DOCSLIB.ORG

Integrated Cytogenetic and High-Resolution Array CGH Analysis of Genomic Alterations Associated with MYCN Amplification

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Integrated Cytogenetic and High-Resolution Array CGH Analysis of Genomic Alterations Associated with MYCN Amplification Original Article Cytogenet Genome Res 2011;134:27–39 Accepted: November 3, 2010 DOI: 10.1159/000324698 by M. Schmid Published online: April 18, 2011 Integrated Cytogenetic and High-Resolution Array CGH Analysis of Genomic Alterations Associated with MYCN Amplification a b c c b d A. Pandita J. Bayani J. Paderova P. Marrano C. Graham M. Barrett e f g M. Prasad M. Zielenska J.A. Squire a b Department of Oncology Diagnostics, Genentech, South San Francisco, Calif. , USA; Department of c Laboratory Medicine and Pathobiology, University of Toronto, and Department of Applied Molecular Oncology, d Ontario Cancer Institute, Toronto, Ont. , Canada; Pharmaceutical Genomics Division, Translational Genomics e Research Institute, Scottsdale, Ariz. , Agilent Technologies Inc. Headquarters, Santa Clara, Calif. , USA; f Department of Pathology and Laboratory Medicine, The Hospital for Sick Children, Toronto, Ont. , and g Department of Pathology and Molecular Medicine, Queen’s University and Kingston General Hospital, Kingston, Ont. , Canada Key Words plicon is quite intriguing. MYCN is usually centrally located in aCGH ؒ FISH ؒ mBAND ؒ MYCN ؒ Neuroblastoma ؒ the amplicon; however, the structure and complexity of the Retinoblastoma amplicons were highly variable. It is noteworthy that clusters of unstable repetitive regions characterized by CNV se- quences were present throughout the regions encompassed Abstract by MYCN gene amplification, and these sequences could Amplification of oncogenes and closely linked flanking provide a mechanism to destabilize this region of the ge- genes is common in some types of cancer and can be asso- nome. Complex structural rearrangements involving ge- ciated with complex chromosome rearrangements and/or nomic losses and gains in the 2p24 region lead to MYCN am- co-amplification of non-syntenic chromosomal regions. To plification and that these rearrangements can trigger ampli- better understand the etiology and structural complexity of fication events. Copyright © 2011 S. Karger AG, Basel focal MYCN amplicons in human neuronal cancer, we inves- tigated the precise chromosomal locations of high copy number genomic regions in MYCN amplified cell lines. An integrated cytogenetic map of the MYCN amplicon was cre- Gene amplification is a major mechanism of oncogene ated using high-resolution array CGH, spectral karyotyping activation, which in many cases directly contributes to (SKY), multi-color banding (mBAND), and fluorescence in situ the capacity of cancer cells to grow autonomously [Al- hybridization (FISH) in 4 human neuronal tumor cell lines. bertson et al., 2003]. High copy number MYCN amplifi- The evidence of complex intra- and inter-chromosomal cation has been observed in neuroblastomas [Brodeur et events, providing clues concerning the nature of the genom- al., 1984; Schwab and Amler, 1990] and retinoblastomas ic mechanisms that contributed to the process of MYCN am- plification, was observed. The presence of multiple co-am- plified syntenic or non-syntenic sequences in the MYCN am- A. Pandita and J. Bayani contributed equally to this work. © 2011 S. Karger AG, Basel Jeremy A. Squire, PhD 1424–8581/11/1341–0027$38.00/0 Richardson Laboratories, Room 201e Fax +41 61 306 12 34 88 Stuart St, Queen’s University E-Mail [email protected] Accessible online at: Kingston, ON K7L 3N6 (Canada) www.karger.com www.karger.com/cgr Tel. +1 613 533 2345, E-Mail squirej @ queensu.ca [Squire et al., 1986] and is associated with poor prognosis copy number genomic regions in 4 human neuronal tu- of neuroblastomas. In primary neuronal tumors, MYCN mor cell lines (Y79, GOTO, LAN5 and IMR32). High copy amplicons often exist as autonomously replicating extra- number focal amplification of multiple chromosome re- chromosomal elements called double minutes (dmins) gions were observed in Y79, GOTO and IMR32 cell lines. [Moreau et al., 2006], while in neuronal cell lines, MYCN These amplifications were associated with structural re- amplicons are usually integrated into the chromosome arrangements proximal to MYCN and deletions within and appear as homogeneously staining regions (hsrs) and distal to 2p24. LAN5 carried one dmin population [Kitajima et al., 2001; Shimizu et al., 2001]. It has been with focal amplification centered at MYCN and a second proposed that MYCN -containing hsrs may arise during dmin population with a focal amplicon from 6p12. Inter- in vitro cell growth by a process involving the reintegra- estingly, in all 4 cell lines, unstable repetitive regions char- tion of dmins at a site that underwent amplification by acterized by copy-number variation (CNV sequences) oc- unequal sister-chromatid exchange [Narayanan et al., curred in close proximity to the copy-number transition 2006]; such chromosomal breaks and/or excision of ge- zones of high copy number amplicons. These data suggest nomic sequences play roles in amplicon formation in can- that complex structural rearrangements involving ge- cer cells. Neither the complexity of MYCN amplicons nor nomic losses and gains in the 2p24 region lead to MYCN the mechanisms by which they form in primary tumors amplification in neuronal cancer cells, and that these re- and tumor-derived cell lines are well characterized. arrangements can be accompanied by intra- or inter- M o s t MYCN amplicons contain 50–100 tandem re- chromosomal alterations which facilitate high copy num- peats of a unit that is 100 kb to 1 MB in size [Akiyama et ber focal amplifications of MYCN . al., 1993; Noguchi et al., 1996]. MYCN maps to the central core of amplicons and co-amplified genomic regions vary considerably in size and complexity [Kohl et al., 1983; Materials and Methods Schwab et al., 1983, 1984; Pandita et al., 1997]. Studies have shown that despite the high levels of complexity be- Cell Lines The neuroblastoma cell lines LAN5, GOTO, IMR32, and reti- tween different cell lines, the high-expression level of noblastoma cell line Y79 were maintained as previously described MYCN is considered to be driven by DNA copy-number by Pandita et al. [1997] and processed for cytogenetic harvest increases, with the most amplified cell lines expressing [Bayani and Squire, 2004c]. DNA was extracted by standard the highest levels of the gene [reviewed in Schwab, 2000]. methods [Bayani and Squire, 2004b]. Normal human lympho- Array comparative genomic hybridization (aCGH) has cytes were also prepared for cytogenetic harvest. recently been used to precisely characterize the structure Array Comparative Genomic Hybridization and location of high copy number focal MYCN amplicons DNAs were extracted from each cell line using standard ex- in cancer cells [Mosse et al., 2007; Caren et al., 2008; Fix traction methods. aCGH was performed using the Agilent 44K et al., 2008]. These studies revealed single continuous fo- and 244K platform (Agilent Technologies, Santa Clara, Calif., USA), according to the manufacturer’s instructions and as de- cal amplicons centered on the gene at 2p24, with or with- scribed by Prasad et al [2008]. Slides were dried and further out multiple discrete co-amplifications in 2p and/or ad- scanned using an Agilent 2565AA DNA microarray scanner. Mi- ditional non-syntenic chromosome regions [Mosse et al., croarray images were analyzed using Agilent Feature Extraction 2007; Caren et al., 2008; Fix et al., 2008]. However, these software version 8.1. Default settings for CGH arrays were used aCGH studies did not provide sufficient data to deter- according to the supplier’s recommendations. CGH Analytics software version 3.4 (Agilent Technologies) was used for analysis. mine the cytogenetic relationships between genomic se- The data quality of each microarray was assessed using the Qual- quences co-amplified with MYCN or to deduce putative ity Metrics report generated by the Agilent CGH analytics soft- mechanisms by which these amplicons formed. ware (v.3.4). This report provides acceptable ranges for quality- The goal of this study was to apply aCGH and advanced control parameters from each microarray experiment, based on molecular cytogenetic methods to better understand the analysis of numerous well-characterized cell lines. All CGH data represent the average of dye-flip experiments for each of the sam- etiology and structural complexity of focal MYCN ampli- ples, using the aberration detection method 1 (ADM-1), which is cons in human neuronal cancer. Because each molecular based on computing significance ratios for all genomic intervals cytogenetic technique possesses its own set of limitations [Lipson et al., 2006]. To make aberration calls, a robust estimate [Bayani and Squire, 2007], aCGH, spectral karyotyping of the noise was obtained by calculating the spread of the ratio differences between consecutive probes (DLRSpread) along all (SKY), multi-color banding (mBAND) and fluorescence chromosomes. The ability of the DLRSpread to measure the noise in situ hybridization (FISH) analyses were used to better of the ratios independently of the number and severity of aberra- determine the precise chromosomal locations of all high tions was used to assess the overall quality of each experiment. 28 Cytogenet Genome Res 2011;134:27–39 Pandita et al. The ADM-1 algorithm searches for chromosomal intervals of any R e s u l t s length for which the mean interval ratio is significantly different from zero. An interval has a ratio significantly different from zero if it is more than the threshold standard deviations. For this study, The following experiments were designed to identify the threshold was optimized to a value of 10 to reduce inherent and fine-map MYCN amplicons and all associated high sample noise, without negating true consistent imbalances along copy-number variations in Y79, GOTO, IMR32, and each chromosome. Further details concerning these principles LAN5. For this purpose, SKY, mBAND, aCGH, and FISH are available at the Agilent website (www.agilent.com/chem/ analyses were conducted for each cell line (see Materials goCGH). Aberrations were assigned as either gain (ratio 6 0.5), loss ( ^ –1.0) or amplification (6 2.0). Copy number variation and Methods and legends to figures for detailed experi- (CNV) loci were identified using the Agilent supplied annotated mental procedures).
Load more

Recommended publications
  • Role of RUNX1 in Aberrant Retinal Angiogenesis Jonathan D
    Page 1 of 25 Diabetes Identification of RUNX1 as a mediator of aberrant retinal angiogenesis Short Title: Role of RUNX1 in aberrant retinal angiogenesis Jonathan D. Lam,†1 Daniel J. Oh,†1 Lindsay L. Wong,1 Dhanesh Amarnani,1 Cindy Park- Windhol,1 Angie V. Sanchez,1 Jonathan Cardona-Velez,1,2 Declan McGuone,3 Anat O. Stemmer- Rachamimov,3 Dean Eliott,4 Diane R. Bielenberg,5 Tave van Zyl,4 Lishuang Shen,1 Xiaowu Gai,6 Patricia A. D’Amore*,1,7 Leo A. Kim*,1,4 Joseph F. Arboleda-Velasquez*1 Author affiliations: 1Schepens Eye Research Institute/Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, 20 Staniford St., Boston, MA 02114 2Universidad Pontificia Bolivariana, Medellin, Colombia, #68- a, Cq. 1 #68305, Medellín, Antioquia, Colombia 3C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital, 55 Fruit St., Boston, MA 02114 4Retina Service, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles St., Boston, MA 02114 5Vascular Biology Program, Boston Children’s Hospital, Department of Surgery, Harvard Medical School, 300 Longwood Ave., Boston, MA 02115 6Center for Personalized Medicine, Children’s Hospital Los Angeles, Los Angeles, 4650 Sunset Blvd, Los Angeles, CA 90027, USA 7Department of Pathology, Harvard Medical School, 25 Shattuck St., Boston, MA 02115 Corresponding authors: Joseph F. Arboleda-Velasquez: [email protected] Ph: (617) 912-2517 Leo Kim: [email protected] Ph: (617) 912-2562 Patricia D’Amore: [email protected] Ph: (617) 912-2559 Fax: (617) 912-0128 20 Staniford St. Boston MA, 02114 † These authors contributed equally to this manuscript Word Count: 1905 Tables and Figures: 4 Diabetes Publish Ahead of Print, published online April 11, 2017 Diabetes Page 2 of 25 Abstract Proliferative diabetic retinopathy (PDR) is a common cause of blindness in the developed world’s working adult population, and affects those with type 1 and type 2 diabetes mellitus.
    [Show full text]
  • Analysis of the Indacaterol-Regulated Transcriptome in Human Airway
    Supplemental material to this article can be found at: http://jpet.aspetjournals.org/content/suppl/2018/04/13/jpet.118.249292.DC1 1521-0103/366/1/220–236$35.00 https://doi.org/10.1124/jpet.118.249292 THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS J Pharmacol Exp Ther 366:220–236, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Analysis of the Indacaterol-Regulated Transcriptome in Human Airway Epithelial Cells Implicates Gene Expression Changes in the s Adverse and Therapeutic Effects of b2-Adrenoceptor Agonists Dong Yan, Omar Hamed, Taruna Joshi,1 Mahmoud M. Mostafa, Kyla C. Jamieson, Radhika Joshi, Robert Newton, and Mark A. Giembycz Departments of Physiology and Pharmacology (D.Y., O.H., T.J., K.C.J., R.J., M.A.G.) and Cell Biology and Anatomy (M.M.M., R.N.), Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada Received March 22, 2018; accepted April 11, 2018 Downloaded from ABSTRACT The contribution of gene expression changes to the adverse and activity, and positive regulation of neutrophil chemotaxis. The therapeutic effects of b2-adrenoceptor agonists in asthma was general enriched GO term extracellular space was also associ- investigated using human airway epithelial cells as a therapeu- ated with indacaterol-induced genes, and many of those, in- tically relevant target. Operational model-fitting established that cluding CRISPLD2, DMBT1, GAS1, and SOCS3, have putative jpet.aspetjournals.org the long-acting b2-adrenoceptor agonists (LABA) indacaterol, anti-inflammatory, antibacterial, and/or antiviral activity. Numer- salmeterol, formoterol, and picumeterol were full agonists on ous indacaterol-regulated genes were also induced or repressed BEAS-2B cells transfected with a cAMP-response element in BEAS-2B cells and human primary bronchial epithelial cells by reporter but differed in efficacy (indacaterol $ formoterol .
    [Show full text]
  • New Basal Cell Carcinoma Susceptibility Loci
    ARTICLE Received 5 Nov 2014 | Accepted 3 Mar 2015 | Published 9 Apr 2015 DOI: 10.1038/ncomms7825 OPEN New basal cell carcinoma susceptibility loci Simon N. Stacey1, Hannes Helgason1, Sigurjon A. Gudjonsson1, Gudmar Thorleifsson1, Florian Zink1, Asgeir Sigurdsson1, Birte Kehr1, Julius Gudmundsson1, Patrick Sulem1, Bardur Sigurgeirsson2,3, Kristrun R. Benediktsdottir2,3, Kristin Thorisdottir2,3, Rafn Ragnarsson2,3, Victoria Fuentelsaz4, Cristina Corredera5, Yolanda Gilaberte6, Matilde Grasa7, Dolores Planelles8, Onofre Sanmartin9,10, Peter Rudnai11, Eugene Gurzau12, Kvetoslava Koppova13, Bjørn A. Nexø14, Anne Tjønneland15, Kim Overvad16, Jon G. Jonasson2,3,17, Laufey Tryggvadottir3,17, Hrefna Johannsdottir1, Anna M. Kristinsdottir1, Hreinn Stefansson1, Gisli Masson1, Olafur T. Magnusson1, Bjarni V. Halldorsson1,18, Augustine Kong1, Thorunn Rafnar1, Unnur Thorsteinsdottir1,3, Ulla Vogel19, Rajiv Kumar20, Eduardo Nagore9,10, Jose´ I. Mayordomo21, Daniel F. Gudbjartsson1, Jon H. Olafsson2,3 & Kari Stefansson1,3 In an ongoing screen for DNA sequence variants that confer risk of cutaneous basal cell carcinoma (BCC), we conduct a genome-wide association study (GWAS) of 24,988,228 SNPs and small indels detected through whole-genome sequencing of 2,636 Icelanders and imputed into 4,572 BCC patients and 266,358 controls. Here we show the discovery of four new BCC susceptibility loci: 2p24 MYCN (rs57244888[C], OR ¼ 0.76, P ¼ 4.7 Â 10 À 12), 2q33 CASP8-ALS2CR12 (rs13014235[C], OR ¼ 1.15, P ¼ 1.5 Â 10 À 9), 8q21 ZFHX4 (rs28727938[G], OR ¼ 0.70, P ¼ 3.5 Â 10 À 12) and 10p14 GATA3 (rs73635312[A], OR ¼ 0.74, P ¼ 2.4 Â 10 À 16). Fine mapping reveals that two variants correlated with rs73635312[A] occur in conserved binding sites for the GATA3 transcription factor.
    [Show full text]
  • Mouse Fam49a Conditional Knockout Project (CRISPR/Cas9)
    https://www.alphaknockout.com Mouse Fam49a Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Fam49a conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Fam49a gene (NCBI Reference Sequence: NM_029758 ; Ensembl: ENSMUSG00000020589 ) is located on Mouse chromosome 12. 13 exons are identified, with the ATG start codon in exon 4 and the TAG stop codon in exon 13 (Transcript: ENSMUST00000069066). Exon 5 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Fam49a gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-184A24 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 5 starts from about 7.33% of the coding region. The knockout of Exon 5 will result in frameshift of the gene. The size of intron 4 for 5'-loxP site insertion: 17286 bp, and the size of intron 5 for 3'-loxP site insertion: 1046 bp. The size of effective cKO region: ~622 bp. The cKO region does not have any other known gene. Page 1 of 7 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele gRNA region 5' gRNA region 3' 1 5 6 13 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Fam49a Homology arm cKO region loxP site Page 2 of 7 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats.
    [Show full text]
  • Dnp63a Represses Anti-Proliferative Genes Via H2A.Z Deposition
    Downloaded from genesdev.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press DNp63a represses anti-proliferative genes via H2A.Z deposition Corrie L. Gallant-Behm,1,2 Matthew R. Ramsey,3 Claire L. Bensard,1,2 Ignacio Nojek,1,2 Jack Tran,1,2 Minghua Liu,1,2 Leif W. Ellisen,3 and Joaquı´n M. Espinosa1,2,4 1Howard Hughes Medical Institute, 2Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA; 3Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts 02114, USA DNp63a is a member of the p53 family of transcription factors that functions as an oncogene in squamous cell carcinomas (SCCs). Because DNp63a and p53 bind virtually identical DNA sequence motifs, it has been proposed that DNp63a functions as a dominant-negative inhibitor of p53 to promote proliferation and block apoptosis. However, most SCCs concurrently overexpress DNp63a and inactivate p53, suggesting the autonomous action of these oncogenic events. Here we report the discovery of a novel mechanism of transcriptional repression by DNp63a that reconciles these observations. We found that although both proteins bind the same genomic sites, they regulate largely nonoverlapping gene sets. Upon activation, p53 binds all enhancers regardless of DNp63a status but fails to transactivate genes repressed by DNp63a. We found that DNp63a associates with the SRCAP chromatin regulatory complex involved in H2A/H2A.Z exchange and mediates H2A.Z deposition at its target loci. Interestingly, knockdown of SRCAP subunits or H2A.Z leads to specific induction of DNp63a-repressed genes. We identified SAMD9L as a key anti-proliferative gene repressed by DNp63a and H2A.Z whose depletion suffices to reverse the arrest phenotype caused by DNp63a knockdown.
    [Show full text]
  • Gene Amplification As Double Minutes Or Homogeneously Staining Regions in Solid Tumors: Origin and Structure
    Downloaded from genome.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press Research Gene amplification as double minutes or homogeneously staining regions in solid tumors: Origin and structure Clelia Tiziana Storlazzi,1 Angelo Lonoce,1 Maria C. Guastadisegni,1 Domenico Trombetta,1 Pietro D’Addabbo,1 Giulia Daniele,1 Alberto L’Abbate,1 Gemma Macchia,1 Cecilia Surace,1,7 Klaas Kok,2 Reinhard Ullmann,3 Stefania Purgato,4 Orazio Palumbo,5 Massimo Carella,5 Peter F. Ambros,6 and Mariano Rocchi1,8 1Department of Genetics and Microbiology, University of Bari, Bari 70126, Italy; 2Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen 9700 RR, The Netherlands; 3Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany; 4Department of Biology, University of Bologna, Bologna 40126, Italy; 5Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo (FG) 71013, Italy; 6Children’s Cancer Research Institute (CCRI), St. Anna Kinderkrebsforschung, Vienna A-1090, Austria Double minutes (dmin) and homogeneously staining regions (hsr) are the cytogenetic hallmarks of genomic amplification in cancer. Different mechanisms have been proposed to explain their genesis. Recently, our group showed that the MYC-containing dmin in leukemia cases arise by excision and amplification (episome model). In the present paper we investigated 10 cell lines from solid tumors showing MYCN amplification as dmin or hsr. Particularly revealing results were provided by the two subclones of the neuroblastoma cell line STA-NB-10, one showing dmin-only and the second hsr-only amplification. Both subclones showed a deletion, at 2p24.3, whose extension matched the amplicon extension.
    [Show full text]
  • Skeletal Muscle Transcriptome in Healthy Aging
    ARTICLE https://doi.org/10.1038/s41467-021-22168-2 OPEN Skeletal muscle transcriptome in healthy aging Robert A. Tumasian III 1, Abhinav Harish1, Gautam Kundu1, Jen-Hao Yang1, Ceereena Ubaida-Mohien1, Marta Gonzalez-Freire1, Mary Kaileh1, Linda M. Zukley1, Chee W. Chia1, Alexey Lyashkov1, William H. Wood III1, ✉ Yulan Piao1, Christopher Coletta1, Jun Ding1, Myriam Gorospe1, Ranjan Sen1, Supriyo De1 & Luigi Ferrucci 1 Age-associated changes in gene expression in skeletal muscle of healthy individuals reflect accumulation of damage and compensatory adaptations to preserve tissue integrity. To characterize these changes, RNA was extracted and sequenced from muscle biopsies col- 1234567890():,; lected from 53 healthy individuals (22–83 years old) of the GESTALT study of the National Institute on Aging–NIH. Expression levels of 57,205 protein-coding and non-coding RNAs were studied as a function of aging by linear and negative binomial regression models. From both models, 1134 RNAs changed significantly with age. The most differentially abundant mRNAs encoded proteins implicated in several age-related processes, including cellular senescence, insulin signaling, and myogenesis. Specific mRNA isoforms that changed sig- nificantly with age in skeletal muscle were enriched for proteins involved in oxidative phosphorylation and adipogenesis. Our study establishes a detailed framework of the global transcriptome and mRNA isoforms that govern muscle damage and homeostasis with age. ✉ 1 National Institute on Aging–Intramural Research Program, National
    [Show full text]
  • WO 2016/130600 A2 18 August 2016 (18.08.2016) P O P C T
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2016/130600 A2 18 August 2016 (18.08.2016) P O P C T (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, C12Q 1/68 (2006.0 1) C12N 9/22 (2006.0 1) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (21) International Application Number: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, PCT/US20 16/0 17221 KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, (22) International Filing Date: MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, ' February 2016 (09.02.2016) PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, (25) Filing Language: English TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (26) Publication Language: English (84) Designated States (unless otherwise indicated, for every (30) Priority Data: kind of regional protection available): ARIPO (BW, GH, 62/1 13,569 February 2015 (09.02.2015) US GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, (71) Applicant: DUKE UNIVERSITY [US/US]; 2812 Erwin TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, Road, Suite 306, Durham, NC 27705 (US).
    [Show full text]
  • CYRI1-Mediated Inhibition of RAC1 Signalling Restricts Salmonella
    bioRxiv preprint doi: https://doi.org/10.1101/238733; this version posted December 22, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. CYRI1-mediated inhibition of RAC1 signalling restricts Salmonella Typhimurium infection Kyoko E Yuki1,2,†, Hadir Marei3,†, Evgenij Fiskin3,†, Megan M Eva1,2,†, Angelica A Gopal2,4, Jeremy A Schwartzentruber1, Jacek Majewski1, Mathieu Cellier5, Judith N Mandl2,4, Silvia M Vidal1,2, Danielle Malo1,2,6,* and Ivan Dikic3,7,* 1 Department of Human Genetics, McGill University, Montreal, QC Canada H3G 0B1. 2 McGill University Research Centre on Complex Traits, Montreal, QC Canada H3G 0B1. 3 Institute of Biochemistry II, Goethe University Faculty of Medicine, Theodor-Stern- Kai 7, 60590 Frankfurt am Main, Germany. 4 Department of Physiology, McGill University, Montreal, QC Canada H3G 0B1. 5 Centre INRS-Institut Armand-Frappier, Laval, QC, Canada H7V 1B7. 6 Department of Medicine, McGill University, Montreal, QC Canada H3G 0B1. 7 Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany. † These authors contributed equally to this work. * These authors jointly supervised this work. Correspondence should be addressed to: [email protected] or [email protected] Keywords: FAM49B, CYRI1, Salmonella, RAC1 GTPase, cytoskeletal modulation, actin polymerisation, WRC. 1 bioRxiv preprint doi: https://doi.org/10.1101/238733; this version posted December 22, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved.
    [Show full text]
  • Early Vertebrate Whole Genome Duplications Were Predated by a Period of Intense Genome Rearrangement
    Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement Andrew L. Hufton1, Detlef Groth1,2, Martin Vingron1, Hans Lehrach1, Albert J. Poustka1, Georgia Panopoulou1* 1. Max Planck for Molecular Genetics, Ihnestr. 73, 12169 Berlin, Germany. 2. Potsdam University, Bioinformatics Group, c/o Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany * Corresponding author: Max-Planck Institut für Molekulare Genetik, Ihnestrasse 73, D- 14195 Berlin Germany. email: [email protected], Tel: +49-30-84131235, Fax: +49- 30-84131128 Running title: Early vertebrate genome duplications and rearrangements Keywords: synteny, amphioxus, genome duplications, rearrangement rate, genome instability Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Hufton et al. Abstract Researchers, supported by data from polyploid plants, have suggested that whole genome duplication (WGD) may induce genomic instability and rearrangement, an idea which could have important implications for vertebrate evolution. Benefiting from the newly released amphioxus genome sequence (Branchiostoma floridae), an invertebrate which researchers have hoped is representative of the ancestral chordate genome, we have used gene proximity conservation to estimate rates of genome rearrangement throughout vertebrates and some of their invertebrate ancestors. We find that, while amphioxus remains the best single source of invertebrate information about the early chordate genome, its genome structure is not particularly well conserved and it cannot be considered a fossilization of the vertebrate pre- duplication genome. In agreement with previous reports, we identify two WGD events in early vertebrates and another in teleost fish.
    [Show full text]
  • The Glomerular Transcriptome and a Predicted Protein–Protein Interaction Network
    BASIC RESEARCH www.jasn.org The Glomerular Transcriptome and a Predicted Protein–Protein Interaction Network Liqun He,* Ying Sun,* Minoru Takemoto,* Jenny Norlin,* Karl Tryggvason,* Tore Samuelsson,† and Christer Betsholtz*‡ *Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, and ‡Department of Medicine, Karolinska Institutet, Stockholm, and †Department of Medical Biochemistry, Go¨teborg University, Go¨teborg, Sweden ABSTRACT To increase our understanding of the molecular composition of the kidney glomerulus, we performed a meta-analysis of available glomerular transcriptional profiles made from mouse and man using five different methodologies. We generated a combined catalogue of glomerulus-enriched genes that emerged from these different sources and then used this to construct a predicted protein–protein interaction network in the glomerulus (GlomNet). The combined glomerulus-enriched gene catalogue provides the most comprehensive picture of the molecular composition of the glomerulus currently available, and GlomNet contributes an integrative systems biology approach to the understanding of glomerular signaling networks that operate during development, function, and disease. J Am Soc Nephrol 19: 260–268, 2008. doi: 10.1681/ASN.2007050588 Many kidney diseases and, importantly, approxi- nins have been shown to be mutated in Alport syn- mately two thirds of all cases of ESRD originate with drome and Pierson congenital nephrotic syndromes, glomerular disease. Most cases of glomerular disease respectively.11,12 Genetic studies in mice have further are caused by systemic disorders (e.g., diabetes, hyper- revealed genes and proteins of importance for glomer- tension, lupus, obesity) for which the molecular ulus development and function, such as podoca- pathogeneses of the glomerular complications are un- lyxin,13 CD2AP,14 NEPH1,15 FAT1,16 forkhead box known.
    [Show full text]
  • Structure-Function Relationships of Rna and Protein in Synaptic Plasticity
    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2017 Structure-Function Relationships Of Rna And Protein In Synaptic Plasticity Sarah Middleton University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, Biology Commons, and the Neuroscience and Neurobiology Commons Recommended Citation Middleton, Sarah, "Structure-Function Relationships Of Rna And Protein In Synaptic Plasticity" (2017). Publicly Accessible Penn Dissertations. 2474. https://repository.upenn.edu/edissertations/2474 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/2474 For more information, please contact [email protected]. Structure-Function Relationships Of Rna And Protein In Synaptic Plasticity Abstract Structure is widely acknowledged to be important for the function of ribonucleic acids (RNAs) and proteins. However, due to the relative accessibility of sequence information compared to structure information, most large genomics studies currently use only sequence-based annotation tools to analyze the function of expressed molecules. In this thesis, I introduce two novel computational methods for genome-scale structure-function analysis and demonstrate their application to identifying RNA and protein structures involved in synaptic plasticity and potentiation—important neuronal processes that are thought to form the basis of learning and memory. First, I describe a new method for de novo identification of RNA secondary structure motifs enriched in co-regulated transcripts. I show that this method can accurately identify secondary structure motifs that recur across three or more transcripts in the input set with an average recall of 0.80 and precision of 0.98. Second, I describe a tool for predicting protein structural fold from amino acid sequence, which achieves greater than 96% accuracy on benchmarks and can be used to predict protein function and identify new structural folds.
    [Show full text]