151
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Witkowski L, Lalonde E, Zhang J, Albrecht S, Hamel N, Cavallone L, May ST, Nicholson JC, Coleman N, Murray MJ, Tauber PF, Huntsman DG, Schönberger S, Yandell D, Hasselblatt M, Tischkowitz MD, Majewski J, Foulkes WD. Familial rhabdoid tumour 'avant la lettre
'-from pathology review to exome sequencing and back again. J Pathol 2013; 231:35-43. [DOI: 10.1002/path.4225] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 06/06/2013] [Accepted: 06/10/2013] [Indexed: 01/08/2023]
Affiliation(s)
- Leora Witkowski
- Program in Cancer Genetics, Department of Oncology and Human Genetics; McGill University, Montreal; Quebec Canada
- Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital; McGill University, Montreal; Quebec Canada
- Department of Human Genetics; McGill University, Montreal; Quebec Canada
| | - Emilie Lalonde
- Department of Human Genetics; McGill University, Montreal; Quebec Canada
- McGill University and Genome Quebec Innovation Center, Montreal; Quebec Canada
| | - Jian Zhang
- Department of Human Genetics; McGill University, Montreal; Quebec Canada
- McGill University and Genome Quebec Innovation Center, Montreal; Quebec Canada
| | - Steffen Albrecht
- Department of Pathology, Montreal Children's Hospital; McGill University Health Centre, Montreal; Quebec Canada
| | - Nancy Hamel
- Program in Cancer Genetics, Department of Oncology and Human Genetics; McGill University, Montreal; Quebec Canada
- Research Institute; McGill University Health Centre, Montreal; Quebec Canada
| | - Luca Cavallone
- Program in Cancer Genetics, Department of Oncology and Human Genetics; McGill University, Montreal; Quebec Canada
- Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital; McGill University, Montreal; Quebec Canada
| | - Sandra Thompson May
- Vermont Cancer Center; University of Vermont College of Medicine; Burlington VT USA
| | - James C Nicholson
- Department of Paediatric Oncology and Haematology; Cambridge University Hospitals NHS Foundation Trust; Cambridge UK
| | | | - Matthew J Murray
- Department of Paediatric Oncology and Haematology; Cambridge University Hospitals NHS Foundation Trust; Cambridge UK
- Department of Pathology; University of Cambridge; UK
| | - Peter F Tauber
- Department of Obstetrics and Gynecology; St. Mary's Hospital; Siegen Germany
| | - David G Huntsman
- British Columbia Cancer Research Center; British Columbia Cancer Agency, Vancouver; BC Canada
- Genetic Pathology Evaluation Center of the Departments of Pathology of Vancouver General Hospital; the Center for Translational and Applied Genomics, and Pathology and Laboratory Medicine; Vancouver BC Canada
| | - Stefan Schönberger
- Department of Paediatric Haematology and Oncology; University Children's Hospital; University of Bonn Germany
| | - David Yandell
- Vermont Cancer Center; University of Vermont College of Medicine; Burlington VT USA
| | | | | | - Jacek Majewski
- Department of Human Genetics; McGill University, Montreal; Quebec Canada
- McGill University and Genome Quebec Innovation Center, Montreal; Quebec Canada
| | - William D Foulkes
- Program in Cancer Genetics, Department of Oncology and Human Genetics; McGill University, Montreal; Quebec Canada
- Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital; McGill University, Montreal; Quebec Canada
- Department of Human Genetics; McGill University, Montreal; Quebec Canada
- Research Institute; McGill University Health Centre, Montreal; Quebec Canada
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152
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Kouskoumvekaki I, Shublaq N, Brunak S. Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics. Brief Bioinform 2013; 15:942-52. [PMID: 23908249 DOI: 10.1093/bib/bbt055] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
As both the amount of generated biological data and the processing compute power increase, computational experimentation is no longer the exclusivity of bioinformaticians, but it is moving across all biomedical domains. For bioinformatics to realize its translational potential, domain experts need access to user-friendly solutions to navigate, integrate and extract information out of biological databases, as well as to combine tools and data resources in bioinformatics workflows. In this review, we present services that assist biomedical scientists in incorporating bioinformatics tools into their research. We review recent applications of Cytoscape, BioGPS and DAVID for data visualization, integration and functional enrichment. Moreover, we illustrate the use of Taverna, Kepler, GenePattern, and Galaxy as open-access workbenches for bioinformatics workflows. Finally, we mention services that facilitate the integration of biomedical ontologies and bioinformatics tools in computational workflows.
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153
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Iwagami Y, Eguchi H, Nagano H, Akita H, Hama N, Wada H, Kawamoto K, Kobayashi S, Tomokuni A, Tomimaru Y, Mori M, Doki Y. miR-320c regulates gemcitabine-resistance in pancreatic cancer via SMARCC1. Br J Cancer 2013; 109:502-11. [PMID: 23799850 PMCID: PMC3721395 DOI: 10.1038/bjc.2013.320] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 06/02/2013] [Accepted: 06/04/2013] [Indexed: 12/14/2022] Open
Abstract
Background: Gemcitabine-based chemotherapy is the standard treatment for pancreatic cancer. However, the issue of resistance remains unresolved. The aim of this study was to identify microRNAs (miRNAs) that govern the resistance to gemcitabine in pancreatic cancer. Methods: miRNA microarray analysis using gemcitabine-resistant clones of MiaPaCa2 (MiaPaCa2-RGs), PSN1 (PSN1-RGs), and their parental cells (MiaPaCa2-P, PSN1-P) was conducted. Changes in the anti-cancer effects of gemcitabine were studied after gain/loss-of-function analysis of the candidate miRNA. Further assessment of the putative target gene was performed in vitro and in 66 pancreatic cancer clinical samples. Results: miR-320c expression was significantly higher in MiaPaCa2-RGs and PSN1-RGs than in their parental cells. miR-320c induced resistance to gemcitabine in MiaPaCa2. Further experiments showed that miR-320c-related resistance to gemcitabine was mediated through SMARCC1, a core subunit of the switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex. In addition, clinical examination revealed that only SMARCC1-positive patients benefited from gemcitabine therapy with regard to survival after recurrence (P=0.0463). Conclusion: The results indicate that miR-320c regulates the resistance of pancreatic cancer cells to gemcitabine through SMARCC1, suggesting that miR-320c/SMARCC1 could be suitable for prediction of the clinical response and potential therapeutic target in pancreatic cancer patients on gemcitabine-based therapy.
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Affiliation(s)
- Y Iwagami
- Department of Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, Japan
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154
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The SWI/SNF genetic blockade: effects in cell differentiation, cancer and developmental diseases. Oncogene 2013; 33:2681-9. [PMID: 23752187 DOI: 10.1038/onc.2013.227] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 04/17/2013] [Accepted: 04/17/2013] [Indexed: 12/26/2022]
Abstract
Our rapidly growing knowledge about cancer genetics attests to the widespread occurrence of alterations at genes encoding different components of the SWI/SNF complex. This reveals an important new feature that sustains cancer development: the blockade of chromatin remodeling. Here, we provide an overview of our current knowledge on the gene alterations of chromatin-remodeling factors, and how they relate to cancer and human developmental diseases. We also consider the functional repercussions, particularly how the inactivation of the SWI/SNF complex impairs the appropriate cell response to nuclear receptor signaling, which, in turn, prevents cell differentiation and sustains cell growth independently of the environment.
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155
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Khursheed M, Kolla JN, Kotapalli V, Gupta N, Gowrishankar S, Uppin SG, Sastry RA, Koganti S, Sundaram C, Pollack JR, Bashyam MD. ARID1B, a member of the human SWI/SNF chromatin remodeling complex, exhibits tumour-suppressor activities in pancreatic cancer cell lines. Br J Cancer 2013; 108:2056-62. [PMID: 23660946 PMCID: PMC3670478 DOI: 10.1038/bjc.2013.200] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: The human ATP-dependent SWItch/sucrose nonfermentable (SWI/SNF) complex functions as a primary chromatin remodeler during ontogeny, as well as in adult life. Several components of the complex have been suggested to function as important regulators of tumorigenesis in various cancers. In the current study, we have characterised a possible tumour suppressor role for the largest subunit of the complex, namely the AT-rich interaction domain 1B (ARID1B). Methods: We performed Azacytidine and Trichostatin A treatments, followed by bisulphite sequencing to determine the possible DNA methylation-induced transcription repression of the gene in pancreatic cancer (PaCa) cell lines. Functional characterisation of effect of ARID1B ectopic expression in MiaPaCa2 PaCa cell line, which harboured ARID1B homozygous deletion, was carried out. Finally, we evaluated ARID1B protein expression in pancreatic tumour samples using immunohistochemistry on a tissue microarray. Results: ARID1B was transcriptionally repressed due to promoter hypermethylation, and ectopic expression severely compromised the ability of MiaPaCa2 cells to form colonies in liquid culture and soft agar. In addition, ARID1B exhibited significantly reduced/loss of expression in PaCa tissue, especially in samples from advanced-stage tumours, when compared with normal pancreas. Conclusion: The results therefore suggest a possible tumour-suppressor function for ARID1B in PaCa, thus adding to the growing list of SWI/SNF components with a similar function. Given the urgent need to design efficient targeted therapies for PaCa, our study assumes significance.
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Affiliation(s)
- M Khursheed
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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156
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Balbás-Martínez C, Rodríguez-Pinilla M, Casanova A, Domínguez O, Pisano DG, Gómez G, Lloreta J, Lorente JA, Malats N, Real FX. ARID1A alterations are associated with FGFR3-wild type, poor-prognosis, urothelial bladder tumors. PLoS One 2013; 8:e62483. [PMID: 23650517 PMCID: PMC3641081 DOI: 10.1371/journal.pone.0062483] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 03/20/2013] [Indexed: 02/06/2023] Open
Abstract
Urothelial bladder cancer (UBC) is heterogeneous at the clinical, pathological, genetic, and epigenetic levels. Exome sequencing has identified ARID1A as a novel tumor suppressor gene coding for a chromatin remodeling protein that is mutated in UBC. Here, we assess ARID1A alterations in two series of patients with UBC. In the first tumor series, we analyze exons 2–20 in 52 primary UBC and find that all mutant tumors belong to the aggressive UBC phenotype (high grade non-muscle invasive and muscle invasive tumors) (P = 0.05). In a second series (n = 84), we assess ARID1A expression using immunohistochemistry, a surrogate for mutation analysis, and find that loss of expression increases with higher stage/grade, it is inversely associated with FGFR3 overexpression (P = 0.03) but it is not correlated with p53 overexpression (P = 0.30). We also analyzed the expression of cytokeratins in the same set of tumor and find, using unsupervised clustering, that tumors with ARID1A loss of expression are generally KRT5/6-low. In this patient series, loss of ARID1A expression is also associated with worse prognosis, likely reflecting the higher prevalence of losses found in tumors of higher stage and grade. The independent findings in these two sets of patients strongly support the notion that ARID1A inactivation is a key player in bladder carcinogenesis occurring predominantly in FGFR3 wild type tumors.
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MESH Headings
- Aged
- Aged, 80 and over
- Base Sequence
- Carcinoma, Transitional Cell/genetics
- Carcinoma, Transitional Cell/mortality
- Carcinoma, Transitional Cell/pathology
- Cell Line, Tumor
- DNA Mutational Analysis
- DNA-Binding Proteins
- Female
- HEK293 Cells
- Humans
- Kaplan-Meier Estimate
- Male
- Middle Aged
- Mutation, Missense
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Prognosis
- Receptor, Fibroblast Growth Factor, Type 3/genetics
- Receptor, Fibroblast Growth Factor, Type 3/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- Urinary Bladder Neoplasms/genetics
- Urinary Bladder Neoplasms/mortality
- Urinary Bladder Neoplasms/pathology
- Urothelium/pathology
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Affiliation(s)
- Cristina Balbás-Martínez
- Epithelial Carcinogenesis Group, Molecular Pathology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - María Rodríguez-Pinilla
- Lymphoma Group, Molecular Pathology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Ariel Casanova
- Epithelial Carcinogenesis Group, Molecular Pathology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Orlando Domínguez
- Genomics Unit, Biotechnology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - David G. Pisano
- Bioinformatics Unit, Structural and Computational Biology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Gonzalo Gómez
- Bioinformatics Unit, Structural and Computational Biology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Josep Lloreta
- Department of Pathology, Hospital del Mar, Barcelona, Spain
- Departament de Ciències Experimentals de i la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Núria Malats
- Genetic and Molecular Epidemiology Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Francisco X. Real
- Epithelial Carcinogenesis Group, Molecular Pathology Programme, Spanish National Cancer Research Centre, Madrid, Spain
- Departament de Ciències Experimentals de i la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- * E-mail:
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157
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Hakimi AA, Ostrovnaya I, Reva B, Schultz N, Chen YB, Gonen M, Liu H, Takeda S, Voss MH, Tickoo SK, Reuter VE, Russo P, Cheng EH, Sander C, Motzer RJ, Hsieh JJ. Adverse outcomes in clear cell renal cell carcinoma with mutations of 3p21 epigenetic regulators BAP1 and SETD2: a report by MSKCC and the KIRC TCGA research network. Clin Cancer Res 2013; 19:3259-67. [PMID: 23620406 DOI: 10.1158/1078-0432.ccr-12-3886] [Citation(s) in RCA: 271] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PURPOSE To investigate the impact of newly identified chromosome 3p21 epigenetic tumor suppressors PBRM1, SETD2, and BAP1 on cancer-specific survival (CSS) of 609 patients with clear cell renal cell carcinoma (ccRCC) from 2 distinct cohorts. EXPERIMENTAL DESIGN Select sequencing on 3p tumor suppressors of 188 patients who underwent resection of primary ccRCC at the Memorial Sloan-Kettering Cancer Center (MSKCC) was conducted to interrogate the genotype-phenotype associations. These findings were compared with analyses of the genomic and clinical dataset from our nonoverlapping The Cancer Genome Atlas (TCGA) cohort of 421 patients with primary ccRCC. RESULTS 3p21 tumor suppressors are frequently mutated in both the MSKCC (PBRM1, 30.3%; SETD2, 7.4%; BAP1, 6.4%) and the TCGA (PBRM1, 33.5%; SETD2, 11.6%; BAP1, 9.7%) cohorts. BAP1 mutations are associated with worse CSS in both cohorts [MSKCC, P = 0.002; HR 7.71; 95% confidence interval (CI)2.08-28.6; TCGA, P = 0.002; HR 2.21; 95% CI 1.35-3.63]. SETD2 are associated with worse CSS in the TCGA cohort (P = 0.036; HR 1.68; 95% CI 1.04-2.73). On the contrary, PBRM1 mutations, the second most common gene mutations of ccRCC, have no impact on CSS. CONCLUSION The chromosome 3p21 locus harbors 3 frequently mutated ccRCC tumor suppressor genes. BAP1 and SETD2 mutations (6%-12%) are associated with worse CSS, suggesting their roles in disease progression. PBRM1 mutations (30%-34%) do not impact CSS, implicating its principal role in the tumor initiation. Future efforts should focus on therapeutic interventions and further clinical, pathologic, and molecular interrogation of this novel class of tumor suppressors.
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Affiliation(s)
- A Ari Hakimi
- Urology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
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158
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Giacomini CP, Sun S, Varma S, Shain AH, Giacomini MM, Balagtas J, Sweeney RT, Lai E, Del Vecchio CA, Forster AD, Clarke N, Montgomery KD, Zhu S, Wong AJ, van de Rijn M, West RB, Pollack JR. Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types. PLoS Genet 2013; 9:e1003464. [PMID: 23637631 PMCID: PMC3636093 DOI: 10.1371/journal.pgen.1003464] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 03/05/2013] [Indexed: 02/07/2023] Open
Abstract
Gene fusions, like BCR/ABL1 in chronic myelogenous leukemia, have long been recognized in hematologic and mesenchymal malignancies. The recent finding of gene fusions in prostate and lung cancers has motivated the search for pathogenic gene fusions in other malignancies. Here, we developed a “breakpoint analysis” pipeline to discover candidate gene fusions by tell-tale transcript level or genomic DNA copy number transitions occurring within genes. Mining data from 974 diverse cancer samples, we identified 198 candidate fusions involving annotated cancer genes. From these, we validated and further characterized novel gene fusions involving ROS1 tyrosine kinase in angiosarcoma (CEP85L/ROS1), SLC1A2 glutamate transporter in colon cancer (APIP/SLC1A2), RAF1 kinase in pancreatic cancer (ATG7/RAF1) and anaplastic astrocytoma (BCL6/RAF1), EWSR1 in melanoma (EWSR1/CREM), CDK6 kinase in T-cell acute lymphoblastic leukemia (FAM133B/CDK6), and CLTC in breast cancer (CLTC/VMP1). Notably, while these fusions involved known cancer genes, all occurred with novel fusion partners and in previously unreported cancer types. Moreover, several constituted druggable targets (including kinases), with therapeutic implications for their respective malignancies. Lastly, breakpoint analysis identified new cell line models for known rearrangements, including EGFRvIII and FIP1L1/PDGFRA. Taken together, we provide a robust approach for gene fusion discovery, and our results highlight a more widespread role of fusion genes in cancer pathogenesis. Gene fusions represent an important class of cancer genes, created by rearrangements of the genome that bring together two different genes. Because they are unique to cancer cells, gene fusions are ideal diagnostic markers and therapeutic targets. While gene fusions were once thought restricted mainly to blood cancers, recent discoveries suggest they are more widespread. Here, we have developed an approach for mining DNA microarray data to detect the tell-tale signatures of gene fusions, as “breakpoints” occurring within the encoding DNA or expressed transcripts. We apply this approach to a large collection of nearly 1,000 human cancer specimens. From this analysis, we discover and verify twelve new gene fusions occurring in diverse cancer types. We verify that some of these rearrangements recur in other samples of the same cancer type (supporting a causal role) and that the cancers show dependency on the fusion for cancer cell growth. Notably, some of these fusions (e.g. CEP85L/ROS1 in angiosarcoma) represent the first for that cancer type and thus provide important new biological insight. Some are also good drug targets (including rearrangements of ROS1, RAF1, and CDK6 kinases), with clear implications for therapy.
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Affiliation(s)
- Craig P. Giacomini
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Steven Sun
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - A. Hunter Shain
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Marilyn M. Giacomini
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Jay Balagtas
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Robert T. Sweeney
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Everett Lai
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Catherine A. Del Vecchio
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Andrew D. Forster
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nicole Clarke
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Kelli D. Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Shirley Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Albert J. Wong
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Robert B. West
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jonathan R. Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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159
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Abstract
Ovarian clear cell carcinomas (OCCCs) account for about 5–13% of all epithelial ovarian carcinomas in Western populations. It is characterised by resistance to conventional platinum-based chemotherapy, and new therapeutic strategies are urgently required. This article will focus on how recent discoveries have enhanced our understanding of the molecular pathogenesis of OCCCs, leading to new therapeutic opportunities. These include mutations in ARID1A, which provides a link to endometriosis, upregulation of the phosphatidylinositol 3-kinase/AKT pathway, particularly through mutations of PIK3CA and inactivation of PTEN, and increased activity of pathways involved in angiogenesis. Targeting HER2, apoptotic escape mechanisms and mismatch repair defects offer additional opportunities for treating this enigmatic tumour subtype.
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160
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Makohon-Moore A, Brosnan JA, Iacobuzio-Donahue CA. Pancreatic cancer genomics: insights and opportunities for clinical translation. Genome Med 2013; 5:26. [PMID: 23673020 PMCID: PMC4064313 DOI: 10.1186/gm430] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Pancreatic cancer is a highly lethal tumor type for which there are few viable therapeutic options. It is also caused by the accumulation of mutations in a variety of genes. These genetic alterations can be grouped into those that accumulate during pancreatic intraepithelial neoplasia (precursor lesions) and thus are present in all cells of the infiltrating carcinoma, and those that accumulate specifically within the infiltrating carcinoma during subclonal evolution, resulting in genetic heterogeneity. Despite this heterogeneity there are nonetheless commonly altered cellular functions, such as pathways controlling the cell cycle, DNA damage repair, intracellular signaling and development, which could provide for a variety of drug targets. This review aims to summarize current knowledge of the genetics and genomics of pancreatic cancer from its inception to metastatic colonization, and to provide examples of how this information can be translated into the clinical setting for therapeutic benefit and personalized medicine.
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Affiliation(s)
- Alvin Makohon-Moore
- Graduate Program in Pathobiology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Jacqueline A Brosnan
- Graduate Program in Pathobiology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Christine A Iacobuzio-Donahue
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
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161
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Cho H, Kim JSY, Chung H, Perry C, Lee H, Kim JH. Loss of ARID1A/BAF250a expression is linked to tumor progression and adverse prognosis in cervical cancer. Hum Pathol 2013; 44:1365-74. [PMID: 23427874 DOI: 10.1016/j.humpath.2012.11.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 11/11/2012] [Accepted: 11/13/2012] [Indexed: 02/08/2023]
Abstract
The tumor suppressor gene ARID1A encodes BAF250a, a component of human SWI/SNF chromatin-remodeling complexes. Loss of BAF250a expression has recently been reported in several tumor types. To investigate the potential correlation between BAF250a and various clinicopathologic parameters, we assessed the expression of BAF250a in archival tumor tissue specimens from 147 patients with cervical cancer and 191 with cervical intraepithelial neoplasia as well as 376 matched nonadjacent normal tissues by immunohistochemical staining. Messenger RNA expression level for BAF250a was decreased in cervical cancer cell lines (P = .013) and tissues (P = .010), when compared with normal cervical epithelial tissue using SYBR Green real-time polymerase chain reaction. BAF250a was also detected in nuclear fractions of HeLa cells and in nuclei of cervical cancer tissue samples by Western blotting and immunohistochemistry, respectively. BAF250a expression gradually decreased in transitioning from normal to cervical carcinoma (P < .001), and this loss of expression was significantly associated with tumor stage (P = .005), tumor grade (P = .029), tumor size (P = .003), and lymph node metastasis (P = .020). In multivariate analysis, overall survival in cervical cancer was significantly reduced in cases with BAF250a loss (hazard ratio, 2.78 [1.01-7.63]; P = .047). Our findings suggest a potential role for BAF250a in providing valuable prognostic information to clinicians for risk assessment in cervical cancer.
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Affiliation(s)
- Hanbyoul Cho
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 135-720, Korea
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162
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Yachida S, Iacobuzio-Donahue CA. Evolution and dynamics of pancreatic cancer progression. Oncogene 2013; 32:5253-60. [PMID: 23416985 DOI: 10.1038/onc.2013.29] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/02/2013] [Accepted: 01/03/2013] [Indexed: 02/08/2023]
Abstract
Efficient metastasis is believed as the result of multiple genetic, epigenetic and/or post-translational events in the lifetime of a carcinoma. At the genetic level, these events may be categorized into those that occur during carcinogenesis, and those that occur during subclonal evolution. This review summarizes current knowledge of the genetics of pancreatic cancer from its initiation within a normal cell until the time that is has disseminated to distant organs, many features of which can be extrapolated to other solid tumor types. The implications of these findings to personalize genome analyses of an individual patient's tumor are also discussed.
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Affiliation(s)
- S Yachida
- 1] Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA [2] Division of Refractory Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
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163
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Gao X, Huang M, Liu L, He Y, Yu Q, Zhao H, Zhou C, Zhang J, Zhu Z, Wan J, Jiang X, Gao Y. Insertion/deletion polymorphisms in the promoter region of BRM contribute to risk of hepatocellular carcinoma in Chinese populations. PLoS One 2013; 8:e55169. [PMID: 23359823 PMCID: PMC3554679 DOI: 10.1371/journal.pone.0055169] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 12/19/2012] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND BRM (Brahma homologue) is well known for its critical role in tumor suppression and cancer development. Genetic variations in the promoter region of BRM have been suggested to be associated with loss of BRM expression and lung cancer risk. To the authors' knowledge, no study on the role of BRM genetic polymorphisms in hepatocellular carcinoma (HCC) risk has been performed. METHODOLOGY/PRINCIPAL FINDINGS In two independent case-control studies containing 796 HCC cases and 806 cancer-free individuals, we genotyped two putative functional insertion/deletion (indel) polymorphisms [BRM-1321 (rs3832613) and BRM-741 (rs34480940)] within promoter region of BRM in Chinese populations using a PCR-based method. Real-time RT-PCR analysis was used to explore the genotype-phenotype correlation between these polymorphisms and BRM expression in both tissue samples and HCC cell lines. Logistic regression analysis showed that compared to BRM-1321del/del genotype, the ins/del and ins/ins variant genotypes had an increased HCC risk [adjusted odds ratio (OR) = 1.47, 95% confidence interval (CI) = 1.19-1.82; adjusted OR = 2.55, 95% CI = 1.75-3.72, respectively]. No significant association between BRM-741 and HCC incidence was observed. However, stratification analysis revealed a significant association between ins/ins genotype of BRM-741 and increased HCC susceptibility in smokers (adjusted OR = 2.07, 95% CI = 1.33-3.22). Quantitative PCR analyses demonstrated that the genotypes of BRM-1321 and the corresponding haplotypes were significantly correlated with BRM expression in vivo. Compared with ins/ins genotype, subjects carrying ins/del and del/del genotype had 2.30 and 4.99 fold higher BRM expression in HCC tissue samples, respectively. Similar trends were observed in western blot analysis at protein level. CONCLUSIONS/SIGNIFICANCE Our findings suggest that BRM promoter polymorphism (BRM-1321) could regulate BRM expression and may serve as a potential marker for genetic susceptibility to HCC.
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Affiliation(s)
- Xueren Gao
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Moli Huang
- Department of Bioinformatics, Medical College of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Limin Liu
- Department of Pathophysiology, Medical College of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Yan He
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Qiang Yu
- Department of Gastroenterology, Affiliated Hospital of Nanjing Medical University, Suzhou, Jiangsu, People’s Republic of China
| | - Hua Zhao
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Chunxiao Zhou
- Department of Gastroenterology, Affiliated Hospital of Nanjing Medical University, Suzhou, Jiangsu, People’s Republic of China
| | - Jinkun Zhang
- Department of Gastroenterology, Affiliated Hospital of Nanjing Medical University, Suzhou, Jiangsu, People’s Republic of China
| | - Zhansheng Zhu
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Jiao Wan
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Xinghong Jiang
- Department of Neurobiology and Psychology, Key Laboratory of Pain Research & Therapy, Medical College of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Yuzhen Gao
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, Jiangsu, People’s Republic of China
- * E-mail:
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164
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The spectrum of SWI/SNF mutations, ubiquitous in human cancers. PLoS One 2013; 8:e55119. [PMID: 23355908 PMCID: PMC3552954 DOI: 10.1371/journal.pone.0055119] [Citation(s) in RCA: 406] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 12/19/2012] [Indexed: 02/06/2023] Open
Abstract
SWI/SNF is a multi-subunit chromatin remodeling complex that uses the energy of ATP hydrolysis to reposition nucleosomes, thereby modulating gene expression. Accumulating evidence suggests that SWI/SNF functions as a tumor suppressor in some cancers. However, the spectrum of SWI/SNF mutations across human cancers has not been systematically investigated. Here, we mined whole-exome sequencing data from 24 published studies representing 669 cases from 18 neoplastic diagnoses. SWI/SNF mutations were widespread across diverse human cancers, with an excess of deleterious mutations, and an overall frequency approaching TP53 mutation. Mutations occurred most commonly in the SMARCA4 enzymatic subunit, and in subunits thought to confer functional specificity (ARID1A, ARID1B, PBRM1, and ARID2). SWI/SNF mutations were not mutually-exclusive of other mutated cancer genes, including TP53 and EZH2 (both previously linked to SWI/SNF). Our findings implicate SWI/SNF as an important but under-recognized tumor suppressor in diverse human cancers, and provide a key resource to guide future investigations.
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165
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Zhang X, Sun Q, Shan M, Niu M, Liu T, Xia B, Liang X, Wei W, Sun S, Zhang Y, Liu XS, Song Q, Yang Y, Ma Y, Liu Y, Yang L, Ren Y, Zhang G, Pang D. Promoter hypermethylation of ARID1A gene is responsible for its low mRNA expression in many invasive breast cancers. PLoS One 2013; 8:e53931. [PMID: 23349767 PMCID: PMC3549982 DOI: 10.1371/journal.pone.0053931] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Accepted: 12/07/2012] [Indexed: 11/25/2022] Open
Abstract
ARID1A (AT-rich interactive domain 1A) has recently been identified as a tumor suppressor gene. Its mRNA expression is significantly low in many breast cancers; this is often associated with more aggressive phenotypes. However, the underlying molecular mechanism for its low expression has not been fully understood. This study was undertaken to evaluate the contribution of gene copy number variation, mutations, promoter methylation and histone modification to ARID1A’s low expression. 38 pairs of breast invasive ductal carcinomas and their normal breast tissue counterparts from the same patients were randomly selected for gene expression and copy number variation detection. Promoter methylation and histone modification levels were evaluated by MeDIP-qPCR and ChIP-qPCR, respectively. PCR product Sanger sequencing was carried out to detect the exon mutation rate. Twenty-two out of 38 invasive ductal carcinomas in the study (57.9%) revealed ARID1A mRNA low expression by realtime RT-PCR. The relative promoter methylation level was, significantly higher in ARID1A mRNA low expression group compared with its high expression group (p<0.001). In the low expression group, nineteen out of 22 invasive ductal carcinomas (86.4%) exhibited ARID1A promoter hypermthylation. In addition, the promoter hypermethylation was accompanied with repressive histone modification (H3K27Me3). Although five out of 38 invasive ductal carcinomas (13.2%) exhibited loss of ARID1A gene copy number by realtime PCR and nine exon novel mutations are seen from eight out of 33 invasive ductal carcinomas (24.2%), there was no statistically significant difference in both ARID1A mRNA low and high expression groups (p = 0.25,and p = 0.68, respectively). We demonstrate that promoter hypermethylation was the main culprit for ARID1A mRNA low expression in invasive ductal carcinomas. The influence of mutation and copy number variation on the expression were statistically insignificant at mRNA level, and were, therefore, not considered the main causes for ARID1A mRNA low expression in invasive breast cancer.
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MESH Headings
- Adult
- Base Sequence
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- DNA Copy Number Variations
- DNA Methylation
- DNA-Binding Proteins
- Female
- Gene Expression Regulation, Neoplastic
- Histones/metabolism
- Humans
- Methylation
- Middle Aged
- Mutation
- Neoplasm Invasiveness
- Nuclear Proteins/genetics
- Promoter Regions, Genetic/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Transcription Factors/genetics
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Affiliation(s)
- Xianyu Zhang
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Qian Sun
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Ming Shan
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Ming Niu
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Tong Liu
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Bingshu Xia
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaoshuan Liang
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Wei Wei
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Shanshan Sun
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Youxue Zhang
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaolong Sean Liu
- Department of Pathology, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Qingbin Song
- Department of Medicine, Mount Sinai School of Medicine, New York, United States of America
| | - Yanmei Yang
- Key Laboratory, Heilongjiang Institute for Cancer Research, Harbin, Heilongjiang, China
| | - Yuyan Ma
- Key Laboratory, Heilongjiang Institute for Cancer Research, Harbin, Heilongjiang, China
| | - Yang Liu
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Long Yang
- ICFC Custom Service, Life Technologies Corporation, Beijing, China
| | - Yanlv Ren
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Guoqiang Zhang
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Da Pang
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory, Heilongjiang Institute for Cancer Research, Harbin, Heilongjiang, China
- * E-mail:
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Tzatsos A, Paskaleva P, Ferrari F, Deshpande V, Stoykova S, Contino G, Wong KK, Lan F, Trojer P, Park PJ, Bardeesy N. KDM2B promotes pancreatic cancer via Polycomb-dependent and -independent transcriptional programs. J Clin Invest 2013; 123:727-39. [PMID: 23321669 DOI: 10.1172/jci64535] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 11/26/2012] [Indexed: 12/13/2022] Open
Abstract
Epigenetic mechanisms mediate heritable control of cell identity in normal cells and cancer. We sought to identify epigenetic regulators driving the pathogenesis of pancreatic ductal adenocarcinoma (PDAC), one of the most lethal human cancers. We found that KDM2B (also known as Ndy1, FBXL10, and JHDM1B), an H3K36 histone demethylase implicated in bypass of cellular senescence and somatic cell reprogramming, is markedly overexpressed in human PDAC, with levels increasing with disease grade and stage, and highest expression in metastases. KDM2B silencing abrogated tumorigenicity of PDAC cell lines exhibiting loss of epithelial differentiation, whereas KDM2B overexpression cooperated with KrasG12D to promote PDAC formation in mouse models. Gain- and loss-of-function experiments coupled to genome-wide gene expression and ChIP studies revealed that KDM2B drives tumorigenicity through 2 different transcriptional mechanisms. KDM2B repressed developmental genes through cobinding with Polycomb group (PcG) proteins at transcriptional start sites, whereas it activated a module of metabolic genes, including mediators of protein synthesis and mitochondrial function, cobound by the MYC oncogene and the histone demethylase KDM5A. These results defined epigenetic programs through which KDM2B subverts cellular differentiation and drives the pathogenesis of an aggressive subset of PDAC.
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Affiliation(s)
- Alexandros Tzatsos
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA.
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167
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Gonzalez-Perez A, Jene-Sanz A, Lopez-Bigas N. The mutational landscape of chromatin regulatory factors across 4,623 tumor samples. Genome Biol 2013; 14:r106. [PMID: 24063517 PMCID: PMC4054018 DOI: 10.1186/gb-2013-14-9-r106] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 09/24/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Chromatin regulatory factors are emerging as important genes in cancer development and are regarded as interesting candidates for novel targets for cancer treatment. However, we lack a comprehensive understanding of the role of this group of genes in different cancer types. RESULTS We have analyzed 4,623 tumor samples from thirteen anatomical sites to determine which chromatin regulatory factors are candidate drivers in these different sites. We identify 34 chromatin regulatory factors that are likely drivers in tumors from at least one site, all with relatively low mutational frequency. We also analyze the relative importance of mutations in this group of genes for the development of tumorigenesis in each site, and indifferent tumor types from the same site. CONCLUSIONS We find that, although tumors from all thirteen sites show mutations in likely driver chromatin regulatory factors, these are more prevalent in tumors arising from certain tissues. With the exception of hematopoietic, liver and kidney tumors, as a median, the mutated factors are less than one fifth of all mutated drivers across all sites analyzed. We also show that mutations in two of these genes, MLL and EP300, correlate with broad expression changes across cancer cell lines, thus presenting at least one mechanism through which these mutations could contribute to tumorigenesis in cells of the corresponding tissues.
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Affiliation(s)
- Abel Gonzalez-Perez
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain
| | - Alba Jene-Sanz
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain
| | - Nuria Lopez-Bigas
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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168
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Abstract
UNLABELLED Although disordered chromatin organization has long been recognized as a feature of cancer, the molecular underpinnings of chromatin structure, epigenetic regulation, and their relationships to transcription are only beginning to be understood. Cancer genome sequencing studies have revealed a novel theme: frequent mutation of epigenetic regulators. Among these, the ARID1A/BAF250A subunit of the SWI/SNF (BRG1-associated factors) chromatin remodeling complex has emerged as recurrently mutated in a broad array of tumor types. We review the genomic and functional data supporting classification of ARID1A as a tumor suppressor. SIGNIFICANCE Mutations in chromatin remodeling complex genes are increasingly recognized in many cancer types. However, the mechanisms by which chromatin remodeling complexes contribute to gene expression and the cancer phenotype are poorly understood. Understanding how mutation of chromatin remodelers facilitates transformation may offer the potential for development and implementation of novel therapies for cancer.
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Affiliation(s)
- Jennifer N Wu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA
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169
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Nair SS, Kumar R. Chromatin remodeling in cancer: a gateway to regulate gene transcription. Mol Oncol 2012; 6:611-9. [PMID: 23127546 PMCID: PMC3538127 DOI: 10.1016/j.molonc.2012.09.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 09/30/2012] [Indexed: 01/01/2023] Open
Abstract
Cancer cells are remarkably adaptive to diverse survival strategies, probably due to its ability to interpret signaling cues differently than the normal cells. It appears as if cancer cells are constantly sampling, selecting and adapting signaling pathways to favor its proliferation. This process of successful adaptive evolution eventually renders a retractile nature to therapeutic regimens, fueling to the process of cancer progression. Based on plethora of available information, it is now evident that multiple signaling pathways eventually converge, perhaps, in a tempo-spatial manner, onto DNA template-dependent dynamic processes. Considering the complexity and packaging of eukaryotic genome, this process involves energy-dependent sub-events mediated by chromatin remodelers. Chromatin remodeler proteins function as gatekeepers and constitute a major determinant of accessibility of accessory factors to nucleosome DNA, allowing a wide repertoire of biological functions. And thus, aberrant expression or epigenetic modulation of remodeler proteins confers a unique ability to cancer cells to reprogram its genome for the maintenance of oncogenic phenotypes. Cancer cells can uniquely select a multi-subunit remodeler proteome for oncogenic advantage. This review summarizes our current understanding and importance of remodeler and chromatin proteins in cancer biology and also highlights the paradoxical role of proteins with or without dual-regulator functions. It is our hope that an in-depth understanding of these events is likely to provide a next set of opportunities for novel strategies for targeted cancer therapeutics.
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Affiliation(s)
- Sujit S Nair
- Department of Biochemistry and Molecular Biology, The McCormick Genomic and Proteomic Center, The School of Medicine & Health Sciences, The George Washington University, Washington, DC 20037, USA
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170
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Le Gallo M, O'Hara AJ, Rudd ML, Urick ME, Hansen NF, O'Neil NJ, Price JC, Zhang S, England BM, Godwin AK, Sgroi DC, Hieter P, Mullikin JC, Merino MJ, Bell DW. Exome sequencing of serous endometrial tumors identifies recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes. Nat Genet 2012; 44:1310-5. [PMID: 23104009 PMCID: PMC3515204 DOI: 10.1038/ng.2455] [Citation(s) in RCA: 326] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 10/04/2012] [Indexed: 12/12/2022]
Abstract
Endometrial cancer is the 6th most commonly diagnosed cancer among women worldwide, causing ~74,000 deaths annually 1. Serous endometrial cancers are a clinically aggressive subtype with a poorly defined genetic etiology 2-4. We used whole exome sequencing (WES) to comprehensively search for somatic mutations within ~22,000 protein-encoding genes among 13 primary serous endometrial tumors. We subsequently resequenced 18 genes that were mutated in more than one tumor, and/or were genes that formed an enriched functional grouping, from 40 additional serous tumors. We identified high frequencies of somatic mutations in CHD4 (17%), EP300 (8%), ARID1A (6%), TSPYL2 (6%), FBXW7 (29%), SPOP (8%), MAP3K4 (6%) and ABCC9 (6%). Overall, 36.5% of serous tumors had mutated a chromatin-remodeling gene and 35% had mutated a ubiquitin ligase complex gene, implicating the frequent mutational disruption of these processes in the molecular pathogenesis of one of the deadliest forms of endometrial cancer.
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Affiliation(s)
- Matthieu Le Gallo
- Cancer Genetics Branch, National Human Genome Research Institute, US National Institutes of Health (NIH), Bethesda, MD, USA
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171
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McCleary-Wheeler AL, Lomberk GA, Weiss FU, Schneider G, Fabbri M, Poshusta TL, Dusetti NJ, Baumgart S, Iovanna JL, Ellenrieder V, Urrutia R, Fernandez-Zapico ME. Insights into the epigenetic mechanisms controlling pancreatic carcinogenesis. Cancer Lett 2012; 328:212-21. [PMID: 23073473 DOI: 10.1016/j.canlet.2012.10.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 10/02/2012] [Accepted: 10/08/2012] [Indexed: 12/14/2022]
Abstract
During the last couple decades, we have significantly advanced our understanding of mechanisms underlying the development of pancreatic ductual adenocarcinoma (PDAC). In the late 1990s into the early 2000s, a model of PDAC development and progression was developed as a multi-step process associated with the accumulation of somatic mutations. The correlation and association of these particular genetic aberrations with the establishment and progression of PDAC has revolutionized our understanding of this process. However, this model leaves out other molecular events involved in PDAC pathogenesis that contribute to its development and maintenance, specifically those being epigenetic events. Thus, a new model considering the new scientific paradigms of epigenetics will provide a more comprehensive and useful framework for understanding the pathophysiological mechanisms underlying this disease. Epigenetics is defined as the type of inheritance not based on a particular DNA sequence but rather traits that are passed to the next generation via DNA and histone modifications as well as microRNA-dependent mechanisms. Key tumor suppressors that are well established to play a role in PDAC may be altered through hypermethylation, and oncogenes can be upregulated secondary to permissive histone modifications. Factors involved in tumor invasiveness can be aberrantly expressed through dysregulated microRNAs. A noteworthy characteristic of epigenetic-based inheritance is its reversibility, which is in contrast to the stable nature of DNA sequence-based alterations. Given this nature of epigenetic alterations, it becomes imperative that our understanding of epigenetic-based events promoting and maintaining PDAC continues to grow.
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Affiliation(s)
- Angela L McCleary-Wheeler
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Department of Oncology, Rochester, MN, USA
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172
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Hakimi AA, Chen YB, Wren J, Gonen M, Abdel-Wahab O, Heguy A, Liu H, Takeda S, Tickoo SK, Reuter VE, Voss MH, Motzer RJ, Coleman JA, Cheng EH, Russo P, Hsieh JJ. Clinical and pathologic impact of select chromatin-modulating tumor suppressors in clear cell renal cell carcinoma. Eur Urol 2012; 63:848-54. [PMID: 23036577 DOI: 10.1016/j.eururo.2012.09.005] [Citation(s) in RCA: 174] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 09/03/2012] [Indexed: 01/17/2023]
Abstract
BACKGROUND Historically, VHL was the only frequently mutated gene in clear cell renal cell carcinoma (ccRCC), with conflicting clinical relevance. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC including PBRM1, SETD2, BAP1, and KDM5C. PBRM1, SETD2, and BAP1 are located in close proximity to VHL within a commonly lost (approximately 90%) 3p locus. To date, the clinical and pathologic significance of mutations in these novel candidate tumor suppressors is unknown. OBJECTIVE To determine the frequency of and render the first clinical and pathologic outcome associated with mutations of these novel candidate tumor suppressors in ccRCC. DESIGN, SETTING, AND PARTICIPANTS Targeted sequencing was performed in 185 ccRCCs and matched normal tissues from a single institution. Pathologic features, baseline patient characteristics, and follow-up data were recorded. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The linkage between mutations and clinical and pathologic outcomes was interrogated with the Fisher exact test (for stage and Fuhrman nuclear grade) and the permutation log-rank test (for cancer-specific survival [CSS]). RESULTS AND LIMITATIONS PBRM1, BAP1, SETD2, and KDM5C are mutated at 29%, 6%, 8%, and 8%, respectively. Tumors with mutations in PBRM1 or any of BAP1, SETD2, or KDM5C (19%) are more likely to present with stage III disease or higher (p = 0.01 and p = 0.001, respectively). Small tumors (<4 cm) with PBRM1 mutations are more likely to exhibit stage III pathologic features (odds ratio: 6.4; p = 0.001). BAP1 mutations tend to occur in Fuhrman grade III-IV tumors (p = 0.052) and are associated with worse CSS (p = 0.01). Clinical outcome data are limited by the number of events. CONCLUSIONS Most mutations of chromatin modulators discovered in ccRCC are loss of function, associated with advanced stage, grade, and possibly worse CSS. Further studies validating the clinical impact of these novel mutations and future development of therapeutics remedying these tumor suppressors are warranted.
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Affiliation(s)
- A Ari Hakimi
- Urology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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173
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Emerging frontiers in pancreatic cancer research: elaboration of key genes, cells and the extracellular milieu. Curr Opin Gastroenterol 2012; 28:516-22. [PMID: 22759592 PMCID: PMC3680108 DOI: 10.1097/mog.0b013e3283567f69] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
PURPOSE OF REVIEW We review recent literature with a view to forge an integrative understanding of the molecular, cellular and extracellular milieu of pancreatic cancer, and discuss them in the context of development of novel, personalized therapeutic options. RECENT FINDINGS Pancreatic tumorigenesis, examined using genetically engineered mouse models, appears to be driven by local inflammation, in concert with the 'big four' mutations involving oncogenic KRAS, SMAD4, CDKN2A, and TP53, through induction of epithelial-to-mesenchymal transition (EMT) and cancer stem cells, and accompanied by metastasis. High-throughput sequencing of pancreatic ductal adenocarcinoma as well as neuroendocrine tumors and rarer subtypes of cancers of the pancreas has revealed several novel mutations in genes like PALB2, guanine nucleotide-binding protein, alpha stimulating, death-domain-associated protein, α thalassemia/mental retardation syndrome X linked, switch/sucrose nonfermentable pathway related, and in genes in the ubiquitin-dependent pathways such as USP9X. Therapeutic targeting of the tumor-stroma axis by cytokines and immune response modulators and the role of autophagy in pancreatic cancer are some other salient themes explored in the recent publications. SUMMARY Recent publications shed new light on the mutational landscape of pancreatic cancer and further delineate the distinctive pancreatic cancer-stroma ecosystem as determined by the dynamic interplay of inflammation, hallmark mutations, EMT, and cancer stem cells.
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174
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Macgregor-Das AM, Iacobuzio-Donahue CA. Molecular pathways in pancreatic carcinogenesis. J Surg Oncol 2012; 107:8-14. [PMID: 22806689 DOI: 10.1002/jso.23213] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/13/2012] [Indexed: 12/21/2022]
Abstract
Pancreatic cancer is a genetic disease. Pancreatic cancers develop from one of three precursor lesions, pancreatic intraepithelial neoplasia (PanIN), intraductal papillary mucinous neoplasms (IPMNs), and mucinous cystic neoplasms (MCNs), and each arises in association with distinct genetic alterations. These alterations not only provide insight into the fundamental origins of pancreatic cancer but provide ample opportunity for improving early diagnosis and management of cystic precursors.
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Affiliation(s)
- Anne M Macgregor-Das
- Pathobiology Program, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
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