Functional annotation of colon cancer risk SNPs

Nature Communications

Volumn 5, Issue , 2014, Pages

  Yao, Lijing ^a   Tak, Yu Gyoung ^a   Berman, Benjamin P ^a   Farnham, Peggy J ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CANCER; GENE EXPRESSION; GENETIC VARIATION; GENOME; GENOMICS; MOLECULAR ANALYSIS; RISK FACTOR; TUMOR;

ARTICLE; CANCER RISK; COLON CANCER; ENHANCER REGION; EXON; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC RISK; GENETIC VARIABILITY; HISTONE MODIFICATION; HUMAN; HYPOTHESIS; POSITION WEIGHT MATRIX; PROMOTER REGION; QUANTITATIVE TRAIT LOCUS; SIGMOID; SINGLE NUCLEOTIDE POLYMORPHISM; COLON TUMOR; GENETIC PREDISPOSITION; GENETICS;

COLONIC NEOPLASMS; ENHANCER ELEMENTS, GENETIC; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS, GENETIC;

EID: 84922581297     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms6114     Document Type: Article

References (61)

1. Fearon, E. R. Molecular genetics of colorectal cancer. Annu. Rev. Pathol. 6, 479-507 (2011).
2. TheCancerGenomeAtlas. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330-337 (2012).
3. Hindorff, L. A. et al. Potential etiologic and functional implications of genomewide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA 106, 9362-9367 (2009).
4. Manolio, T. A. Genomewide association studies and assessment of the risk of disease. New Engl. J. Med. 363, 166-176 (2010).
5. Zanke, B. W. et al. Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24. Nat. Genet. 39, 989-994 (2007).
6. Tomlinson, I. P. et al. A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3. Nat. Genet. 40, 623-630 (2008).
7. Tenesa, A. et al. Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21. Nat. Genet. 40, 631-637 (2008).
8. Peters, U. et al. Identification of genetic susceptibility loci for colorectal tumors in a genome-wide meta-analysis. Gastroenterology 144, 799-807 e724 (2013).
9. Jia, W. H. et al. Genome-wide association analyses in East Asians identify new susceptibility loci for colorectal cancer. Nat. Genet. 45, 191-196 (2013).
10. Houlston, R. S. et al. Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. Nat. Genet. 40, 1426-1435 (2008).
11. Houlston, R. S. et al. Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33. Nat. Genet. 42, 973-977 (2010).
12. Dunlop, M. G. et al. Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk. Nat. Genet. 44, 770-776 (2012).
13. Schaub, M. A., Boyle, A. P., Kundaje, A., Batzoglou, S. & Snyder, M. Linking disease associations with regulatory information in the human genome. Genome Res. 22, 1748-1759 (2012).
14. Zentner, G. E. & Scacheri, P. C. The chromatin fingerprint of gene enhancer elements. J. Biol. Chem. 287, 30888-30896 (2012).
15. ENCODEConsortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
16. Frietze, S. et al. Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3. Genome. Biol. 13, R52 (2012).
17. Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190-1195 (2012).
18. Akhtar-Zaidi, B. et al. Epigenomic enhancer profiling defines a signature of colon cancer. Science 336, 736-739 (2012).
19. Hardison, R. C. Genome-wide epigenetic data facilitate understanding of disease susceptibility association studies. J. Biol. Chem. 287, 30932-30940 (2012).
20. Farnham, P. J. Thematic minireview series on results from the ENCODE project: integrative global analyses of regulatory regions in the human genome. J. Biol. Chem. 287, 30885-30887 (2012).
21. Coetzee, S. G., Rhie, S. K., Berman, B. P., Coetzee, G. A. & Noushmehr, H. FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs. Nucleic Acids Res. 40, e139 (2012).
22. Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6, 80-92 (2012).
23. Adzhubei, I. A. et al. A method and server for predicting damaging missense mutations. Nat. Methods 7, 248-249 (2010).
24. Choi, Y., Sims, G. E., Murphy, S., Miller, J. R. & Chan, A. P. Predicting the functional effect of amino acid substitutions and indels. PLoS ONE 7, e46688 (2012).
25. Koudritsky, M. & Domany, E. Positional distribution of human transcription factor binding sites. Nucleic Acids Res. 36, 6795-6805 (2008).
26. Stergachis, A. B. et al. Exonic transcription factor binding directs codon choice and affects protein evolution. Science 342, 1367-1372 (2013).
27. Blahnik, K. R. et al. Sole-search: An integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res. 38, e13 (2010).
28. Blahnik, K. R. et al. Characterization of the contradictory chromatin signatures at the 30 exons of zinc finger genes. PLoS ONE 6, e17121 (2011).
29. Wang, J. et al. Factorbook.org: a Wiki-based database for transcription factorbinding data generated by the ENCODE consortium. Nucleic Acids Res. 41, D171-D176 (2013).
30. Sanyal, A., Lajoie, B. R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109-113 (2012).
31. Sur, I. K. et al. Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors. Science 338, 1360-1363 (2012).
32. Breyer, J. P. et al. An expressed retrogene of the master embryonic stem cell gene POU5F1 is associated with prostate cancer susceptibility. Am. J. Hum. Genet. 94, 395-404 (2014).
33. Cao, Y., Bryan, T. M. & Reddel, R. R. Increased copy number of the TERT and TERC telomerase subunit genes in cancer cells. Cancer Sci. 99, 1092-1099 (2008).
34. Paredes, J. et al. Epithelial E- and P-cadherins: role and clinical significance in cancer. Biochim. Biophys. Acta 1826, 297-311 (2012).
35. Zhang, L., Smit-McBride, Z., Pan, X., Rheinhardt, J. & Hershey, J. W. An oncogenic role for the phosphorylated h-subunit of human translation initiation factor eIF3. J. Biol. Chem. 283, 24047-24060 (2008).
36. Li, X. et al. The atypical histone macroH2A1.2 interacts with HER-2 protein in cancer cells. J. Biol. Chem. 287, 23171-23183 (2012).
37. Li, Q. et al. MicroRNA-25 functions as a potential tumor suppressor in colon cancer by targeting Smad7. Cancer Lett. 335, 168-174 (2013).
38. Karagiannis, G. S., Berk, A., Dimitromanolakis, A. & Diamandis, E. P. Enrichment map profiling of the cancer invasion front suggests regulation of colorectal cancer progression by the bone morphogenetic protein antagonist, gremlin-1. Mol. Oncol. 7, 826-839 (2013).
39. Huang, G. L. et al. Activating transcription factor 1 is a prognostic marker of colorectal cancer. Asian Pac. J. Cancer Prev. 13, 1053-1057 (2012).
40. Hu, Y., Sun, Z., Zhang, A. & Zhang, J. SMAD7 rs12953717 polymorphism contributes to increased risk of colorectal cancer. Tumour Biol. 35, 695-699 (2013).
41. Deng, H. et al. Bone morphogenetic protein-4 is overexpressed in colonic adenocarcinomas and promotes migration and invasion of HCT116 cells. Exp. Cell. Res. 313, 1033-1044 (2007).
42. Danussi, C. et al. RHPN2 drives mesenchymal transformation in malignant glioma by triggering RhoA activation. Cancer Res. 73, 5140-5150 (2013).
43. Carneiro, P. et al. Therapeutic targets associated to E-cadherin dysfunction in gastric cancer. Expert Opin. Ther. Targets 17, 1187-1201 (2013).
44. Garte, S. J. The c-myc oncogene in tumor progression. Crit. Rev. Oncog. 4, 435-449 (1993).
45. Cheung, E. C. et al. TIGAR is required for efficient intestinal regeneration and tumorigenesis. Dev. Cell 25, 463-477 (2013).
46. Aumailley, M. The laminin family. Cell Adh. Migr. 7, 48-55 (2013).
47. Carvajal-Carmona, L. G. et al. Fine-mapping of colorectal cancer susceptibility loci at 8q23.3, 16q22.1 and 19q13.11: refinement of association signals and use of in silico analysis to suggest functional variation and unexpected candidate target genes. Hum. Mol. Genet. 20, 2879-2888 (2011).
48. Ernst, J. & Kellis, M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat. Biotechnol. 28, 817-825 (2010).
49. Calo, E. & Wysocka, J. Modification of enhancer chromatin: what, how, and why? Mol. Cell 49, 825-837 (2013).
50. Bonn, S. et al. Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat. Genet. 44, 148-156 (2012).
51. Home, P. et al. Altered subcellular localization of transcription factor TEAD4 regulates first mammalian cell lineage commitment. Proc. Natl Acad. Sci. USA 109, 7362-7367 (2012).
52. Jeon, B. N. et al. KR-POK interacts with p53 and represses its ability to activate transcription of p21WAF1/CDKN1A. Cancer Res. 72, 1137-1148 (2012).
53. Knosel, T. et al. Loss of desmocollin 1-3 and homeobox genes PITX1 and CDX2 are associated with tumor progression and survival in colorectal carcinoma. Int. J. Colorectal. Dis. 27, 1391-1399 (2012).
54. Qi, D. L. et al. Identification of PITX1 as a TERT suppressor gene located on human chromosome 5. Mol. Cell Biol. 31, 1624-1636 (2011).
55. Guan, Y. et al. Amplification of PVT1 contributes to the pathophysiology of ovarian and breast cancer. Clin. Cancer Res. 13, 5745-5755 (2007).
56. Huppi, K., Pitt, J. J., Wahlberg, B. M. & Caplen, N. J. The 8q24 gene desert: an oasis of non-coding transcriptional activity. Front. Genet. 3, 69 (2012).
57. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
58. Hazelett, D. J. et al. Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet. 10, e1004102 (2014).
59. Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 490, 61-70 (2012).
60. Li, Q. et al. Integrative eQTL-based analyses reveal the biology of breast cancer risk loci. Cell 152, 633-641 (2013).
61. Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645 (2009).