MITF: Master Regulator of Melanocyte Development and Melanoma Oncogene
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Molecular Cytogenetic Analysis for TFE3 Rearrangement In
Modern Pathology (2014) 27, 113–127 & 2014 USCAP, Inc. All rights reserved 0893-3952/14 $32.00 113 Molecular cytogenetic analysis for TFE3 rearrangement in Xp11.2 renal cell carcinoma and alveolar soft part sarcoma: validation and clinical experience with 75 cases Jennelle C Hodge, Kathryn E Pearce, Xiaoke Wang, Anne E Wiktor, Andre M Oliveira and Patricia T Greipp Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA Renal cell carcinoma with TFE3 rearrangement at Xp11.2 is a distinct subtype manifesting an indolent clinical course in children, with recent reports suggesting a more aggressive entity in adults. This subtype is morphologically heterogeneous and can be misclassified as clear cell or papillary renal cell carcinoma. TFE3 is also rearranged in alveolar soft part sarcoma. To aid in diagnosis, a break-apart strategy fluorescence in situ hybridization (FISH) probe set specific for TFE3 rearrangement and a reflex dual-color, single-fusion strategy probe set involving the most common TFE3 partner gene, ASPSCR1, were validated on formalin-fixed, paraffin- embedded tissues from nine alveolar soft part sarcoma, two suspected Xp11.2 renal cell carcinoma, and nine tumors in the differential diagnosis. The impact of tissue cut artifact was reduced through inclusion of a chromosome X centromere control probe. Analysis of the UOK-109 renal carcinoma cell line confirmed the break-apart TFE3 probe set can distinguish the subtle TFE3/NONO fusion-associated inversion of chromosome X. Subsequent extensive clinical experience was gained through analysis of 75 cases with an indication of Xp11.2 renal cell carcinoma (n ¼ 54), alveolar soft part sarcoma (n ¼ 13), perivascular epithelioid cell neoplasms (n ¼ 2), chordoma (n ¼ 1), or unspecified (n ¼ 5). -
Enhancer-Targeted Genome Editing Selectively Blocks Innate Resistance to Oncokinase Inhibition
Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Webster et al. Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition Dan E. Webster1, Brook Barajas1*, Rose T. Bussat1*, Karen J. Yan1, Poornima H. Neela1, Ross J. Flockhart1, Joanna Kovalski1, Ashley Zehnder1, and Paul A. Khavari1, ¶ 1The Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305 USA *These authors made equal and independent contributions. ¶ Correspondence to: P.A.K. at [email protected] Running title: Enhancer disruption blocks oncokinase resistance Keywords: Cancer Epigenomics, Enhancer, TALE nuclease, Chromosome conformation, BRAF, MITF Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press ABSTRACT Thousands of putative enhancers are characterized in the human genome, yet few have been shown to have a functional role in cancer progression. Inhibiting oncokinases, such as EGFR, ALK, ERBB2, and BRAF, is a mainstay of current cancer therapy but is hindered by innate drug resistance mediated by upregulation of the HGF receptor, MET. The mechanisms mediating such genomic responses to targeted therapy are unknown. Here, we identify lineage- specific enhancers at the MET locus for multiple common tumor types, including a melanoma lineage-specific enhancer 63kb downstream of the MET TSS. This enhancer displays inducible chromatin looping with the MET promoter to upregulate MET expression upon BRAF inhibition. Epigenomic analysis demonstrated that the melanocyte-specific transcription factor, MITF, mediates this enhancer function. Targeted genomic deletion (<7bp) of the MITF motif within the MET enhancer suppressed inducible chromatin looping and innate drug resistance, while maintaining MITF-dependent, inhibitor-induced melanoma cell differentiation. -
Gene Section Short Communication
Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL INIST-CNRS Gene Section Short Communication TYRP1 (tyrosinase-related protein 1) Kunal Ray, Mainak Sengupta, Sampurna Ghosh Academy of Scientific and Innovative Research (AcSIR), Campus at CSIR - Central Road Research Institute, Mathura Road, New Delhi - 110 025, [email protected] (KR); University of Calcutta, Department of Genetics, 35, Ballygunge Circular Road, Kolkata - 700 019, [email protected]); [email protected] (MS, SG) India. Published in Atlas Database: April 2016 Online updated version : http://AtlasGeneticsOncology.org/Genes/TYRP1ID46370ch9p23.html Printable original version : http://documents.irevues.inist.fr/bitstream/handle/2042/68125/04-2016-TYRP1ID46370ch9p23.pdf DOI: 10.4267/2042/68125 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2016 Atlas of Genetics and Cytogenetics in Oncology and Haematology Abstract Location: 9p23 TYRP1 gene, having a chromosomal location of 9p23, encodes a melanosomal enzyme belonging to DNA/RNA the tyrosinase family. TYRP1 catalyses oxidation of 5,6-dihydroxyindole-2-carboxylic acid (DHICA) Description into indole-5,6-quinone-2-carboxylic acid. TYRP1 In Chromosome 9, the 24,852 bases long gene starts is also thought to play a role in stabilizing tyrosinase from12,685,439 bp from pter and ends at 12,710,290 and modulates its catalytic activity, in maintenance bp from pter; Orientation: Plus strand. The gene of melanosome structure, affecting melanocyte contains 8 exons and spans ~24.8 kb of the genome. proliferation and melanocyte cell death. Defects in this gene cause oculocutaneous albinism type III; Transcription OCA III (also known as rufous oculocutaneous The gene encodes a 2876 bp mRNA. -
Dog Coat Colour Genetics: a Review Date Published Online: 31/08/2020; 1,2 1 1 3 Rashid Saif *, Ali Iftekhar , Fatima Asif , Mohammad Suliman Alghanem
www.als-journal.com/ ISSN 2310-5380/ August 2020 Review Article Advancements in Life Sciences – International Quarterly Journal of Biological Sciences ARTICLE INFO Open Access Date Received: 02/05/2020; Date Revised: 20/08/2020; Dog Coat Colour Genetics: A Review Date Published Online: 31/08/2020; 1,2 1 1 3 Rashid Saif *, Ali Iftekhar , Fatima Asif , Mohammad Suliman Alghanem Authors’ Affiliation: 1. Institute of Abstract Biotechnology, Gulab Devi Educational anis lupus familiaris is one of the most beloved pet species with hundreds of world-wide recognized Complex, Lahore - Pakistan breeds, which can be differentiated from each other by specific morphological, behavioral and adoptive 2. Decode Genomics, traits. Morphological characteristics of dog breeds get more attention which can be defined mostly by 323-D, Town II, coat color and its texture, and considered to be incredibly lucrative traits in this valued species. Although Punjab University C Employees Housing the genetic foundation of coat color has been well stated in the literature, but still very little is known about the Scheme, Lahore - growth pattern, hair length and curly coat trait genes. Skin pigmentation is determined by eumelanin and Pakistan 3. Department of pheomelanin switching phenomenon which is under the control of Melanocortin 1 Receptor and Agouti Signaling Biology, Tabuk Protein genes. Genetic variations in the genes involved in pigmentation pathway provide basic understanding of University - Kingdom melanocortin physiology and evolutionary adaptation of this trait. So in this review, we highlighted, gathered and of Saudi Arabia comprehend the genetic mutations, associated and likely to be associated variants in the genes involved in the coat color and texture trait along with their phenotypes. -
Renal Cell Carcinoma – Detection of PRCC-TFE3 and Alpha-TFEB Gene Fusions Using RT-PCR on Tissues (Odes 60153 and 60154) Notice of Assessment
Renal Cell Carcinoma – Detection of PRCC-TFE3 and Alpha-TFEB Gene Fusions Using RT-PCR on Tissues (odes 60153 and 60154) Notice of Assessment June 2013 DISCLAIMER: This document was originally drafted in French by the Institut national d'excellence en santé et en services sociaux (INESSS), and that version can be consulted at http://www.inesss.qc.ca/fileadmin/doc/INESSS/Analyse_biomedicale/Juin_2013/INESSS_Analyse_15.pdf http://www.inesss.qc.ca/fileadmin/doc/INESSS/Analyse_biomedicale/Juin_2013/INESSS_Analyse_16.pdf It was translated into English by the Canadian Agency for Drugs and Technologies in Health (CADTH) with INESSS’s permission. INESSS assumes no responsibility with regard to the quality or accuracy of the translation. While CADTH has taken care in the translation of the document to ensure it accurately represents the content of the original document, CADTH does not make any guarantee to that effect. CADTH is not responsible for any errors or omissions or injury, loss, or damage arising from or relating to the use (or misuse) of any information, statements, or conclusions contained in or implied by the information in this document, the original document, or in any of the source documentation. 1 GENERAL INFORMATION 1.1 Requestor: Centre hospitalier universitaire de Québec (CHUQ). 1.2 Application Submitted: August 1, 2012. 1.3 Notice Issued: April 12, 2013. Note: This notice is based on the scientific and commercial information (submitted by the requestor[s]) and on a complementary review of the literature according to the data available at the time that this test was assessed by INESSS. 2 TECHNOLOGY, COMPANY, AND LICENCE(S) 2.1 Name of the Technology Reverse transcription of messenger RNA and amplification (RT-PCR). -
GABPA Is a Master Regulator of Luminal Identity and Restrains Aggressive Diseases in Bladder Cancer
Cell Death & Differentiation (2020) 27:1862–1877 https://doi.org/10.1038/s41418-019-0466-7 ARTICLE GABPA is a master regulator of luminal identity and restrains aggressive diseases in bladder cancer 1,2,3 3,4 5 2,5 5 3 5 5 Yanxia Guo ● Xiaotian Yuan ● Kailin Li ● Mingkai Dai ● Lu Zhang ● Yujiao Wu ● Chao Sun ● Yuan Chen ● 5 6 3 1,2 1,2 3,7 Guanghui Cheng ● Cheng Liu ● Klas Strååt ● Feng Kong ● Shengtian Zhao ● Magnus Bjorkhölm ● Dawei Xu 3,7 Received: 3 June 2019 / Revised: 20 November 2019 / Accepted: 21 November 2019 / Published online: 4 December 2019 © The Author(s) 2019. This article is published with open access Abstract TERT promoter mutations occur in the majority of glioblastoma, bladder cancer (BC), and other malignancies while the ETS family transcription factors GABPA and its partner GABPB1 activate the mutant TERT promoter and telomerase in these tumors. GABPA depletion or the disruption of the GABPA/GABPB1 complex by knocking down GABPB1 was shown to inhibit telomerase, thereby eliminating the tumorigenic potential of glioblastoma cells. GABPA/B1 is thus suggested as a cancer therapeutic target. However, it is unclear about its role in BC. Here we unexpectedly observed that GABPA ablation 1234567890();,: 1234567890();,: inhibited TERT expression, but robustly increased proliferation, stem, and invasive phenotypes and cisplatin resistance in BC cells, while its overexpression exhibited opposite effects, and inhibited in vivo metastasizing in a xenograft transplant model. Mechanistically, GABPA directly activates the transcription of FoxA1 and GATA3, key transcription factors driving luminal differentiation of urothelial cells. Consistently, TCGA/GEO dataset analyses show that GABPA expression is correlated positively with luminal while negatively with basal signatures. -
22 Ultra-Conserved Elements in Vertebrate and Fly Genomes Mathias Drton Nicholas Eriksson Garmay Leung
22 Ultra-Conserved Elements in Vertebrate and Fly Genomes Mathias Drton Nicholas Eriksson Garmay Leung Ultra-conserved elements in an alignment of multiple genomes are consecutive nucleotides that are in perfect agreement across all the genomes. For aligned vertebrate and fly genomes, we give descriptive statistics of ultra-conserved elements, explain their biological relevance, and show that the existence of ultra-conserved elements is highly improbable in neutrally evolving regions. 22.1 The data Our analyses of ultra-conserved elements are based on multiple sequence align- ments produced by MAVID [Bray and Pachter, 2004]. Prior to the alignment of multiple genomes, homology mappings (from Mercator [Dewey, 2005]) group into bins genomic regions that are anchored together by neighboring homolo- gous exons. A multiple sequence alignment is then produced for each of these alignment bins. MAVID is a global multiple alignment program, and therefore homologous regions with more than one homologous hit to another genome may not be found aligned together. Table 22.1 shows an example of Merca- tor’s output for a single region along with the beginning of the resulting MAVID multiple sequence alignment. Species Chrom. Start End Alignment Dog chrX 752057 864487 + A----AACCAAA--------- Chicken chr1 122119382 122708162 − TGCTGAGCTAAAGATCAGGCT Zebrafish chr9 19018916 19198136 + ------ATGCAACATGCTTCT Pufferfish chr2 7428614 7525502 + ---TAGATGGCAGACGATGCT Fugufish asm1287 21187 82482 + ---TCAAGGG----------- Table 22.1. Mercator output for a single bin, giving the position and orientation on the chromosome. Notice that the Fugu fish genome has not been fully assembled into chromosomes (cf. Section 4.2). The vertebrate dataset consists of 10,279 bins over 9 genomes (Table 22.2). -
A Novel Partner of TFE3 in the Xp11 Translocation Renal Cell Carcinoma: Clinicopathological Analyses and Detection of EWSR1-TFE3 Fusion
Virchows Archiv (2019) 474:389–393 https://doi.org/10.1007/s00428-018-2509-8 BRIEF REPORT A novel partner of TFE3 in the Xp11 translocation renal cell carcinoma: clinicopathological analyses and detection of EWSR1-TFE3 fusion Hironori Fukuda1 & Ikuma Kato2 & Mitsuko Furuya2 & Reiko Tanaka3 & Toshio Takagi1 & Tsunenori Kondo1,4 & Yoji Nagashima5 Received: 28 August 2018 /Revised: 13 November 2018 /Accepted: 10 December 2018 /Published online: 14 December 2018 # Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract The renal cell carcinomas associated with Xp11 translocations (Xp11 translocation RCCs) harbor gene fusions involving TFE3,a member of the microphthalmia-associated transcription factor (MiTF) family. In the present study, we identified a novel partner of TFE3, Ewing sarcoma breakpoint region 1 (EWSR1), in an Xp11 translocation RCC. A 57-year-old Japanese woman without special disease history was referred to us for treatment of an RCC. The resected tumor displayed an alveolar growth pattern with high-grade nuclei. The tumor was diffusely positive for TFE3 and cathepsin K. Anchored multiplex PCR revealed a novel fusion, EWSR1-TFE3. Fluorescent in situ hybridization analysis demonstrated the rearrangements of EWSR1 and TFE3. RT-PCR analysis confirmed the chimeric transcript. No neoplasm with EWSR1-TFE3 has been reported so far, in any organ. The results will expand the genomic spectrums of Xp11 translocation RCCs and contribute to better understanding of the roles of the MiTF family in the oncogenic process. Keywords -
Endolysosomal Cation Channels and MITF in Melanocytes and Melanoma
biomolecules Review Endolysosomal Cation Channels and MITF in Melanocytes and Melanoma Carla Abrahamian and Christian Grimm * Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-University, 80336 Munich, Germany; [email protected] * Correspondence: [email protected] Abstract: Microphthalmia-associated transcription factor (MITF) is the principal transcription fac- tor regulating pivotal processes in melanoma cell development, growth, survival, proliferation, differentiation and invasion. In recent years, convincing evidence has been provided attesting key roles of endolysosomal cation channels, specifically TPCs and TRPMLs, in cancer, including breast cancer, glioblastoma, bladder cancer, hepatocellular carcinoma and melanoma. In this review, we provide a gene expression profile of these channels in different types of cancers and decipher their roles, in particular the roles of two-pore channel 2 (TPC2) and TRPML1 in melanocytes and melanoma. We specifically discuss the signaling cascades regulating MITF and the relationship between endolysosomal cation channels, MAPK, canonical Wnt/GSK3 pathways and MITF. Keywords: TPC; two-pore; lysosome; TPC1; TPC2; TRPML; mucolipin; MCOLN; TRPML1; MITF; melanocytes; melanoma; mTOR; TFEB; calcium Citation: Abrahamian, C.; Grimm, C. 1. Introduction Endolysosomal Cation Channels and Melanocytes are neural-crest derived cells that produce melanin, the primary de- MITF in Melanocytes and Melanoma. terminant of skin color. Melanin is also found in hair, in the iris of the eye, and in the Biomolecules 2021, 11, 1021. https:// stria vascularis of the inner ear and, to a lesser degree, in a broad range of other tissues doi.org/10.3390/biom11071021 throughout the body [1]. There are two major types of melanin called eumelanin (dark, brown, black) and pheomelanin (yellow, red, light brown). -
Association of Gene Ontology Categories with Decay Rate for Hepg2 Experiments These Tables Show Details for All Gene Ontology Categories
Supplementary Table 1: Association of Gene Ontology Categories with Decay Rate for HepG2 Experiments These tables show details for all Gene Ontology categories. Inferences for manual classification scheme shown at the bottom. Those categories used in Figure 1A are highlighted in bold. Standard Deviations are shown in parentheses. P-values less than 1E-20 are indicated with a "0". Rate r (hour^-1) Half-life < 2hr. Decay % GO Number Category Name Probe Sets Group Non-Group Distribution p-value In-Group Non-Group Representation p-value GO:0006350 transcription 1523 0.221 (0.009) 0.127 (0.002) FASTER 0 13.1 (0.4) 4.5 (0.1) OVER 0 GO:0006351 transcription, DNA-dependent 1498 0.220 (0.009) 0.127 (0.002) FASTER 0 13.0 (0.4) 4.5 (0.1) OVER 0 GO:0006355 regulation of transcription, DNA-dependent 1163 0.230 (0.011) 0.128 (0.002) FASTER 5.00E-21 14.2 (0.5) 4.6 (0.1) OVER 0 GO:0006366 transcription from Pol II promoter 845 0.225 (0.012) 0.130 (0.002) FASTER 1.88E-14 13.0 (0.5) 4.8 (0.1) OVER 0 GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism3004 0.173 (0.006) 0.127 (0.002) FASTER 1.28E-12 8.4 (0.2) 4.5 (0.1) OVER 0 GO:0006357 regulation of transcription from Pol II promoter 487 0.231 (0.016) 0.132 (0.002) FASTER 6.05E-10 13.5 (0.6) 4.9 (0.1) OVER 0 GO:0008283 cell proliferation 625 0.189 (0.014) 0.132 (0.002) FASTER 1.95E-05 10.1 (0.6) 5.0 (0.1) OVER 1.50E-20 GO:0006513 monoubiquitination 36 0.305 (0.049) 0.134 (0.002) FASTER 2.69E-04 25.4 (4.4) 5.1 (0.1) OVER 2.04E-06 GO:0007050 cell cycle arrest 57 0.311 (0.054) 0.133 (0.002) -
Stem Cell Differentiation As a Many-Body Problem
Stem cell differentiation as a many-body problem Bin Zhanga,b and Peter G. Wolynesa,b,c,1 Departments of aChemistry and cPhysics and Astronomy, and bCenter for Theoretical Biological Physics, Rice University, Houston, TX 77005 Contributed by Peter G. Wolynes, May 9, 2014 (sent for review March 25, 2014) Stem cell differentiation has been viewed as coming from transitions transcription factors function as pioneers that can directly bind between attractors on an epigenetic landscape that governs the with the chromatin sites occupied by the nucleosome, slow dynamics of a regulatory network involving many genes. Rigorous DNA binding (14, 15) is still a good approximation to describe definition of such a landscape is made possible by the realization the effect of the progressive change of the chromatin structure that gene regulation is stochastic, owing to the small copy number of and histone modification induced by the pioneer factors on gene the transcription factors that regulate gene expression and because regulation (16). As a result, DNA binding must be treated on of the single-molecule nature of the gene itself. We develop an ap- equal footing together with protein synthesis and degradation proximation that allows the quantitative construction of the epige- to fully understand eukaryotic gene regulation (14–18). netic landscape for large realistic model networks. Applying this By increasing the dimensionality of the problem, investigating approach to the network for embryonic stem cell development ex- the effects arising from slow DNA-binding -
Cloning of an Alpha-TFEB Fusion in Renal Tumors Harboring the T(6;11)(P21;Q13) Chromosome Translocation
Cloning of an Alpha-TFEB fusion in renal tumors harboring the t(6;11)(p21;q13) chromosome translocation Ian J. Davis*†, Bae-Li Hsi‡, Jason D. Arroyo*, Sara O. Vargas§, Y. Albert Yeh§, Gabriela Motyckova*, Patricia Valencia*, Antonio R. Perez-Atayde§, Pedram Argani¶, Marc Ladanyiʈ, Jonathan A. Fletcher*‡, and David E. Fisher*†** *Department of Pediatric Oncology, Dana–Farber Cancer Institute, Boston, MA 02115; Departments of †Medicine and §Pathology, Children’s Hospital Boston, Boston, MA 02115; ‡Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115; ʈDepartment of Pathology, Memorial Sloan–Kettering Cancer Center, New York, NY 10021; and ¶Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD 21287 Communicated by Phillip A. Sharp, Massachusetts Institute of Technology, Cambridge, MA, March 12, 2003 (received for review January 28, 2003) MITF, TFE3, TFEB, and TFEC comprise a transcription factor family Among members of the MiT family, TFE3 has previously been (MiT) that regulates key developmental pathways in several cell implicated in cancer-associated translocations. TFE3 transloca- lineages. Like MYC, MiT members are basic helix-loop-helix-leucine tions occur in distinctive renal carcinomas of childhood and zipper transcription factors. MiT members share virtually perfect young adults and in alveolar soft part sarcoma. In these trans- homology in their DNA binding domains and bind a common DNA locations, the DNA binding domain of TFE3 is fused to various motif. Translocations of TFE3 occur in specific subsets of human N-terminal partners, including PRCC, NonO (p54nrb), PSF, or renal cell carcinomas and in alveolar soft part sarcomas. Although ASPL (15–20). Although the mechanism through which these multiple translocation partners are fused to TFE3, each transloca- fusions contribute to oncogenesis remains unclear, several stud- tion product retains TFE3’s basic helix–loop–helix leucine zipper.