Somatic gene copy number alterations in colorectal cancer: New quest for cancer drivers and biomarkers

Oncogene

Volumn 35, Issue 16, 2016, Pages 2011-2019

  Wang, H ^a   Liang, L ^a   Fang, J Y ^a   Xu, J ^a  

^a SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA; TUMOR MARKER;

CANCER GENETICS; CARCINOGENESIS; CHROMOSOME 1; CHROMOSOME 10; CHROMOSOME 11; CHROMOSOME 12; CHROMOSOME 13; CHROMOSOME 15; CHROMOSOME 16; CHROMOSOME 17; CHROMOSOME 18; CHROMOSOME 19; CHROMOSOME 2; CHROMOSOME 20; CHROMOSOME 22; CHROMOSOME 3; CHROMOSOME 4; CHROMOSOME 5; CHROMOSOME 6; CHROMOSOME 7; CHROMOSOME 8; COLORECTAL CANCER; COPY NUMBER VARIATION; GAIN OF FUNCTION MUTATION; GENE FREQUENCY; GENETIC ASSOCIATION; HUMAN; NONHUMAN; PRIORITY JOURNAL; REVIEW; SEX CHROMOSOME; SOMATIC MUTATION; SYSTEMATIC REVIEW; COLORECTAL TUMOR; GENETIC VARIATION; GENETICS; HUMAN CHROMOSOME;

BIOMARKERS, TUMOR; CHROMOSOMES, HUMAN; COLORECTAL NEOPLASMS; GENOMIC STRUCTURAL VARIATION; HUMANS;

EID: 84938873541     PISSN: 09509232     EISSN: 14765594     Source Type: Journal    
DOI: 10.1038/onc.2015.304     Document Type: Review

References (154)

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. Issa JP. Colon cancer: it's CIN or CIMP. Clin Cancer Res 2008; 14: 5939-5940.
3. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD et al. Global variation in copy number in the human genome. Nature 2006; 444: 444-454.
4. Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nat Rev Genet 2009; 10: 551-564.
5. Pillaire MJ, Selves J, Gordien K, Gourraud PA, Gentil C, Danjoux M et al. A 'DNA replication' signature of progression and negative outcome in colorectal cancer. Oncogene 2010; 29: 876-887.
6. Carvalho B, Postma C, Mongera S, Hopmans E, Diskin S, van de Wiel MA et al. Multiple putative oncogenes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression. Gut 2009; 58: 79-89.
7. Diep CB, Kleivi K, Ribeiro FR, Teixeira MR, Lindgjaerde OC, Lothe RA. The order of genetic events associated with colorectal cancer progression inferred from meta-analysis of copy number changes. Genes, Chromosomes Cancer 2006; 45: 31-41.
8. Sheffer M, Bacolod MD, Zuk O, Giardina SF, Pincas H, Barany F et al. Association of survival and disease progression with chromosomal instability: a genomic exploration of colorectal cancer. Proc Natl Acad Sci USA 2009; 106: 7131-7136.
9. Brosens RP, Belt EJ, Haan JC, Buffart TE, Carvalho B, Grabsch H et al. Deletion of chromosome 4q predicts outcome in stage II colon cancer patients. Analyt Cell Pathol 2010; 33: 95-104.
10. Sapkota Y, Ghosh S, Lai R, Coe BP, Cass CE, Yasui Y et al. Germline DNA copy number aberrations identified as potential prognostic factors for breast cancer recurrence. PLoS One 2013; 8: e53850.
11. Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B et al. Pan-cancer patterns of somatic copy number alteration. Nat Genet 2013; 45: 1134-1140.
12. Lin CH, Lin JK, Chang SC, Chang YH, Chang HM, Liu JH et al. Molecular profile and copy number analysis of sporadic colorectal cancer in Taiwan. J Biomed Sci 2011; 18: 36.
13. Postma C, Koopman M, Buffart TE, Eijk PP, Carvalho B, Peters GJ et al. DNA copy number profiles of primary tumors as predictors of response to chemotherapy in advanced colorectal cancer. Ann Oncol 2009; 20: 1048-1056.
14. Eldai H, Periyasamy S, Al Qarni S, Al Rodayyan M, Muhammed Mustafa S, Deeb A et al. Novel genes associated with colorectal cancer are revealed by high resolution cytogenetic analysis in a patient specific manner. PLoS One 2013; 8: e76251.
15. Henningham A, Yamaguchi M, Aziz RK, Kuipers K, Buffalo CZ, Dahesh S et al. Mutual exclusivity of hyaluronan and hyaluronidase in invasive group A Streptococcus. J Biol Chem 2014; 289: 32303-32315.
16. Little SE, Popov S, Jury A, Bax DA, Doey L, Al-Sarraj S et al. Receptor tyrosine kinase genes amplified in glioblastoma exhibit a mutual exclusivity in variable proportions reflective of individual tumor heterogeneity. Cancer Res 2012; 72: 1614-1620.
17. Ciriello G, Cerami E, Sander C, Schultz N. Mutual exclusivity analysis identifies oncogenic network modules. Genome Res 2012; 22: 398-406.
18. Hou JP, Ma J. DawnRank: discovering personalized driver genes in cancer. Genome Med 2014; 6: 56.
19. Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R et al. Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods 2013; 10: 723-729.
20. Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol 2011; 12: R41.
21. Amgalan B, Lee H. DEOD: uncovering dominant effects of cancer-driver genes based on a partial covariance selection method. Bioinformatics 2015; 31: 2452-2460.
22. Gonzalez-Perez A, Lopez-Bigas N. Functional impact bias reveals cancer drivers. Nucleic Acids Res 2012; 40: e169.
23. Tamborero D, Lopez-Bigas N, Gonzalez-Perez A. Oncodrive-CIS: a method to reveal likely driver genes based on the impact of their copy number changes on expression. PLoS One 2013; 8: e55489.
24. Reimand J, Bader GD. Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Mol Syst Biol 2013; 9: 637.
25. Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J et al. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep 2013; 3: 2650.
26. Ali Hassan NZ, Mokhtar NM, Kok Sin T, Mohamed Rose I, Sagap I, Harun R et al. Integrated analysis of copy number variation and genome-wide expression profiling in colorectal cancer tissues. PLoS One 2014; 9: e92553.
27. Loo LW, Tiirikainen M, Cheng I, Lum-Jones A, Seifried A, Church JM et al. Integrated analysis of genome-wide copy number alterations and gene expression in microsatellite stable, CpG island methylator phenotype-negative colon cancer. Genes Chromosomes Cancer 2013; 52: 450-466.
28. Ali RH, Marafie MJ, Bitar MS, Al-Dousari F, Ismael S, Bin Haider H et al. Genderassociated genomic differences in colorectal cancer: clinical insight from feminization of male cancer cells. Int J Mol Sci 2014; 15: 17344-17365.
29. Xie T, Cho YB, Wang K, Huang D, Hong HK, Choi YL et al. Patterns of somatic alterations between matched primary and metastatic colorectal tumors characterized by whole-genome sequencing. Genomics 2014; 104: 234-241.
30. Gonzalez-Gonzalez M, Fontanillo C, Abad MM, Gutierrez ML, Mota I, Bengoechea O et al. Identification of a characteristic copy number alteration profile by high-resolution single nucleotide polymorphism arrays associated with metastatic sporadic colorectal cancer. Cancer 2014; 120: 1948-1959.
31. Liang L, Fang JY, Xu J. Gastric cancer and gene copy number variation: emerging cancer drivers for targeted therapy. Oncogene 2016; 35: 1475-1482.
32. Hu Y, Wang J, Qian J, Kong X, Tang J, Wang Y et al. Long noncoding RNA GAPLINC regulates CD44-dependent cell invasiveness and associates with poor prognosis of gastric cancer. Cancer Res 2014; 74: 6890-6902.
33. Liang WC, Fu WM, Wong CW, Wang Y, Wang WM, Hu GX et al. The LncRNA H19 promotes epithelial to mesenchymal transition by functioning as MiRNA sponges in colorectal cancer. Oncotarget 2015; e-pub ahead of print 5 June 2015.
34. Iguchi T, Uchi R, Nambara S, Saito T, Komatsu H, Hirata H et al. A long noncoding RNA, lncRNA-ATB, is involved in the progression and prognosis of colorectal cancer. Anticancer Res 2015; 35: 1385-1388.
35. Xue Y, Gu D, Ma G, Zhu L, Hua Q, Chu H et al. Genetic variants in lncRNA HOTAIR are associated with risk of colorectal cancer. Mutagenesis 2015; 30: 303-310.
36. Shi D, Zheng H, Zhuo C, Peng J, Li D, Xu Y et al. Low expression of novel lncRNA RP11-462C24.1 suggests a biomarker of poor prognosis in colorectal cancer. Med Oncol 2014; 31: 31.
37. Xiang JF, Yin QF, Chen T, Zhang Y, Zhang XO, Wu Z et al. Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res 2014; 24: 513-531.
38. Chen H, Xu J, Hong J, Tang R, Zhang X, Fang JY. Long noncoding RNA profiles identify five distinct molecular subtypes of colorectal cancer with clinical relevance. Mol Oncol 2014; 8: 1393-1403.
39. Hu Y, Chen HY, Yu CY, Xu J, Wang JL, Qian J et al. A long non-coding RNA signature to improve prognosis prediction of colorectal cancer. Oncotarget 2014; 5: 2230-2242.
40. Liang L, Ai L, Qian J, Fang JY, Xu J. Long noncoding RNA expression profiles in gut tissues constitute molecular signatures that reflect the types of microbes. Sci Rep 2015; 5: 11763.
41. Postma C, Terwischa S, Hermsen MA, van der Sijp JR, Meijer GA. Gain of chromosome 20q is an indicator of poor prognosis in colorectal cancer. Cell Oncol 2007; 29: 73-75.
42. Maffei M, Mongera S, Terpstra L, Donadini A, Voorham QJ, Meijer GA et al. Chromosome 20 aberrations at the diploid-aneuploid transition in sporadic colorectal cancer. Cytogenet Genome Res 2014; 144: 9-14.
43. Sillars-Hardebol AH, Carvalho B, Tijssen M, Belien JA, de Wit M, Delis-van Diemen PM et al. TPX2 and AURKA promote 20q amplicon-driven colorectal adenoma to carcinoma progression. Gut 2012; 61: 1568-1575.
44. Fu J, Bian M, Jiang Q, Zhang C. Roles of Aurora kinases in mitosis and tumorigenesis. Mol Cancer Res 2007; 5: 1-10.
45. Hossini AM, Eberle J. Apoptosis induction by Bcl-2 proteins independent of the BH3 domain. Biochem Pharmacol 2008; 76: 1612-1619.
46. Wang JC. Cellular roles of DNA topoisomerases: a molecular perspective. Nat Rev Mol Cell Biol 2002; 3: 430-440.
47. Thomas SM, Coppelli FM, Wells A, Gooding WE, Song J, Kassis J et al. Epidermal growth factor receptor-stimulated activation of phospholipase Cgamma-1 promotes invasion of head and neck squamous cell carcinoma. Cancer Res 2003; 63: 5629-5635.
48. Jones NP, Peak J, Brader S, Eccles SA, Katan M. PLCgamma1 is essential for early events in integrin signalling required for cell motility. J Cell Sci 2005; 118: 2695-2706.
49. Wells A, Grandis JR. Phospholipase C-gamma1 in tumor progression. Clin Exp Metastasis 2003; 20: 285-290.
50. Blume-Jensen P, Hunter T. Oncogenic kinase signalling. Nature 2001; 411: 355-365.
51. Yue SQ, Yang YL, Dou KF, Li KZ. Expression of PCNA and CD44mRNA in colorectal cancer with venous invasion and its relationship to liver metastasis. World J Gastroenterol 2003; 9: 2863-2865.
52. Fernandez-Sanchez ME, Gonatopoulos-Pournatzis T, Preston G, Lawlor MA, Cowling VH. S-adenosyl homocysteine hydrolase is required for Myc-induced mRNA cap methylation, protein synthesis, and cell proliferation. Mol Cell Biol 2009; 29: 6182-6191.
53. Cowling VH. Regulation of mRNA cap methylation. Biochem J 2010; 425: 295-302.
54. Darsigny M, Babeu JP, Seidman EG, Gendron FP, Levy E, Carrier J et al. Hepatocyte nuclear factor-4alpha promotes gut neoplasia in mice and protects against the production of reactive oxygen species. Cancer Res 2010; 70: 9423-9433.
55. Sabbah M, Prunier C, Ferrand N, Megalophonos V, Lambein K, De Wever O et al. CCN5, a novel transcriptional repressor of the transforming growth factor beta signaling pathway. Mol Cell Biol 2011; 31: 1459-1469.
56. Motoyama K, Tanaka F, Kosaka Y, Mimori K, Uetake H, Inoue H et al. Clinical significance of BMP7 in human colorectal cancer. Ann Surg Oncol 2008; 15: 1530-1537.
57. Quinlan KG, Verger A, Yaswen P, Crossley M. Amplification of zinc finger gene 217 (ZNF217) and cancer: when good fingers go bad. Biochim Biophys Acta 2007; 1775: 333-340.
58. Zhang ZC, Zheng LQ, Pan LJ, Guo JX, Yang GS. ZNF217 is overexpressed and enhances cell migration and invasion in colorectal carcinoma. Asian Pac J Cancer Prev 2015; 16: 2459-2463.
59. Ramirez-Ramirez R, Gutierrez-Angulo M, Magana MT, Moreno-Ortiz JM, Partida-Perez M, Muniz-Mendoza R et al. Effect of ZNF217 gene polymorphisms on colorectal cancer development in a Mexican population. Genet Mol Res 2015; 14: 362-367.
60. Horvath HC, Lakatos P, Kosa JP, Bacsi K, Borka K, Bises G et al. The candidate oncogene CYP24A1: a potential biomarker for colorectal tumorigenesis. J Histochem Cytochem 2010; 58: 277-285.
61. King AN, Beer DG, Christensen PJ, Simpson RU, Ramnath N. The vitamin D/CYP24A1 story in cancer. Anticancer Agents Med Chem 2010; 10: 213-224.
62. Fang Z, Xiong Y, Zhang C, Li J, Liu L, Li M et al. Coexistence of copy number increases of ZNF217 and CYP24A1 in colorectal cancers in a Chinese population. Oncol Lett 2010; 1: 925-930.
63. Guilmeau S, Flandez M, Bancroft L, Sellers RS, Tear B, Stanley P et al. Intestinal deletion of Pofut1 in the mouse inactivates notch signaling and causes enterocolitis. Gastroenterology 2008; 135: 849-860 860 e841-846.
64. Stahl M, Uemura K, Ge C, Shi S, Tashima Y, Stanley P. Roles of Pofut1 and O-fucose in mammalian Notch signaling. J Biol Chem 2008; 283: 13638-13651.
65. Yao D, Huang Y, Huang X, Wang W, Yan Q, Wei L et al. Protein O-fucosyltransferase 1 (Pofut1) regulates lymphoid and myeloid homeostasis through modulation of Notch receptor ligand interactions. Blood 2011; 117: 5652-5662.
66. Honma K, Iwao-Koizumi K, Takeshita F, Yamamoto Y, Yoshida T, Nishio K et al. RPN2 gene confers docetaxel resistance in breast cancer. Nat Med 2008; 14: 939-948.
67. Cano A, Perez-Moreno MA, Rodrigo I, Locascio A, Blanco MJ, del Barrio MG et al. The transcription factor snail controls epithelial-mesenchymal transitions by repressing E-cadherin expression. Nat Cell Biol 2000; 2: 76-83.
68. Stemmer V, de Craene B, Berx G, Behrens J. Snail promotes Wnt target gene expression and interacts with beta-catenin. Oncogene 2008; 27: 5075-5080.
69. Berg M, Agesen TH, Thiis-Evensen EINFAC-study group, Merok MA, Teixeira MR et al. Distinct high resolution genome profiles of early onset and late onset colorectal cancer integrated with gene expression data identify candidate susceptibility loci. Mol Cancer 2010; 9: 100.
70. Han SW, Kim HP, Shin JY, Jeong EG, Lee WC, Lee KH et al. Targeted sequencing of cancer-related genes in colorectal cancer using next-generation sequencing. PLoS One 2013; 8: e64271.
71. Cancer Genome Atlas Network, Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012; 487: 330-337.
72. Yoshida T, Kobayashi T, Itoda M, Muto T, Miyaguchi K, Mogushi K et al. Clinical omics analysis of colorectal cancer incorporating copy number aberrations and gene expression data. Cancer Inform 2010; 9: 147-161.
73. Sillars-Hardebol AH, Carvalho B, Belien JA, de Wit M, Delis-van Diemen PM, Tijssen M et al. BCL2L1 has a functional role in colorectal cancer and its protein expression is associated with chromosome 20q gain. J Pathol 2012; 226: 442-450.
74. Keino-Masu K, Masu M, Hinck L, Leonardo ED, Chan SS, Culotti JG et al. Deleted in Colorectal Cancer (DCC) encodes a netrin receptor. Cell 1996; 87: 175-185.
75. Fazeli A, Dickinson SL, Hermiston ML, Tighe RV, Steen RG, Small CG et al. Phenotype of mice lacking functional Deleted in colorectal cancer (Dcc) gene. Nature 1997; 386: 796-804.
76. Cho KR, Oliner JD, Simons JW, Hedrick L, Fearon ER, Preisinger AC et al. The DCC gene: structural analysis and mutations in colorectal carcinomas. Genomics 1994; 19: 525-531.
77. Fleming NI, Jorissen RN, Mouradov D, Christie M, Sakthianandeswaren A, Palmieri M et al. SMAD2, SMAD3 and SMAD4 mutations in colorectal cancer. Cancer Res 2013; 73: 725-735.
78. Ma Y, Yan F, Li L, Liu L, Sun J. Deletion and down-regulation of SMAD4 gene in colorectal cancers in a Chinese population. Chin J Cancer Res 2014; 26: 525-531.
79. Takagi Y, Kohmura H, Futamura M, Kida H, Tanemura H, Shimokawa K et al. Somatic alterations of the DPC4 gene in human colorectal cancers in vivo. Gastroenterology 1996; 111: 1369-1372.
80. Takagi Y, Koumura H, Futamura M, Aoki S, Ymaguchi K, Kida H et al. Somatic alterations of the SMAD-2 gene in human colorectal cancers. Br J Cancer 1998; 78: 1152-1155.
81. Wu CL, Kirley SD, Xiao H, Chuang Y, Chung DC, Zukerberg LR. Cables enhances cdk2 tyrosine 15 phosphorylation by Wee1, inhibits cell growth, and is lost in many human colon and squamous cancers. Cancer Res 2001; 61: 7325-7332.
82. Park, do Y, Sakamoto H, Kirley SD, Ogino S, Kawasaki T, Kwon E et al. The Cables gene on chromosome 18q is silenced by promoter hypermethylation and allelic loss in human colorectal cancer. Am J Pathol 2007; 171: 1509-1519.
83. Molina JR, Agarwal NK, Morales FC, Hayashi Y, Aldape KD, Cote G et al. PTEN, NHERF1 and PHLPP form a tumor suppressor network that is disabled in glioblastoma. Oncogene 2012; 31: 1264-1274.
84. Liu J, Weiss HL, Rychahou P, Jackson LN, Evers BM, Gao T. Loss of PHLPP expression in colon cancer: role in proliferation and tumorigenesis. Oncogene 2009; 28: 994-1004.
85. Liu XP, Kawauchi S, Oga A, Sato T, Ikemoto K, Ikeda E et al. Chromosomal aberrations detected by comparative genomic hybridization predict outcome in patients with colorectal carcinoma. Oncol Rep 2007; 17: 261-267.
86. Poulogiannis G, Ichimura K, Hamoudi RA, Luo F, Leung SY, Yuen ST et al. Prognostic relevance of DNA copy number changes in colorectal cancer. J Pathol 2010; 220: 338-347.
87. Storojeva I, Boulay JL, Ballabeni P, Buess M, Terracciano L, Laffer U et al. Prognostic and predictive relevance of DNAM-1, SOCS6 and CADH-7 genes on chromosome 18q in colorectal cancer. Oncology 2005; 68: 246-255.
88. Orsetti B, Selves J, Bascoul-Mollevi C, Lasorsa L, Gordien K, Bibeau F et al. Impact of chromosomal instability on colorectal cancer progression and outcome. BMC Cancer 2014; 14: 121.
89. Singhal SS, Singhal J, Yadav S, Dwivedi S, Boor PJ, Awasthi YC et al. Regression of lung and colon cancer xenografts by depleting or inhibiting RLIP76 (Ral-binding protein 1). Cancer Res 2007; 67: 4382-4389.
90. Knosel T, Schluns K, Stein U, Schwabe H, Schlag PM, Dietel M et al. Chromosomal alterations during lymphatic and liver metastasis formation of colorectal cancer. Neoplasia 2004; 6: 23-28.
91. Ogunbiyi OA, Goodfellow PJ, Gagliardi G, Swanson PE, Birnbaum EH, Fleshman JW et al. Prognostic value of chromosome 1p allelic loss in colon cancer. Gastroenterology 1997; 113: 761-766.
92. Stawski R, Piaskowski S, Stoczynska-Fidelus E, Wozniak K, Bienkowski M, Zakrzewska M et al. Reduced expression of ELAVL4 in male meningioma patients. Brain Tumor Pathol 2013; 30: 160-166.
93. Liu J, Li X, Dong GL, Zhang HW, Chen DL, Du JJ et al. In silico analysis and verification of S100 gene expression in gastric cancer. BMC Cancer 2008; 8: 261.
94. Rand V, Prebble E, Ridley L, Howard M, Wei W, Brundler MA et al. Investigation of chromosome 1q reveals differential expression of members of the S100 family in clinical subgroups of intracranial paediatric ependymoma. Br J Cancer 2008; 99: 1136-1143.
95. Feng Z, Hu W, de Stanchina E, Teresky AK, Jin S, Lowe S et al. The regulation of AMPK beta1, TSC2, and PTEN expression by p53: stress, cell and tissue specificity, and the role of these gene products in modulating the IGF-1-AKT-mTOR pathways. Cancer Res 2007; 67: 3043-3053.
96. Hoang D, Sue GR, Xu F, Li P, Narayan D. Absence of aneuploidy and gastrointestinal tumours in a man with a chromosomal 2q13 deletion and BUB1 monoallelic deficiency. BMJ Case Rep 2013; e-pub ahead of print, 25 February 2013; doi:10.1136/bcr-2013-008684.
97. Bavi P, Jehan Z, Bu R, Prabhakaran S, Al-Sanea N, Al-Dayel F et al. ALK gene amplification is associated with poor prognosis in colorectal carcinoma. Br J Cancer 2013; 109: 2735-2743.
98. Wierzbicki PM, Adrych K, Kartanowicz D, Dobrowolski S, Stanislawowski M, Chybicki J et al. Fragile histidine triad (FHIT) gene is overexpressed in colorectal cancer. J Physiol Pharmacol 2009; 60(Suppl 4): 63-70.
99. Xie T, D' Ario G, Lamb JR, Martin E, Wang K, Tejpar S et al. A comprehensive characterization of genome-wide copy number aberrations in colorectal cancer reveals novel oncogenes and patterns of alterations. PLoS One 2012; 7: e42001.
100. Thean LF, Loi C, Ho KS, Koh PK, Eu KW, Cheah PY. Genome-wide scan identifies a copy number variable region at 3q26 that regulates PPM1L in APC mutationnegative familial colorectal cancer patients. Genes Chromosomes Cancer 2010; 49: 99-106.
101. Iwatsuki M, Mimori K, Ishii H, Yokobori T, Takatsuno Y, Sato T et al. Loss of FBXW7, a cell cycle regulating gene, in colorectal cancer: clinical significance. Int J Cancer 2010; 126: 1828-1837.
102. Lam AK, Gopalan V, Nassiri MR, Kasim K, Dissanayake J, Tang JC et al. Altered JS-2 expression in colorectal cancers and its clinical pathological relevance. Mol Oncol 2011; 5: 475-481.
103. Ungerback J, Belenki D, Jawad ul-Hassan A, Fredrikson M, Fransen K, Elander N et al. Genetic variation and alterations of genes involved in NFkappaB/TNFAIP3- and NLRP3-inflammasome signaling affect susceptibility and outcome of colorectal cancer. Carcinogenesis 2012; 33: 2126-2134.
104. Lu Y, Jingyan G, Baorong S, Peng J, Xu Y, Cai S. Expression of EGFR, Her2 predict lymph node metastasis (LNM)-associated metastasis in colorectal cancer. Cancer Biomark 2012; 11: 219-226.
105. Flora M, Piana S, Bassano C, Bisagni A, De Marco L, Ciarrocchi A et al. Epidermal growth factor receptor (EGFR) gene copy number in colorectal adenomacarcinoma progression. Cancer Genet 2012; 205: 630-635.
106. Kumarakulasingham M, Rooney PH, Dundas SR, Telfer C, Melvin WT, Curran S et al. Cytochrome p450 profile of colorectal cancer: identification of markers of prognosis. Clin Cancer Res 2005; 11: 3758-3765.
107. Meng X, Ezzati P, Wilkins JA. Requirement of podocalyxin in TGF-beta induced epithelial mesenchymal transition. PLoS One 2011; 6: e18715.
108. Larsson A, Fridberg M, Gaber A, Nodin B, Leveen P, Jonsson G et al. Validation of podocalyxin-like protein as a biomarker of poor prognosis in colorectal cancer. BMC Cancer 2012; 12: 282.
109. Rebhun JF, Castro AF, Quilliam LA. Identification of guanine nucleotide exchange factors (GEFs) for the Rap1 GTPase. Regulation of MR-GEF by M-Ras-GTP interaction. J Biol Chem 2000; 275: 34901-34908.
110. Mitra AK, Sawada K, Tiwari P, Mui K, Gwin K, Lengyel E. Ligand-independent activation of c-Met by fibronectin and alpha(5)beta(1)-integrin regulates ovarian cancer invasion and metastasis. Oncogene 2011; 30: 1566-1576.
111. Benedettini E, Sholl LM, Peyton M, Reilly J, Ware C, Davis L et al. Met activation in non-small cell lung cancer is associated with de novo resistance to EGFR inhibitors and the development of brain metastasis. Am J Pathol 2010; 177: 415-423.
112. Han CB, Ma JT, Li F, Zhao JZ, Jing W, Zhou Y et al. EGFR and KRAS mutations and altered c-Met gene copy numbers in primary non-small cell lung cancer and associated stage N2 lymph node-metastasis. Cancer Lett 2012; 314: 63-72.
113. Zhao D, Wang SH, Feng Y, Hua CG, Zhao J, Tang XF. Intratumoral c-Met expression is associated with vascular endothelial growth factor C expression, lymphangiogenesis, and lymph node metastasis in oral squamous cell carcinoma: implications for use as a prognostic marker. Hum Pathol 2011; 42: 1514-1523.
114. Grady WM, Carethers JM. Genomic and epigenetic instability in colorectal cancer pathogenesis. Gastroenterology 2008; 135: 1079-1099.
115. Hermsen M, Postma C, Baak J, Weiss M, Rapallo A, Sciutto A et al. Colorectal adenoma to carcinoma progression follows multiple pathways of chromosomal instability. Gastroenterology 2002; 123: 1109-1119.
116. Hornstein M, Hoffmann MJ, Alexa A, Yamanaka M, Muller M, Jung V et al. Protein phosphatase and TRAIL receptor genes as new candidate tumor genes on chromosome 8p in prostate cancer. Cancer Genomics Proteomics 2008; 5: 123-136.
117. Westermarck J, Hahn WC. Multiple pathways regulated by the tumor suppressor PP2A in transformation. Trends Mol Med 2008; 14: 152-160.
118. Zuern C, Heimrich J, Kaufmann R, Richter KK, Settmacher U, Wanner C et al. Down-regulation of MTUS1 in human colon tumors. Oncol Rep 2010; 23: 183-189.
119. Bacolod MD, Barany F. Gene dysregulations driven by somatic copy number aberrations-biological and clinical implications in colon tumors: a paper from the 2009 William Beaumont Hospital Symposium on Molecular Pathology. J Mol Diagn 2010; 12: 552-561.
120. Kruszewski W, Kowara R, Rzepko R, Warezak C, Zielinski J, Gryglewski G et al. KRAS point mutation, and amplification of C-MYC and C-ERBB2 in colon adenocarcinoma. Folia Histochem Cytobiol 2004; 42: 173-179.
121. Price TJ, Hardingham JE, Lee CK, Townsend AR, Wrin JW, Wilson K et al. Prognostic impact and the relevance of PTEN copy number alterations in patients with advanced colorectal cancer (CRC) receiving bevacizumab. Cancer Med 2013; 2: 277-285.
122. Cui H, Cruz-Correa M, Giardiello FM, Hutcheon DF, Kafonek DR, Brandenburg S et al. Loss of IGF2 imprinting: a potential marker of colorectal cancer risk. Science 2003; 299: 1753-1755.
123. Nakagawa H, Chadwick RB, Peltomaki P, Plass C, Nakamura Y, de La Chapelle A. Loss of imprinting of the insulin-like growth factor II gene occurs by biallelic methylation in a core region of H19-associated CTCF-binding sites in colorectal cancer. Proc Natl Acad Sci USA 2001; 98: 591-596.
124. Veronese A, Lupini L, Consiglio J, Visone R, Ferracin M, Fornari F et al. Oncogenic role of miR-483-3p at the IGF2/483 locus. Cancer Res 2010; 70: 3140-3149.
125. Berteaux N, Aptel N, Cathala G, Genton C, Coll J, Daccache A et al. A novel H19 antisense RNA overexpressed in breast cancer contributes to paternal IGF2 expression. Mol Cell Biol 2008; 28: 6731-6745.
126. Deng Q, He B, Gao T, Pan Y, Sun H, Xu Y et al. Up-regulation of 91H promotes tumor metastasis and predicts poor prognosis for patients with colorectal cancer. PLoS One 2014; 9: e103022.
127. Mekenkamp LJ, Tol J, Dijkstra JR, de Krijger I, Vink-Borger ME, van Vliet S et al. Beyond KRAS mutation status: influence of KRAS copy number status and microRNAs on clinical outcome to cetuximab in metastatic colorectal cancer patients. BMC Cancer 2012; 12: 292.
128. Finlin BS, Gau CL, Murphy GA, Shao H, Kimel T, Seitz RS et al. RERG is a novel ras-related, estrogen-regulated and growth-inhibitory gene in breast cancer. J Biol Chem 2001; 276: 42259-42267.
129. Yang R, Chen B, Pfutze K, Buch S, Steinke V, Holinski-Feder E et al. Genome-wide analysis associates familial colorectal cancer with increases in copy number variations and a rare structural variation at 12p12.3. Carcinogenesis 2014; 35: 315-323.
130. Schunke D, Span P, Ronneburg H, Dittmer A, Vetter M, Holzhausen HJ et al. Cyclooxygenase-2 is a target gene of rho GDP dissociation inhibitor beta in breast cancer cells. Cancer Res 2007; 67: 10694-10702.
131. Moniz S, Jordan P. Emerging roles for WNK kinases in cancer. Cell Mol Life Sci 2010; 67: 1265-1276.
132. Aytekin T, Ozaslan M, Cengiz B. Deletion mapping of chromosome region 12q13-24 in colorectal cancer. Cancer Genet Cytogenet 2010; 201: 32-38.
133. Zhang C, Zhang S, Zhang D, Zhang Z, Xu Y, Liu S. A lung cancer gene GPC5 could also be crucial in breast cancer. Mol Genet Metabol 2011; 103: 104-105.
134. Sokolenko AP, Iyevleva AG, Preobrazhenskaya EV, Mitiushkina NV, Abysheva SN, Suspitsin EN et al. High prevalence and breast cancer predisposing role of the BLM c.1642 C4T (Q548X) mutation in Russia. Int J Cancer 2012; 130: 2867-2873.
135. Zhu J, Shi Z, Wang J, Zhang B. Empowering biologists with multi-omics data: colorectal cancer as a paradigm. Bioinformatics 2014; 31: 1436-1443.
136. Gruber SB, Ellis NA, Scott KK, Almog R, Kolachana P, Bonner JD et al. BLM heterozygosity and the risk of colorectal cancer. Science 2002; 297: 2013.
137. Kurashina K, Yamashita Y, Ueno T, Koinuma K, Ohashi J, Horie H et al. Chromosome copy number analysis in screening for prognosis-related genomic regions in colorectal carcinoma. Cancer Sci 2008; 99: 1835-1840.
138. Satoh S, Daigo Y, Furukawa Y, Kato T, Miwa N, Nishiwaki T et al. AXIN1 mutations in hepatocellular carcinomas, and growth suppression in cancer cells by virusmediated transfer of AXIN1. Nat Genet 2000; 24: 245-250.
139. Segditsas S, Tomlinson I. Colorectal cancer and genetic alterations in the Wnt pathway. Oncogene 2006; 25: 7531-7537.
140. Bouteille N, Driouch K, Hage PE, Sin S, Formstecher E, Camonis J et al. Inhibition of the Wnt/beta-catenin pathway by the WWOX tumor suppressor protein. Oncogene 2009; 28: 2569-2580.
141. Andersen CL, Lamy P, Thorsen K, Kjeldsen E, Wikman F, Villesen P et al. Frequent genomic loss at chr16p13.2 is associated with poor prognosis in colorectal cancer. Int J Cancer 2011; 129: 1848-1858.
142. Silva FP, Hamamoto R, Nakamura Y, Furukawa Y. WDRPUH, a novel WD-repeatcontaining protein, is highly expressed in human hepatocellular carcinoma and involved in cell proliferation. Neoplasia 2005; 7: 348-355.
143. Chen W, Yuan L, Cai Y, Chen X, Chi Y, Wei P et al. Identification of chromosomal copy number variations and novel candidate loci in hereditary nonpolyposis colorectal cancer with mismatch repair proficiency. Genomics 2013; 102: 27-34.
144. Nehls O, Okech T, Hsieh CJ, Enzinger T, Sarbia M, Borchard F et al. Studies on p53, BAX and Bcl-2 protein expression and microsatellite instability in stage III (UICC) colon cancer treated by adjuvant chemotherapy: major prognostic impact of proapoptotic BAX. Br J Cancer 2007; 96: 1409-1418.
145. Miyabe I, Kunkel TA, Carr AM. The major roles of DNA polymerases epsilon and delta at the eukaryotic replication fork are evolutionarily conserved. PLoS Genet 2011; 7: e1002407.
146. Liu Z, Lu H, Jiang Z, Pastuszyn A, Hu CA. Apolipoprotein l6, a novel proapoptotic Bcl-2 homology 3-only protein, induces mitochondria-mediated apoptosis in cancer cells. Mol Cancer Res 2005; 3: 21-31.
147. Muscatelli F, Walker AP, De Plaen E, Stafford AN, Monaco AP. Isolation and characterization of a MAGE gene family in the Xp21.3 region. Proc Natl Acad Sci USA 1995; 92: 4987-4991.
148. Choi J, Chang H. The expression of MAGE and SSX, and correlation of COX2, VEGF, and survivin in colorectal cancer. Anticancer Res 2012; 32: 559-564.
149. Yamada S, Nomoto S, Fujii T, Kaneko T, Takeda S, Inoue S et al. Correlation between copy number of mitochondrial DNA and clinico-pathologic parameters of hepatocellular carcinoma. Eur J Surg Oncol 2006; 32: 303-307.
150. Park SY, Shin MG, Kim HR, Oh JY, Kim SH, Shin JH et al. Alteration of mitochondrial DNA sequence and copy number in nasal polyp tissue. Mitochondrion 2009; 9: 318-325.
151. Feng S, Xiong L, Ji Z, Cheng W, Yang H. Correlation between increased copy number of mitochondrial DNA and clinicopathological stage in colorectal cancer. Oncol Lett 2011; 2: 899-903.
152. Cui H, Huang P, Wang Z, Zhang Y, Zhang Z, Xu W et al. Association of decreased mitochondrial DNA content with the progression of colorectal cancer. BMC Cancer 2013; 13: 110.
153. Chen T, He J, Shen L, Fang H, Nie H, Jin T et al. The mitochondrial DNA 4,977-bp deletion and its implication in copy number alteration in colorectal cancer. BMC Med Genet 2011; 12: 8.
154. Han D, Wang M, Ma N, Xu Y, Jiang Y, Gao X. Long noncoding RNAs: novel players in colorectal cancer. Cancer Lett 2015; 361: 13-21.