Identification of novel mutations by exome sequencing in African American colorectal cancer patients

Cancer

Volumn 121, Issue 1, 2015, Pages 34-42

  Ashktorab, Hassan ^a   Daremipouran, Mohammad ^a   Devaney, Joe ^b   Varma, Sudhir ^c   Rahi, Hamed ^a   Lee, Edward ^a   Shokrani, Babak ^a   Schwartz, Russell ^d   Nickerson, Michael L ^e   Brim, Hassan ^a  

^a HOWARD UNIVERSITY COLLEGE OF MEDICINE   (United States)

^b CHILDREN'S NATIONAL MEDICAL CENTER   (United States)

^c Hithru LLC   (United States)

^d CARNEGIE MELLON UNIVERSITY   (United States)

^e NATIONAL CANCER INSTITUTE   (United States)

Author keywords

APC; Cancer pathways; Mutation; Oncogene; Tumor suppressors

Indexed keywords

APC PROTEIN; B RAF KINASE; K RAS PROTEIN; WNT PROTEIN; APC PROTEIN, HUMAN; BRAF PROTEIN, HUMAN; KRAS PROTEIN, HUMAN; ONCOPROTEIN; PHOSPHATIDYLINOSITOL 3 KINASE; PIK3CA PROTEIN, HUMAN; RAS PROTEIN;

ADULT; AFRICAN AMERICAN; AGED; ARTICLE; BRAF GENE; CANCER INCIDENCE; CANCER PATIENT; CLINICAL ARTICLE; COLORECTAL CANCER; CONTROLLED STUDY; DISEASE ACTIVITY; DISEASE ASSOCIATION; DNA SEQUENCE; EXOME; FEMALE; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCATION; GENE MUTATION; GENETIC ASSOCIATION; GENETIC VARIABILITY; HUMAN; KRAS GENE; MALE; MIDDLE AGED; MOLECULAR PATHOLOGY; ONCOGENE; OUTCOME ASSESSMENT; PIK3CA GENE; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SPECTROSCOPY; TUMOR SUPPRESSOR GENE; VERY ELDERLY; WHOLE EXOME SEQUENCING; WNT GENE; ADENOCARCINOMA; COLORECTAL NEOPLASMS; COPY NUMBER VARIATION; ETHNOLOGY; GENETICS; MUTATION; PROCEDURES; SIGNAL TRANSDUCTION;

ADENOCARCINOMA; ADENOMATOUS POLYPOSIS COLI PROTEIN; ADULT; AFRICAN AMERICANS; AGED; AGED, 80 AND OVER; COLORECTAL NEOPLASMS; DNA COPY NUMBER VARIATIONS; EXOME; FEMALE; HUMANS; MALE; MIDDLE AGED; MUTATION; PHOSPHATIDYLINOSITOL 3-KINASES; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTO-ONCOGENE PROTEINS; PROTO-ONCOGENE PROTEINS B-RAF; RAS PROTEINS; SEQUENCE ANALYSIS, DNA; SIGNAL TRANSDUCTION;

EID: 84918779211     PISSN: 0008543X     EISSN: 10970142     Source Type: Journal    
DOI: 10.1002/cncr.28922     Document Type: Article

References (48)

1. Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D. Global cancer statistics. CA Cancer J Clin. 2011;61:69-90.
2. Siegel R, Desantis C, Virgo K, et al. Cancer treatment and survivorship statistics, 2012. CA Cancer J Clin. 2012;62:220-241.
3. Ashktorab H, Paydar M, Namin HH, et al. Prevalence of colorectal neoplasia among young African Americans and Hispanic Americans. Dig Dis Sci. 2014;59:446-450.
4. Fearon ER. Molecular genetics of colorectal cancer. Annu Rev Pathol. 2011;6:479-507.
5. Jones S, Chen WD, Parmigiani G, et al. Comparative lesion sequencing provides insights into tumor evolution. Proc Natl Acad Sci U S A. 2008;105:4283-4288.
6. Network CGA. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487:330-337.
7. Wood LD, Parsons DW, Jones S, et al. The genomic landscapes of human breast and colorectal cancers. Science. 2007;318:1108-1113
8. Bass AJ, Lawrence MS, Brace LE, et al. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat Genet. 2011;43:964-968.
9. Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA Jr, Kinzler KW. Cancer genome landscapes. Science. 2013;339:1546-1558.
10. Ashktorab H, Rahi H, Soltani S, et al. Novel mutation and hypome-thylation define distinct biological subgroups of altered KRAS colon tumors. AACR. 2013.
11. Ashktorab H, Rahi H, Wansley D, et al. Toward a comprehensive and systematic methylome signature in colorectal cancers. Epigenetics. 2013;8:807-815
12. Ashktorab H, Smoot DT, Farzanmehr H, et al. Clinicopathological features and microsatellite instability (MSI) in colorectal cancers from African Americans. Int J Cancer. 2005;116:914-919.
13. Brim H, Hasszadeh H, Schaffer AA, et al. Genomic aberrations in an African American colorectal cancer cohort reveals a MSI-specific profile and chromosome X amplification in male patients. PLoS One. 2012;7:e40392
14. Kumar K, Brim H, Mokarram P, et al. Distinct BRAF (V600E) and KRAS mutations in high microsatellite instability sporadic colorectal cancer in African Americans. Clin Cancer Res. 2009;15:1155-1161
15. Chun SY, Johnson C, Washburn JG, Cruz-Correa MR, Dang DT, Dang LH. Oncogenic KRAS modulates mitochondrial metabolism in human colon cancer cells by inducing HIF-1alpha and HIF-2alpha target genes. Mol Cancer. 2010;9:293.
16. Femia AP, Dolara P, Giannini A, Salvadori M, Biggeri A, Caderni G. Frequent mutation of Apc gene in rat colon tumors and mucin-depleted foci, preneoplastic lesions in experimental colon carcinogen-esis. Cancer Res. 2007;67:445-449.
17. Moreno-Bueno G, Hardisson D, Sanchez C, et al. Abnormalities of the APC/beta-catenin pathway in endometrial cancer. Oncogene. 2002;21:7981-7990.
18. Nagel R, le Sage C, Diosdado B, et al. Regulation of the adenoma-tous polyposis coli gene by the miR-135 family in colorectal cancer. Cancer Res. 2008;68:5795-5802.
19. Segditsas S, Rowan AJ, Howarth K, et al. APC and the three-hit hypothesis. Oncogene. 2009;28:146-155.
20. Bacolod MD, Barany F. Molecular profiling of colon tumors: the search for clinically relevant biomarkers of progression, prognosis, therapeutics, and predisposition. Ann Surg Oncol. 2011;18:3694-3700.
21. Seshagiri S, Stawiski EW, Durinck S, et al. Recurrent R-spondin fusions in colon cancer. Nature. 2012;488:660-664.
22. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589-595.
23. McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297-1303.
24. DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491-498.
25. Dees ND, Zhang Q, Kandoth C, et al. MuSiC: identifying mutational significance in cancer genomes. Genome Res. 2012;22:1589-1598.
26. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754-1760.
27. Eckhardt F, Lewin J, Cortese R, et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet. 2006;38:1378-1385.
28. Olivier M, Hussain SP, Caron de Fromentel C, Hainaut P, Harris CC. TP53 mutation spectra and load: a tool for generating hypotheses on the etiology of cancer. IARC Sci Publ. 2004:247-270.
29. Costello JF, Fruhwald MC, Smiraglia DJ, et al. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet. 2000;24:132-138.
30. Clevers H, Nusse R. Wnt/beta-catenin signaling and disease. Cell. 2012;149:1192-1205.
31. Vogelstein B, Kinzler KW. Winning the war: science parkour. Sci Transl Med. 2012;4:127ed122.
32. Diaz LA Jr, Williams RT, Wu J, et al. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 2012;486:537-540.
33. Perreault N, Katz JP, Sackett SD, Kaestner KH. Foxl1 controls the Wnt/beta-catenin pathway by modulating the expression of proteo-glycans in the gut. J Biol Chem. 2001;276:43328-43333.
34. Reya T, Clevers H. Wnt signalling in stem cells and cancer. Nature. 2005;434:843-850.
35. van Es JH, Jay P, Gregorieff A, et al. Wnt signalling induces maturation of Paneth cells in intestinal crypts. Nat Cell Biol. 2005;7:381-386.
36. Choi K, Chen J, Mitra S, Sarna SK. Impaired integrity of DNA after recovery from inflammation causes persistent dysfunction of colo-nic smooth muscle. Gastroenterology. 2011;141:1293-1301.
37. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144:646-674.
38. Kandoth C, McLellan MD, Vandin F, et al. Mutational landscape and significance across 12 major cancer types. Nature. 2013;502: 333-339.
39. Tamborero D, Gonzalez-Perez A, Perez-Llamas C, et al. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep. 2013;3:2650.
40. Lawrence MS, Stojanov P, Mermel CH, et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature. 2014; 505:495-501.
41. Chevillard-Briet M, Quaranta M, Grezy A, et al. Interplay between chromatin-modifying enzymes controls colon cancer progression through Wnt signaling. Hum Mol Genet. 2014;23:2120-2131
42. Fatemi M, Brim H, Ashktorab H. Epigenetic silencing of CHD5, a novel tumor suppressor gene, occurs in early colorectal cancer stages. Cancer. 2014;120:172-180
43. Ashktorab H, Belgrave K, Hosseinkhah F, et al. Global histone H4 acetylation and HDAC2 expression in colon adenoma and carcinoma. Dig Dis Sci. 2009;54:2109-2117.
44. Kume K, Iizumi Y, Shimada M, et al. Role of N-end rule ubiquitin ligases UBR1 and UBR2 in regulating the leucine-mTOR signaling pathway. Genes Cells. 2010;15:339-349.
45. Brim H, Mokarram P, Naghibalhossaini F, et al. Impact of BRAF, MLH1 on the incidence of microsatellite instability high colorectal cancer in populations based study. Mol Cancer. 2008;7:68.
46. Ashktorab H, Schaffer AA, Daremipouran M, Smoot DT, Lee E, Brim H. Distinct genetic alterations in colorectal cancer. PLoS One. 2010;5:e8879.
47. Smits R, Kielman MF, Breukel C, et al. Apc1638T: a mouse model delineating critical domains of the adenomatous polyposis coli protein involved in tumorigenesis and development. Genes Dev. 1999; 13:1309-1321.
48. Valenta T, Hausmann G, Basler K. The many faces and functions of beta-catenin. EMBO J. 2012;31:2714-2736.