The 14q22.2 colorectal cancer variant rs4444235 shows cis-acting regulation of BMP4

Oncogene

Volumn 31, Issue 33, 2012, Pages 3777-3784

  Lubbe, S J ^a   Pittman, A M ^a   Olver, B ^a   Lloyd, A ^a   Vijayakrishnan, J ^a   Naranjo, S ^b   Dobbins, S ^a   Broderick, P ^a   Gomez Skarmeta J L ^b   Houlston, R S ^a  

^a INSTITUTE OF CANCER RESEARCH   (United Kingdom)

^b Departamento de Biología Molecular e Ingeniería Bioquímica   (Spain)

Author keywords

bone morphogenetic protein 4; cis regulatory; colorectal cancer

Indexed keywords

BONE MORPHOGENETIC PROTEIN 4; DEOXYRIBONUCLEASE I;

ADULT; ALLELE; ARTICLE; BIOINFORMATICS; BMP4 GENE; CANCER CELL; CHROMATIN; CHROMOSOME 14Q; COLORECTAL CANCER; ENHANCER REGION; FEMALE; GENE; GENE CONTROL; GENE EXPRESSION; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC RISK; GENETIC VARIABILITY; HETEROZYGOSITY; HUMAN; HUMAN CELL; MAJOR CLINICAL STUDY; MALE; PRIORITY JOURNAL; REPORTER GENE; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION REGULATION;

ALLELES; BONE MORPHOGENETIC PROTEIN 4; CHROMOSOMES, HUMAN, PAIR 14; COLORECTAL NEOPLASMS; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84865247240     PISSN: 09509232     EISSN: 14765594     Source Type: Journal    
DOI: 10.1038/onc.2011.564     Document Type: Article

References (36)

1. Aaltonen L, Johns L, Jarvinen H, Mecklin JP, Houlston R. (2007). Explaining the familial colorectal cancer risk associated with mismatch repair (MMR)-deficient and MMR-stable tumors. Clin Cancer Res 13: 356-361. (Pubitemid 46121890)
2. Abdel-Rahman WM, Katsura K, Rens W, Gorman PA, Sheer D, Bicknell D et al. (2001). Spectral karyotyping suggests additional subsets of colorectal cancers characterized by pattern of chromosome rearrangement. Proc Natl Acad Sci USA 98: 2538-2543. (Pubitemid 32209517)
3. Broderick P, Carvajal-Carmona L, Pittman AM, Webb E, Howarth K, Rowan A et al. (2007). A genome-wide association study shows that common alleles of SMAD7 influence colorectal cancer risk. Nat Genet 39: 1315-1317. (Pubitemid 350034998)
4. Deng H, Makizumi R, Ravikumar TS, Dong H, Yang W, Yang WL. (2007). Bone morphogenetic protein-4 is overexpressed in colonic adenocarcinomas and promotes migration and invasion of HCT116 cells. Exp Cell Res 313: 1033-1044. (Pubitemid 46273448)
5. Eisen T, Matakidou A, Houlston R. (2008). Identification of low penetrance alleles for lung cancer: the GEnetic Lung CAncer Predisposition Study (GELCAPS). BMC Cancer 8: 244.
6. Fried M, Crothers DM. (1981). Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res 9: 6505-6525.
7. GaasenbeekM, Howarth K, Rowan AJ, Gorman PA, Jones A, Chaplin T et al. (2006). Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex changes and multiple forms of chromosomal instability in colorectal cancers. Cancer Res 66: 3471-3479.
8. Garner MM, Revzin A. (1981). A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res 9: 3047-3060.
9. Gomez-Skarmeta JL, Lenhard B, Becker TS. (2006). New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences. Dev Dyn 235: 870-885.
10. He XC, Zhang J, Tong WG, Tawfik O, Ross J, Scoville DH et al. (2004). BMP signaling inhibits intestinal stem cell self-renewal through suppression of Wnt-beta-catenin signaling. Nat Genet 36: 1117-1121. (Pubitemid 41184475)
11. Heinemeyer T, Wingender E, Reuter I, Hermjakob H, Kel AE, Kel OV et al. (1998). Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res 26: 362-367. (Pubitemid 28295292)
12. Houlston RS, Cheadle J, Dobbins SE, Tenesa A, Jones AM, Howarth K et al. (2010). 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.
13. Houlston RS, Webb E, Broderick P, Pittman AM, Di Bernardo MC, Lubbe S et al. (2008). Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. Nat Genet 40: 1426-1435.
14. Jaeger E, Webb E, Howarth K, Carvajal-Carmona L, Rowan A, Broderick P et al. (2008). Common genetic variants at the CRAC1 (HMPS) locus on chromosome 15q13.3 influence colorectal cancer risk. Nat Genet 40: 26-28.
15. Kawai K, Viars C, Arden K, Tarin D, Urquidi V, Goodison S. (2002). Comprehensive karyotyping of the HT-29 colon adenocarcinoma cell line. Genes Chromosomes Cancer 34: 1-8. (Pubitemid 34260590)
16. Kosinski C, Li VS, Chan AS, Zhang J, Ho C, Tsui WY et al. (2007). Gene expression patterns of human colon tops and basal crypts and BMP antagonists as intestinal stem cell niche factors. Proc Natl Acad Sci USA 104: 15418-15423. (Pubitemid 47502932)
17. Lichtenstein P, Holm NV, Verkasalo PK, Iliadou A, Kaprio J, Koskenvuo M et al. (2000). Environmental and heritable factors in the causation of cancer - analyses of cohorts of twins from Sweden, Denmark, and Finland. N Engl J Med 343: 78-85. (Pubitemid 30451850)
18. Liu C, Calogero A, Ragona G, Adamson E, Mercola D. (1996). EGR-1, the reluctant suppression factor: EGR-1 is known to function in the regulation of growth, differentiation, and also has significant tumor suppressor activity and a mechanism involving the induction of TGF-beta1 is postulated to account for this suppressor activity. Crit Rev Oncog 7: 101-125.
19. Lo HS, Wang Z, Hu Y, Yang HH, Gere S, Buetow KH et al. (2003). Allelic variation in gene expression is common in the human genome. Genome Res 13: 1855-1862. (Pubitemid 36987191)
20. Lubbe SJ, Webb EL, Chandler IP, Houlston RS. (2009). Implications of familial colorectal cancer risk profiles and microsatellite instability status. J Clin Oncol 27: 2238-2244.
21. Milani L, Gupta M, Andersen M, Dhar S, Fryknas M, Isaksson A et al. (2007). Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells. Nucleic Acids Res 35: e34.
22. Palin K, Taipale J, Ukkonen E. (2006). Locating potential enhancer elements by comparative genomics using the EEL software. Nat Protoc 1: 368-374.
23. Penegar S, Wood W, Lubbe S, Chandler I, Broderick P, Papaemmanuil E et al. (2007). National study of colorectal cancer genetics. Br J Cancer 97: 1305-1309. (Pubitemid 350035800)
24. Pittman AM, Naranjo S, Jalava SE, Twiss P, Ma Y, Olver B et al. (2010). Allelic variation at the 8q23.3 colorectal cancer risk locus functions as a cis-acting regulator of EIF3H. PLoS Genet 6: e1001126.
25. Pittman AM, Naranjo S, Webb E, Broderick P, Lips EH, van Wezel T et al. (2009). The colorectal cancer risk at 18q21 is caused by a novel variant altering SMAD7 expression. Genome Res 19: 987-993.
26. Polakis P. (2000). Wnt signaling and cancer. Genes Dev 14: 1837-1851. (Pubitemid 30639518)
27. Pomerantz MM, Ahmadiyeh N, Jia L, Herman P, Verzi MP, Doddapaneni H et al. (2009). The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat Genet 41: 882-884.
28. Pregizer S, Mortlock DP. (2009). Control of BMP gene expression by long-range regulatory elements. Cytokine Growth Factor Rev 20: 509-515.
29. Takash W, Canizares J, Bonneaud N, Poulat F, Mattei MG, Jay P et al. (2001). SOX7 transcription factor: sequence, chromosomal localisation, expression, transactivation and interference with Wnt signalling. Nucleic Acids Res 29: 4274-4283. (Pubitemid 33064768)
30. Tenesa A, Farrington SM, Prendergast JG, Porteous ME, Walker M, Haq N et al. (2008). 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. (Pubitemid 351601219)
31. Tomlinson I, Carvajal-Carmona L, Dobbins SE, Tenesa A, Jones A, Howarth K et al. (2011). Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4 and BMP2 explain part of the missing heritability of colorectal cancer. PLoS Genet 7: e1002105.
32. Tomlinson I, Webb E, Carvajal-Carmona L, Broderick P, Kemp Z, Spain S et al. (2007). A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21. Nat Genet 39: 984-988. (Pubitemid 47185182)
33. Tomlinson IP, Webb E, Carvajal-Carmona L, Broderick P, Howarth K, Pittman AM et al. (2008). A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3. Nat Genet 40: 623-630. (Pubitemid 351601204)
34. Tsushimi T, Noshima S, Oga A, Esato K, Sasaki K. (2001). DNA amplification and chromosomal translocations are accompanied by chromosomal instability: analysis of seven human colon cancer cell lines by comparative genomic hybridization and spectral karyotyping. Cancer Genet Cytogenet 126: 34-38. (Pubitemid 32416523)
35. Tuupanen S, Turunen M, Lehtonen R, Hallikas O, Vanharanta S, Kivioja T et al. (2009). The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. Nat Genet 41: 885-890.
36. Zanke BW, Greenwood CM, Rangrej J, Kustra R, Tenesa A, Farrington SM et al. (2007). Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24. Nat Genet 39: 989-994. (Pubitemid 47185183)