Journal
CANCER RESEARCH
Volume 76, Issue 2, Pages 216-226Publisher
AMER ASSOC CANCER RESEARCH
DOI: 10.1158/0008-5472.CAN-15-0484
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Funding
- Japan Society for the Promotion of Science (JSPS)
- Foreign Postdoctoral Researcher (FPR) program from RIKEN, Japan
- Ministry of Education, Culture, Sports, Science, and Technology
- European Research Council (ERC) under the European Union [638273]
- Novo Nordisk Foundation
- Lundbeck Foundation
- MEXT
- MEXT, Japan
- Japanese Ministry of Education, Culture, Sports, Science and Technology through RIKEN Preventive Medicine and Diagnosis Innovation Program
- RIKEN Centre for Life Science, Division of Genomic Technologies
- Cancer Research Trust
- MACA Ride to Conquer Cancer
- Novo Nordisk Fonden [NNF10SA1016550] Funding Source: researchfish
- European Research Council (ERC) [638273] Funding Source: European Research Council (ERC)
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Genes that are commonly deregulated in cancer are clinically attractive as candidate pan-diagnostic markers and therapeutic targets. To globally identify such targets, we compared Cap Analysis of Gene Expression profiles from 225 different cancer cell lines and 339 corresponding primary cell samples to identify transcripts that are deregulated recurrently in a broad range of cancer types. Comparing RNA-seq data from 4,055 tumors and 563 normal tissues profiled in the The Cancer Genome Atlas and FANTOM5 datasets, we identified a core transcript set with theranostic potential. Our analyses also revealed enhancer RNAs, which are upregulated in cancer, defining promoters that overlap with repetitive elements (especially SINE/Alu and LTR/ERV1 elements) that are often upregulated in cancer. Lastly, we documented for the first time upregulation of multiple copies of the REP522 interspersed repeat in cancer. Overall, our genome-wide expression profiling approach identified a comprehensive set of candidate biomarkers with pan-cancer potential, and extended the perspective and pathogenic significance of repetitive elements that are frequently activated during cancer progression. (C) 2015 AACR.
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