The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling

Nature Genetics

Volumn 41, Issue 8, 2009, Pages 885-890

  Tuupanen, Sari ^a   Turunen, Mikko ^a,b   Lehtonen, Rainer ^a   Hallikas, Outi ^a,b   Vanharanta, Sakari ^a,h   Kivioja, Teemu ^a,b   Björklund, Mikael ^a,b   Wei, Gonghong ^a,b   Yan, Jian ^a,b   Niittymäki, Iina ^a   Mecklin, Jukka Pekka ^c   Järvinen, Heikki ^d   Ristimäki, Ari ^a,e   Di Bernardo, Mariachiara ^f   East, Phil ^g   Carvajal Carmona, Luis ^g   Houlston, Richard S ^f   Tomlinson, Ian ^g   Palin, Kimmo ^a,i   Ukkonen, Esko ^a   Karhu, Auli ^a   Taipale, Jussi ^a,b   Aaltonen, Lauri A ^a   more..

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

^c JYVÄSKYLÄ CENTRAL HOSPITAL   (Finland)

^d HELSINKI UNIVERSITY CENTRAL HOSPITAL   (Finland)

^e UNIVERSITY OF OULU   (Finland)

^f INSTITUTE OF CANCER RESEARCH   (United Kingdom)

^g UNIVERSITY OF OXFORD   (United Kingdom)

^h MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

ⁱ WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BETA CATENIN; DNA; DNA BINDING PROTEIN; IMMUNOGLOBULIN G; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR 4; UNCLASSIFIED DRUG; WNT PROTEIN;

ALGORITHM; ALLELE; ANIMAL EXPERIMENT; ARTICLE; BINDING SITE; CANCER CELL CULTURE; CANCER RISK; CANCER SUSCEPTIBILITY; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME 8Q; COLON ADENOMA; COLON CARCINOGENESIS; COLORECTAL CANCER; COMPUTER ANALYSIS; EMBRYO; ENHANCER REGION; GENOME; GENOME WIDE ASSOCIATION; GENOTYPE; HUMAN; HUMAN CELL; HUMAN GENOME; MOUSE; NONHUMAN; ONCOGENE MYC; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION; REAL TIME POLYMERASE CHAIN REACTION; REPORTER GENE; SINGLE NUCLEOTIDE POLYMORPHISM; TISSUE SPECIFICITY; TRANSCRIPTION REGULATION; TRANSGENIC MOUSE; TUMOR SUPPRESSOR GENE;

ANIMALS; BASE SEQUENCE; BETA CATENIN; BINDING SITES; CHROMOSOMES, HUMAN, PAIR 8; COLORECTAL NEOPLASMS; CONSERVED SEQUENCE; EMBRYO, MAMMALIAN; ENHANCER ELEMENTS, GENETIC; GENE DOSAGE; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MICE; MICE, TRANSGENIC; MOLECULAR SEQUENCE DATA; ORGAN SPECIFICITY; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN BINDING; PROTO-ONCOGENE PROTEINS C-MYC; REPRODUCIBILITY OF RESULTS; SIGNAL TRANSDUCTION; TCF TRANSCRIPTION FACTORS; WNT PROTEINS;

EID: 68149170044     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.406     Document Type: Article

References (54)

1. Couzin, J. & Kaiser, J. Genome-wide association. Closing the net on common disease genes. Science 316, 820-822 (2007).
2. Easton, D.F. & Eeles, R.A. Genome-wide association studies in cancer. Hum. Mol. Genet. 17, R109-R115 (2008).
3. Tomlinson, I. et al. A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21. Nat. Genet. 39, 984-988 (2007).
4. Zanke, B.W. et al. Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24. Nat. Genet. 39, 989-994 (2007).
5. Haiman, C.A. et al. A common genetic risk factor for colorectal and prostate cancer. Nat. Genet. 39, 954-956 (2007).
6. Yeager, M. et al. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat. Genet. 39, 645-649 (2007).
7. Zheng, S.L. et al. Cumulative association of five genetic variants with prostate cancer. N. Engl. J. Med. 358, 910-919 (2008).
8. Gruber, S.B. et al. Genetic variation in 8q24 associated with risk of colorectal cancer. Cancer Biol. Ther. 6, 1143-1147 (2007).
9. Poynter, J.N. et al. Variants on 9p24 and 8q24 are associated with risk of colorectal cancer: results from the Colon Cancer Family Registry. Cancer Res. 67, 11128-11132 (2007).
10. Tuupanen, S. et al. Allelic imbalance at rs6983267 suggests selection of the risk allele in somatic colorectal tumor evolution. Cancer Res. 68, 14-17 (2008).
11. Li, L. et al. A common 8q24 variant and the risk of colon cancer: a population-based case-control study. Cancer Epidemiol. Biomarkers Prev. 17, 339-342 (2008).
12. Schafmayer, C. et al. Investigation of the colorectal cancer susceptibility region on chromosome 8q24.21 in a large German case-control sample. Int. J. Cancer 124, 75-80 (2009).
13. Berndt, S.I. et al. Pooled analysis of genetic variation at chromosome 8q24 and colorectal neoplasia risk. Hum. Mol. Genet. 17, 2665-2672 (2008).
14. Yeager, M. et al. Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers. Hum. Genet. 124, 161-170 (2008).
15. He, T.C. et al. Identification of c-MYC as a target of the APC pathway. Science 281, 1509-1512 (1998).
16. Bienz, M. & Clevers, H. Linking colorectal cancer to Wnt signaling. Cell 103, 311-320 (2000).
17. 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).
18. Hallikas, O. et al. Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124, 47-59 (2006).
19. Palin, K., Taipale, J. & Ukkonen, E. Locating potential enhancer elements by comparative genomics using the EEL software. Nat. Protocols 1, 368-374 (2006).
20. Barrett, J.C., Fry, B., Maller, J. & Daly, M.J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263-265 (2005).
21. Lickert, H. & Kemler, R. Functional analysis of cis-regulatory elements controlling initiation and maintenance of early Cdx1 gene expression in the mouse. Dev. Dyn. 225, 216-220 (2002).
22. Jiang, J. & Levine, M. Binding affinities and cooperative interactions with bHLH activators delimit threshold responses to the dorsal gradient morphogen. Cell 72, 741-752 (1993).
23. Yochum, G.S. et al. Serial analysis of chromatin occupancy identifies b-catenin target genes in colorectal carcinoma cells. Proc. Natl. Acad. Sci. USA 104, 3324-3329 (2007).
24. Robertson, G. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4, 651-657 (2007).
25. Heintzman, N.D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39, 311-318 (2007).
26. Barrow, J.R. et al. Ectodermal Wnt3/b-catenin signalling is required for the establishment and maintenance of the apical ectodermal ridge. Genes Dev. 17, 394-409 (2003).
27. Huelsken, J. et al. Requirement for b-catenin in anterior-posterior axis formation in mice. J. Cell Biol. 148, 567-578 (2000).
28. 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).
29. Broderick, P. et al. A genome-wide association study shows that common alleles of SMAD7 influence colorectal cancer risk. Nat. Genet. 39, 1315-1317 (2007).
30. Jaeger, E. et al. Common genetic variants at the CRAC1 (HMPS) locus on chromosome 15q13.3 influence colorectal cancer risk. Nat. Genet. 40, 26-28 (2008).
31. 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).
32. Kiemeney, L.A. et al. Sequence variant on 8q24 confers susceptibility to urinary bladder cancer. Nat. Genet. 40, 1307-1312 (2008).
33. Pomerantz, M.M. et al. The 8q24 cancer risk variant rs6983267 demonstrates long-range interaction with MYC in colorectal cancer. Nat. Genet. advance online publication, doi:10.1038/ng.403 (28 June 2009).
34. Korinek, V. et al. Constitutive transcriptional activation by a b-catenin-Tcf complex in APC/colon carcinoma. Science 275, 1784-1787 (1997).
35. Sansom, O.J. et al. Myc deletion rescues Apc deficiency in the small intestine. Nature 446, 676-679 (2007).
36. Herbst, A. & Kolligs, F.T. Wnt signaling as a therapeutic target for cancer. Methods Mol. Biol. 361, 63-91 (2007).
37. Soucek, L. et al. Modelling Myc inhibition as a cancer therapy. Nature 455, 679-683 (2008).
38. Van der Flier, L.G. et al. The intestinal Wnt/TCF signature. Gastroenterology 132, 628-635 (2007).
39. Otero, J.J., Fu, W., Kan, L., Cuadra, A.E. & Kessler, J.A. b-catenin signaling is required for neural differentiation of embryonic stem cells. Development 131, 3545-3557 (2004).
40. Miller, C. & Sassoon, D.A. Wnt-7a maintains appropriate uterine patterning during the delopment of the mouse female reproductive tract. Development 125, 3201-3211 (1998).
41. Lei, Q. et al. Wnt signaling inhibitors regulate the transcriptional response to morphogenetic Shh-Gli signaling in the neural tube. Dev. Cell 11, 325-337 (2006).
42. Kioussi, C. et al. Identification of a Wnt/Dvl/b-catenin - Pitx2 pathway mediating cell-type-specific proliferation during development. Cell 111, 673-685 (2002).
43. Aaltonen, L.A. et al. Incidence of hereditary nonpolyposis colorectal cancer and the feasibility of molecular screening for the disease. N. Engl. J. Med. 338, 1481-1487 (1998).
44. Salovaara, R. et al. Population-based molecular detection of hereditary nonpolyposis colorectal cancer. J. Clin. Oncol. 18, 2193-2200 (2000).
45. Badis, G. et al. Diversity and complexity in DNA recognition by transcription factors. Science advance online publication, doi:10.1126/science.1162327 (14 May 2009).
46. Hallikas, O. & Taipale, J. High-throughput assay for determining specificity and affinity of protein-DNA binding interactions. Nat. Protoc. 1, 215-222 (2006).
47. Taipale, J., Cooper, M.K., Maiti, T. & Beachy, P.A. Patched acts catalytically to suppress the activity of Smoothened. Nature 418, 892-897 (2002).
48. Turunen, M.M., Dunlop, T.W., Carlberg, C. & Va ̈isanen, S. Selective use of multiple vitamin D response elements underlies the 1 a, 25-dihydroxyvitamin D3-mediated negative regulation of the human CYP27B1 gene. Nucleic Acids Res. 35, 2734-2747 (2007).
49. Audic, S. & Claverie, J.M. The significance of digital gene expression profiles. Genome Res. 7, 986-995 (1997).
50. Kwan, T. et al. Genome-wide analysis of transcript isoform variation in humans. Nat. Genet. 40, 225-231 (2008).
51. The International HapMap Consortium. The International HapMap Project. Nature 426, 789-796 (2003).
52. Smyth, G.K. in Bioinformatics and Computional Biology Solutions using R and Bioconductor (ed. Gentleman. R.) Limma: linear models for microarray data (Springer, New York, 2005).
53. Laiho, P. et al. Serrated carcinomas form a subclass of colorectal cancer with distinct molecular basis. Oncogene 26, 312-320 (2007).
54. Dai, M. et al. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res. 33, e175 (2005).