Journal article
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
Cell reports (Cambridge), Vol.23(1), pp.297-312.e12
04/03/2018
DOI: 10.1016/j.celrep.2018.03.064
PMCID: PMC5906131
PMID: 29617668
Abstract
Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles in cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors (cancer genes) by modeling their effects on the activity of transcription factors, RNA-binding proteins, and microRNAs in 5,185 TCGA tumors and 1,019 ENCODE assays. Our predictions included hundreds of candidate onco- and tumor-suppressor lncRNAs (cancer lncRNAs) whose somatic alterations account for the dysregulation of dozens of cancer genes and pathways in each of 14 tumor contexts. To demonstrate proof of concept, we showed that perturbations targeting OIP5-AS1 (an inferred tumor suppressor) and TUG1 and WT1-AS (inferred onco-lncRNAs) dysregulated cancer genes and altered proliferation of breast and gynecologic cancer cells. Our analysis indicates that, although most lncRNAs are dysregulated in a tumor-specific manner, some, including OIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergistically dysregulate cancer pathways in multiple tumor contexts.
Details
- Title: Subtitle
- Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
- Creators
- Hua-Sheng Chiu - Baylor College of MedicineSonal Somvanshi - Baylor College of MedicineEktaben Patel - Baylor College of MedicineTing-Wen Chen - Chang Gung UniversityVivek P Singh - Baylor College of MedicineBarry Zorman - Baylor College of MedicineSagar L Patil - University of HoustonYinghong Pan - University of HoustonSujash S Chatterjee - University of HoustonAnil K Sood - The University of Texas MD Anderson Cancer CenterPreethi H Gunaratne - University of HoustonPavel Sumazin - Baylor College of Medicine
- Contributors
- Cancer Genome Atlas Research Network (Contributor)Deqin Ma (Contributor) - University of Iowa, PathologyMohammed M Milhem (Contributor) - University of Iowa, Internal MedicineAaron D Bossler (Contributor) - University of Iowa, Pathology
- Resource Type
- Journal article
- Publication Details
- Cell reports (Cambridge), Vol.23(1), pp.297-312.e12
- DOI
- 10.1016/j.celrep.2018.03.064
- PMID
- 29617668
- PMCID
- PMC5906131
- ISSN
- 2211-1247
- eISSN
- 2211-1247
- Grant note
- U24 CA143843 / NCI NIH HHS U24 CA143867 / NCI NIH HHS U24 CA143858 / NCI NIH HHS U24 CA143882 / NCI NIH HHS U24 CA210957 / NCI NIH HHS U54 HG003067 / NHGRI NIH HHS U24 CA143845 / NCI NIH HHS U54 HG003079 / NHGRI NIH HHS U24 CA143835 / NCI NIH HHS U24 CA143840 / NCI NIH HHS U54 HG003273 / NHGRI NIH HHS U24 CA144025 / NCI NIH HHS U24 CA210950 / NCI NIH HHS U24 CA143866 / NCI NIH HHS U24 CA143883 / NCI NIH HHS U24 CA210990 / NCI NIH HHS U24 CA143799 / NCI NIH HHS U24 CA210949 / NCI NIH HHS R01 CA163722 / NCI NIH HHS U24 CA143848 / NCI NIH HHS
- Language
- English
- Date published
- 04/03/2018
- Academic Unit
- Hematology, Oncology, and Blood & Marrow Transplantation; Pathology; Internal Medicine
- Record Identifier
- 9984185281002771
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