Putative cis-regulatory drivers in colorectal cancer

Nature

Volumn 512, Issue 1, 2014, Pages 87-90

  Ongen, Halit ^a,b,c   Andersen, Claus L ^d   Bramsen, Jesper B ^d   Oster, Bodil ^d   Rasmussen, Mads H ^d   Ferreira, Pedro G ^a,b,c   Sandoval, Juan ^e   Vidal, Enrique ^e   Whiffin, Nicola ^f   Planchon, Alexandra ^a,b,c   Padioleau, Ismael ^a,b,c   Bielser, Deborah ^a,b,c   Romano, Luciana ^a,b,c   Tomlinson, Ian ^g   Houlston, Richard S ^f   Esteller, Manel ^e,h,i   Orntoft, Torben F ^d   Dermitzakis, Emmanouil T ^a,b,c  

^a UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^b UNIVERSITY OF GENEVA   (Switzerland)

^c SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^d AARHUS UNIVERSITY HOSPITAL   (Denmark)

^e BELLVITGE BIOMEDICAL RESEARCH INSTITUTE IDIBELL   (Spain)

^f INSTITUTE OF CANCER RESEARCH   (United Kingdom)

^g UNIVERSITY OF OXFORD   (United Kingdom)

^h UNIVERSITY OF BARCELONA   (Spain)

ⁱ INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELES; CELL TRANSFORMATION, NEOPLASTIC; COLORECTAL NEOPLASMS; DNA METHYLATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; GERM-LINE MUTATION; HUMANS; INTESTINAL MUCOSA; QUANTITATIVE TRAIT LOCI; REGULATORY SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION FACTORS; TRANSCRIPTOME;

EID: 84905581513     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature13602     Document Type: Article

References (20)

1. Huang, F. W. et al. Highly recurrent TERT promoter mutations in human melanoma. Science 339, 957-959 (2013).
2. Dvinge, H. et al. The shaping and functional consequences of the microRNA landscape in breast cancer. Nature 497, 378-382 (2013).
3. Grundberg, E. et al. Mapping cis-and trans-regulatory effects across multiple tissues in twins. Nature Genet. 44, 1084-1089 (2012).
4. Lappalainen, T., Montgomery, S. B., Nica, A. C. & Dermitzakis, E. T. Epistatic selection between coding and regulatory variation in human evolution and disease. Am. J. Hum. Genet. 89, 459-463 (2011).
5. The 1000 Genomes Project Consortium An integrated map of genetic variation from 1, 092 human genomes. Nature 491, 56-65 (2012).
6. The Cancer Genome AtlasComprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330-337 (2012).
7. Perez-Llamas, C. & Lopez-Bigas, N. Gitools: analysis and visualisation of genomic data using interactive heat-maps. PLoS ONE 6, e19541 (2011).
8. Tamborero, D. et al. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Scientific Rep. 2, 2650 (2013).
9. Ma, C. et al. Extracellular matrix protein big-h3/TGFBI promotes metastasis of colon cancer by enhancing cell extravasation. Genes Dev. 22, 308-321 (2008).
10. Sun, D. et al. MicroRNA-31 activates the RAS pathway and functions as an oncogenic MicroRNA in human colorectal cancerby repressing RAS p21 GTPase activating protein 1 (RASA1). J. Biol. Chem. 288, 9508-9518 (2013).
11. Schweinfest, C. W., Henderson, K. W., Suster, S., Kondoh, N. & Papas, T. S. Identification of a colon mucosa gene that is down-regulated in colon adenomas and adenocarcinomas. Proc. Natl Acad. Sci. USA 90, 4166-4170 (1993).
12. Thorsen, K. et al. Alternative splicing ofSLC39A14 in colorectal cancer is regulated by the Wnt pathway. Mol. Cell. Proteom. 10, M110. 002998 (2011).
13. Lappalainen, T. et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501, 506-511 (2013).
14. Emi, M. et al. Frequent loss of heterozygosity for loci on chromosome 8p in hepatocellular carcinoma, colorectal cancer, and lung cancer. Cancer Res. 52, 5368-5372 (1992).
15. Matsuzaki, K. et al. The relationship between global methylation level, loss of heterozygosity, and microsatellite instability in sporadic colorectal cancer. Clin. Cancer Res. 11, 8564-8569 (2005).
16. Bamford, S. et al. The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br. J. Cancer 91, 355-358 (2004).
17. Nica, A. C. et al. The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet. 7, e1002003 (2011).
18. Aerts, S. & Cools, J. Cancer: Mutations close in on gene regulation. Nature 499, 35-36 (2013).
19. Dalla-Torre, C. A. et al. Effects of THBS3, SPARC and SPP1 expression on biological behavior and survival in patients with osteosarcoma. BMC Cancer 6, 237 (2006).
20. Yan, J. et al. Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. Cell 154, 801-813 (2013).