Document Detail


Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer.
MedLine Citation:
PMID:  23028188     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Endometrial cancer is the most common gynecological malignancy, with more than 280,000 cases occurring annually worldwide. Although previous studies have identified important common somatic mutations in endometrial cancer, they have primarily focused on a small set of known cancer genes and have thus provided a limited view of the molecular basis underlying this disease. Here we have developed an integrated systems-biology approach to identifying novel cancer genes contributing to endometrial tumorigenesis. We first performed whole-exome sequencing on 13 endometrial cancers and matched normal samples, systematically identifying somatic alterations with high precision and sensitivity. We then combined bioinformatics prioritization with high-throughput screening (including both shRNA-mediated knockdown and expression of wild-type and mutant constructs) in a highly sensitive cell viability assay. Our results revealed 12 potential driver cancer genes including 10 tumor-suppressor candidates (ARID1A, INHBA, KMO, TTLL5, GRM8, IGFBP3, AKTIP, PHKA2, TRPS1, and WNT11) and two oncogene candidates (ERBB3 and RPS6KC1). The results in the "sensor" cell line were recapitulated by siRNA-mediated knockdown in endometrial cancer cell lines. Focusing on ARID1A, we integrated mutation profiles with functional proteomics in 222 endometrial cancer samples, demonstrating that ARID1A mutations frequently co-occur with mutations in the phosphatidylinositol 3-kinase (PI3K) pathway and are associated with PI3K pathway activation. siRNA knockdown in endometrial cancer cell lines increased AKT phosphorylation supporting ARID1A as a novel regulator of PI3K pathway activity. Our study presents the first unbiased view of somatic coding mutations in endometrial cancer and provides functional evidence for diverse driver genes and mutations in this disease.
Authors:
Han Liang; Lydia W T Cheung; Jie Li; Zhenlin Ju; Shuangxing Yu; Katherine Stemke-Hale; Turgut Dogruluk; Yiling Lu; Xiuping Liu; Chao Gu; Wei Guo; Steven E Scherer; Hannah Carter; Shannon N Westin; Mary D Dyer; Roeland G W Verhaak; Fan Zhang; Rachel Karchin; Chang-Gong Liu; Karen H Lu; Russell R Broaddus; Kenneth L Scott; Bryan T Hennessy; Gordon B Mills
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't     Date:  2012-10-01
Journal Detail:
Title:  Genome research     Volume:  22     ISSN:  1549-5469     ISO Abbreviation:  Genome Res.     Publication Date:  2012 Nov 
Date Detail:
Created Date:  2012-11-05     Completed Date:  2013-04-11     Revised Date:  2014-09-18    
Medline Journal Info:
Nlm Unique ID:  9518021     Medline TA:  Genome Res     Country:  United States    
Other Details:
Languages:  eng     Pagination:  2120-9     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Case-Control Studies
Cell Transformation, Neoplastic / genetics
Endometrial Neoplasms / genetics*
Exome*
Female
Genes, Tumor Suppressor*
Genomics*
High-Throughput Nucleotide Sequencing*
Humans
Mutation
Oncogenes*
Phosphatidylinositol 3-Kinase / metabolism
Phosphorylation
RNA, Small Interfering
Sequence Analysis, DNA
Systems Biology
Grant Support
ID/Acronym/Agency:
P30 CA016672/CA/NCI NIH HHS; P30 CA016672/CA/NCI NIH HHS; P50 CA098258/CA/NCI NIH HHS; P50 CA098258/CA/NCI NIH HHS; R21CA152432/CA/NCI NIH HHS; U01 CA168394/CA/NCI NIH HHS; U24 CA143883/CA/NCI NIH HHS; UL1 RR024148/RR/NCRR NIH HHS
Chemical
Reg. No./Substance:
0/RNA, Small Interfering; EC 2.7.1.137/Phosphatidylinositol 3-Kinase
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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