP2, and the splice downregulated in human breast cancer samples as isoform of ASPP2, BBP, share homology in both compared to adjacent normal tissue (Sgroi et al., their N-terminal and C-terminal domains while the 1999; Samuels-Lev et al., 2001; Cobleigh et al., family member iASPP only retains C-terminal 2005). Reduced levels of ASPP2 expression are homology (Samuels-Lev et al., 2001; Bergamaschi seen in both invasive and metastatic breast tumor et al., 2003). tissue (Sgroi et al., 1999) and ASPP2 downregulation may be favored in tumor cells Mutations expressing wild type but not mutant p53 (Samuels- Note Lev et al., 2001). No mutations at the ASPP2 locus, TP53BP2, have been reported. However, single nucleotide

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 689

TP53BP2 (tumor protein p53 binding protein, 2) Van Hook K, et al.

Prognosis Iwabuchi K, Li B, Massa HF, Trask BJ, Date T, Fields S. Stimulation of p53-mediated transcriptional activation by Elevated levels of ASPP2 mRNA were correlated the p53-binding proteins, 53BP1 and 53BP2. J Biol Chem. with a lower risk of distant recurrence of disease 1998 Oct 2;273(40):26061-8 among a panel of 78 patients with extensive lymph Sachdev S, Hoffmann A, Hannink M. Nuclear localization node involvement (Cobleigh et al., 2005). of IkappaB alpha is mediated by the second ankyrin Non-Hodgkin's lymphoma repeat: the IkappaB alpha ankyrin repeats define a novel class of cis-acting nuclear import sequences. Mol Cell Biol. specifically diffuse large B-cell 1998 May;18(5):2524-34 lymphoma, follicular center Sgroi DC, Teng S, Robinson G, LeVangie R, Hudson JR lymphoma, and Burkitt's lymphoma Jr, Elkahloun AG. In vivo gene expression profile analysis of human breast cancer progression. Cancer Res. 1999 Note Nov 15;59(22):5656-61 Overall, ASPP2 expression (as measured by Real- Yang JP, Hori M, Takahashi N, Kawabe T, Kato H, time RT-PCR) was found to be significantly higher Okamoto T. NF-kappaB subunit p65 binds to 53BP2 and in diffuse large B-cell lymphoma as compared to inhibits cell death induced by 53BP2. Oncogene. 1999 Sep follicular center lymphoma. However, the 16;18(37):5177-86 variability of ASPP2 expression in diffuse large B- Lopez CD, Ao Y, Rohde LH, Perez TD, O'Connor DJ, Lu cell lymphoma was much greater than that seen in X, Ford JM, Naumovski L. Proapoptotic p53-interacting follicular center lymphoma. ASPP2 expression protein 53BP2 is induced by UV irradiation but suppressed by p53. Mol Cell Biol. 2000 Nov;20(21):8018-25 appeared inversely proportional to serum lactate dehydrogenase levels. Additionally, levels of Mori T, Okamoto H, Takahashi N, Ueda R, Okamoto T. Aberrant overexpression of 53BP2 mRNA in lung cancer ASPP2 expression are extremely low or cell lines. FEBS Lett. 2000 Jan 14;465(2-3):124-8 undetectable in cell lines derived from Burkitt's lymphoma (Lossos et al., 2002). Nakagawa H, Koyama K, Murata Y, Morito M, Akiyama T, Nakamura Y. APCL, a central nervous system-specific Prognosis homologue of adenomatous polyposis coli tumor In general, patients with high ASPP2 expression suppressor, binds to p53-binding protein 2 and translocates it to the perinucleus. Cancer Res. 2000 Jan tended to have a longer median survival than those 1;60(1):101-5 with low ASPP2 expression (Lossos et al., 2002). Espanel X, Sudol M. Yes-associated protein and p53- Gastric cancer binding protein-2 interact through their WW and SH3 domains. J Biol Chem. 2001 Apr 27;276(17):14514-23 Note Four single nucleotide polymorphisms within the Samuels-Lev Y, O'Connor DJ, Bergamaschi D, Trigiante G, Hsieh JK, Zhong S, Campargue I, Naumovski L, Crook ASPP2 gene locus, TP53BP2, show significant T, Lu X. ASPP proteins specifically stimulate the apoptotic correlation with gastric cancer susceptibility (Ju et function of p53. Mol Cell. 2001 Oct;8(4):781-94 al., 2005). Lossos IS, Natkunam Y, Levy R, Lopez CD. Apoptosis Hepatitis B virus-positive stimulating protein of p53 (ASPP2) expression differs in diffuse large B-cell and follicular center lymphoma: hepatocellular carcinoma correlation with clinical outcome. Leuk Lymphoma. 2002 Note Dec;43(12):2309-17 Downregulation of ASPP2 (and ASPP1) as a result Bergamaschi D, Samuels Y, O'Neil NJ, Trigiante G, Crook of promoter hypermethylation (as measured by T, Hsieh JK, O'Connor DJ, Zhong S, Campargue I, methylation-specific PCR) is frequently observed in Tomlinson ML, Kuwabara PE, Lu X. iASPP oncoprotein is a key inhibitor of p53 conserved from worm to human. Nat human patient samples of HBV-positive Genet. 2003 Feb;33(2):162-7 hepatocellular carcinoma as compared to Chen Y, Liu W, Naumovski L, Neve RL. ASPP2 inhibits surrounding non-tumor tissue (Zhao et al., 2010). APP-BP1-mediated NEDD8 conjugation to cullin-1 and decreases APP-BP1-induced cell proliferation and References neuronal apoptosis. J Neurochem. 2003 May;85(3):801-9 Iwabuchi K, Bartel PL, Li B, Marraccino R, Fields S. Two Bergamaschi D, Samuels Y, Jin B, Duraisingham S, Crook cellular proteins that bind to wild-type but not mutant p53. T, Lu X. ASPP1 and ASPP2: common activators of p53 Proc Natl Acad Sci U S A. 1994 Jun 21;91(13):6098-102 family members. Mol Cell Biol. 2004 Feb;24(3):1341-50 Helps NR, Barker HM, Elledge SJ, Cohen PT. Protein Cao Y, Hamada T, Matsui T, Date T, Iwabuchi K. Hepatitis phosphatase 1 interacts with p53BP2, a protein which C virus core protein interacts with p53-binding protein, binds to the tumour suppressor p53. FEBS Lett. 1995 Dec 53BP2/Bbp/ASPP2, and inhibits p53-mediated apoptosis. 27;377(3):295-300 Biochem Biophys Res Commun. 2004 Mar 19;315(4):788- 95 Naumovski L, Cleary ML. The p53-binding protein 53BP2 also interacts with Bc12 and impedes cell cycle Meek SE, Lane WS, Piwnica-Worms H. Comprehensive progression at G2/M. Mol Cell Biol. 1996 Jul;16(7):3884-92 proteomic analysis of interphase and mitotic 14-3-3- binding proteins. J Biol Chem. 2004 Jul 30;279(31):32046- Yang JP, Ono T, Sonta S, Kawabe T, Okamoto T. 54 Assignment of p53 binding protein (TP53BP2) to human chromosome band 1q42.1 by in situ hybridization. Sarraf SA, Stancheva I. Methyl-CpG binding protein MBD1 Cytogenet Cell Genet. 1997;78(1):61-2 couples histone H3 methylation at lysine 9 by SETDB1 to

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 690

TP53BP2 (tumor protein p53 binding protein, 2) Van Hook K, et al.

DNA replication and chromatin assembly. Mol Cell. 2004 Langton PF, Colombani J, Aerne BL, Tapon N. Drosophila Aug 27;15(4):595-605 ASPP regulates C-terminal Src kinase activity. Dev Cell. 2007 Dec;13(6):773-82 Takahashi N, Kobayashi S, Jiang X, Kitagori K, Imai K, Hibi Y, Okamoto T. Expression of 53BP2 and ASPP2 Tidow H, Andreeva A, Rutherford TJ, Fersht AR. Solution proteins from TP53BP2 gene by alternative splicing. structure of ASPP2 N-terminal domain (N-ASPP2) reveals Biochem Biophys Res Commun. 2004 Mar 5;315(2):434-8 a ubiquitin-like fold. J Mol Biol. 2007 Aug 24;371(4):948-58 Chen D, Padiernos E, Ding F, Lossos IS, Lopez CD. Sun WT, Hsieh PC, Chiang ML, Wang MC, Wang FF. p53 Apoptosis-stimulating protein of p53-2 (ASPP2/53BP2L) is target DDA3 binds ASPP2 and inhibits its stimulation on an E2F target gene. Cell Death Differ. 2005 Apr;12(4):358- p53-mediated BAX activation. Biochem Biophys Res 68 Commun. 2008 Nov 14;376(2):395-8 Cobleigh MA, Tabesh B, Bitterman P, Baker J, Cronin M, Kampa KM, Bonin M, Lopez CD. New insights into the Liu ML, Borchik R, Mosquera JM, Walker MG, Shak S. expanding complexity of the tumor suppressor ASPP2. Tumor gene expression and prognosis in breast cancer Cell Cycle. 2009a Sep 15;8(18):2871-6 patients with 10 or more positive lymph nodes. Clin Cancer Res. 2005 Dec 15;11(24 Pt 1):8623-31 Kampa KM, Acoba JD, Chen D, Gay J, Lee H, Beemer K, Padiernos E, Boonmark N, Zhu Z, Fan AC, Bailey AS, Fogal V, Kartasheva NN, Trigiante G, Llanos S, Yap D, Fleming WH, Corless C, Felsher DW, Naumovski L, Lopez Vousden KH, Lu X. ASPP1 and ASPP2 are new CD. Apoptosis-stimulating protein of p53 (ASPP2) transcriptional targets of E2F. Cell Death Differ. 2005 heterozygous mice are tumor-prone and have attenuated Apr;12(4):369-76 cellular damage-response thresholds. Proc Natl Acad Sci U S A. 2009b Mar 17;106(11):4390-5 Hershko T, Chaussepied M, Oren M, Ginsberg D. Novel link between E2F and p53: proapoptotic cofactors of p53 Uhlmann-Schiffler H, Kiermayer S, Stahl H. The DEAD box are transcriptionally upregulated by E2F. Cell Death Differ. protein Ddx42p modulates the function of ASPP2, a 2005 Apr;12(4):377-83 stimulator of apoptosis. Oncogene. 2009 May 21;28(20):2065-73 Ju H, Lee KA, Yang M, Kim HJ, Kang CP, Sohn TS, Rhee JC, Kang C, Kim JW. TP53BP2 locus is associated with Cong W, Hirose T, Harita Y, Yamashita A, Mizuno K, gastric cancer susceptibility. Int J Cancer. 2005 Dec Hirano H, Ohno S. ASPP2 regulates epithelial cell polarity 20;117(6):957-60 through the PAR complex. Curr Biol. 2010 Aug 10;20(15):1408-14 Kobayashi S, Kajino S, Takahashi N, Kanazawa S, Imai K, Hibi Y, Ohara H, Itoh M, Okamoto T. 53BP2 induces Sottocornola R, Royer C, Vives V, Tordella L, Zhong S, apoptosis through the mitochondrial death pathway. Genes Wang Y, Ratnayaka I, Shipman M, Cheung A, Gaston- Cells. 2005 Mar;10(3):253-60 Massuet C, Ferretti P, Molnár Z, Lu X. ASPP2 binds Par-3 and controls the polarity and proliferation of neural Liu ZJ, Lu X, Zhang Y, Zhong S, Gu SZ, Zhang XB, Yang progenitors during CNS development. Dev Cell. 2010 Jul X, Xin HM. Downregulated mRNA expression of ASPP and 20;19(1):126-37 the hypermethylation of the 5'-untranslated region in cancer cell lines retaining wild-type p53. FEBS Lett. 2005 Zhao J, Wu G, Bu F, Lu B, Liang A, Cao L, Tong X, Lu X, Mar 14;579(7):1587-90 Wu M, Guo Y. Epigenetic silence of ankyrin-repeat- containing, SH3-domain-containing, and proline-rich- Takahashi N, Kobayashi S, Kajino S, Imai K, Tomoda K, region- containing protein 1 (ASPP1) and ASPP2 genes Shimizu S, Okamoto T. Inhibition of the 53BP2S-mediated promotes tumor growth in hepatitis B virus-positive apoptosis by nuclear factor kappaB and Bcl-2 family hepatocellular carcinoma. Hepatology. 2010 proteins. Genes Cells. 2005 Aug;10(8):803-11 Jan;51(1):142-53 Zhu Z, Ramos J, Kampa K, Adimoolam S, Sirisawad M, Yu Liu CY, Lv X, Li T, Xu Y, Zhou X, Zhao S, Xiong Y, Lei QY, Z, Chen D, Naumovski L, Lopez CD. Control of Guan KL. PP1 cooperates with ASPP2 to dephosphorylate ASPP2/(53BP2L) protein levels by proteasomal and activate TAZ. J Biol Chem. 2011 Feb 18;286(7):5558- degradation modulates p53 apoptotic function. J Biol 66 Chem. 2005 Oct 14;280(41):34473-80 Wang XD, Lapi E, Sullivan A, Ratnayaka I, Goldin R, Hay Vives V, Su J, Zhong S, Ratnayaka I, Slee E, Goldin R, Lu R, Lu X. SUMO-modified nuclear cyclin D1 bypasses Ras- X. ASPP2 is a haploinsufficient tumor suppressor that induced senescence. Cell Death Differ. 2011 cooperates with p53 to suppress tumor growth. Genes Feb;18(2):304-14 Dev. 2006 May 15;20(10):1262-7 Hakuno F, Kurihara S, Watson RT, Pessin JE, Takahashi This article should be referenced as such: S. 53BP2S, interacting with insulin receptor substrates, Van Hook K, Wang Z, Lopez C. TP53BP2 (tumor protein modulates insulin signaling. J Biol Chem. 2007 Dec p53 binding protein, 2). Atlas Genet Cytogenet Oncol 28;282(52):37747-58 Haematol. 2011; 15(8):687-691.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 691

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Leukaemia Section Review

8p11 myeloproliferative syndrome (EMS, eight p11 myeloproliferative syndrome) Paula Aranaz, José Luis Vizmanos Department of Genetics, School of Sciences, University of Navarra, E-31008 Pamplona, Spain (PA, JLV)

Published in Atlas Database: December 2010 Online updated version : http://AtlasGeneticsOncology.org/Anomalies/8p11inMPDID1091.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI 8p11inMPDID1091.txt

NSD3) (Rosati et al., 2002; Romana et al., 2006; Identity Taketani et al., 2009), both of them in 8p11. In Alias addition, aberrations in 8p11-p12 are also frequent Stem cell leukemia-lymphoma syndrome (SCLL); events in breast cancer, but the loci responsible are 8p11 stem cell syndrome; 8p11 stem cell not well known (Yang et al., 2004; Garcia et al., leukemia/lymphoma syndrome; Myeloid and 2005; Gelsi-Boyer et al., 2005; Pole et al., 2006; lymphoid neoplasms FGFR1 abnormalities (WHO Yang et al., 2006; Yang et al., 2010). 2008 proposal) Disease Note Clinical entity defined by the disruption of the Although "8p11 myeloproliferative syndrome" FGFR1 gene located at 8p11 with generation of a (EMS) (Macdonald et al., 1995) is the most fusion gene between the 3' part of FGFR1 and the 5' frequent name for this disease in the literature, it part of the partner gene that also provides its must be designated as "myeloid and lymphoid promoter. The partner gene is always expressed in neoplasm with FGFR1 abnormalities" under the the haematopietic system and codes for a protein current 2008 World Health Organization with oligomerization domains. As a result of classification (Tefferi and Vardiman, 2008; Tefferi oligomerization, chimeric proteins show et al., 2009). This disease has been referred to as constitutive and ligand-independent activation of "stem cell leukemia/lymphoma" (SCLL) (Inhorn et FGFR1 kinase activity. al., 1995) which remark the coexistence of The 8p11 myeloproliferative syndrome (EMS) is a lymphoma, myeloid malignancy and lymphoblastic myeloproliferative disease with multilineage leukemia. involvement characterized by chronic myelomonocytic leukemia (CMML)-like myeloid Clinics and pathology hyperplasia, marked peripheral blood eosinophilia and associated with a high incidence of non- Note Hodgkin's lymphoma, usually of the T-cell This disease is related to fusion genes between lymphoblastic subtype. Occasional cases also show FGFR1, located in 8p11, and several partner genes. a B-cell lymphoproliferative disorder (Macdonald However there are some other aberrations affecting et al., 2002). this chromosomal band and 8p12 in other EMS cases were already described in the 1970s and neoplasms. Some acute myeloid leukemia (AML) 1980s, but cytogenetic and molecular analyses were cases have been described related to translocations not available (Manthorpe et al., 1977; Kjeldsberg et affecting MYST3 (also known as MOZ) (Borrow et al., 1979; Catovsky et al., 1980; Posner et al., al., 1996; Carapeti et al., 1998; Chaffanet et al., 1982). In 1992, 3 cases of T-cell lymphoblastic 2000; Murati et al., 2007; Esteyries et al., 2008; lymphoma associated with eosinophilia that Gervais et al., 2008) and WHSC1L1 (also known as subsequently developed acute myeloid leukemia or

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 692

8p11 myeloproliferative syndrome (EMS, eight p11 Aranaz P, Vizmanos JL myeloproliferative syndrome) myelodysplastic/myeloproliferative neoplasms were myeloproliferative neoplasms (Macdonald et al., reported (Abruzzo et al., 1992). One of them 2002; Jackson et al., 2010). showed a t(8;13) by conventional cytogenetics. Cytology Later it was shown that one of the breakpoints involved one 8p11 locus (Xiao et al., 1998). In the It seems that neoplastic cells present in lymph same year, Rao et al. reported a patient with nodes are predominantly small or medium t(8;13)(p11;q12) who presented with leukocytosis, lymphoblasts with a small cytoplasm (Jackson et monocytosis, myeloid hyperplasia of bone marrow, al., 2010). and generalized lymphadenopathy due to T-cell Pathology lymphoblastic lymphoma (Rao et al., 1998). The The blood counts reported are variable. More than term 8p11 myeloproliferative syndrome was 90% of patients have leukocytosis and less than suggested in 1995 by Macdonald et al. (Aguiar et 10% have leukopenia but some cases have been al., 1995; Macdonald et al., 1995) and confirmed as reported with normal leukocyte counts. clinical entity (SCLL) by Inhorn et al. (Inhorn et al., Eosinophilia is frequent, but monocytosis appears 1995). only in one third of patients. Basophils are Phenotype/cell stem origin increased only in cases with the t(8;22)(p11;q11). The presence of the cytogenetic aberration in 8p11 Blasts have been detected in half of the patients and both in myeloid and lymphoid cells, suggest a some cases show blast counts typical of an acute bilineage differentiation from a pluripotent and leukemia. These blasts are mainly of a myeloid or common stem cell (Macdonald et al., 2002). myeloid and lymphoid (bilineal) lineage although some of them are also of an immature lymphoid Etiology lineage. The FGFR1 fusion proteins that result from Most of the patients show a hypercellular bone chromosomal translocations affecting 8p11 have marrow that leads to a diagnosis of myeloid constitutive and ligand-independent FGFR1 hyperplasia or a myeloproliferative neoplasm. But enzymatic activity. FGFR1 is a receptor tyrosine in some cases, the dysplastic features lead to a kinase that dimerizes upon ligand binding, diagnosis of myelodysplastic syndrome or a activating multiple signalling pathways like myelodisplastic syndrome/myeloproliferative Ras/MAPK, PI3K, PLCgamma and STAT. These neoplasm. pathways could be abnormally activated as Most of the cases with lymph node biopsies consequence of FGFR1 aberration (Macdonald et reported had T-lymphoblastic lymphoma and the al., 2002) resulting in cell transformation. In fact, rest had myeloid sarcoma. In some cases evidence expression of ZMYM2-FGFR1 and BCR-FGFR1 of bilineal T-cell/myeloid or B-and T- cell fusions in immunodeficient mice are capable of lymphoblastic lymphoma has been reported. For a initiating an EMS-like disease (Agerstam et al., review see Jackson et al., 2010. 2010). Different fusion proteins could activate these Treatment pathways in a different way and could explain the phenotypic variability of the disease (Roumiantsev This is a very aggressive disease with a high rate of et al., 2004; Cross and Reiter, 2008; Jackson et al., progression to an AML resistant to conventional 2010). chemotherapy with a median survival time of less than 12 months (Macdonald et al., 2002; Cross and Epidemiology Reiter, 2008; Jackson, 2010). This is a very rare disease with less than 100 There are very few cases (Martinez-Climent et al., patients reported around the world and it can be 1998; Zhou et al., 2010) responding to interferon found at any age. It has been reported at ages alpha, this treatment could be useful at early stages. ranging from 3 to 84 years (median: 44 years). However, to date, only stem cell transplant remains There is a slightly male-to-female predominance effective to eradicate or suppress the malignant (Macdonald et al., 2002; Jackson et al., 2010). clone (Macdonald et al., 2002; Jackson et al., Clinics 2010). Median survival time for patients who received transplant after transformation to AML is Around 20-25% of patients show systemic and 24 months (range 6-46 months) but median survival unspecific symptoms like fatigue, night sweats, time is 12 months for the patients who did not weight loss and fever and around 20% are received transplant (range 0-60 months) (Jackson et asymptomatic (and the disease is detected in routine al., 2010). Currently there are no specific inhibitors analyses). Near two thirds of patients show for clinical use effective in this disease. Patients lymphadenopathy, generalized or localized. with FGFR1 fusions do not respond to drugs Hepato- and/or splenomegaly are also frequent developed for other tyrosine kinases like imatinib, events in these patients. One of the distinctive although several FGFR1 inhibitors have been features of this disease is the high frequency of tested, some of them with promising effects (Zhang lymphoblastic lymphoma, uncommon in other et al., 2010; Zhou et al., 2010; Bhide et al., 2010;

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 693

8p11 myeloproliferative syndrome (EMS, eight p11 Aranaz P, Vizmanos JL myeloproliferative syndrome)

Risuleo et al., 2009; Ma et al., 2008; Cai et al., 2008; Chase et al., 2007; Kammasud et al., 2007; Cytogenetics Klenke et al., 2007; Chen et al., 2004; Aviezier et Variants al., 2000). t(8;13)(p11;q12) ZMYM2-FGFR1 Evolution This is the first translocation described (Xiao et al., This disease has a chronic phase characterized by 1998; Reiter et al., 1998; Smedley et al., 1998; myeloid hyperplasia and overproduction of myeloid Popovici et al., 1998) and the most common one. In cells that can differentiate, but without treatment fact, it has been described in 33 of the 65 cases the disease progresses rapidly (1 to 2 years after described until now (Jackson et al., 2010). diagnosis) to an acute myeloid leukemia (AML) or This translocation generates a fusion gene sometimes to a B-lineage ALL (Macdonald et al., ZMYM2-FGFR1. 1995; Inhorn et al., 1995; Macdonald et al., 2002; Patients with this translocation develop Jackson et al., 2010). lymphadenopathy and T-cell lymphoblastic Gain of an additional copy of chromosome 21 is a lymphoma (Macdonald et al., 2002; Cross and non-random cytogenetic event apparently Reiter, 2008; Jackson et al., 2010). associated with progression of this disease t(6;8)(q27;p11) FGFR1OP-FGFR1 (Agerstam et al., 2007; Goradia et al., 2008) but its This translocation was first described by Popovici role remains unclear (Jackson et al., 2010). This et al. (1999) and fuses FGFR1OP (previously abnormality is reported in only 5 of 47 (10.6%) known as FOP -FGFR1 oncogene partner-) with karyotypes at the time of diagnosis but in 10 of 13 FGFR1. (76.9%) karyotypes reported in follow-up. These As other FGFR1 fusion variants, the chimeric karyotypes were mostly derived during clinical FGFR1OP-FGFR1 protein retains the N-terminus deterioration. In addition, some findings at the time leucine-rich region of FGFR1OP (an of transformation from EMS to acute leukemia oligomerization domain) fused to the catalytic include the addition of various marker domain of FGFR1 driving the abnormal chromosomes, as well as trisomy of chromosomes oligomerization of the chimeric protein and a 8, 9, 12 or 19 and deletions of chromosome 7 or constitutive and ligand-independent activation. either the 7p or 7q arms, and derivative This translocation has been reported in 8 cases until chromosome 9 (Jackson et al., 2010). date (Vizmanos et al., 2004). Eosinophilia is frequent in these patients. Four of these patients had Prognosis features at presentation and/or a clinical course As mentioned before, this is a devastating disease, typical of EMS, but three showed polycythemia which transforms to acute leukemia in a few vera (PV) and another one B-ALL. months if left untreated, and in which the malignant t(8;9)(p12;q33) CEP110-FGFR1 clone cannot be eradicated by conventional This translocation was described in 1983 but chemotherapy. So at this moment, without specific molecularly characterized by Guasch et al. in 2000 FGFR1 inhibitors for clinical use, the stem cell (Guasch et al., 2000). transplant remains as the only possibility to a long- This translocation has been reported in more than term survival (Macdonald et al., 1995; Inhorn et al., ten cases until date (Mozziconazzi et al., 2008; 1995; Macdonald et al., 2002; Jackson et al., 2010). Jackson et al., 2010) and the MPD caused by this aberration transforms rapidly and always in Genetics myelomonocytic leukemia, with a possible B- or T- lymphoid involvement. In addition, tonsillar Note involvement and monocytosis also correlates with This disease is defined by the fusion of FGFR1 this variant (Mozziconazzi et al., 2008; Jackson et (8p11) with other partner genes, as consequence of al., 2010). Recently a complete haematological and a cytogenetic aberration, mainly chromosomal molecular remission has been reported after two translocations. FGFR1 codes for a receptor tyrosine years in a patient with this translocation treated kinase. The gene fusion maintains the 3' terminal early with interferon alpha (Zhou et al., 2010). part of the FGFR1 gene (from exon 9) joined to the t(8;22)(p11;q11) BCR-FGFR1 5' terminal part of the partner gene. Partner genes This translocation was reported simultaneously by are widely expressed and fusion genes have also two groups in 2001 (Fioretos et al., 2001; this expression pattern. The chimeric gene codes for Demiroglu et al., 2001) and fuses BCR with a protein which retains the TK domain from FGFR1 FGFR1. and oligomerization domains provided by the As in the case of the other FGFR1 fusions, BCR is partner gene. This protein has a constitutive and also widely expressed and BCR-FGFR1 retains ligand-independent activity and activates multiple oligomerization domains from BCR and the signal transduction pathways. catalytic domain from FGFR1,

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 694

8p11 myeloproliferative syndrome (EMS, eight p11 Aranaz P, Vizmanos JL myeloproliferative syndrome) leading to constitutive and ligand-independent located at 12p11.23 and FGFR1. Fusion structure activity of the chimeric protein. However it seems was identical to other FGFR1 variants. that BCR not only drives this oligomerization but This fusion has been reported only in one case could also play some role in triggering the (Sohal et al., 2001; Grand et al., 2004) but it has downstream signalling pathways. Patients with been also found in the cell line KG-1 (Gu et al., BCR-FGFR1 fusions have a slightly different 2006; DSMZ ACC 14) that can be used to assay in clinical phenotype from other FGFR1 fusion vitro specific FGFR1 inhibitors (Gu et al., 2006; variants. In fact, these patients have a clinical and Chase et al., 2007). This cell line was derived from morphological picture similar to typical BCR-ABL the bone marrow of a 59-year-old man with positive chronic myeloid leukemia (Roumiantsev et erythroleukemia transformed to AML at relapse in al., 2004; Cross and Reiter, 2008; Baldazzi et al., 1977 (Koeffler and Golde, 1978). 2010; Jackson et al., 2010). t(7;8)(q34;p11) TRIM24-FGFR1 t(8;11)(p11;p15) NUP98-FGFR1 This translocation was described and molecularly This translocation was described by Sohal et al. in characterized by Belloni et al. (2005) in a 49-year- 2001, in a patient with AML with additional old woman with a putative chronic MPD with cytogenetic aberrations (patient UPN6, eosinophilia which transformed to an AML-M4 and 47,XY,t(8;11)(p11;p15),+8,-17,+i(17q)) (Sohal et died in a few days. As other FGFR1 fusions, this is al., 2001). Only interphase cells were available to the only case reported to date. perform FISH analysis, and the results obtained The consequence of the t(7,8)(q34;p11) is the indicated a breakpoint within or in the vicinity of fusion gene TRIM24-FGFR1. NUP98 but definite molecular characterization t(8;17)(p11;q23) MYO18A-FGFR1 could not be done. Other patient with AML and the This translocation was described by Walz et al. same translocation had been reported previously (2005) in a 74-year-old female with a 2 years (Larson et al., 1983), indicating that this was a history of an unusual recurrent abnormality. However no new cases have myelodysplastic/myeloproliferative disease been described since these reports so NUP98- (MDS/MPD) with thrombocytopenia, markedly FGFR1 fusion has not been confirmed definitely. reduced size and numbers of megakaryocytes and NUP98 has a small coiled-coil region that could elevated numbers of monocytes, eosinophils and drive the constitutive activation of the chimeric basophils. Her karyotype showed an additional NUP98-FGFR1 protein but it is possible that trisomy 20 and she died after a treatment-resistant disruption of NUP98 was also involved in the disease progression of two years. oncogenic process. This translocation fuses MYO18A, located in t(8;19)(p11;q13) HERVK-FGFR1 17q11.2 with FGFR1. However, the breakpoint in This aberration was firstly described in 2000, chromosome 17 was cytogenetically located to associated with loss of the Y chromosome in a man 17q23. FISH and molecular analysis showed that with an AML M0, probably secondary to a this fusion gene was consequence of a complex myeloproliferative disorder, who died 15 months cytogenetic aberration with an additional inversion after diagnosis (Mugneret et al., 2000). Later, the in 17q region between 17q11 and 17q23. same group identified the chromosome 19 partner t(8;12)(p11;q15) CPSF6-FGFR1 showing that a long terminal repeat of human This translocation targeting FGFR1 was first endogenous retrovirus gene (HERV-K) was fused described by Sohal et al. (2001). Later the same in frame with FGFR1 (Guasch et al., 2003). This group identified the partner gene as CPSF6 (located fusion has been described only in this case. at 12q15) (Hidalgo-Curtis et al., 2008) and again, ins(12;8)(p11;p11p22) FGFR1OP2-FGFR1 only this case has been described. The patient was a This FGFR1 fusion is not caused by a chromosomal 75-year-old female with lymphadenopathy, translocation but an inversion. splenomegaly, neutrophilia and eosinophilia in Ins(12;8)(p11;p11p22) targeting FGFR1 was first peripheral blood and also an increase of eosinophils described by Sohal et al. (2001) in a 75-years old and eosinophil precursors in the bone marrow. patient diagnosed with a T-cell lymphoblastic After a rapid clinical deterioration the patient died lymphoma and marked lymph node infiltration with in 10 weeks. atypical eosinophils. Whole blood count was t(2;8)(q37;p11) LRRFIP1-FGFR1 normal except for very mild eosinophilia and the In 2009, Soler et al. identified and characterized the bone marrow also showed some atypical t(2;8)(q37;p11) in an 82-year-old man with 10% eosinophils. After complete remission, this patient eosinophils, 2-4% myelocytes and metamyelocytes, relapsed and transformed to an AML with the same and 8% circulating blasts and an hypocellular bone chromosomal aberration and died. Later this marrow with moderate dysgranulopoiesis and 15% aberration was molecularly characterized by the blasts (Soler et al., 2009). Some years before, this same group (Grand et al., 2004) as a fusion between patient had displayed pancitopenia and a bone FGFR1OP2 (from FGFR1 oncogene partner 2) marrow showing a refractory anemia with an excess

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 695

8p11 myeloproliferative syndrome (EMS, eight p11 Aranaz P, Vizmanos JL myeloproliferative syndrome) of blasts (15%). The disease transformed to AML BCR in one year and the patient died. FISH analysis on Location retrospective samples showed that the 22q11.2 t(2;8)(q37;p11) was not present in early stages (pancitopenia) of the disease. Protein BCR is, like ETV6, a common fusion partner of Genes involved and several tyrosine kinase genes rearranged in myeloid disorders (BCR-ABL, BCR-JAK2, BCR-PDGFRA proteins and BCR-FGFR1 have been described to date). ZMYM2 However function of the protein encoded by this gene is not clear and its name comes from Location breakpoint cluster region. 13q12 NUP98 Protein Location ZMYM2 (also known as ZNF198, RAMP - 11p15 rearranged in atypical myeloproliferative disorder-, or FIM - fused in myeloproliferative disorder) HERVK codes for a zinc finger protein that may act as a Location transcription factor involved in ribosomal RNA 7p22.1 transcription and also could be part of a BHC histone deacetylase complex. The chimeric protein Protein retains the proline-rich domain of ZMYM2 (an HERV-K is also ubiquitously expressed. The oligomerization domain) and the tyrosine kinase HERV-Ks are human specific endogenous domain of FGFR1. The abnormal oligomerization retrovirus that have been proposed as etiological of the chimeric protein leads to constitutive and cofactors in some chronic diseases like cancer ligand-independent activation. In addition, this because they are mobile elements that could disrupt abnormal protein is located in the cytoplasm and tumor suppressor and/or DNA repair genes. In this not in the membrane as native FGFR1. case, it seems that the part of the HERV-K sequence fused showed similarities with a retroviral FGFR1OP envelope protein whose dimerization would induce Location the constitutive activation of the chimeric protein 6q27 HERVK-FGFR1 (Guasch et al., 2003). Protein FGFR1OP2 FGFR1OP, widely expressed, codes for a Location hydrophilic centrosomal protein that could be a 12p11.23 member of a leucine-rich protein family, and it is involved in the anchoring of microtubules (MTS) to Protein subcellular structures. FGFR1OP could play a role As other FGFR1 partners, FGFR1OP2 is also in lung cancer growth and progression and has been widely expressed but its function is unknown. It proposed as a prognostic biomarker for this disease could code for a cytoskeleton molecule (Lin et al., (Mano et al., 2007). 2010). However, the putative protein coded by this gene has four potential coiled-coil domains and the CEP110 first two are retained in the chimeric protein, so Location they could mediate its oligomerization and 9q33.2 constitutive activation (Grand et al., 2004). Protein TRIM24 CEP110 encodes also a centrosomal protein with Location several leucine zipper motifs required for the 7q34 centrosome to function as a microtubule organizing center. CEP110 is also widely expressed and Protein CEP110-FGFR1 retains the leucine zipper motifs of TRIM24 (previously known as TIF1) codes for a CEP110 at its N-terminus which could mediate the protein of the tripartite motif (TRIM) family that consititutive activation of the FGFR1 catalytic mediates transcriptional control by interaction with domain at its C-terminus. In addition the CEP110- several nuclear receptors and localizes to nuclear FGFR1 fusion protein has been found in the bodies. The tripartite motif includes three zinc- cytoplasm, whereas both CEP110 and FGFR1 wild- binding domains - a RING, a B-box type 1 and a B- type proteins are centrosome and plasma box type 2 - and a coiled-coil region that is retained membrane-bound proteins respectively (Guasch et in the chimeric protein so it could promote, as other al., 2000). FGFR1 fusion proteins, its constitutive and ligand- independent activation

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 696

8p11 myeloproliferative syndrome (EMS, eight p11 Aranaz P, Vizmanos JL myeloproliferative syndrome)

MYO18A Result of the chromosomal Location 17q11.2 anomaly Protein Hybrid gene MYO18A is a widely expressed gene that codes for Detection a protein of unknown function of the myosin Methods of detection superfamily. It has been recently described that this 1. Conventional cytogenetics to identify protein is a novel PAK2 (p21-activated kinase 2) translocations or other rearrangements involving binding partner (Hsu et al., 2010). PAK2 has many 8p11. biological functions, including the regulation of 2. Fluorescent in situ hibridization (FISH) with actin reorganization and cell motility. MYO18A probes flanking or covering FGFR1 to demonstrate contains several functional motifs that are retained disruption of this gene. in MYO18A-FGFR1, including an N-terminal PDZ 3. 5' RACE PCR to identify FGFR1 partner gene. (PSD-95/Dlg/ZO-1) protein-protein interaction 4. RT-PCR with primers located in both genes domain, a myosin head domain and a region that is fused. predicted to form multiple coiled-coils. Some of these coiled-coils could drive oligomerization of References MYO18A-FGFR1, with consequent constitutive activation of the FGFR1 kinase activity. Manthorpe R, Jonsson V, Christensen BE, Hesselvik M, Recently, MYO18A has also been found fused to Egeberg J, Videbaek A. A case of T-cell lymphoma with Sézary cells in the blood and bone marrow accompanied PDGFRB as consequence of a t(5;17)(q33-q34;q11) by peripheral T and B lymphocytosis. Scand J Haematol. but with a different breakpoint in which all the 1977 May;18(5):449-54 predicted coiled-coil domains of normal MYO18A Koeffler HP, Golde DW. Acute myelogenous leukemia: a are retained in the chimeric protein (Walz et al., human cell line responsive to colony-stimulating activity. 2009). Science. 1978 Jun 9;200(4346):1153-4 CPSF6 Kjeldsberg CR, Nathwani BN, Rappaport H. Acute myeloblastic leukemia developing in patients with Location mediastinal lymphoblastic lymphoma. Cancer. 1979 12q15 Dec;44(6):2316-23 Protein Catovsky D, Bernasconi C, Verdonck PJ, Postma A, Hows The protein encoded by CPSF6 is the 68 kD subunit J, van der Does-van den Berg A, Rees JK, Castelli G, Morra E, Galton DA. The association of eosinophilia with of a cleavage factor required for 3' RNA cleavage lymphoblastic leukaemia or lymphoma: a study of seven and polyadenylation processing. Unlike other patients. Br J Haematol. 1980 Aug;45(4):523-34 partners of FGFR1, CPSF6 does not have any Posner MR, Said J, Pinkus GS, Nadler LM, Hardy R, identifiable oligomerisation motifs. However RNA Flatow F, Skarin AT. T-cell lymphoblastic lymphoma with recognition motifs (RRM) such as the one retained subsequent acute nonlymphocytic leukemia: a case report. in CPSF6-FGFR1, could mediate the dimerization Cancer. 1982 Jul 1;50(1):118-24 needed for constitutive activation of the CPSF6- Larson RA, Le Beau MM, Vardiman JW, Testa JR, Golomb FGFR1 kinase activity. HM, Rowley JD. The predictive value of initial cytogenetic studies in 148 adults with acute nonlymphocytic leukemia: LRRFIP1 a 12-year study (1970-1982). Cancer Genet Cytogenet. Location 1983 Nov;10(3):219-36 2q37.3 Abruzzo LV, Jaffe ES, Cotelingam JD, Whang-Peng J, Del Duca V Jr, Medeiros LJ. T-cell lymphoblastic lymphoma Protein with eosinophilia associated with subsequent myeloid LRRFIP1 (Leucine-rich repeat Flightless- malignancy. Am J Surg Pathol. 1992 Mar;16(3):236-45 Interacting Protein 1) is a ubiquitously expressed Rao PH, Cesarman G, Coleman M, Acaron S, Verma RS. gene that encodes for a nuclear and cytoplasmatic Cytogenetic evidence for extramedullary blast crisis with protein with multiple functions. In the nucleus, it t(8;13)(q11;p11) in chronic myelomonocytic leukemia. Acta acts as a transcriptional repressor that decreases the Haematol. 1992;88(4):201-3 expression of EGFR, PDGFRA and TNF. In the Inhorn RC, Aster JC, Roach SA, Slapak CA, Soiffer R, cytoplasm, it interacts with actin-binding proteins. Tantravahi R, Stone RM. A syndrome of lymphoblastic lymphoma, eosinophilia, and myeloid It has an N-terminal coiled-coil domain that, as hyperplasia/malignancy associated with t(8;13)(p11;q11): other FGFR1 partners, could drive the dimerization description of a distinctive clinicopathologic entity. Blood. of LRRFIP1-FGFR1 leading to the constitutive 1995 Apr 1;85(7):1881-7 activation of the kinase activity.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 697

8p11 myeloproliferative syndrome (EMS, eight p11 Aranaz P, Vizmanos JL myeloproliferative syndrome)

Macdonald D, Aguiar RC, Mason PJ, Goldman JM, Cross translocation involving the FGFR1 gene. Br J Haematol. NC. A new myeloproliferative disorder associated with 2000 Nov;111(2):647-9 chromosomal translocations involving 8p11: a review. Leukemia. 1995 Oct;9(10):1628-30 Demiroglu A, Steer EJ, Heath C, Taylor K, Bentley M, Allen SL, Koduru P, Brody JP, Hawson G, Rodwell R, Borrow J, Stanton VP Jr, Andresen JM, Becher R, Behm Doody ML, Carnicero F, Reiter A, Goldman JM, Melo JV, FG, Chaganti RS, Civin CI, Disteche C, Dubé I, Frischauf Cross NC. The t(8;22) in chronic myeloid leukemia fuses AM, Horsman D, Mitelman F, Volinia S, Watmore AE, BCR to FGFR1: transforming activity and specific inhibition Housman DE. The translocation t(8;16)(p11;p13) of acute of FGFR1 fusion proteins. Blood. 2001 Dec myeloid leukaemia fuses a putative acetyltransferase to 15;98(13):3778-83 the CREB-binding protein. Nat Genet. 1996 Sep;14(1):33- 41 Fioretos T, Panagopoulos I, Lassen C, Swedin A, Billström R, Isaksson M, Strömbeck B, Olofsson T, Mitelman F, Carapeti M, Aguiar RC, Goldman JM, Cross NC. A novel Johansson B. Fusion of the BCR and the fibroblast growth fusion between MOZ and the nuclear receptor coactivator factor receptor-1 (FGFR1) genes as a result of TIF2 in acute myeloid leukemia. Blood. 1998 May t(8;22)(p11;q11) in a myeloproliferative disorder: the first 1;91(9):3127-33 fusion gene involving BCR but not ABL. Genes Chromosomes Cancer. 2001 Dec;32(4):302-10 Martinez-Climent JA, Vizcarra E, Benet I, Marugan I, Terol MJ, Solano C, Arbona C, Tormo M, Comes AM, García- Sohal J, Chase A, Mould S, Corcoran M, Oscier D, Iqbal S, Conde J. Cytogenetic response induced by interferon Parker S, Welborn J, Harris RI, Martinelli G, Montefusco V, alpha in the myeloproliferative disorder with eosinophilia, T Sinclair P, Wilkins BS, van den Berg H, Vanstraelen D, cell lymphoma and the chromosomal translocation Goldman JM, Cross NC. Identification of four new t(8;13)(p11;q12) Leukemia. 1998 Jun;12(6):999-1000 translocations involving FGFR1 in myeloid disorders. Genes Chromosomes Cancer. 2001 Oct;32(2):155-63 Popovici C, Adélaïde J, Ollendorff V, Chaffanet M, Guasch G, Jacrot M, Leroux D, Birnbaum D, Pébusque MJ. Macdonald D, Reiter A, Cross NC. The 8p11 Fibroblast growth factor receptor 1 is fused to FIM in stem- myeloproliferative syndrome: a distinct clinical entity cell myeloproliferative disorder with t(8;13). Proc Natl Acad caused by constitutive activation of FGFR1. Acta Sci U S A. 1998 May 12;95(10):5712-7 Haematol. 2002;107(2):101-7 Reiter A, Sohal J, Kulkarni S, Chase A, Macdonald DH, Rosati R, La Starza R, Veronese A, Aventin A, Aguiar RC, Gonçalves C, Hernandez JM, Jennings BA, Schwienbacher C, Vallespi T, Negrini M, Martelli MF, Goldman JM, Cross NC. Consistent fusion of ZNF198 to Mecucci C. NUP98 is fused to the NSD3 gene in acute the fibroblast growth factor receptor-1 in the myeloid leukemia associated with t(8;11)(p11.2;p15). t(8;13)(p11;q12) myeloproliferative syndrome. Blood. 1998 Blood. 2002 May 15;99(10):3857-60 Sep 1;92(5):1735-42 Guasch G, Popovici C, Mugneret F, Chaffanet M, Smedley D, Hamoudi R, Clark J, Warren W, Abdul-Rauf M, Pontarotti P, Birnbaum D, Pébusque MJ. Endogenous Somers G, Venter D, Fagan K, Cooper C, Shipley J. The retroviral sequence is fused to FGFR1 kinase in the 8p12 t(8;13)(p11;q11-12) rearrangement associated with an stem-cell myeloproliferative disorder with atypical myeloproliferative disorder fuses the fibroblast t(8;19)(p12;q13.3). Blood. 2003 Jan 1;101(1):286-8 growth factor receptor 1 gene to a novel gene RAMP. Hum Mol Genet. 1998 Apr;7(4):637-42 Chen J, Deangelo DJ, Kutok JL, Williams IR, Lee BH, Wadleigh M, Duclos N, Cohen S, Adelsperger J, Okabe R, Xiao S, Nalabolu SR, Aster JC, Ma J, Abruzzo L, Jaffe ES, Coburn A, Galinsky I, Huntly B, Cohen PS, Meyer T, Stone R, Weissman SM, Hudson TJ, Fletcher JA. FGFR1 Fabbro D, Roesel J, Banerji L, Griffin JD, Xiao S, Fletcher is fused with a novel zinc-finger gene, ZNF198, in the JA, Stone RM, Gilliland DG. PKC412 inhibits the zinc t(8;13) leukaemia/lymphoma syndrome. Nat Genet. 1998 finger 198-fibroblast growth factor receptor 1 fusion Jan;18(1):84-7 tyrosine kinase and is active in treatment of stem cell myeloproliferative disorder. Proc Natl Acad Sci U S A. Popovici C, Zhang B, Grégoire MJ, Jonveaux P, Lafage- 2004 Oct 5;101(40):14479-84 Pochitaloff M, Birnbaum D, Pébusque MJ. The t(6;8)(q27;p11) translocation in a stem cell Grand EK, Grand FH, Chase AJ, Ross FM, Corcoran MM, myeloproliferative disorder fuses a novel gene, FOP, to Oscier DG, Cross NC. Identification of a novel gene, fibroblast growth factor receptor 1. Blood. 1999 Feb FGFR1OP2, fused to FGFR1 in 8p11 myeloproliferative 15;93(4):1381-9 syndrome. Genes Chromosomes Cancer. 2004 May;40(1):78-83 Aviezer D, Cotton S, David M, Segev A, Khaselev N, Galili N, Gross Z, Yayon A. Porphyrin analogues as novel Roumiantsev S, Krause DS, Neumann CA, Dimitri CA, antagonists of fibroblast growth factor and vascular Asiedu F, Cross NC, Van Etten RA. Distinct stem cell endothelial growth factor receptor binding that inhibit myeloproliferative/T lymphoma syndromes induced by endothelial cell proliferation, tumor progression, and ZNF198-FGFR1 and BCR-FGFR1 fusion genes from 8p11 metastasis. Cancer Res. 2000 Jun 1;60(11):2973-80 translocations. Cancer Cell. 2004 Mar;5(3):287-98 Chaffanet M, Gressin L, Preudhomme C, Soenen-Cornu V, Vizmanos JL, Hernández R, Vidal MJ, Larráyoz MJ, Odero Birnbaum D, Pébusque MJ. MOZ is fused to p300 in an MD, Marín J, Ardanaz MT, Calasanz MJ, Cross NC. acute monocytic leukemia with t(8;22). Genes Clinical variability of patients with the t(6;8)(q27;p12) and Chromosomes Cancer. 2000 Jun;28(2):138-44 FGFR1OP-FGFR1 fusion: two further cases. Hematol J. 2004;5(6):534-7 Guasch G, Mack GJ, Popovici C, Dastugue N, Birnbaum D, Rattner JB, Pébusque MJ. FGFR1 is fused to the Yang ZQ, Albertson D, Ethier SP. Genomic organization of centrosome-associated protein CEP110 in the 8p12 stem the 8p11-p12 amplicon in three breast cancer cell lines. cell myeloproliferative disorder with t(8;9)(p12;q33). Blood. Cancer Genet Cytogenet. 2004 Nov;155(1):57-62 2000 Mar 1;95(5):1788-96 Belloni E, Trubia M, Gasparini P, Micucci C, Tapinassi C, Mugneret F, Chaffanet M, Maynadié M, Guasch G, Favre Confalonieri S, Nuciforo P, Martino B, Lo-Coco F, Pelicci B, Casasnovas O, Birnbaum D, Pébusque MJ. The 8p12 PG, Di Fiore PP. 8p11 myeloproliferative syndrome with a myeloproliferative disorder. t(8;19)(p12;q13.3): a novel novel t(7;8) translocation leading to fusion of the FGFR1

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 698

8p11 myeloproliferative syndrome (EMS, eight p11 Aranaz P, Vizmanos JL myeloproliferative syndrome)

and TIF1 genes. Genes Chromosomes Cancer. 2005 acute myeloid leukemias. Haematologica. 2007 Mar;42(3):320-5 Feb;92(2):262-3 Garcia MJ, Pole JC, Chin SF, Teschendorff A, Naderi A, Cai ZW, Zhang Y, Borzilleri RM, Qian L, Barbosa S, Wei Ozdag H, Vias M, Kranjac T, Subkhankulova T, Paish C, D, Zheng X, Wu L, Fan J, Shi Z, Wautlet BS, Mortillo S, Ellis I, Brenton JD, Edwards PA, Caldas C. A 1 Mb minimal Jeyaseelan R Sr, Kukral DW, Kamath A, Marathe P, amplicon at 8p11-12 in breast cancer identifies new D'Arienzo C, Derbin G, Barrish JC, Robl JA, Hunt JT, candidate oncogenes. Oncogene. 2005 Aug Lombardo LJ, Fargnoli J, Bhide RS. Discovery of brivanib 4;24(33):5235-45 alaninate ((S)-((R)-1-(4-(4-fluoro-2-methyl-1H-indol-5- yloxy)-5-methylpyrrolo[2,1-f][1,2,4]triazin-6-yloxy)propan-2- Gelsi-Boyer V, Orsetti B, Cervera N, Finetti P, Sircoulomb yl)2-aminopropanoate), a novel prodrug of dual vascular F, Rougé C, Lasorsa L, Letessier A, Ginestier C, Monville endothelial growth factor receptor-2 and fibroblast growth F, Esteyriès S, Adélaïde J, Esterni B, Henry C, Ethier SP, factor receptor-1 kinase inhibitor (BMS-540215). J Med Bibeau F, Mozziconacci MJ, Charafe-Jauffret E, Chem. 2008 Mar 27;51(6):1976-80 Jacquemier J, Bertucci F, Birnbaum D, Theillet C, Chaffanet M. Comprehensive profiling of 8p11-12 Cross NC, Reiter A. Fibroblast growth factor receptor and amplification in breast cancer. Mol Cancer Res. 2005 platelet-derived growth factor receptor abnormalities in Dec;3(12):655-67 eosinophilic myeloproliferative disorders. Acta Haematol. 2008;119(4):199-206 Walz C, Chase A, Schoch C, Weisser A, Schlegel F, Hochhaus A, Fuchs R, Schmitt-Gräff A, Hehlmann R, Esteyries S, Perot C, Adelaide J, Imbert M, Lagarde A, Cross NC, Reiter A. The t(8;17)(p11;q23) in the 8p11 Pautas C, Olschwang S, Birnbaum D, Chaffanet M, myeloproliferative syndrome fuses MYO18A to FGFR1. Mozziconacci MJ. NCOA3, a new fusion partner for Leukemia. 2005 Jun;19(6):1005-9 MOZ/MYST3 in M5 acute myeloid leukemia. Leukemia. 2008 Mar;22(3):663-5 Gu TL, Goss VL, Reeves C, Popova L, Nardone J, Macneill J, Walters DK, Wang Y, Rush J, Comb MJ, Gervais C, Murati A, Helias C, Struski S, Eischen A, Druker BJ, Polakiewicz RD. Phosphotyrosine profiling Lippert E, Tigaud I, Penther D, Bastard C, Mugneret F, identifies the KG-1 cell line as a model for the study of Poppe B, Speleman F, Talmant P, VanDen Akker J, FGFR1 fusions in acute myeloid leukemia. Blood. 2006 Baranger L, Barin C, Luquet I, Nadal N, Nguyen-Khac F, Dec 15;108(13):4202-4 Maarek O, Herens C, Sainty D, Flandrin G, Birnbaum D, Mozziconacci MJ, Lessard M. Acute myeloid leukaemia Pole JC, Courtay-Cahen C, Garcia MJ, Blood KA, Cooke with 8p11 (MYST3) rearrangement: an integrated SL, Alsop AE, Tse DM, Caldas C, Edwards PA. High- cytologic, cytogenetic and molecular study by the groupe resolution analysis of chromosome rearrangements on 8p francophone de cytogénétique hématologique. Leukemia. in breast, colon and pancreatic cancer reveals a complex 2008 Aug;22(8):1567-75 pattern of loss, gain and translocation. Oncogene. 2006 Sep 14;25(41):5693-706 Goradia A, Bayerl M, Cornfield D. The 8p11 myeloproliferative syndrome: review of literature and an Romana SP, Radford-Weiss I, Ben Abdelali R, Schluth C, illustrative case report. Int J Clin Exp Pathol. 2008 Jan Petit A, Dastugue N, Talmant P, Bilhou-Nabera C, 1;1(5):448-56 Mugneret F, Lafage-Pochitaloff M, Mozziconacci MJ, Andrieu J, Lai JL, Terre C, Rack K, Cornillet-Lefebvre P, Hidalgo-Curtis C, Chase A, Drachenberg M, Roberts MW, Luquet I, Nadal N, Nguyen-Khac F, Perot C, Van den Finkelstein JZ, Mould S, Oscier D, Cross NC, Grand FH. Akker J, Fert-Ferrer S, Cabrol C, Charrin C, Tigaud I, The t(1;9)(p34;q34) and t(8;12)(p11;q15) fuse pre-mRNA Poirel H, Vekemans M, Bernard OA, Berger R. NUP98 processing proteins SFPQ (PSF) and CPSF6 to ABL and rearrangements in hematopoietic malignancies: a study of FGFR1. Genes Chromosomes Cancer. 2008 the Groupe Francophone de Cytogénétique May;47(5):379-85 Hématologique. Leukemia. 2006 Apr;20(4):696-706 Ma J, Xin X, Meng L, Tong L, Lin L, Geng M, Ding J. The Yang ZQ, Streicher KL, Ray ME, Abrams J, Ethier SP. marine-derived oligosaccharide sulfate (MdOS), a novel Multiple interacting oncogenes on the 8p11-p12 amplicon multiple tyrosine kinase inhibitor, combats tumor in human breast cancer. Cancer Res. 2006 Dec angiogenesis both in vitro and in vivo. PLoS One. 15;66(24):11632-43 2008;3(11):e3774 Chase A, Grand FH, Cross NC. Activity of TKI258 against Mozziconacci MJ, Carbuccia N, Prebet T, Charbonnier A, primary cells and cell lines with FGFR1 fusion genes Murati A, Vey N, Chaffanet M, Birnbaum D. Common associated with the 8p11 myeloproliferative syndrome. features of myeloproliferative disorders with Blood. 2007 Nov 15;110(10):3729-34 t(8;9)(p12;q33) and CEP110-FGFR1 fusion: report of a new case and review of the literature. Leuk Res. 2008 Kammasud N, Boonyarat C, Tsunoda S, Sakurai H, Saiki I, Aug;32(8):1304-8 Grierson DS, Vajragupta O. Novel inhibitor for fibroblast growth factor receptor tyrosine kinase. Bioorg Med Chem Tefferi A, Vardiman JW. Classification and diagnosis of Lett. 2007 Sep 1;17(17):4812-8 myeloproliferative neoplasms: the 2008 World Health Organization criteria and point-of-care diagnostic Klenke FM, Abdollahi A, Bertl E, Gebhard MM, Ewerbeck algorithms. Leukemia. 2008 Jan;22(1):14-22 V, Huber PE, Sckell A. Tyrosine kinase inhibitor SU6668 represses chondrosarcoma growth via antiangiogenesis in Risuleo G, Ciacciarelli M, Castelli M, Galati G. The vivo. BMC Cancer. 2007 Mar 17;7:49 synthetic inhibitor of fibroblast growth factor receptor PD166866 controls negatively the growth of tumor cells in Mano Y, Takahashi K, Ishikawa N, Takano A, Yasui W, culture. J Exp Clin Cancer Res. 2009 Dec 11;28:151 Inai K, Nishimura H, Tsuchiya E, Nakamura Y, Daigo Y. Fibroblast growth factor receptor 1 oncogene partner as a Soler G, Nusbaum S, Varet B, Macintyre EA, Vekemans novel prognostic biomarker and therapeutic target for lung M, Romana SP, Radford-Weiss I. LRRFIP1, a new FGFR1 cancer. Cancer Sci. 2007 Dec;98(12):1902-13 partner gene associated with 8p11 myeloproliferative syndrome. Leukemia. 2009 Jul;23(7):1359-61 Murati A, Adélaïde J, Quilichini B, Rémy V, Sainty D, Stoppa AM, Bernard P, Olschwang S, Birnbaum D, Taketani T, Taki T, Nakamura H, Taniwaki M, Masuda J, Chaffanet M, Mozziconacci MJ. New types of MYST3-CBP Hayashi Y. NUP98-NSD3 fusion gene in radiation- and CBP-MYST3 fusion transcripts in t(8;16)(p11;p13) associated myelodysplastic syndrome with

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 699

8p11 myeloproliferative syndrome (EMS, eight p11 Aranaz P, Vizmanos JL myeloproliferative syndrome)

t(8;11)(p11;p15) and expression pattern of NSD family modulating epithelial cell migration. Mol Biol Cell. 2010 Jan genes. Cancer Genet Cytogenet. 2009 Apr 15;190(2):108- 15;21(2):287-301 12 Jackson CC, Medeiros LJ, Miranda RN. 8p11 Tefferi A, Thiele J, Vardiman JW. The 2008 World Health myeloproliferative syndrome: a review. Hum Pathol. 2010 Organization classification system for myeloproliferative Apr;41(4):461-76 neoplasms: order out of chaos. Cancer. 2009 Sep 1;115(17):3842-7 Lin A, Hokugo A, Choi J, Nishimura I. Small cytoskeleton- associated molecule, fibroblast growth factor receptor 1 Walz C, Haferlach C, Hänel A, Metzgeroth G, Erben P, oncogene partner 2/wound inducible transcript-3.0 Gosenca D, Hochhaus A, Cross NC, Reiter A. (FGFR1OP2/wit3.0), facilitates fibroblast-driven wound Identification of a MYO18A-PDGFRB fusion gene in an closure. Am J Pathol. 2010 Jan;176(1):108-21 eosinophilia-associated atypical myeloproliferative neoplasm with a t(5;17)(q33-34;q11.2). Genes Yang ZQ, Liu G, Bollig-Fischer A, Giroux CN, Ethier SP. Chromosomes Cancer. 2009 Feb;48(2):179-83 Transforming properties of 8p11-12 amplified genes in human breast cancer. Cancer Res. 2010 Nov Agerstam H, Järås M, Andersson A, Johnels P, Hansen N, 1;70(21):8487-97 Lassen C, Rissler M, Gisselsson D, Olofsson T, Richter J, Fan X, Ehinger M, Fioretos T. Modeling the human 8p11- Zhang J, Zhou J, Ren X, Diao Y, Li H, Jiang H, Ding K, Pei myeloproliferative syndrome in immunodeficient mice. D. A new diaryl urea compound, D181, induces cell cycle Blood. 2010 Sep 23;116(12):2103-11 arrest in the G1 and M phases by targeting receptor tyrosine kinases and the microtubule skeleton. Invest New Baldazzi C, Iacobucci I, Luatti S, Ottaviani E, Marzocchi G, Drugs. 2010 Nov 16; Paolini S, Stacchini M, Papayannidis C, Gamberini C, Martinelli G, Baccarani M, Testoni N. B-cell acute Zhou W, Hur W, McDermott U, Dutt A, Xian W, Ficarro SB, lymphoblastic leukemia as evolution of a 8p11 Zhang J, Sharma SV, Brugge J, Meyerson M, Settleman J, myeloproliferative syndrome with t(8;22)(p11;q11) and Gray NS. A structure-guided approach to creating covalent BCR-FGFR1 fusion gene. Leuk Res. 2010 FGFR inhibitors. Chem Biol. 2010 Mar 26;17(3):285-95 Oct;34(10):e282-5 Zhou L, Fu W, Yuan Z, Hou J. Complete molecular Bhide RS, Lombardo LJ, Hunt JT, Cai ZW, Barrish JC, remission after interferon alpha treatment in a case of Galbraith S, Jeyaseelan R Sr, Mortillo S, Wautlet BS, 8p11 myeloproliferative syndrome. Leuk Res. 2010 Krishnan B, Kukral D, Malone H, Lewin AC, Henley BJ, Nov;34(11):e306-7 Fargnoli J. The antiangiogenic activity in xenograft models of brivanib, a dual inhibitor of vascular endothelial growth This article should be referenced as such: factor receptor-2 and fibroblast growth factor receptor-1 Aranaz P, Vizmanos JL. 8p11 myeloproliferative syndrome kinases. Mol Cancer Ther. 2010 Feb;9(2):369-78 (EMS, eight p11 myeloproliferative syndrome). Atlas Genet Hsu RM, Tsai MH, Hsieh YJ, Lyu PC, Yu JS. Identification Cytogenet Oncol Haematol. 2011; 15(8):692-700. of MYO18A as a novel interacting partner of the PAK2/betaPIX/GIT1 complex and its potential function in

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 700

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Leukaemia Section Mini Review i(5)(p10) in acute myeloid leukemia Nathalie Douet-Guilbert, Angèle Herry, Audrey Basinko, Marie-Josée Le Bris, Nadia Guéganic, Clément Bovo, Frédéric Morel, Marc De Braekeleer Laboratory of Histology, Embryology, and Cytogenetics, Faculty of Medicine and Health Sciences, Université de Bretagne Occidentale, 22, avenue Camille Desmoulins, CS 93837, F-29238 Brest cedex 3, France (NDG, AH, AB, MJL, NG, CB, FM, MD)

Published in Atlas Database: December 2010 Online updated version : http://AtlasGeneticsOncology.org/Anomalies/i5pID1376.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI i5pID1376.txt

This article is an update of : Schoch C. i(5)(p10) in acute myeloid leukemia. Atlas Genet Cytogenet Oncol Haematol 2005;9(2)

Identity

i(5)(p10) G-banding - Claudia Schoch (left), and R-banding - Nathalie Douet-Guilbert (right).

Note Type 2: classified as acute myeloid leukemia (5 In literature, two types of i(5)(p10) are observed: cases), predominantly AML M5a. Type 1: i(5)(p10) inducing a loss of the long arm of Etiology chromosome 5 (5q) and a trisomy of the short arm Unclear of the chromosome 5 (5p); Type 2: +i(5)(p10) (or supernumerary i(5)(p10) or Epidemiology gain of i(5)(p10)) inducing a tetrasomy of the short Type 1: it is found in young adults in MDS arm of chromosome 5 (5p). The i(5)(p10) occurred (average age: 35 years; range: 19-67) and in older in addition to two normal chromosomes 5. patients in AML (average age: 66 years; range: 50- The isochromosome of the short arm of 85). chromosome 5 - i(5)(p10) - has only been described Type 2: the +i(5)(p10) is found in patients with an in a few cases of myeloid leukemia. average age of 48.5 years (range : 24-78). Clinics and pathology Prognosis Prognosis of patients with i(5)(p10) seems to be Phenotype/cell stem origin poor compared to patients with del(5q), but it is Type 1: classified as myelodysplastic syndrome (4 unclear due to the very small number of cases and cases), acute myeloid leukemia (4 cases) the usually associated complex chromosomal predominantly AML M2; abnormalities.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 701 i(5)(p10) in acute myeloid leukemia Douet-Guilbert N, et al.

A - FISH with partial chromosome painting 5p (pcp 5p) (Green signal) and 5q (pcp 5q) (Red signal). B - FISH with LSI 5p15.2 (Green signal) / 5q31 (Red signal). Nathalie Douet-Guilbert.

number in refractory acute myeloid leukemia. Leukemia. Cytogenetics 1997 Jul;11(7):958-63 Cytogenetics morphological Tamura S, Takemoto Y, Hashimoto-Tamaoki T, Mimura K, Sugahara Y, Senoh J, Furuyama JI, Kakishita E. The formation of i(5p) results from the loss of the Cytogenetic analysis of de novo acute myeloid leukemia long arm of chromosome 5 and duplication of its with trilineage myelodysplasia in comparison with short arm inducing trisomy 5p and monosomy 5q in myelodysplastic syndrome evolving to acute myeloid leukemia. Int J Oncol. 1998 Jun;12(6):1259-62 type 1 and tetrasomy 5p in type 2. A metacentric del(5q) could be an isochromosome Markovic VD, Bouman D, Bayani J, Al-Maghrabi J, Kamel- Reid S, Squire JA. Lack of BCR/ABL reciprocal fusion in of the short arm of chromosome 5. FISH technique variant Philadelphia chromosome translocations: a use of with specific probes of chromosome 5p/5q used as double fusion signal FISH and spectral karyotyping. a complement of conventional karyotype is Leukemia. 2000 Jun;14(6):1157-60 necessary to identify i(5)(p10). The i(5p) is a Schoch C, Bursch S, Kern W, Schnittger S, Hiddemann W, variant of del(5q). The i(5p) is monocentric or Haferlach T. Gain of an isochromosome 5p: a new dicentric. recurrent chromosome abnormality in acute monoblastic leukemia. Cancer Genet Cytogenet. 2001 May;127(1):85-8 Additional anomalies Christodoulou J, Schoch C, Schnittger S, Haferlach T. In one case, i(5)(p10) was the sole anomaly but Myelodysplastic syndrome (RARS) with +i(12p) rapidly evolved into a complex karyotype. Complex abnormality in a patient 10 months after diagnosis and karyotypes were present in the other cases: - successful treatment of a mediastinal germ cell tumor (MGCT). Ann Hematol. 2004 Jun;83(6):386-9 12/del12p (3 cases), -17/del17p (2 cases), del9q (2 cases). Schmidt HH, Strehl S, Thaler D, Strunk D, Sill H, Linkesch W, Jäger U, Sperr W, Greinix HT, König M, Emberger W, Supernumerary +i(5)(p10) was accompanied by Haas OA. RT-PCR and FISH analysis of acute myeloid several additional anomalies, especially trisomy 8 leukemia with t(8;16)(p11;p13) and chimeric MOZ and CBP transcripts: breakpoint cluster region and clinical Genes involved and implications. Leukemia. 2004 Jun;18(6):1115-21 Panani AD. Gain of an isochromosome 5p: a rare recurrent proteins abnormality in acute myeloid leukemia. In Vivo. 2006 May- Jun;20(3):359-60 Note Type 1: to explain the specific phenotype of Herry A, Douet-Guilbert N, Morel F, Le Bris MJ, Guéganic N, Berthou C, De Braekeleer M. Isochromosome 5p and i(5)(p10), loss of tumor suppressor genes in the related anomalies: a novel recurrent chromosome deleted region (5q) associated with gene dosage abnormality in myeloid disorders. Cancer Genet effect of genes located on 5p is suggested. Cytogenet. 2010 Jul 15;200(2):134-9 Type 2: gene dosage effect of genes located on the This article should be referenced as such: short arm of chromosome 5. Douet-Guilbert N, Herry A, Basinko A, Le Bris MJ, Guéganic N, Bovo C, Morel F, De Braekeleer M. i(5)(p10) References in acute myeloid leukemia. Atlas Genet Cytogenet Oncol El-Rifai W, Elonen E, Larramendy M, Ruutu T, Knuutila S. Haematol. 2011; 15(8):701-702. Chromosomal breakpoints and changes in DNA copy

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 702

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Leukaemia Section Mini Review

+20 or trisomy 20 (solely) Jean-Loup Huret Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France (JLH)

Published in Atlas Database: January 2011 Online updated version : http://AtlasGeneticsOncology.org/Anomalies/tri20ID1572.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI tri20ID1572.txt

neuroblastoma, diagnosed 32 months before onset Clinics and pathology of the leukaemia. A cryptic rearrangement of MLL Disease was found. Survival was short (Jaing et al., 1999). The 8 lympoid cases were: three acute Myeloid and lymphoid malignancies (Shabtai et al., lymphoblastic leukaemias (ALL) (two of which 1978; Kristoffersson et al., 1985; Michalová et al., involved the T-cell lineage), one chronic 1987; Palka et al., 1987; Speaks et al., 1987; Attas lymphocytic leukaemia (CLL), three non Hodgkin et al., 1989; Cuneo et al., 1989; Nayak et al., 1990; lymphomas (NHL) : one follicular (FL), one diffuse Cuneo et al., 1992; Cuneo et al., 1995; Hashimoto large B-cell (DLBL), and one T-cell lymphoma); et al., 1995; Rigolin et al., 1997; Jaing et al., 1999; and one Waldenstrom macroglobulinemia. Mauritzson et al., 2001; Tamura et al., 2001; Mikhail et al., 2002; Farag et al., 2006; Paulsson et Epidemiology al., 2008). In the myeloid group, there were 7 male and 5 Note female patients, median age was 68-72 years Trisomy 20 solely has also been reported in various (range: 8-79 years, 8 of the 10 documented cases benign and malignant solid tumours, in particular in were above 60 years). In the lymploid group, there desmoid fibromatosis, colonic adenomatous polyps, was an unbalanced sex ratio: 6 male and 2 female colorectal adenocarcinomas, fibroadenomas of the patients; median age was 33-53 years (range: 7-76 breast, breast adenocarcinoma, transitional cell years). carcinoma of the urinary tract, squamous cell Prognosis carcinoma of the oro-pharynx and naso-pharynx; it Data is very scarce, and not conclusive, inasmuch has also been found more rarely in many other solid as the genes involved in these cases are unknown, tumours (see records in the Mitelman Database). and as the trisomy 20 group is probably Phenotype/cell stem origin heterogeneous from that view point. Trisomy 20 solely has been described in 20 cases of hematological malignancies: Genes involved and This was a myeloid malignancy in 12 cases: six proteins acute myeloid leukaemias (AML), four myelodysplastic syndromes (MDS), and two Note myeloproliferative disorders (MPD). They were: Genes involved are unknown. two M4-AML, two M5-AML, one M0-AML, one AML not otherwise specified (NOS), one refractory References anaemia (RA), one RA with excess of blasts (RAEB), one chronic myelomonocytic leukaemia Shabtai F, Weiss S, van der Lijn E, Lewinski U, Djaldetti M, Halbrecht I. A new cytogenetic aspect of polycythemia (CMML), one MDS-NOS, and two polycytemia vera. Hum Genet. 1978 Apr 24;41(3):281-7 vera (PV). One AML, a M5-AML, appeared to be treatment-related, in a 8-year-old girl with

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 703

+20 or trisomy 20 (solely) Huret JL

Kristoffersson U, Heim S, Heldrup J, Akerman M, Garwicz hematologic and cytogenetic characterization. S, Mitelman F. Cytogenetic studies of childhood non- Haematologica. 1997 Jan-Feb;82(1):25-30 Hodgkin lymphomas. Hereditas. 1985;103(1):77-84 Jaing TH, Yang CP, Hung IJ. Acute monoblastic leukemia Michalová K, Kobylka P, Lukásová M, Neuwirt J. in a child following chemotherapy for neuroblastoma. J Cytogenetic study of circulating blasts in leukemias. Formos Med Assoc. 1999 Oct;98(10):688-91 Cancer Genet Cytogenet. 1987 Apr;25(2):329-39 Mauritzson N, Johansson B, Rylander L, Albin M, Palka G, Spadano A, Geraci L, Fioritoni G, Dragani A, Strömberg U, Billström R, Ahlgren T, Mikoczy Z, Mitelman Calabrese G, Guanciali Franchi P, Stuppia L. F, Hagmar L, Nilsson PG. The prognostic impact of Chromosome changes in 19 patients with Waldenström's karyotypic subgroups in myelodysplastic syndromes is macroglobulinemia. Cancer Genet Cytogenet. 1987 strongly modified by sex. Br J Haematol. 2001 Dec;29(2):261-9 May;113(2):347-56 Speaks SL, Sanger WG, Linder J, Johnson DR, Armitage Tamura A, Miura I, Iida S, Yokota S, Horiike S, Nishida K, JO, Weisenburger D, Purtilo D. Chromosomal Fujii H, Nakamura S, Seto M, Ueda R, Taniwaki M. abnormalities in indolent lymphoma. Cancer Genet Interphase detection of immunoglobulin heavy chain gene Cytogenet. 1987 Aug;27(2):335-44 translocations with specific oncogene loci in 173 patients with B-cell lymphoma. Cancer Genet Cytogenet. 2001 Attas L, Lichtman SM, Budman DR, Verma RS. Trisomy Aug;129(1):1-9 20 in acute myelogenous leukemia. Cancer Genet Cytogenet. 1989 May;39(1):25-8 Mikhail FM, Serry KA, Hatem N, Mourad ZI, Farawela HM, El Kaffash DM, Coignet L, Nucifora G. AML1 gene over- Cuneo A, Tomasi P, Ferrari L, Balboni M, Piva N, Fagioli expression in childhood acute lymphoblastic leukemia. F, Castoldi G. Cytogenetic analysis of different cellular Leukemia. 2002 Apr;16(4):658-68 populations in chronic myelomonocytic leukemia. Cancer Genet Cytogenet. 1989 Jan;37(1):29-37 Farag SS, Archer KJ, Mrózek K, Ruppert AS, Carroll AJ, Vardiman JW, Pettenati MJ, Baer MR, Qumsiyeh MB, Nayak BN, Sokal J, Ray M. Clonal chromosomal changes Koduru PR, Ning Y, Mayer RJ, Stone RM, Larson RA, in chronic lymphocytic leukemia. Cancer Lett. 1990 Bloomfield CD. Pretreatment cytogenetics add to other Feb;49(2):99-105 prognostic factors predicting complete remission and long- Cuneo A, Fagioli F, Pazzi I, Tallarico A, Previati R, Piva N, term outcome in patients 60 years of age or older with Carli MG, Balboni M, Castoldi G. Morphologic, acute myeloid leukemia: results from Cancer and immunologic and cytogenetic studies in acute myeloid Leukemia Group B 8461. Blood. 2006 Jul 1;108(1):63-73 leukemia following occupational exposure to pesticides Paulsson K, Cazier JB, Macdougall F, Stevens J, and organic solvents. Leuk Res. 1992 Aug;16(8):789-96 Stasevich I, Vrcelj N, Chaplin T, Lillington DM, Lister TA, Cuneo A, Ferrant A, Michaux JL, Boogaerts M, Demuynck Young BD. Microdeletions are a general feature of adult H, Van Orshoven A, Criel A, Stul M, Dal Cin P, Hernandez and adolescent acute lymphoblastic leukemia: Unexpected J. Cytogenetic profile of minimally differentiated (FAB M0) similarities with pediatric disease. Proc Natl Acad Sci U S acute myeloid leukemia: correlation with clinicobiologic A. 2008 May 6;105(18):6708-13 findings. Blood. 1995 Jun 15;85(12):3688-94 Mitelman F, Johansson B and Mertens F (Eds.).. Mitelman Hashimoto K, Miura I, Chyubachi A, Saito M, Miura AB. Database of Chromosome Aberrations and Gene Fusions Correlations of chromosome abnormalities with histologic in Cancer (2011). and immunologic characteristics in 49 patients from Akita, http://cgap.nci.nih.gov/Chromosomes/Mitelman Japan with non-Hodgkin lymphoma. Cancer Genet Cytogenet. 1995 May;81(1):56-65 This article should be referenced as such: Rigolin GM, Cuneo A, Roberti MG, Bardi A, Castoldi G. Huret JL. +20 or trisomy 20 (solely). Atlas Genet Myelodysplastic syndromes with monocytic component: Cytogenet Oncol Haematol. 2011; 15(8):703-704.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 704

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Deep Insight Section Review

TMPRSS2:ETS gene fusions in prostate cancer Julia L Williams, Maisa Yoshimoto, Alexander H Boag, Jeremy A Squire, Paul C Park Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada (JLW, MY, AHB, JAS), Kingston General Hospital, 76 Stuart Street, Douglas 4, Room 8-431, Kingston, Ontario, K7L 2V7 Canada (PCP)

Published in Atlas Database: December 2010 Online updated version : http://AtlasGeneticsOncology.org/Deep/TMPRSS2ERGinCancerID20091.html Printable original version : http://documents.irevues.inist.fr/bitstream/DOI TMPRSS2ERGinCancerID20091.txt

Table of Contents I. Background I.i. Prostate cancer oncogenomics II. Discovery of TMPRSS2:ETS fusion genes in prostate cancer III. Frequency of TMPRSS2:ETS gene fusions in prostate cancer IV. TMPRSS2:ETS gene fusions: genes and protein structure IV.i. TMPRSS2 and the androgen receptor IV.ii. ETS transcription factors V. Fusion variants VI. Detection and classification VI.i. FISH VI.ii. Other methods of detection VII. Fusion gene formation and chromosomal instability VIII. Heterogeneity of multifocal disease IX. Prognostic significance X. Clinical utility XI. Role of ETS in prostate tumourigenesis: Driver? XII. Concluding remarks

I. Background Clinicopathological criteria, including Gleason grading, are not sufficient to differentiate men Prostate cancer (CaP) is the most commonly whose tumours require immediate and aggressive diagnosed male malignancy and a leading cause of therapy from those that would suffice with vigilant cancer deaths in developed countries. With one in clinical observation, thereby causing the latter six men diagnosed, CaP remains a serious global group enormous amounts of unnecessary treatment public health issue (Jemal et al., 2008). CaP is a (Yao and Lu-Yao, 2002). In this regard, the clinically heterogeneous disease, with emerging data on the genetics of CaP hold great manifestations ranging from a rapid and often fatal promise not only in stratifying this heterogeneous progression, to the typical, indolent disease which group of patients, but also in providing the remains relatively insignificant to a patient's health.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 705

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

groundwork for future development of targeted ERG or ETV1 (Tomlins et al., 2005). Interestingly, therapy. just months prior, Petrovics et al. (2005) reported I. i. Prostate cancer oncogenomics that ERG was the most commonly overexpressed Advances in cytogenetics and genomics facilitated oncogene in CaP by microarray and qPCR analysis. the characterization of common genomic alterations Subsequent studies showed that the frequency of in CaP, which are predominantly characterized by the TMPRSS2:ERG fusion gene (or ERG deletions (10q, PTEN; 13q, RB1; 8p, NKX3.1 (a rearrangement) is exceptionally variable and prostate-specific tumour suppressor); 5q; 2q; 17p; inconsistent in the literature, ranging from 27% to and less commonly 6q; 7p; 16q; 18q) with only a 79% in radical prostatectomy (RP) and biopsy small number of recurrent gains (8q, MYC; and samples, generally from prostate-specific antigen chromosome 7). More complex patterns as well as (PSA) screened cohorts (Tomlins et al., 2005; an accumulation in the number of genomic gains Yoshimoto et al., 2008; Mehra et al., 2007b; and amplifications (Xq11.2-q12, androgen receptor Watson et al., 2009; Barwick et al., 2010; Magi- (AR)) emerge as the disease advances. Genomic Galluzzi et al., 2010). rearrangements leading to the formation of Some of the discrepancies in frequency relate to TMPRSS2:ETS gene fusions and deletion of the differences in the patient cohort (race as well as PTEN tumour suppressor are the two most frequent global geographical location or PSA-screened alterations observed in CaP (Tomlins et al., 2005; versus population based) or the type of specimen Yoshimoto et al., 2007; Yoshimoto et al., 2008). examined, as well as the technique used to detect The TMPRSS2:ERG gene fusion is the principle the fusion gene. This concept is clearly illustrated genomic alteration and a characteristic signature in when comparing population based cohorts, which approximately half of prostatic malignancies. have a lower reported frequency of 15-35%, as compared to RP cohorts (Attard et al., 2008a; II. Discovery of TMPRSS2:ETS Demichelis et al., 2007; Fitzgerald et al., 2008). fusion genes in prostate cancer The TMPRSS2:ERG gene fusion is found in approximately half of Caucasian patients, with a The discovery of the TMPRSS2:ERG gene fusion lower reported frequency in African-American men exemplifies the current shift in the strategy in and is less common in Asian cohorts (Mosquera et cancer genomics from experimental to al., 2009; Magi-Galluzzi et al., 2010; Lee K et al., bioinformatics approaches. By surveying 132 gene- 2010; Miyagi et al., 2010). An excellent example of expression CaP datasets from the Oncomine discrepancies based on patient populations was database (Compendia Bioscience) using the data demonstrated in a study that compared patients transformation algorithm cancer outlier profile from the United Kingdom (UK) and China, wherein analysis (COPA), Chinnaiyan and colleagues 41.3% of the UK patients but only 7.5% of Chinese identified genes with aberrant expression profiles in cohort were found to harbour ERG rearrangements a subset of samples (Tomlins et al., 2005). COPA detected by FISH (Mao et al., 2010). The recent, allowed the systematic investigation of cancer- contradicting report that 90% of the Chinese RP related genes known to participate in chromosomal specimens harboured ETS rearrangements further rearrangements in haematological malignancies and emphasize the multifactorial nature of the sarcomas. Two mutually exclusive Erythroblastosis variability in the frequency of this gene fusion (Sun virus E26 transformation-specific (ETS) et al., 2010). transcription factors, ETS variant 1 (ETV1, 7p21.3) TMPRSS2:ERG gene fusions are reported in 10- and ETS-related gene (ERG, 21q22.2), were 21% of high-grade prostatic intraepithelial identified as high-ranking outliers in several neoplastic (HGPIN) lesions, but are identified independent gene-expression profiling datasets. almost exclusively adjacent to fusion-positive Exon-walking quantitative PCR (qPCR) of patient cancer (Cerveira et al., 2006; Perner et al., 2007; samples found the 3' regions of ERG and ETV1 to Carver et al., 2009b; Han et al., 2009; Zhang et al., be overexpressed but the corresponding 5' regions 2010; Mosquera et al., 2008). Benign prostatic were absent. 5' RNA ligase-mediated rapid hyperplasia (BPH) and normal epithelium are amplification of cDNA ends identified the 5' end of negative for ERG rearrangements and fusion these transcripts as the promoter sequences transcripts, with the exception of the report by belonging to the prostate-specific, androgen Clark and colleagues (Rajput et al., 2007; Wang et regulated transmembrane protease, serine II al., 2006; Cerveira et al., 2006; Clark et al., 2007; (TMPRSS2, 21q22.3). Perner et al., 2007; Dai et al., 2008; Han et al., III. Frequency of TMPRSS2:ETS 2009; Mosquera et al., 2009; Zhang et al., 2010; gene fusions in prostate cancer Sun et al., 2010; Lu et al., 2009). This study found that eight of 17 (47%) normal epithelial samples This breakthrough study reported that 79% of adjacent to fusion-positive CaP were also positive radical prostatectomy (RP) samples harboured a for TMPRSS2:ERG rearrangements and found a fusion of the 5' untranslated region (UTR) of 6% fusion-positive rate in BPH samples (Clark et TMPRSS2 with the coding sequences of either

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 706

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

al., 2007). Hormone refractory and/or metastatic epithelia and interacts with cell surface proteins, the CaP exhibits less variability in the occurrence of extracellular matrix and proteins of neighbouring TMPRSS2:ERG rearrangements with reported cells (Vaarala et al., 2001; Wilson et al., 2005; Afar frequencies ranging from 29-59% (Perner et al., et al., 2001). The TMPRSS2 (21q22.3) gene is 2007; Mehra et al., 2008; Gopalan et al., 2009; Han composed of 14 exons, with protein coding et al., 2009; Boormans et al., 2010; Saramaki et al., sequences only in the latter half. Importantly, 2008; Attard et al., 2009; Stott et al., 2010). TMPRSS2 harbours androgen responsive elements Additionally, minute prostatic adenocarcinoma, a (ARE) in its 5' UTR. Prostate epithelial cells form of CaP that is considered less clinically express TMPRSS2 at higher levels relative to other significant, harbours ETS fusions in approximately tissues, while TMPRSS2 gene expression is further half of reported cases, underscoring the necessity of elevated in CaP relative to BPH and normal examining all prostatic malignancies for aggressive prostatic epithelium (Afar et al., 2001). Androgens features such as the fusion gene (Albadine et al., and the AR are essential to the growth and 2009). development of the prostate gland but also play an Investigators have also evaluated this important role in the initiation and progression of rearrangement in the peripheral and transitional CaP (Balk et al., 2008). It is well established that zones of the prostate. Nearly half of the peripheral despite chemical castration the AR functions to tumours (43.3%) derived from RP samples were drive CaP, likely through a variety of mechanisms ERG rearrangement positive, whereas all 30 such as hypersensitivity to low levels of androgens, corresponding transitional tumours displayed a activation in absence of, or via unconventional normal ERG locus by FISH (Guo et al., 2009). In ligands, or amplification of the AR gene locus, contrast, other studies found TMPRSS2:ERG resulting in elevated levels of AR protein. All of (13.3%) and ERG rearrangements (11.9%) are these mechanisms could potentially allow AR present in transitional zone tumours, despite being activation in the presence of low androgen identified at a lower rate compared to peripheral concentration (Ai et al., 2009; Kawata et al., 2010; zone lesions (Bismar and Trpkov, 2010; Falzarano Vis and Schroder, 2009). Consequently, TMPRSS2 et al., 2010). These data illustrate the enormous in turn plays an important role in CaP progression variability in the frequency of TMPRSS2:ERG in spite of hormonal ablation regimens as its fusion positivity with respect to the cohort, disease promoter region drives the expression of the fused stage, origin of sample as well as the method of ETS gene. detection. IV. ii. ETS transcription factors Interestingly, a comprehensive study of patient Twenty-seven human ETS transcription factor samples from 54 tumour types, including sarcomas family members have been identified, all of which and haematological malignancies, for ETS gene share a conserved DNA binding domain that fusions and ERG rearrangements by FISH found recognizes unique sequences containing GGA(A/T) these alterations to be exclusive to CaP samples (Nye et al., 1992). ERG (21q22.2) is the ETS (Scheble et al., 2010). The same result was obtained transcription factor most commonly known to when RT-PCR was performed to detect participate in CaP gene fusions. The ERG gene TMPRSS2:ERG and TMPRSS2:ETV1 fusion contains 11 exons, with the transcriptional start site transcripts in gastric and colorectal carcinomas in exon 3. The ERG protein can interact with ETS (Yoo et al., 2007). These findings provide strong members as well as other transcription factors, such evidence that TMPRSS2:ETS gene fusions are as Jun and Fos, through its protein-protein specific to CaP. interacting domain, SAM-PNT (Carrere et al., IV. TMPRSS2:ETS gene fusions: 1998; Verger et al., 2001; Basuyaux et al., 1997). genes and protein structure The conserved ETS DNA binding domain permits binding to purine rich DNA sequences (Reddy et IV. i. TMPRSS2 and the androgen receptor al., 1991; Reddy et al., 1987), and in this manner, TMPRSS2, a 70 KDa serine protease family exert its effects in numerous cellular processes member is associated with physiological and including membrane remodelling, angiogenesis, pathological processes such as digestion, tissue differentiation, proliferation, and tumourigenesis remodelling, blood coagulation, fertility, (Carver et al., 2009a; Kruse et al., 2009; Oikawa et inflammatory responses, tumour cell invasion and al., 2003; Randi et al., 2009; Ellett et al., 2009; apoptosis. The normal function of this protein is not Birdsey et al., 2008; Mclaughlin et al., 2001; Sato yet known but is composed of a type II et al., 2001). Emerging evidence suggests that transmembrane domain, receptor class A low formation of the fusion gene may promote prostatic density lipoprotein domain, scavenger receptor tumourigenesis, progression, and invasive disease cysteine-rich domain, protease domain, and and is associated with CaP-related mortality cytoplasmic domain (Paoloni-Giacobino et al., (Demichelis et al., 2007; Klezovitch et al., 2008; 1997). The 32 KDa serine protease domain Wang et al., 2008; Hawksworth et al., 2010). undergoes autocleaveage, secretion into the prostate Functionally, ERG overexpression in CaP is highly

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 707

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

implicated in promoting motility and invasiveness likely owing to their close proximity (2.7 Mb) and (Perner et al., 2007; Singh et al., 2002; identical orientation on chromosome 21. Although, Trojanowska et al., 2000; Tomlins et al., 2008a; the remainder of this review will predominately Sreekumar et al., 2009; Schulz et al., 2010). In CaP, focus on the TMPRSS2:ERG rearrangement, ERG expression has been associated with elevated numerous alternative ETS members also can fuse to levels of histone deactylase 1 (HDAC1) and TMPRSS2, albeit at a much lower frequency. subsequent down regulation of HDAC1 target Similarly, variability in 5' partners have also been genes, upregulation of WNT pathway proteins, and identified (Table 1). An intensive study examining inhibition of apoptotic signalling (Iljin et al., 2006). ETV1 rearrangements found that only 9 of 23 HDAC1 upregulation is common in CaP, but was samples had previously identified 5' partners, found to be uniformly increased in ERG rearranged demonstrating the dramatic variability in fusion tumours (Iljin et al., 2006; Bjorkman et al., 2008). partners pairing with ETS transcription factors Activation of the WNT pathway leads to other than ERG (Attard et al., 2008b). The transcription of numerous genes involved in combined frequency of the remaining fusion tumourigenesis, including AR, MYC, JUN, variants accounts for approximately 10% of cases. cyclinD1, BMP4 and MMP7 (Terry et al., 2006; Five prime partners are divided into classes based Schweizer et al., 2008). Highlighting the on their tissue specificity and sensitivity to importance of WNT pathway activation in fusion- androgens (Tomlins et al., 2007). Class I is reserved positive CaP is the resultant increase in AR for TMPRSS2; Class II represents other prostate- transcription and expression levels. Consequently specific androgen inducible 5' UTR or endogenous transcription of the fusion gene is increased, further retroviral elements; Class III represents the amplifying ERG expression. Moreover, beta- prostate-specific but androgen repressed partners; catenin and the AR interact in an androgen- Class IV represents the non-tissue-specific dependent manner to regulate AR target genes, promoters that are ubiquitously expressed, (i.e. whereas in androgen-insensitive tumours, both house-keeping genes-this class often forms a beta-catenin and AR target genes are expressed chimeric or fusion protein, unlike the previous (Schweizer et al., 2008). divisions of gene fusions); and finally Class V ERG overexpression has recently been shown to consists of ETV1-specific rearrangements, activate C-MYC and result in its overexpression. including the localization of the entire ETV1 locus These experiments revealed that C-MYC is to prostate specific locus, 14q13.3-14q21.1 activated by ERG and together their co- (Tomlins et al., 2007; Attard et al., 2008b). To date overexpression results in the suppression of only a single study has identified fusion genes in prostate-epithelial differentiation genes and shorter CaP devoid of ETS transcription factor time to biochemical recurrence (Hawksworth et al., participation (Palanisamy et al., 2010). 2010; Sun et al., 2008). ERG can also induce ICAM2 expression, resulting in AKT activation via VI. Detection and classification PDK1 and subsequent inhibition of BAD leading to VI. i. FISH suppression of apoptotic signals (Mclaughlin et al., Two strategies for FISH experiments are frequently 2001). In addition, ERG can bind BRCA1, a co- used to detect the TMPRSS2:ERG fusion gene in activator of the AR, and together were shown to CaP. The three-colour break-apart strategy, regulate IGFR expression (Chai et al., 2001; developed by Yoshimoto et al. (2006), uses Schayek et al., 2009). IGFR expression eventually differentially labelled bacterial artificial leads to activation of AKT upon IGFR ligand- chromosome (BAC) clones as probes for the 3' binding. ERG regulates MMPs thus influencing (RP11-476D17) and 5' (RP11-95I21) segments of extracellular matrix (ECM) remodelling and the ERG with an additional BAC probe specific for the invasive potential of the cell (Ellett et al., 2009; 5' region of TMPRSS2 (RP11-535H11) or for the Hawksworth et al., 2010; Singh et al., 2002; Schulz transcriptional regulatory sequences (telomeric) of et al., 2010). Recently, Carver and colleagues have TMPRSS2 (RP11-35C4, RP11-891L10; RP11- identified ETS binding sites in the promoter regions 260O11; Figure 1) (Yoshimoto et al., 2006). Using of CXCR4 and ADAMTS1, two genes involved in this probe configuration enables not only the cellular motility and invasion (Carver et al., 2009a). detection of ERG rearrangement, but also allows Furthermore, it was shown that ERG directly confirmation that ERG's coding sequences are upregulates the expression level of CXCR4 and juxtaposed to the transcriptional regulatory region ADAMTS1 (Carver et al., 2009b). Together, these of TMPRSS2. Moreover, the mechanism of studies provide a compelling evidence for a central, rearrangement can also be deduced by this approach functional role of the fusion gene in the biology of (Yoshimoto et al., 2006; Yoshimoto et al., 2007). prostatic carcinoma. Characterization of rearrangement method is essential as differential clinical impacts are V. Fusion variants observed with the various mechanisms resulting in The TMPRSS2:ERG fusion gene constitutes the ETS gene fusions. majority (>85%) of ETS rearrangements in CaP,

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 708

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

1Table 1 5' partner Class 3' partner Initial reference TMPRSS2 I ERG Tomlins et al.(2005) TMPRSS2 I ETV1 Tomlins et al. (2005) TMPRSS2 I ETV4 Tomlins et al. (2006) HERV-K_22q11.23 II ETV1 Tomlins et al. (2007) SLC45A3 II ETV1 Tomlins et al (2007) C15orf21 III ETV1 Tomlins et al. (2007) HNRPA2B1 IV ETV1 Tomlins et al. (2007) KLK2 II ETV4 Hermans et al. (2008a) CANT1 II ETV4 Hermans et al. (2008a) ACSL3 II ETV1 Attard et al. (2008b) SLC45A3 II ERG Han et al. (2008) FLJ35294 II ETV1 Han et al. (2008) DDX5 IV ETV1 Han et al. (2008) TMPRSS2 I ETV5 Helgeson et al. (2008) SLC45A3 II ETV5 Helgeson et al. (2008) EST14 II ETV1 Hermans et al. (2008b) HERVK17 II ETV1 Hermans et al. (2008b)

FOXP1 II ETV1 Hermans et al. (2008b)

SLC45A3 II ELK4 Rickman et al. (2009)

NDRG1 II ERG Pflueger et al. (2009) SLC45A3 ETS neg BRAF* Palanisamy et al. (2010)

ESRP1 ETS neg RAF1* Palanisamy et al. (2010)

*Only 3' partners identified to date that are not a member of the ETS transcription factor family.

Figure 1: In house BAC probe configuration for three-colour break-apart TMPRSS2:ERG gene fusion FISH This schematic ideogram depicts the positions of differentially labelled bacterial artificial chromosome (BAC) clones specific for 3' and 5' regions of the ERG gene (RP11-476D17 in spectrum orange and RP11-95I21 in spectrum green, respectively), within the 21q22.2-3 region. Telomeric to this, the TMPRSS2 gene locus is represented by RP11-535H11 (spectrum red) which spans the gene, or by three BAC clones downstream (telomeric) of the TMPRSS2 gene (RP11-35C4, RP11-891L10 and RP11-260O11 in spectrum aqua). This probe design permits the accurate identification of TMPRSS2:ERG gene fusions as well as ERG rearrangements independent of fusion with TMPRSS2 fusion.

Work by Attard and colleagues classified the ERG locus, therefore co-localization of the two TMPRSS2:ERG rearrangement mechanisms ERG probe signals in close proximity to the according to the pattern of interphase FISH signals TMPRSS2 signal (less than one signal diameter) (Attard et al., 2008a). Class N describes the normal (Figure 2A). The majority of fusion-positive cases

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 709

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

present with a heterozygous deletion at cytoband genomic rearrangement leading to insertion of those 21q22.2-3, termed Class Edel (Figure 2B). The sequences elsewhere in the genome to an unknown deletion typically spans ERG, exons 1-3 and a chromosome location can occur resulting in the partial deletion of exon 4, the known intervening separation of the 5' ERG signals from the co- genes (based on RefSeq Genes: NCRNA00114, localization of the 3' ERG and TMPRSS2 signals, ETS2, PSMG1, BRWD1, NCRNA00257, HMGN1, thus described as ERG split or Class Esplit (Figure WRB, LCA5L, SH3BGR, C21orf88, B3GALT5, 2C). In both types of TMPRSS2:ERG IGSF5, PCP4, DSCAM, C21orf130, MIR3197, rearrangements the unaffected chromosome 21 BACE2, PLAC4, FAM3B, MX2, and MX1) and generally display a Class N signal configuration. the coding exons of TMPRSS2. The three-colour Finally, additional copies of TMPRSS2:ERG gene FISH of an Edel rearrangement displays co- fusions is identified as Class 2+Edel (Attard et al., localization of the 3' ERG and TMPRSS2 signals, 2008a). and absence of the 5' ERG signal. Less frequently a

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 710

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

Figure 2: Classification of TMPRSS2:ERG gene fusion by interphase FISH. Prostate cancer patient samples were hybridized with the three-colour probe set, described in Figure 1, and counterstained with DAPI. The nuclei of interest (in dashed boxes) are magnified in the insets. A) Class N, where no ERG rearrangement has occurred. Co-localization of 3' and 5' ERG probes (often visualized as a yellow signal), with the 5' TMPRSS2 BAC probe signals (red) indicates a normal Chr21q22.2-3 locus. Frequently, the signals for the TMPRSS2 probe, situated 2.7 Mb away from the ERG locus, may be separated from the ERG signals by up to one probe signal width. B) Class Edel is characterized by the co- localization of 3' ERG probe to the TMPRSS2 probe signals, and the absence of the 5' ERG signal. This represents rearrangement with the loss of the intervening sequence. The unaffected Chr21 displays Class N configuration. C) Class Esplit is characterized by the co-localization of the 3' ERG and TMPRSS2 signals, with the retention of the 5' ERG signal elsewhere in the nucleus. The unaffected Chr21 displays Class N configuration.

The second strategy employs a two-colour break- 39-99 amino acids, while the few that initiate apart FISH design to identify rearrangements in translation from the native start codon in exon 3 specific ETS genes (Mehra et al., 2007; Zhang et produce full length ERG (Tomlins et al., 2005; al., 2010). By this method, confirmation of fusion Soller et al., 2006; Wang et al., 2006; Clark et al., between two genes and identification of the specific 2007; Clark et al., 2008a). One of the transcripts 5' partner is not possible because the probes are produces a genuine TMPRSS2:ERG fusion protein specific for a single gene, and therefore, this and eight contain premature stop codons and are strategy is an indirect method for the detection of unlikely to result in ERG overexpression (Tomlins fusion genes in CaP. et al., 2005; Soller et al., 2006; Wang et al., 2006; VI.ii. Other methods of detection Clark et al., 2007; Clark et al., 2008a). These RT-PCR is another technique frequently employed studies further revealed that elaborate heterogeneity to determine the fusion status of prostatic tissue exists in hybrid transcripts present, between foci samples. However, this approach is limited to the and within individual tumour foci of the same detection of the hybrid transcripts, and is unable to patient. Variability in the translation start site obtain important cytogenetic information such as consequentially affects the size of the mRNA the genomic mechanism that generated the gene transcript (373-885 bp) and therefore the protein fusion (Edel vs Esplit). To date, as many as 17 product potentially modifying the functional fusion transcripts and splice variations have been capacity of the gene fusion product (Wang et al., characterized, the most common fusion transcript is 2006). Distinct transcript variants display composed of exon 1 of TMPRSS2 fused to exon 4 differential prognostic influence based on the of ERG (T1:E4 (Wang et al., 2006; Jhavar et al., resultant biological activities (Hermans et al., 2009; 2008)). The majority of the remaining transcripts Wang et al., 2008). A significant challenge remains result in truncation of the ERG protein product by in relating the clinical prognosis to the fusion gene and will be addressed in the subsequent section.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 711

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

Indirect methods suggestive of gene fusions in CaP TMPRSS2 loci, followed by sequencing, revealed are being employed to broadly determine ETS the presence of consensus sequences homologous to rearrangement status with perhaps the anticipation the human Alu-Sq and Alu-Sp subfamily (Liu et al., of implementing a high-throughput method of 2006). The presence of these consensus sequences detection. Analysis of array comparative genomic within intronic regions correlated with the presence hybridization (aCGH) data, specifically the of the fusion gene and may be a factor contributing 21q22.2-3 region may permit identification of Class to the deletion at 21q22.2-3, resulting in the fusion Edel TMPRSS2:ERG gene fusions (Watson et al., gene. More recently, genotyping of familial CaP 2009; Ishkanian et al., 2009). Class Esplit retains revealed that the fusion gene associates with the intervening sequences within the nuclei, in a polymorphisms in DNA repair genes, specifically copy neutral manner and consequently aCGH POLI and ESCO1 (Luedeke et al., 2009). cannot identify this rearrangement. Overexpression Using FISH, the AR was shown to induce of ETS transcription factors by gene expression chromosomal proximity of TMPRSS2 and ERG by microarrays may also imply an ETS rearrangement binding to the promoter region of TMPRSS2 (Mani has occurred. Due to inconclusive results, FISH or et al., 2009). Subsequently, LnCaP cells were RT-PCR assays are necessary to validate irradiated to induce double-strand breaks inducing microarray findings pertaining to the ETS gene the formation of the TMPRSS2:ERG gene fusion fusions. A novel multiplexing technology recently upon dihydrotestosterone stimulation in the developed uses nanostructured microelectrodes previously fusion-negative cell line (Mani et al., integrated onto a chip and has the capability to 2009). The DNA-bound AR is also implicated in detect disease-specific biomarkers, including chromatin architecture modifications that can cause differentiation of various fusion transcripts (Fang et double-strand breaks, commonly repaired by non al., 2009). More recently, immunohistochemistry homologous end joining machinery, and may result (IHC) is also being explored as a means to detect in the formation of gene fusions (Lin et al., 2009). the fusion by ERG protein overexpression, in the Also recently, androgen signalling was shown to absence of confirming fusion at the genomic or recruit topoisomerase II beta with the AR to the transcript level (Furusato et al., 2010; Park et al., breakpoints resulting TMPRSS2:ERG fusion genes 2010). Of the numerous direct (three-colour FISH, (Haffner et al., 2009). Undoubtedly, specific RT-PCR) and indirect (two-colour FISH, nucleotide sequences within the 21q22.2-3 region microarrays, IHC) methods employed to determine are of great importance and further elucidation as to fusion status to date, the three-colour FISH yields their role in the formation of gene fusions is the most cytogenetic and genomic information. In essential. The TMPRSS2:ERG gene fusion is an addition, to identifying the fusion status and class, unique model to query sequence level the inherent cell-by-cell analysis addresses the polymorphisms that may lead to the formation of heterogeneous nature of the disease, and provides a intra-chromosomal rearrangements largely due to biological context for such information. the close proximity and orientation of the involved genes as well as the high rate of recurrence. VII. Fusion gene formation and Chromosomal instability, defined as the formation chromosomal instability of novel chromosome alterations and There is increasing research interest and effort rearrangements at an elevated rate, compared to focusing on the genomic events and attributes that normal cells may also be a factor contributing to the lead to the formation of ETS gene fusions. A formation of ETS gene fusions in CaP. It is well complex TMPRSS2:ERG rearrangement found in a established that deletion of the tumour suppressor single patient was meticulously examined and PTEN (10q23.31), a common genomic aberration in described by Yoshimoto et al. (2007). This patient CaP, results in an elevated level of chromosomal had a microdeletion of the sequences from 5' ERG instability through activation of AKT. One of to and including the TMPRSS2 coding sequences sequelae of this change is the phosphorylation and with a concurrent translocation of the region inhibition of the cell cycle check point kinase 1 immediately telomeric of 5' untranslated TMPRSS2 (Chk1), an important kinase preventing cell cycle sequences. A detailed multicolour FISH assay progression in response to DNA damage (Puc et al., mapped the region between ERG and TMPRSS2, 2005; Sanchez et al., 1997). Furthermore, nuclear revealing the complexity of chromosomal PTEN interacts with kinetochore proteins and rearrangements that can lead to the formation of induces the expression of RAD51, a protein fusion genes in CaP. This case demonstrates the required to reduce the incidence of spontaneous valuable information available through the use of double-strand breaks (Shen et al., 2007). PTEN complex multicolour FISH assays. deficiency ultimately alters multiple cell cycle The molecular mechanisms that underlie this checkpoints, which could potentially delay DNA recurrent translocation are just beginning to be damage repair and/or chromosome segregation understood. For example, fine mapping of the (Gupta et al., 2009). Overall, PTEN has a variety of deletion breakpoints located within the ERG and roles in maintaining chromosomal stability and

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 712

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

integrity, and the recurrent PTEN loss in CaP may et al., 2008; Lee et al., 2010; Sun et al., 2010; represent an important trigger in the events leading Rouzier et al., 2008) with clinical outcomes. When to the formation of TMPRSS2:ETS gene fusions. no association between clinicopathological criteria and the presence of the fusion gene was found, it VIII. Heterogeneity of multifocal was often attributable to small sample sizes. The disease most compelling evidence suggests a trend towards CaP, one of the most heterogeneous epithelial unfavourable factors outcome in CaP progression. carcinomas, is also notoriously multifocal in nature. Notably, an interesting comparison of two studies As a multifocal disease, CaP permits the looking at conservatively managed men had investigation and comparison of recurrent genomic opposing results from an association with CaP- events within distinct foci of individual patients. In specific death (Demichelis et al., 2007) to no 32 RP specimens with spatially distinct foci, ERG reduction in CaP-specific survival for patients rearrangement status was examined using two- harbouring this rearrangement (Fitzgerald et al., colour FISH (Barry et al., 2007). Nineteen samples 2008). displayed interfocal homogeneity, with 80% of the The role of deletion (Edel) or retention (Esplit) of samples negative for ERG rearrangement. The intervening sequences in tumour biology has also remaining 13 samples exhibited interfocal been scrutinized with relatively uniform results heterogeneity but intrafocal homogeneity, with two suggesting that Edel is not only the more prevalent samples harbouring three separate foci each with a mechanism but is also associated with more different rearrangement status: Class N, Edel and aggressive disease (Mwamukonda et al., 2010; Esplit. Similarly, whole mount examination of RP Attard et al., 2008a; Mehra et al., 2008). Edel was specimens for fusion transcripts yielded multiple associated with worse prostate-specific survival and fusion transcripts in individual CaP foci with an shorter time to biochemical recurrence than Class identical hybrid transcript profile in the adjacent Esplit (Yoshimoto et al., 2006; Attard et al., 2008a). HGPIN (Furusato et al., 2008). Two other studies While, Class 2+Edel was associated with lethal examining fusion transcript variants found different disease and significantly worse clinical outcome, transcript hybrids in discrete regions of a single particularly when combined with prostate-specific prostate (Wang et al., 2006; Clark et al., 2007). clinicopathological criteria (Yoshimoto et al., 2006; Multiple TMPRSS2:ETS gene fusion-positive foci Attard et al., 2008a). Another study also may arise independently and exhibit interfocal demonstrated that Edel rearrangements have a more heterogeneity. Investigation of ERG rearrangement aggressive tendency since all fusion-positive in multifocal CaP and corresponding metastases androgen-independent metastases had lost 5' ERG provides a glimpse of the potential biological sequences (Mehra et al., 2008) and Edel was impact of this aberration in the context of disease associated with clinically aggressive features of progression (Perner et al., 2009). This study progression (Perner et al., 2006). These findings are reported that the metastatic lesion was always consistent with elevated ERG expression and led positive for ERG rearrangement through the same investigators to speculate that the loss of 5' ERG is mechanism (Edel vs Esplit) as that present in at associated with aggressive CaP. least one of the prostatic tumour foci (not It must be considered that the commonly deleted necessarily the index focus). The authors suggest 2.7 Mb between ERG and TMPRSS2 could contain that this rearrangement may be a factor contributing important tumour suppressor genes (Yoshimoto et to the development of metastases, regardless of al., 2006) and its loss in the Edel rearrangement clinicopathological criteria of the individual foci. leads to haploinsufficiency of a tumour suppressor gene that underlies the aggressive clinical course. IX. Prognostic significance One gene candidate for this effect within this There exists appreciable controversy with respect to region, HMGN1, a nucleosome binding protein has the prognostic significance of the TMPRSS2:ERG previously been associated with CaP progression gene fusion in CaP, with studies suggesting that the (Birger et al., 2005). In agreement with this view, fusion gene has a favourable (Winnes et al., 2007; the Esplit rearrangement has not yet been shown to Petrovics et al., 2005; Winnes et al., 2007; associate with any particular clinical outcome to Saramaki et al., 2008), unfavourable (Yoshimoto et date. However, given the low frequency of this al., 2008; Mehra et al., 2007a; Perner et al., 2006; event (~10% of TMPRSS2:ERG rearrangements), Wang et al., 2006; Nam et al., 2007a; Nam et al., Esplit rearrangements cannot be excluded as a 2007b; Attard et al., 2008a; Mehra et al., 2008; measure of prognosis until further studies are Reid et al., 2010; Demichelis et al., 2007; Rostad et completed (Attard et al., 2008a). al., 2009; Lapointe et al., 2007a) or no association On the other hand, one investigation demonstrated (Mehra et al., 2008; Yoshimoto et al., 2006; Neill et no statistically significant association with al., 2007; Fletcher et al., 2008; Dai et al., 2008; clinicopathological criteria and Edel or Esplit, but Furusato et al., 2008; Darnel et al., 2009; Gopalan evidence did suggest 2+Edel is a factor contributing et al., 2009; Rubio-Briones et al., 2010; Fitzgerald to CaP-specific mortality (Fitzgerald et al., 2008).

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 713

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

Conversely, TMPRSS2:ERG rearrangement alone study confirmed the association that ETS fusion- were associated with lower histological grade, but positive CaP samples were more likely mucin- no other clinical features or CaP-specific death positive than mucin-negative (Tu et al., 2007). (Gopalan et al., 2009). However, the same group These results should be taken, however, in the also found that copy number increases (CNI) of the context of somewhat contradictory reports, such ERG locus with or without TMPRSS2:ERG gene that the TMPRSS2:ERG gene fusion correlates with fusions was associated with high grade and low Gleason grade and is inversely related to high- advanced stage, while cancers with CNI and 2+Edel grade morphological features. These studies hold rearrangements tended to be more clinically promise that morphological markers routinely aggressive (Fine et al., 2010). While the above examined by pathologists could be coupled with the results are conflicting to the previous studies that current clinicopathological criteria for a more showed no association with extra copies of the comprehensive evaluation of biopsy or RP unrearranged ERG locus (Attard et al., 2008a), the specimens providing well-informed judgments on difference may be due to the deletion of the diagnosis, prognosis and treatment decisions. intervening genes potentially generating a more In an attempt to optimize the clinical utility of this aggressive tumourigenic phenotype. biomarker, investigators are turning to less invasive SPINK1 (5q32) is a gene identified in a more recent survey modes, such as urine specimens and COPA meta-analysis as being overexpressed in circulating tumour cells (CTCs). Post-digital rectal 10% of CaP, all of which are exclusively ETS exam (DRE) urine analyzed by qRT-PCR found fusion negative (Tomlins et al., 2008b). For this 17.2% positive rate for ERG overexpression. reason, SPINK1 expression and the Subsequent examination of the corresponding TMPRSS2:ERG fusion gene were evaluated to biopsy samples from the same cohort revealed a determine their relative significance as prognostic 40% positive rate (Rice et al., 2010). The clinical biomarkers in biopsy samples from hormonally yield of this assay can be improved, as indicated by treated men (Leinonen et al., 2010). In this cohort, another study which found a 69% positive rate the fusion gene was associated with Ki-67 staining, following prostatic message versus only 24% when age at diagnosis and tumour area, but not with any no prostatic message was performed before prostate-specific clinicopathological criteria collecting the urine samples (Rostad et al., 2009). (Leinonen et al., 2010). On the other hand, cases Two additional studies report similar results (42% that overexpressed SPINK1 had a significantly and 59%) of fusion-positive transcripts in post-DRE shorter time to biochemical recurrence, but no urine (Hessels et al., 2007; Laxman et al., 2006). association with any other criteria. Expressed prostatic secretion has also been a successful specimen for the non-invasive detection X. Clinical utility of fusion transcripts (Clark et al., 2008b). These Promptly following the emergence of adverse studies demonstrate the potential for ETS gene clinical correlations of fusion-positive CaP fusion detection using non-invasive approaches Mosquera and colleagues evaluated a series of CaP following physical evaluation of the prostate by cases to determine if there was a morphological DRE, adding valuable information to disease phenotype associated with this genomic alteration stratification prior to radical treatments. A handful (Mosquera et al., 2007). Blinded to ERG of studies have also used FISH to detect ERG rearrangement status, the group identified five rearrangement in CTCs in effort to monitor disease histologic criteria that were significantly related to recurrence or treatment efficacy (Mao et al., 2008; ERG rearrangement positive samples: blue-tinged Attard et al., 2009; Stott et al., 2010). mucin, cribriform growth, macronucleoli, intraductal tumour spread, and signet-ring cell XI. Role of ETS in prostate features. Only 24% of ERG rearranged samples did tumourigenesis: Driver? not identify with any of the above mentioned Discrepancies regarding the fusion gene are not morphological features and 93% of samples with limited to its diagnostic potential and prognostic three features were positive for ERG significance. Controversy also exists in the rearrangement. The authors speculate that the sequence of genomic and molecular alterations in morphological characteristics shared by ERG CaP initiation and progression. Several groups rearranged tumours could result from ETS speculate that the formation of the TMPRSS2:ERG dysregulated pathways and could be utilized in the fusion gene is required for CaP initiation in ETS routine assessment performed by pathologists. positive CaP tumours, with other aberrations More recently, the same group published a similar occuring later in the course of disease advancement set of morphological features with the addition of and metastasis (Perner et al., 2007; Tomlins et al., collagenous micronodules (Mosquera et al., 2009). 2007; Attard et al., 2009). Recently, Attard and A significant association between perineural colleagues demonstrated that CTCs from individual invasion, blue-tinged mucin, and intraductal tumor castration-resistant CaP patients were either spread with a positive gene fusion status has been clonally positive or negative for ERG documented (Nigwekar et al., 2008), while another

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 714

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

rearrangement, however, loss of PTEN and increase experiments using cell lines demonstrated ERG in AR gene copy number was heterogeneous in the overexpression provided enhanced motility without CTCs derived from a single patient (Attard et al., affecting proliferation, in agreement with Tomlins 2009). These results suggest that the formation of et al. (2007); Carver et al. (2009b). These findings the fusion gene occurred before PTEN loss and gain corroborate the view that effectors of ERG of the AR locus. However, this study was overexpression affect cellular processes which are performed on a very small cohort of castration- complimentary to unregulated factors downstream resistant CaP and may not necessarily reflect the of AKT as a result of PTEN deficiency, but on their sequence of accumulating genomic alterations in own are not sufficient to provoke the transition CaP. from benign to neoplastic. The implication is not TMPRSS2:ETS fusion status in HGPIN occurs at a that PTEN loss is the driver in CaP, but that ETS low frequency, and almost exclusively only when gene fusions are enhancer alterations significantly juxtaposed to fusion-positive CaP. These HGPIN affecting cellular processes further progressing lesions, however, do not exhibit the chromosomal prostatic tumourigenesis when the background is copy number changes seen in 42% of the paired primed first by a driver event capable of initiating CaP as assessed by CGH (Cerveira et al., 2006). sufficient dysregulation leading to the development These results propose that formation of the fusion of a preneoplastic lesion. However, because PTEN gene may precede chromosomal-level alterations loss and the presence of the fusion gene are and is consistent with the literature indicating that significantly associated events in CaP (Yoshimoto few gross chromosome- or arm-level chromosomal et al., 2008; Carver et al., 2009a; Han et al., 2009; copy alterations are present in localized CaP. King et al., 2009; Bismar et al., 2010) it is likely Another study investigating a range of prostate that PTEN inactivation may be an important driver tissues comprising benign, precursor, malignant and lesion for fusion-positive CaP. Together the driver metastatic samples found that the majority of event and ETS overexpression lead to a patient samples examined showed homogeneity significantly aggressive and invasive lesion. with respect to fusion status and mechanism (Edel Therefore, elucidation of the cellular pathways vs Esplit). The presence of fusion-positive HGPIN affected by ETS overexpression is fundamental to was interpreted as additional evidence that this the comprehension of the aggressive nature entity is a true-precursor to CaP, a notion that has observed in the majority of fusion-positive CaP, eluded indisputable proof (Perner et al., 2007). In and to developing novel therapeutic strategies to contrast, a recent study that examined both PTEN specifically target this subset of CaP. genomic loss and fusion status by FISH observed XII. Concluding remarks PTEN loss in benign and HGPIN lesions, while Difficulty in assigning prognostic significance, ERG rearrangement was identified in HGPIN, diagnostic and therapeutic utility to ETS gene albeit at a lower frequency than PTEN loss, and fusions is a result of a myriad of factors including, absent in BPH lesions (Bismar et al., 2010). the heterogeneity of the disease, the mechanism of Maintaining this model of progression and rearrangement (Edel vs Esplit), the technique used accumulation of genomic changes in CaP it is to assess the presence of the fusion as well as the possible that heterozygous loss of PTEN may be a cohort examined. Nevertheless, continued 'driver lesion', in a subset of CaP, and PTEN controversy between positive and negative clinical haploinsufficiency may facilitate the selective associations of the gene fusion dictates further formation of the fusion gene (Figure 3). studies are required using larger cohorts to TMPRSS2:ERG gene fusion may occur as a determine the absolute potential of this genomic secondary alteration and may function as an aberration as a biomarker for CaP diagnostic utility, 'enhancer' permitting the cell to achieve a higher prognostic significance, and stratification of level of aggressiveness and invasiveness. When this patients to aid in treatment decisions. Furthermore, sequence of events was emulated in transgenic comprehension of the pathways affected by ETS mice, ERG overexpression resulted in marked overexpression will aid in the potential of acceleration of preneoplastic lesions to invasive implementing ETS specific therapies to target this CaP on a Pten deleted background, but ERG aggressive subtype of CaP and benefit many overexpression alone simply displayed slight patients. atypical histology compared to control mice (Carver et al., 2009a; Carver et al., 2009b). In vitro

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 715

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

Figure 3: Model of prostate cancer progression showing ETS gene fusions as an enhancer lesion. Cooperation of unregulated pathways downstream of PTEN with effectors of ERG overexpression is likely a crucial event in the progression of an invasive and aggressive prostatic adenocarcinoma. Heterozygous genomic deletion of PTEN in benign prostatic precursors may represent an early event, and act as a driver lesion leading to proliferation, survival and genomic instability-all initial requisites of cancer. As a consequence of such heightened genomic instability, PTEN haploinsufficiency may facilitate the selective formation of the fusion gene with consequent acquisition of additional invasive properties. The presence of both rearrangements within a lesion is associated with accelerated disease progression and poor prognosis, indicating that synergistic molecular interactions exist between their complementary pathways. Continuing instability generates genotypic heterogeneity and diversity, such that subclones bearing PTEN homozygous deletions and amplified AR loci have further selective advantage for aggressive tumour progression, androgen escape and metastases.

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 716

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

Singh S, Barrett J, Sakata K, Tozer RG, Singh G. ETS References proteins and MMPs: partners in invasion and metastasis. Curr Drug Targets. 2002 Oct;3(5):359-67 Reddy ES, Rao VN, Papas TS. The erg gene: a human Yao SL, Lu-Yao G. Understanding and appreciating gene related to the ets oncogene. Proc Natl Acad Sci U S overdiagnosis in the PSA era. J Natl Cancer Inst. 2002 Jul A. 1987 Sep;84(17):6131-5 3;94(13):958-60 Reddy ES, Rao VN. erg, an ets-related gene, codes for Oikawa T, Yamada T. Molecular biology of the Ets family sequence-specific transcriptional activators. Oncogene. of transcription factors. Gene. 2003 Jan 16;303:11-34 1991 Dec;6(12):2285-9 Birger Y, Catez F, Furusawa T, Lim JH, Prymakowska- Nye JA, Petersen JM, Gunther CV, Jonsen MD, Graves Bosak M, West KL, Postnikov YV, Haines DC, Bustin M. BJ. Interaction of murine ets-1 with GGA-binding sites Increased tumorigenicity and sensitivity to ionizing establishes the ETS domain as a new DNA-binding motif. radiation upon loss of chromosomal protein HMGN1. Genes Dev. 1992 Jun;6(6):975-90 Cancer Res. 2005 Aug 1;65(15):6711-8 Basuyaux JP, Ferreira E, Stéhelin D, Butticè G. The Ets Petrovics G, Liu A, Shaheduzzaman S, Furusato B, Sun C, transcription factors interact with each other and with the c- Chen Y, Nau M, Ravindranath L, Chen Y, Dobi A, Fos/c-Jun complex via distinct protein domains in a DNA- Srikantan V, Sesterhenn IA, McLeod DG, Vahey M, Moul dependent and -independent manner. J Biol Chem. 1997 JW, Srivastava S. Frequent overexpression of ETS-related Oct 17;272(42):26188-95 gene-1 (ERG1) in prostate cancer transcriptome. Paoloni-Giacobino A, Chen H, Peitsch MC, Rossier C, Oncogene. 2005 May 26;24(23):3847-52 Antonarakis SE. Cloning of the TMPRSS2 gene, which Puc J, Keniry M, Li HS, Pandita TK, Choudhury AD, encodes a novel serine protease with transmembrane, Memeo L, Mansukhani M, Murty VV, Gaciong Z, Meek SE, LDLRA, and SRCR domains and maps to 21q22.3. Piwnica-Worms H, Hibshoosh H, Parsons R. Lack of Genomics. 1997 Sep 15;44(3):309-20 PTEN sequesters CHK1 and initiates genetic instability. Sanchez Y, Wong C, Thoma RS, Richman R, Wu Z, Cancer Cell. 2005 Feb;7(2):193-204 Piwnica-Worms H, Elledge SJ. Conservation of the Chk1 Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, checkpoint pathway in mammals: linkage of DNA damage Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, to Cdk regulation through Cdc25. Science. 1997 Sep Kuefer R, Lee C, Montie JE, Shah RB, Pienta KJ, Rubin 5;277(5331):1497-501 MA, Chinnaiyan AM. Recurrent fusion of TMPRSS2 and Carrère S, Verger A, Flourens A, Stehelin D, Duterque- ETS transcription factor genes in prostate cancer. Science. Coquillaud M. Erg proteins, transcription factors of the Ets 2005 Oct 28;310(5748):644-8 family, form homo, heterodimers and ternary complexes Wilson S, Greer B, Hooper J, Zijlstra A, Walker B, Quigley via two distinct domains. Oncogene. 1998 Jun J, Hawthorne S. The membrane-anchored serine protease, 25;16(25):3261-8 TMPRSS2, activates PAR-2 in prostate cancer cells. Trojanowska M. Ets factors and regulation of the Biochem J. 2005 Jun 15;388(Pt 3):967-72 extracellular matrix. Oncogene. 2000 Dec 18;19(55):6464- Cerveira N, Ribeiro FR, Peixoto A, Costa V, Henrique R, 71 Jerónimo C, Teixeira MR. TMPRSS2-ERG gene fusion Afar DE, Vivanco I, Hubert RS, Kuo J, Chen E, Saffran causing ERG overexpression precedes chromosome copy DC, Raitano AB, Jakobovits A. Catalytic cleavage of the number changes in prostate carcinomas and paired androgen-regulated TMPRSS2 protease results in its HGPIN lesions. Neoplasia. 2006 Oct;8(10):826-32 secretion by prostate and prostate cancer epithelia. Iljin K, Wolf M, Edgren H, Gupta S, Kilpinen S, Skotheim Cancer Res. 2001 Feb 15;61(4):1686-92 RI, Peltola M, Smit F, Verhaegh G, Schalken J, Nees M, Chai Y, Chipitsyna G, Cui J, Liao B, Liu S, Aysola K, Kallioniemi O. TMPRSS2 fusions with oncogenic ETS Yezdani M, Reddy ES, Rao VN. c-Fos oncogene regulator factors in prostate cancer involve unbalanced genomic Elk-1 interacts with BRCA1 splice variants BRCA1a/1b and rearrangements and are associated with HDAC1 and enhances BRCA1a/1b-mediated growth suppression in epigenetic reprogramming. Cancer Res. 2006 Nov breast cancer cells. Oncogene. 2001 Mar 15;20(11):1357- 1;66(21):10242-6 67 Laxman B, Tomlins SA, Mehra R, Morris DS, Wang L, McLaughlin F, Ludbrook VJ, Cox J, von Carlowitz I, Brown Helgeson BE, Shah RB, Rubin MA, Wei JT, Chinnaiyan S, Randi AM. Combined genomic and antisense analysis AM. Noninvasive detection of TMPRSS2:ERG fusion reveals that the transcription factor Erg is implicated in transcripts in the urine of men with prostate cancer. endothelial cell differentiation. Blood. 2001 Dec Neoplasia. 2006 Oct;8(10):885-8 1;98(12):3332-9 Liu W, Chang B, Sauvageot J, Dimitrov L, Gielzak M, Li T, Sato Y. Role of ETS family transcription factors in vascular Yan G, Sun J, Sun J, Adams TS, Turner AR, Kim JW, development and angiogenesis. Cell Struct Funct. 2001 Meyers DA, Zheng SL, Isaacs WB, Xu J. Comprehensive Feb;26(1):19-24 assessment of DNA copy number alterations in human prostate cancers using Affymetrix 100K SNP mapping Vaarala MH, Porvari K, Kyllönen A, Lukkarinen O, Vihko P. array. Genes Chromosomes Cancer. 2006 The TMPRSS2 gene encoding transmembrane serine Nov;45(11):1018-32 protease is overexpressed in a majority of prostate cancer patients: detection of mutated TMPRSS2 form in a case of Perner S, Demichelis F, Beroukhim R, Schmidt FH, aggressive disease. Int J Cancer. 2001 Dec 1;94(5):705- Mosquera JM, Setlur S, Tchinda J, Tomlins SA, Hofer MD, 10 Pienta KG, Kuefer R, Vessella R, Sun XW, Meyerson M, Lee C, Sellers WR, Chinnaiyan AM, Rubin MA. Verger A, Buisine E, Carrère S, Wintjens R, Flourens A, TMPRSS2:ERG fusion-associated deletions provide Coll J, Stéhelin D, Duterque-Coquillaud M. Identification of insight into the heterogeneity of prostate cancer. Cancer amino acid residues in the ETS transcription factor Erg that Res. 2006 Sep 1;66(17):8337-41 mediate Erg-Jun/Fos-DNA ternary complex formation. J Biol Chem. 2001 May 18;276(20):17181-9 Soller MJ, Isaksson M, Elfving P, Soller W, Lundgren R, Panagopoulos I. Confirmation of the high frequency of the

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 717

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

TMPRSS2/ERG fusion gene in prostate cancer. Genes with poor clinical outcome. Br J Cancer. 2007 Sep Chromosomes Cancer. 2006 Jul;45(7):717-9 3;97(5):678-85 Terry S, Yang X, Chen MW, Vacherot F, Buttyan R. Mosquera JM, Perner S, Demichelis F, Kim R, Hofer MD, Multifaceted interaction between the androgen and Wnt Mertz KD, Paris PL, Simko J, Collins C, Bismar TA, signaling pathways and the implication for prostate cancer. Chinnaiyan AM, Rubin MA. Morphological features of J Cell Biochem. 2006 Oct 1;99(2):402-10 TMPRSS2-ERG gene fusion prostate cancer. J Pathol. 2007 May;212(1):91-101 Tomlins SA, Mehra R, Rhodes DR, Smith LR, Roulston D, Helgeson BE, Cao X, Wei JT, Rubin MA, Shah RB, Nam RK, Sugar L, Wang Z, Yang W, Kitching R, Klotz LH, Chinnaiyan AM. TMPRSS2:ETV4 gene fusions define a Venkateswaran V, Narod SA, Seth A. Expression of third molecular subtype of prostate cancer. Cancer Res. TMPRSS2:ERG gene fusion in prostate cancer cells is an 2006 Apr 1;66(7):3396-400 important prognostic factor for cancer progression. Cancer Biol Ther. 2007 Jan;6(1):40-5 Wang J, Cai Y, Ren C, Ittmann M. Expression of variant TMPRSS2/ERG fusion messenger RNAs is associated Nam RK, Sugar L, Yang W, Srivastava S, Klotz LH, Yang with aggressive prostate cancer. Cancer Res. 2006 Sep LY, Stanimirovic A, Encioiu E, Neill M, Loblaw DA, 1;66(17):8347-51 Trachtenberg J, Narod SA, Seth A. Expression of the TMPRSS2:ERG fusion gene predicts cancer recurrence Yoshimoto M, Joshua AM, Chilton-Macneill S, Bayani J, after surgery for localised prostate cancer. Br J Cancer. Selvarajah S, Evans AJ, Zielenska M, Squire JA. Three- 2007 Dec 17;97(12):1690-5 color FISH analysis of TMPRSS2/ERG fusions in prostate cancer indicates that genomic microdeletion of Perner S, Mosquera JM, Demichelis F, Hofer MD, Paris chromosome 21 is associated with rearrangement. PL, Simko J, Collins C, Bismar TA, Chinnaiyan AM, De Neoplasia. 2006 Jun;8(6):465-9 Marzo AM, Rubin MA. TMPRSS2-ERG fusion prostate cancer: an early molecular event associated with invasion. Barry M, Perner S, Demichelis F, Rubin MA. TMPRSS2- Am J Surg Pathol. 2007 Jun;31(6):882-8 ERG fusion heterogeneity in multifocal prostate cancer: clinical and biologic implications. Urology. 2007 Rajput AB, Miller MA, De Luca A, Boyd N, Leung S, Oct;70(4):630-3 Hurtado-Coll A, Fazli L, Jones EC, Palmer JB, Gleave ME, Cox ME, Huntsman DG. Frequency of the TMPRSS2:ERG Clark J, Merson S, Jhavar S, Flohr P, Edwards S, Foster gene fusion is increased in moderate to poorly CS, Eeles R, Martin FL, Phillips DH, Crundwell M, differentiated prostate cancers. J Clin Pathol. 2007 Christmas T, Thompson A, Fisher C, Kovacs G, Cooper Nov;60(11):1238-43 CS. Diversity of TMPRSS2-ERG fusion transcripts in the human prostate. Oncogene. 2007 Apr 19;26(18):2667-73 Rouzier C, Haudebourg J, Carpentier X, Valério L, Amiel J, Michiels JF, Pedeutour F. Detection of the TMPRSS2-ETS Demichelis F, Fall K, Perner S, Andrén O, Schmidt F, fusion gene in prostate carcinomas: retrospective analysis Setlur SR, Hoshida Y, Mosquera JM, Pawitan Y, Lee C, of 55 formalin-fixed and paraffin-embedded samples with Adami HO, Mucci LA, Kantoff PW, Andersson SO, clinical data. Cancer Genet Cytogenet. 2008 Chinnaiyan AM, Johansson JE, Rubin MA. May;183(1):21-7 TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort. Oncogene. Shen WH, Balajee AS, Wang J, Wu H, Eng C, Pandolfi 2007 Jul 5;26(31):4596-9 PP, Yin Y. Essential role for nuclear PTEN in maintaining chromosomal integrity. Cell. 2007 Jan 12;128(1):157-70 Hessels D, Smit FP, Verhaegh GW, Witjes JA, Cornel EB, Schalken JA. Detection of TMPRSS2-ERG fusion Tomlins SA, Laxman B, Dhanasekaran SM, Helgeson BE, transcripts and prostate cancer antigen 3 in urinary Cao X, Morris DS, Menon A, Jing X, Cao Q, Han B, Yu J, sediments may improve diagnosis of prostate cancer. Clin Wang L, Montie JE, Rubin MA, Pienta KJ, Roulston D, Cancer Res. 2007 Sep 1;13(17):5103-8 Shah RB, Varambally S, Mehra R, Chinnaiyan AM. Distinct classes of chromosomal rearrangements create oncogenic Lapointe J, Kim YH, Miller MA, Li C, Kaygusuz G, van de ETS gene fusions in prostate cancer. Nature. 2007 Aug Rijn M, Huntsman DG, Brooks JD, Pollack JR. A variant 2;448(7153):595-9 TMPRSS2 isoform and ERG fusion product in prostate cancer with implications for molecular diagnosis. Mod Tu JJ, Rohan S, Kao J, Kitabayashi N, Mathew S, Chen Pathol. 2007 Apr;20(4):467-73 YT. Gene fusions between TMPRSS2 and ETS family genes in prostate cancer: frequency and transcript variant Lapointe J, Li C, Giacomini CP, Salari K, Huang S, Wang analysis by RT-PCR and FISH on paraffin-embedded P, Ferrari M, Hernandez-Boussard T, Brooks JD, Pollack tissues. Mod Pathol. 2007 Sep;20(9):921-8 JR. Genomic profiling reveals alternative genetic pathways of prostate tumorigenesis. Cancer Res. 2007 Sep Winnes M, Lissbrant E, Damber JE, Stenman G. Molecular 15;67(18):8504-10 genetic analyses of the TMPRSS2-ERG and TMPRSS2- ETV1 gene fusions in 50 cases of prostate cancer. Oncol Mehra R, Han B, Tomlins SA, Wang L, Menon A, Wasco Rep. 2007 May;17(5):1033-6 MJ, Shen R, Montie JE, Chinnaiyan AM, Shah RB. Heterogeneity of TMPRSS2 gene rearrangements in Yoo NJ, Lee JW, Lee SH. Absence of fusion of TMPRSS2 multifocal prostate adenocarcinoma: molecular evidence and ETS transcription factor genes in gastric and for an independent group of diseases. Cancer Res. 2007 colorectal carcinomas. APMIS. 2007 Mar;115(3):252-3 Sep 1;67(17):7991-5 Yoshimoto M, Ludkovski O, Bayani J, Graham C, Mehra R, Tomlins SA, Shen R, Nadeem O, Wang L, Wei Zielenska M, Squire JA. Microdeletion and concurrent JT, Pienta KJ, Ghosh D, Rubin MA, Chinnaiyan AM, Shah translocation associated with a complex TMPRSS2:ERG RB. Comprehensive assessment of TMPRSS2 and ETS prostate cancer gene fusion. Genes Chromosomes family gene aberrations in clinically localized prostate Cancer. 2007 Sep;46(9):861-3 cancer. Mod Pathol. 2007 May;20(5):538-44 Attard G, Clark J, Ambroisine L, Fisher G, Kovacs G, Flohr Yoshimoto M, Cunha IW, Coudry RA, Fonseca FP, Torres P, Berney D, Foster CS, Fletcher A, Gerald WL, Moller H, CH, Soares FA, Squire JA. FISH analysis of 107 prostate Reuter V, De Bono JS, Scardino P, Cuzick J, Cooper CS. cancers shows that PTEN genomic deletion is associated Duplication of the fusion of TMPRSS2 to ERG sequences

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 718

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

identifies fatal human prostate cancer. Oncogene. 2008 Hermans KG, van der Korput HA, van Marion R, van de Jan 10;27(3):253-63 Wijngaart DJ, Ziel-van der Made A, Dits NF, Boormans JL, van der Kwast TH, van Dekken H, Bangma CH, Korsten H, Attard G, Clark J, Ambroisine L, Mills IG, Fisher G, Flohr P, Kraaij R, Jenster G, Trapman J. Truncated ETV1, fused to Reid A, Edwards S, Kovacs G, Berney D, Foster C, Massie novel tissue-specific genes, and full-length ETV1 in CE, Fletcher A, De Bono JS, Scardino P, Cuzick J, Cooper prostate cancer. Cancer Res. 2008 Sep 15;68(18):7541-9 CS. Heterogeneity and clinical significance of ETV1 translocations in human prostate cancer. Br J Cancer. Hu Y, Dobi A, Sreenath T, Cook C, Tadase AY, 2008 Jul 22;99(2):314-20 Ravindranath L, Cullen J, Furusato B, Chen Y, Thangapazham RL, Mohamed A, Sun C, Sesterhenn IA, Balk SP, Knudsen KE. AR, the cell cycle, and prostate McLeod DG, Petrovics G, Srivastava S. Delineation of cancer. Nucl Recept Signal. 2008 Feb 1;6:e001 TMPRSS2-ERG splice variants in prostate cancer. Clin Birdsey GM, Dryden NH, Amsellem V, Gebhardt F, Cancer Res. 2008 Aug 1;14(15):4719-25 Sahnan K, Haskard DO, Dejana E, Mason JC, Randi AM. Jemal A, Siegel R, Ward E, Hao Y, Xu J, Murray T, Thun Transcription factor Erg regulates angiogenesis and MJ. Cancer statistics, 2008. CA Cancer J Clin. 2008 Mar- endothelial apoptosis through VE-cadherin. Blood. 2008 Apr;58(2):71-96 Apr 1;111(7):3498-506 Jhavar S, Reid A, Clark J, Kote-Jarai Z, Christmas T, Björkman M, Iljin K, Halonen P, Sara H, Kaivanto E, Nees Thompson A, Woodhouse C, Ogden C, Fisher C, M, Kallioniemi OP. Defining the molecular action of HDAC Corbishley C, De-Bono J, Eeles R, Brewer D, Cooper C. inhibitors and synergism with androgen deprivation in Detection of TMPRSS2-ERG translocations in human ERG-positive prostate cancer. Int J Cancer. 2008 Dec prostate cancer by expression profiling using GeneChip 15;123(12):2774-81 Human Exon 1.0 ST arrays. J Mol Diagn. 2008 Clark J, Attard G, Jhavar S, Flohr P, Reid A, De-Bono J, Jan;10(1):50-7 Eeles R, Scardino P, Cuzick J, Fisher G, Parker MD, Klezovitch O, Risk M, Coleman I, Lucas JM, Null M, True Foster CS, Berney D, Kovacs G, Cooper CS. Complex LD, Nelson PS, Vasioukhin V. A causal role for ERG in patterns of ETS gene alteration arise during cancer neoplastic transformation of prostate epithelium. Proc Natl development in the human prostate. Oncogene. 2008 Mar Acad Sci U S A. 2008 Feb 12;105(6):2105-10 27;27(14):1993-2003 Mao X, Shaw G, James SY, Purkis P, Kudahetti SC, Clark JP, Munson KW, Gu JW, Lamparska-Kupsik K, Chan Tsigani T, Kia S, Young BD, Oliver RT, Berney D, Prowse KG, Yoshida JS, Kawachi MH, Crocitto LE, Wilson TG, DM, Lu YJ. Detection of TMPRSS2:ERG fusion gene in Feng Z, Smith SS. Performance of a single assay for both circulating prostate cancer cells. Asian J Androl. 2008 type III and type VI TMPRSS2:ERG fusions in noninvasive May;10(3):467-73 prediction of prostate biopsy outcome. Clin Chem. 2008 Dec;54(12):2007-17 Mehra R, Tomlins SA, Yu J, Cao X, Wang L, Menon A, Rubin MA, Pienta KJ, Shah RB, Chinnaiyan AM. Dai MJ, Chen LL, Zheng YB, Chen W, Tao ZH, Weng ZL, Characterization of TMPRSS2-ETS gene aberrations in Wu XL, Li CD, Chen ZG, Chen XD, Shi SB. [Frequency androgen-independent metastatic prostate cancer. Cancer and transcript variant analysis of gene fusions between Res. 2008 May 15;68(10):3584-90 TMPRSS2 and ETS transcription factor genes in prostate cancer]. Zhonghua Yi Xue Za Zhi. 2008 Mar Mosquera JM, Perner S, Genega EM, Sanda M, Hofer MD, 11;88(10):669-73 Mertz KD, Paris PL, Simko J, Bismar TA, Ayala G, Shah RB, Loda M, Rubin MA. Characterization of TMPRSS2- FitzGerald LM, Agalliu I, Johnson K, Miller MA, Kwon EM, ERG fusion high-grade prostatic intraepithelial neoplasia Hurtado-Coll A, Fazli L, Rajput AB, Gleave ME, Cox ME, and potential clinical implications. Clin Cancer Res. 2008 Ostrander EA, Stanford JL, Huntsman DG. Association of Jun 1;14(11):3380-5 TMPRSS2-ERG gene fusion with clinical characteristics and outcomes: results from a population-based study of Nigwekar P, Miick S, Rittenhouse H, et al.. Morphologic prostate cancer. BMC Cancer. 2008 Aug 11;8:230 correlates of individual splice variants of TMPRSS2-ERG prostate cancer (PCa) detected by transcription-mediated Furusato B, Gao CL, Ravindranath L, Chen Y, Cullen J, amplification (TMA) in radical prostatectomy (RP) McLeod DG, Dobi A, Srivastava S, Petrovics G, specimens [abstract 797]. in USCAP, 2008. Denver (CO). Sesterhenn IA. Mapping of TMPRSS2-ERG fusions in the context of multi-focal prostate cancer. Mod Pathol. 2008 Saramaki OR, Harjula AE, Martikainen PM, Vessella RL, Feb;21(2):67-75 Tammela TL, Visakorpi T.. TMPRSS2:ERG fusion identifies a subgroup of prostate cancers with a favorable Han B, Mehra R, Dhanasekaran SM, Yu J, Menon A, prognosis. Clin Cancer Res. 2008 Jun 1;14(11):3395-400. Lonigro RJ, Wang X, Gong Y, Wang L, Shankar S, Laxman B, Shah RB, Varambally S, Palanisamy N, Schweizer L, Rizzo CA, Spires TE, Platero JS, Wu Q, Lin Tomlins SA, Kumar-Sinha C, Chinnaiyan AM. A TA, Gottardis MM, Attar RM.. The androgen receptor can fluorescence in situ hybridization screen for E26 signal through Wnt/beta-Catenin in prostate cancer cells transformation-specific aberrations: identification of DDX5- as an adaptation mechanism to castration levels of ETV4 fusion protein in prostate cancer. Cancer Res. 2008 androgens. BMC Cell Biol. 2008 Jan 24;9:4. Sep 15;68(18):7629-37 Sun C, Dobi A, Mohamed A, Li H, Thangapazham RL, Helgeson BE, Tomlins SA, Shah N, Laxman B, Cao Q, Furusato B, Shaheduzzaman S, Tan SH, Vaidyanathan G, Prensner JR, Cao X, Singla N, Montie JE, Varambally S, Whitman E, Hawksworth DJ, Chen Y, Nau M, Patel V, Mehra R, Chinnaiyan AM. Characterization of Vahey M, Gutkind JS, Sreenath T, Petrovics G, TMPRSS2:ETV5 and SLC45A3:ETV5 gene fusions in Sesterhenn IA, McLeod DG, Srivastava S.. TMPRSS2- prostate cancer. Cancer Res. 2008 Jan 1;68(1):73-80 ERG fusion, a common genomic alteration in prostate cancer activates C-MYC and abrogates prostate epithelial Hermans KG, Bressers AA, van der Korput HA, Dits NF, differentiation. Oncogene. 2008 Sep 11;27(40):5348-53. Jenster G, Trapman J. Two unique novel prostate-specific Epub 2008 Jun 9. and androgen-regulated fusion partners of ETV4 in prostate cancer. Cancer Res. 2008 May 1;68(9):3094-8 Tomlins SA, Laxman B, Varambally S, Cao X, Yu J, Helgeson BE, Cao Q, Prensner JR, Rubin MA, Shah RB, Mehra R, Chinnaiyan AM.. Role of the TMPRSS2-ERG

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 719

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

gene fusion in prostate cancer. Neoplasia. 2008a rearranged prostate cancer. Genes Chromosomes Cancer. Feb;10(2):177-88. 2009 Apr;48(4):366-80. Tomlins SA, Rhodes DR, Yu J, Varambally S, Mehra R, Ellett F, Kile BT, Lieschke GJ.. The role of the ETS factor Perner S, Demichelis F, Helgeson BE, Laxman B, Morris erg in zebrafish vasculogenesis. Mech Dev. 2009 Mar- DS, Cao Q, Cao X, Andren O, Fall K, Johnson L, Wei JT, Apr;126(3-4):220-9. Epub 2008 Nov 8. Shah RB, Al-Ahmadie H, Eastham JA, Eggener SE, Fine SW, Hotakainen K, Stenman UH, Tsodikov A, Gerald WL, Fang Z, Soleymani L, Pampalakis G, Yoshimoto M, Squire Lilja H, Reuter VE, Kantoff PW, Scardino PT, Rubin MA, JA, Sargent EH, Kelley SO.. Direct profiling of cancer Bjartell AS, Chinnaiyan AM.. The role of SPINK1 in ETS biomarkers in tumor tissue using a multiplexed rearrangement-negative prostate cancers. Cancer Cell. nanostructured microelectrode integrated circuit. ACS 2008b Jun;13(6):519-28. Nano. 2009 Oct 27;3(10):3207-13. Wang J, Cai Y, Yu W, Ren C, Spencer DM, Ittmann M.. Gopalan A, Leversha MA, Satagopan JM, Zhou Q, Al- Pleiotropic biological activities of alternatively spliced Ahmadie HA, Fine SW, Eastham JA, Scardino PT, Scher TMPRSS2/ERG fusion gene transcripts. Cancer Res. 2008 HI, Tickoo SK, Reuter VE, Gerald WL.. TMPRSS2-ERG Oct 15;68(20):8516-24. gene fusion is not associated with outcome in patients treated by prostatectomy. Cancer Res. 2009 Feb Yoshimoto M, Joshua AM, Cunha IW, Coudry RA, 15;69(4):1400-6. Epub 2009 Feb 3. Fonseca FP, Ludkovski O, Zielenska M, Soares FA, Squire JA.. Absence of TMPRSS2:ERG fusions and PTEN losses Guo CC, Zuo G, Cao D, Troncoso P, Czerniak BA.. in prostate cancer is associated with a favorable outcome. Prostate cancer of transition zone origin lacks TMPRSS2- Mod Pathol. 2008 Dec;21(12):1451-60. Epub 2008 May ERG gene fusion. Mod Pathol. 2009 Jul;22(7):866-71. 23. Epub 2009 Apr 24. Ai J, Wang Y, Dar JA, Liu J, Liu L, Nelson JB, Wang Z.. Gupta A, Yang Q, Pandita RK, Hunt CR, Xiang T, Misri S, HDAC6 regulates androgen receptor hypersensitivity and Zeng S, Pagan J, Jeffery J, Puc J, Kumar R, Feng Z, nuclear localization via modulating Hsp90 acetylation in Powell SN, Bhat A, Yaguchi T, Wadhwa R, Kaul SC, castration-resistant prostate cancer. Mol Endocrinol. 2009 Parsons R, Khanna KK, Pandita TK.. Cell cycle checkpoint Dec;23(12):1963-72. Epub 2009 Oct 23. defects contribute to genomic instability in PTEN deficient cells independent of DNA DSB repair. Cell Cycle. 2009 Jul Albadine R, Latour M, Toubaji A, Haffner M, Isaacs WB, A 15;8(14):2198-210. Epub 2009 Jul 7. Platz E, Meeker AK, Demarzo AM, Epstein JI, Netto GJ.. TMPRSS2-ERG gene fusion status in minute (minimal) Han B, Mehra R, Lonigro RJ, Wang L, Suleman K, Menon prostatic adenocarcinoma. Mod Pathol. 2009 A, Palanisamy N, Tomlins SA, Chinnaiyan AM, Shah RB.. Nov;22(11):1415-22. Epub 2009 Sep 4. Fluorescence in situ hybridization study shows association of PTEN deletion with ERG rearrangement during prostate Attard G, Swennenhuis JF, Olmos D, Reid AH, Vickers E, cancer progression. Mod Pathol. 2009 Aug;22(8):1083-93. A'Hern R, Levink R, Coumans F, Moreira J, Riisnaes R, Epub 2009 May 1. Oommen NB, Hawche G, Jameson C, Thompson E, Sipkema R, Carden CP, Parker C, Dearnaley D, Kaye SB, Hermans KG, Boormans JL, Gasi D, van Leenders GJ, Cooper CS, Molina A, Cox ME, Terstappen LW, de Bono Jenster G, Verhagen PC, Trapman J.. Overexpression of JS.. Characterization of ERG, AR and PTEN gene status prostate-specific TMPRSS2(exon 0)-ERG fusion in circulating tumor cells from patients with castration- transcripts corresponds with favorable prognosis of resistant prostate cancer. Cancer Res. 2009 Apr prostate cancer. Clin Cancer Res. 2009 Oct 1;69(7):2912-8. 15;15(20):6398-403. Epub 2009 Oct 13. Bonaccorsi L, Nesi G, Nuti F, Paglierani M, Krausz C, Hofer MD, Kuefer R, Maier C, Herkommer K, Perner S, Masieri L, Serni S, Proietti-Pannunzi L, Fang Y, Jhanwar Demichelis F, Paiss T, Vogel W, Rubin MA, Hoegel J.. SC, Orlando C, Carini M, Forti G, Baldi E, Luzzatto L.. Genome-wide linkage analysis of TMPRSS2-ERG fusion Persistence of expression of the TMPRSS2:ERG fusion in familial prostate cancer. Cancer Res. 2009 Jan gene after pre-surgery androgen ablation may be 15;69(2):640-6. associated with early prostate specific antigen relapse of Holcomb IN, Young JM, Coleman IM, Salari K, Grove DI, prostate cancer: preliminary results. J Endocrinol Invest. Hsu L, True LD, Roudier MP, Morrissey CM, Higano CS, 2009 Jul;32(7):590-6. Epub 2009 May 5. Nelson PS, Vessella RL, Trask BJ.. Comparative analyses Carver BS, Tran J, Chen Z, Carracedo-Perez A, Alimonti of chromosome alterations in soft-tissue metastases within A, Nardella C, Gopalan A, Scardino PT, Cordon-Cardo C, and across patients with castration-resistant prostate Gerald W, Pandolfi PP.. ETS rearrangements and prostate cancer. Cancer Res. 2009 Oct 1;69(19):7793-802. Epub cancer initiation. Nature. 2009a Feb 12;457(7231):E1; 2009 Sep 22. discussion E2-3. Ishkanian AS, Mallof CA, Ho J, Meng A, Albert M, Syed A, Carver BS, Tran J, Gopalan A, Chen Z, Shaikh S, van der Kwast T, Milosevic M, Yoshimoto M, Squire JA, Carracedo A, Alimonti A, Nardella C, Varmeh S, Scardino Lam WL, Bristow RG.. High-resolution array CGH PT, Cordon-Cardo C, Gerald W, Pandolfi PP.. Aberrant identifies novel regions of genomic alteration in ERG expression cooperates with loss of PTEN to promote intermediate-risk prostate cancer. Prostate. 2009 Jul cancer progression in the prostate. Nat Genet. 2009b 1;69(10):1091-100. May;41(5):619-24. Epub 2009 Apr 26. King JC, Xu J, Wongvipat J, Hieronymus H, Carver BS, Darnel AD, Lafargue CJ, Vollmer RT, Corcos J, Bismar Leung DH, Taylor BS, Sander C, Cardiff RD, Couto SS, TA.. TMPRSS2-ERG fusion is frequently observed in Gerald WL, Sawyers CL.. Cooperativity of TMPRSS2-ERG Gleason pattern 3 prostate cancer in a Canadian cohort. with PI3-kinase pathway activation in prostate Cancer Biol Ther. 2009 Jan;8(2):125-30. Epub 2009 Feb 4. oncogenesis. Nat Genet. 2009 May;41(5):524-6. Epub 2009 Apr 26. Demichelis F, Setlur SR, Beroukhim R, Perner S, Korbel JO, Lafargue CJ, Pflueger D, Pina C, Hofer MD, Sboner A, Kruse EA, Loughran SJ, Baldwin TM, Josefsson EC, Ellis Svensson MA, Rickman DS, Urban A, Snyder M, S, Watson DK, Nurden P, Metcalf D, Hilton DJ, Alexander Meyerson M, Lee C, Gerstein MB, Kuefer R, Rubin MA.. WS, Kile BT.. Dual requirement for the ETS transcription Distinct genomic aberrations associated with ERG factors Fli-1 and Erg in hematopoietic stem cells and the

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 720

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

megakaryocyte lineage. Proc Natl Acad Sci U S A. 2009 steroidogenic pathways. BJU Int. 2009 Aug;104(4):438-48. Aug 18;106(33):13814-9. Epub 2009 Jul 31. Epub 2009 Jun 24. (REVIEW) Lin C, Yang L, Tanasa B, Hutt K, Ju BG, Ohgi K, Zhang J, Watson SK, Woolcock BW, Fee JN, Bainbridge TC, Rose DW, Fu XD, Glass CK, Rosenfeld MG.. Nuclear Webber D, Kinahan TJ, Lam WL, Vielkind JR.. Minimum receptor-induced chromosomal proximity and DNA breaks altered regions in early prostate cancer progression underlie specific translocations in cancer. Cell. 2009 Dec identified by high resolution whole genome tiling path BAC 11;139(6):1069-83. array comparative hybridization. Prostate. 2009 Jun 15;69(9):961-75. Lu B, Maqsodi B, Yang W, McMaster GK, Perner S, Regan M, Bubley GJ, Balk SP, Rubin M, Sanda MG.. Detection of Barwick BG, Abramovitz M, Kodani M, Moreno CS, Nam TMPRSS2-ERG fusion gene expression in prostate cancer R, Tang W, Bouzyk M, Seth A, Leyland-Jones B.. Prostate specimens by a novel assay using branched DNA. cancer genes associated with TMPRSS2-ERG gene fusion Urology. 2009 Nov;74(5):1156-61. Epub 2009 Aug 3. and prognostic of biochemical recurrence in multiple cohorts. Br J Cancer. 2010 Feb 2;102(3):570-6. Epub 2010 Luedeke M, Linnert CM, Hofer MD, Surowy HM, Rinckleb Jan 12. AE, Hoegel J, Kuefer R, Rubin MA, Vogel W, Maier C.. Predisposition for TMPRSS2-ERG fusion in prostate Bismar TA, Trpkov K.. TMPRSS2-ERG gene fusion in cancer by variants in DNA repair genes. Cancer Epidemiol transition zone prostate cancer. Mod Pathol. 2010 Biomarkers Prev. 2009 Nov;18(11):3030-5. Epub 2009 Oct Jul;23(7):1040-1; author reply 1041-2. 27. Boormans JL, Hermans KG, Made AC, van Leenders GJ, Mani RS, Tomlins SA, Callahan K, Ghosh A, Nyati MK, Wildhagen MF, Collette L, Schroder FH, Trapman J, Varambally S, Palanisamy N, Chinnaiyan AM.. Induced Verhagen PC.. Expression of the androgen-regulated chromosomal proximity and gene fusions in prostate fusion gene TMPRSS2-ERG does not predict response to cancer. Science. 2009 Nov 27;326(5957):1230. Epub 2009 endocrine treatment in hormone-naive, node-positive Oct 29. prostate cancer. Eur Urol. 2010 May;57(5):830-5. Epub 2009 Aug 22. Mosquera JM, Mehra R, Regan MM, Perner S, Genega EM, Bueti G, Shah RB, Gaston S, Tomlins SA, Wei JT, Esgueva R, Perner S, J LaFargue C, Scheble V, Stephan Kearney MC, Johnson LA, Tang JM, Chinnaiyan AM, C, Lein M, Fritzsche FR, Dietel M, Kristiansen G, Rubin Rubin MA, Sanda MG.. Prevalence of TMPRSS2-ERG MA.. Prevalence of TMPRSS2-ERG and SLC45A3-ERG fusion prostate cancer among men undergoing prostate gene fusions in a large prostatectomy cohort. Mod Pathol. biopsy in the United States. Clin Cancer Res. 2009 Jul 2010 Apr;23(4):539-46. Epub 2010 Jan 29. 15;15(14):4706-11. Epub 2009 Jul 7. Falzarano SM, Navas M, Simmerman K, Klein EA, Rubin Pflueger D, Rickman DS, Sboner A, Perner S, LaFargue MA, Zhou M, Magi-Galluzzi C.. ERG rearrangement is CJ, Svensson MA, Moss BJ, Kitabayashi N, Pan Y, de la present in a subset of transition zone prostatic tumors. Taille A, Kuefer R, Tewari AK, Demichelis F, Chee MS, Mod Pathol. 2010 Nov;23(11):1499-506. Epub 2010 Aug 6. Gerstein MB, Rubin MA.. N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer. Fine SW, Gopalan A, Leversha MA, Al-Ahmadie HA, Neoplasia. 2009 Aug;11(8):804-11. Tickoo SK, Zhou Q, Satagopan JM, Scardino PT, Gerald WL, Reuter VE.. TMPRSS2-ERG gene fusion is Randi AM, Sperone A, Dryden NH, Birdsey GM.. associated with low Gleason scores and not with high- Regulation of angiogenesis by ETS transcription factors. grade morphological features. Mod Pathol. 2010 Biochem Soc Trans. 2009 Dec;37(Pt 6):1248- Oct;23(10):1325-33. Epub 2010 Jun 18. 53.(REVIEW) Furusato B, Tan SH, Young D, Dobi A, Sun C, Mohamed Rickman DS, Pflueger D, Moss B, VanDoren VE, Chen AA, Thangapazham R, Chen Y, McMaster G, Sreenath T, CX, de la Taille A, Kuefer R, Tewari AK, Setlur SR, Petrovics G, McLeod DG, Srivastava S, Sesterhenn IA.. Demichelis F, Rubin MA.. SLC45A3-ELK4 is a novel and ERG oncoprotein expression in prostate cancer: clonal frequent erythroblast transformation-specific fusion progression of ERG-positive tumor cells and potential for transcript in prostate cancer. Cancer Res. 2009 Apr ERG-based stratification. Prostate Cancer Prostatic Dis. 1;69(7):2734-8. Epub 2009 Mar 17. 2010 Sep;13(3):228-37. Epub 2010 Jun 29. Rostad K, Hellwinkel OJ, Haukaas SA, Halvorsen OJ, Haffner MC, Aryee MJ, Toubaji A, Esopi DM, Albadine R, Oyan AM, Haese A, Budaus L, Albrecht H, Akslen LA, Gurel B, Isaacs WB, Bova GS, Liu W, Xu J, Meeker AK, Schlomm T, Kalland KH.. TMPRSS2:ERG fusion Netto G, De Marzo AM, Nelson WG, Yegnasubramanian transcripts in urine from prostate cancer patients correlate S.. Androgen-induced TOP2B-mediated double-strand with a less favorable prognosis. APMIS. 2009 breaks and prostate cancer gene rearrangements. Nat Aug;117(8):575-82. Genet. 2010 Aug;42(8):668-75. Epub 2010 Jul 4. Schayek H, Haugk K, Sun S, True LD, Plymate SR, Hawksworth D, Ravindranath L, Chen Y, Furusato B, Werner H.. Tumor suppressor BRCA1 is expressed in Sesterhenn IA, McLeod DG, Srivastava S, Petrovics G.. prostate cancer and controls insulin-like growth factor I Overexpression of C-MYC oncogene in prostate cancer receptor (IGF-IR) gene transcription in an androgen predicts biochemical recurrence. Prostate Cancer Prostatic receptor-dependent manner. Clin Cancer Res. 2009 Mar Dis. 2010 Dec;13(4):311-5. Epub 2010 Sep 7. 1;15(5):1558-65. Epub 2009 Feb 17. Kawata H, Ishikura N, Watanabe M, Nishimoto A, Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Tsunenari T, Aoki Y.. Prolonged treatment with Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, bicalutamide induces androgen receptor overexpression Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, and androgen hypersensitivity. Prostate. 2010 May Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger 15;70(7):745-54. A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM.. Metabolomic profiles delineate potential Lee K, Chae JY, Kwak C, Ku JH, Moon KC.. TMPRSS2- role for sarcosine in prostate cancer progression. Nature. ERG gene fusion and clinicopathologic characteristics of 2009 Feb 12;457(7231):910-4. Korean prostate cancer patients. Urology. 2010 Nov;76(5):1268.e7-13. Epub 2010 Aug 30. Vis AN, Schroder FH.. Key targets of hormonal treatment of prostate cancer. Part 1: the androgen receptor and

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 721

TMPRSS2:ETS gene fusions in prostate cancer Williams JL, et al.

Leinonen KA, Tolonen TT, Bracken H, Stenman UH, with radical prostatectomy. J Urol. 2010 May;183(5):2054- Tammela TL, Saramaki OR, Visakorpi T.. Association of 61. Epub 2010 Mar 19. SPINK1 expression and TMPRSS2:ERG fusion with prognosis in endocrine-treated prostate cancer. Clin Scheble VJ, Braun M, Beroukhim R, Mermel CH, Ruiz C, Cancer Res. 2010 May 15;16(10):2845-51. Epub 2010 Wilbertz T, Stiedl AC, Petersen K, Reischl M, Kuefer R, May 4. Schilling D, Fend F, Kristiansen G, Meyerson M, Rubin MA, Bubendorf L, Perner S.. ERG rearrangement is Magi-Galluzzi C, Tsusuki T, Elson P, Simmerman K, specific to prostate cancer and does not occur in any other Lafargue C, Esgueva R, Klein E, Rubin MA, Zhou M.. common tumor. Mod Pathol. 2010 Aug;23(8):1061-7. Epub TMPRSS2-ERG gene fusion prevalence and class are 2010 May 14. significantly different in prostate cancer of caucasian, african-american and japanese patients. Prostate. 2010 Schulz WA, Ingenwerth M, Djuidje CE, Hader C, Sep 28. [Epub ahead of print] Rahnenfuhrer J, Engers R.. Changes in cortical cytoskeletal and extracellular matrix gene expression in Mao X, Yu Y, Boyd LK, Ren G, Lin D, Chaplin T, Kudahetti prostate cancer are related to oncogenic ERG SC, Stankiewicz E, Xue L, Beltran L, Gupta M, Oliver RT, deregulation. BMC Cancer. 2010 Sep 22;10:505. Lemoine NR, Berney DM, Young BD, Lu YJ.. Distinct genomic alterations in prostate cancers in Chinese and Shan L, Ambroisine L, Clark J, Yanez-Munoz RJ, Fisher G, Western populations suggest alternative pathways of Kudahetti SC, Yang J, Kia S, Mao X, Fletcher A, Flohr P, prostate carcinogenesis. Cancer Res. 2010 Jul Edwards S, Attard G, De-Bono J, Young BD, Foster CS, 1;70(13):5207-12. Epub 2010 Jun 1. Reuter V, Moller H, Oliver TD, Berney DM, Scardino P, Cuzick J, Cooper CS, Lu YJ.. The identification of Miyagi Y, Sasaki T, Fujinami K, Sano J, Senga Y, Miura T, chromosomal translocation, t(4;6)(q22;q15), in prostate Kameda Y, Sakuma Y, Nakamura Y, Harada M, Tsuchiya cancer. Prostate Cancer Prostatic Dis. 2010 E.. ETS family-associated gene fusions in Japanese Jun;13(2):117-25. Epub 2010 Feb 23. prostate cancer: analysis of 194 radical prostatectomy samples. Mod Pathol. 2010 Nov;23(11):1492-8. Epub 2010 Stott SL, Lee RJ, Nagrath S, Yu M, Miyamoto DT, Ulkus L, Aug 6. Inserra EJ, Ulman M, Springer S, Nakamura Z, Moore AL, Tsukrov DI, Kempner ME, Dahl DM, Wu CL, Iafrate AJ, Mwamukonda K, Chen Y, Ravindranath L, Furusato B, Hu Smith MR, Tompkins RG, Sequist LV, Toner M, Haber DA, Y, Sterbis J, Osborn D, Rosner I, Sesterhenn IA, McLeod Maheswaran S.. Isolation and characterization of DG, Srivastava S, Petrovics G.. Quantitative expression of circulating tumor cells from patients with localized and TMPRSS2 transcript in prostate tumor cells reflects metastatic prostate cancer. Sci Transl Med. 2010 Mar TMPRSS2-ERG fusion status. Prostate Cancer Prostatic 31;2(25):25ra23. Dis. 2010 Mar;13(1):47-51. Epub 2009 Jul 14. Sun QP, Li LY, Chen Z, Pang J, Yang WJ, Zhou XF, Qiu Park K, Tomlins SA, Mudaliar KM, Chiu YL, Esgueva R, JG, Su ZL, He D, Gao X.. Detection of TMPRSS2-ETS Mehra R, Suleman K, Varambally S, Brenner JC, fusions by a multiprobe fluorescence in situ hybridization MacDonald T, Srivastava A, Tewari AK, Sathyanarayana assay for the early diagnosis of prostate cancer: a pilot U, Nagy D, Pestano G, Kunju LP, Demichelis F, study. J Mol Diagn. 2010 Sep;12(5):718-24. Epub 2010 Jul Chinnaiyan AM, Rubin MA.. Antibody-based detection of 8. ERG rearrangement-positive prostate cancer. Neoplasia. 2010 Jul;12(7):590-8. Palanisamy N, Ateeq B, Kalyana-Sundaram S, Pflueger D, Ramnarayanan K, Shankar S, Han B, Cao Q, Cao X, Perner S, Svensson MA, Hossain RR, Day JR, Groskopf J, Suleman K, Kumar-Sinha C, Dhanasekaran SM, Chen YB, Slaughter RC, Jarleborn AR, Hofer MD, Kuefer R, Esgueva R, Banerjee S, LaFargue CJ, Siddiqui J, Demichelis F, Rickman DS, Rubin MA.. ERG Demichelis F, Moeller P, Bismar TA, Kuefer R, Fullen DR, rearrangement metastasis patterns in locally advanced Johnson TM, Greenson JK, Giordano TJ, Tan P, Tomlins prostate cancer. Urology. 2010 Apr;75(4):762-7. SA, Varambally S, Rubin MA, Maher CA, Chinnaiyan AM.. Rearrangements of the RAF kinase pathway in prostate Reid AH, Attard G, Ambroisine L, Fisher G, Kovacs G, cancer, gastric cancer and melanoma. Nat Med. 2010 Brewer D, Clark J, Flohr P, Edwards S, Berney DM, Foster Jul;16(7):793-8. Epub 2010 Jun 6. CS, Fletcher A, Gerald WL, Moller H, Reuter VE, Scardino PT, Cuzick J, de Bono JS, Cooper CS.. Molecular Zhang S, Pavlovitz B, Tull J, Wang Y, Deng FM, Fuller C.. characterisation of ERG, ETV1 and PTEN gene loci Detection of TMPRSS2 gene deletions and translocations identifies patients at low and high risk of death from in carcinoma, intraepithelial neoplasia, and normal prostate cancer. Br J Cancer. 2010 Feb 16;102(4):678-84. epithelium of the prostate by direct fluorescence in situ Epub 2010 Jan 26. hybridization. Diagn Mol Pathol. 2010 Sep;19(3):151-6. Rice KR, Chen Y, Ali A, Whitman EJ, Blase A, Ibrahim M, Bismar TA, Yoshimoto M, Vollmer RT, Duan Q, Firszt M, Elsamanoudi S, Brassell S, Furusato B, Stingle N, Corcos J, Squire JA.. PTEN genomic deletion is an early Sesterhenn IA, Petrovics G, Miick S, Rittenhouse H, event associated with ERG gene rearrangements in Groskopf J, McLeod DG, Srivastava S.. Evaluation of the prostate cancer. BJU Int. 2011 Feb;107(3):477-485. doi: ETS-related gene mRNA in urine for the detection of 10.1111/j.1464-410X.2010.09470.x. prostate cancer. Clin Cancer Res. 2010 Mar 1;16(5):1572- 6. Epub 2010 Feb 16. This article should be referenced as such: Rubio-Briones J, Fernandez-Serra A, Calatrava A, Garcia- Williams JL, Yoshimoto M, Boag AH, Squire JA, Park PC. Casado Z, Rubio L, Bonillo MA, Iborra I, Solsona E, Lopez- TMPRSS2:ETS gene fusions in prostate cancer. Atlas Guerrero JA.. Clinical implications of TMPRSS2-ERG gene Genet Cytogenet Oncol Haematol. 2011; 15(8):705-722. fusion expression in patients with prostate cancer treated

Atlas Genet Cytogenet Oncol Haematol. 2011; 15(8) 722

Atlas of Genetics and Cytogenetics

in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS

Instructions to Authors Manuscripts submitted to the Atlas must be submitted solely to the Atlas. Iconography is most welcome: there is no space restriction. The Atlas publishes "cards", "deep insights", "case reports", and "educational items". Cards are structured review articles. Detailed instructions for these structured reviews can be found at: http://AtlasGeneticsOncology.org/Forms/Gene_Form.html for reviews on genes, http://AtlasGeneticsOncology.org/Forms/Leukaemia_Form.html for reviews on leukaemias, http://AtlasGeneticsOncology.org/Forms/SolidTumour_Form.html for reviews on solid tumours, http://AtlasGeneticsOncology.org/Forms/CancerProne_Form.html for reviews on cancer-prone diseases. According to the length of the paper, cards are divided, into "reviews" (texts exceeding 2000 words), "mini reviews" (between), and "short communications" (texts below 400 words). The latter category may not be accepted for indexing by bibliographic databases. Deep Insights are written as traditional papers, made of paragraphs with headings, at the author's convenience. No length restriction. Case Reports in haematological malignancies are dedicated to recurrent -but rare- chromosomes abnormalities in leukaemias/lymphomas. Cases of interest shall be: 1- recurrent (i.e. the chromosome anomaly has already been described in at least 1 case), 2- rare (previously described in less than 20 cases), 3- with well documented clinics and laboratory findings, and 4- with iconography of chromosomes. It is mandatory to use the specific "Submission form for Case reports": see http://AtlasGeneticsOncology.org/Reports/Case_Report_Submission.html. Educational Items must be didactic, give full information and be accompanied with iconography. Translations into French, German, Italian, and Spanish are welcome.

Subscription: The Atlas is FREE!

Corporate patronage, sponsorship and advertising Enquiries should be addressed to [email protected].

Rules, Copyright Notice and Disclaimer Conflicts of Interest: Authors must state explicitly whether potential conflicts do or do not exist. Reviewers must disclose to editors any conflicts of interest that could bias their opinions of the manuscript. The editor and the editorial board members must disclose any potential conflict. Privacy and Confidentiality – Iconography: Patients have a right to privacy. Identifying details should be omitted. If complete anonymity is difficult to achieve, informed consent should be obtained. Property: As "cards" are to evolve with further improvements and updates from various contributors, the property of the cards belongs to the editor, and modifications will be made without authorization from the previous contributor (who may, nonetheless, be asked for refereeing); contributors are listed in an edit history manner. Authors keep the rights to use further the content of their papers published in the Atlas, provided that the source is cited. Copyright: The information in the Atlas of Genetics and Cytogenetics in Oncology and Haematology is issued for general distribution. All rights are reserved. The information presented is protected under international conventions and under national laws on copyright and neighbouring rights. Commercial use is totally forbidden. Information extracted from the Atlas may be reviewed, reproduced or translated for research or private study but not for sale or for use in conjunction with commercial purposes. Any use of information from the Atlas should be accompanied by an acknowledgment of the Atlas as the source, citing the uniform resource locator (URL) of the article and/or the article reference, according to the Vancouver convention. Reference to any specific commercial products, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favouring. The views and opinions of contributors and authors expressed herein do not necessarily state or reflect those of the Atlas editorial staff or of the web site holder, and shall not be used for advertising or product endorsement purposes. The Atlas does not make any warranty, express or implied, including the warranties of merchantability and fitness for a particular purpose, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, and shall not be liable whatsoever for any damages incurred as a result of its use. In particular, information presented in the Atlas is only for research purpose, and shall not be used for diagnosis or treatment purposes. No responsibility is assumed for any injury and/or damage to persons or property for any use or operation of any methods products, instructions or ideas contained in the material herein. See also: "Uniform Requirements for Manuscripts Submitted to Biomedical Journals: Writing and Editing for Biomedical Publication - Updated October 2004": http://www.icmje.org.

http://AtlasGeneticsOncology.org

Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS