Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma

Gut

Volumn 60, Issue 10, 2011, Pages 1317-1326

  Goh, X Y ^a,b   Rees, J R E ^a,c   Paterson, A L ^a,b   Chin, S F ^b,d   Marioni, J C ^d   Save, V ^c   O'Donovan, M ^c   Eijk, P P ^e   Alderson, D ^f   Ylstra, B ^e   Caldas, C ^b,d   Fitzgerald, R C ^a  

^a HUTCHISON MRC RESEARCH CENTRE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c ADDENBROOKE S HOSPITAL   (United Kingdom)

^d IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^e VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^f QUEEN ELIZABETH HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ADULT; AGED; ARTICLE; CANCER TISSUE; CARCINOGENESIS; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; EGFR GENE; ESOPHAGEAL ADENOCARCINOMA; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; FOLLOW UP; GENE; GENE DELETION; GENE DOSAGE; GENE EXPRESSION PROFILING; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; KAPLAN MEIER METHOD; MAJOR CLINICAL STUDY; MALE; MBNL1 GENE; MTMR9 GENE; MULTIPLEX POLYMERASE CHAIN REACTION; NEIL2 GENE; PRIORITY JOURNAL; PROGNOSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TISSUE MICROARRAY; WT1 GENE;

ADENOCARCINOMA; AGED; AGED, 80 AND OVER; COMPARATIVE GENOMIC HYBRIDIZATION; DNA, NEOPLASM; ESOPHAGEAL NEOPLASMS; FEMALE; FOLLOW-UP STUDIES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GREAT BRITAIN; HUMANS; IMMUNOHISTOCHEMISTRY; KAPLAN-MEIER ESTIMATE; MALE; MICROARRAY ANALYSIS; MIDDLE AGED; POLYMERASE CHAIN REACTION; PROGNOSIS; RECEPTOR, EPIDERMAL GROWTH FACTOR; RETROSPECTIVE STUDIES; SURVIVAL RATE; TIME FACTORS; TUMOR MARKERS, BIOLOGICAL;

EID: 80052575003     PISSN: 00175749     EISSN: 14683288     Source Type: Journal    
DOI: 10.1136/gut.2010.234179     Document Type: Article

References (44)

1. Pohl H., Welch H.G. The role of overdiagnosis and reclassification in the marked increase of esophageal adenocarcinoma incidence. J Natl Cancer Inst 2005;97:142-146 (Pubitemid 40277094)
2. Mitry E., Rachet B., Quinn M.J., et al. Survival from cancer of the oesophagus in England and Wales up to 2001. Br J Cancer 2008;99(Suppl 1):S11-S13
3. Solomon E., Borrow J., Goddard A.D. Chromosome aberrations and cancer. Science 1991;254:1153-1160 (Pubitemid 21917440)
4. Weir B.A., Woo M.S., Getz G., et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 2007;450:893-898 (Pubitemid 350231325)
5. Classon M., Harlow E. The retinoblastoma tumour suppressor in development and cancer. Nat Rev Cancer 2002;2:910-917 (Pubitemid 37328892)
6. Gu J., Ajani J.A., Hawk E.T., et al. Genome-wide catalogue of chromosomal aberrations in Barrett's esophagus and esophageal adenocarcinoma: A high-density single nucleotide polymorphism array analysis. Cancer Prev Res (Phila) 2010;3:1176-1186
7. Varis A., Puolakkainen P., Savolainen H., et al. DNA copy number profiling in esophageal Barrett adenocarcinoma: Comparison with gastric adenocarcinoma and esophageal squamous cell carcinoma. Cancer Genet Cytogenet 2001;127:53-58 (Pubitemid 32530094)
8. Bang Y.J., Van Cutsem E., Feyereislova A., et al. Trastuzumab in combination with chemotherapy versus chemotherapy alone for treatment of HER2-positive advanced gastric or gastro-oesophageal junction cancer (ToGA): A phase 3, open-label, randomised controlled trial. Lancet 2010;376:687-697
9. Reid B.J., Prevo L.J., Galipeau P.C., et al. Predictors of progression in Barrett's esophagus II: Baseline 17p (p53) loss of heterozygosity identifies a patient subset at increased risk for neoplastic progression. Am J Gastroenterol 2001;96:2839-2848 (Pubitemid 32959522)
10. Powell E.L., Leoni L.M., Canto M.I., et al. Concordant loss of MTAP and p16/CDKN2A expression in gastroesophageal carcinogenesis: Evidence of homozygous deletion in esophageal noninvasive precursor lesions and therapeutic implications. Am J Surg Pathol 2005;29:1497-1504 (Pubitemid 41513300)
11. Wong D.J., Paulson T.G., Prevo L.J., et al. p16(INK4a) lesions are common, early abnormalities that undergo clonal expansion in Barrett's metaplastic epithelium. Cancer Res 2001;61:8284-8289 (Pubitemid 33091623)
12. Michael D., Beer D.G., Wilke C.W., et al. Frequent deletions of FHIT and FRA3B in Barrett's metaplasia and esophageal adenocarcinomas. Oncogene 1997;15:1653-1659 (Pubitemid 27466704)
13. Wiech T., Nikolopoulos E., Weis R., et al. Genome-wide analysis of genetic alterations in Barrett's adenocarcinoma using single nucleotide polymorphism arrays. Lab invest 2009;89:385-397
14. Nancarrow D.J., Handoko H.Y., Smithers B.M., et al. Genome-wide copy number analysis in esophageal adenocarcinoma using high-density single-nucleotide polymorphism arrays. Cancer Res 2008;68:4163-4172
15. Kindler H.L., Burris H.A. 3rd, Sandler A.B., et al. A phase II multicenter study of L-alanosine, a potent inhibitor of adenine biosynthesis, in patients with MTAP-deficient cancer. Invest New Drugs 2009;27:75-81.
16. Snijders A.M., Nowak N., Segraves R., et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 2001;29:263-264 (Pubitemid 33096449)
17. Van den Ijssel P., Tijssen M., Chin S.F., et al. Human and mouse oligonucleotide-based array CGH. Nucleic Acids Res 2005;33:e192. (Pubitemid 43125092)
18. Peters C.J., Rees J.R., Hardwick R.H., et al. A 4-gene signature predicts survival of patients with resected adenocarcinoma of the esophagus, junction, and gastric cardia. Gastroenterology 2010;139:1995-2004e15.
19. Santarius T., Shipley J., Brewer D., et al. A census of amplified and overexpressed human cancer genes. Nat Rev Cancer 2010;10:59-64.
20. Schutze K., Lahr G. Identification of expressed genes by laser-mediated manipulation of single cells. Nat Biotechnol 1998;16:737-742 (Pubitemid 28363754)
21. Caldon C.E., Lee C.S., Sutherland R.L., et al. Wilms' tumor protein 1: An early target of progestin regulation in T-47D breast cancer cells that modulates proliferation and differentiation. Oncogene 2008;27:126-138
22. Chung-man Ho J, Zheng S, Comhair SA, et al. Differential expression of manganese superoxide dismutase and catalase in lung cancer. Cancer Res 2001;61:8578-8585
23. Hill A., McFarlane S., Mulligan K., et al. Cortactin underpins CD44-promoted invasion and adhesion of breast cancer cells to bone marrow endothelial cells. Oncogene 2006;25:6079-6091 (Pubitemid 44562406)
24. Yamada H., Yanagisawa K., Tokumaru S., et al. Detailed characterization of a homozygously deleted region corresponding to a candidate tumor suppressor locus at 21q11-21 in human lung cancer. Genes Chromosomes Cancer 2008;47:810-818
25. Anders M., Vieth M., Rocken C., et al. Loss of the coxsackie and adenovirus receptor contributes to gastric cancer progression. Br J Cancer 2009;100:352-359
26. Fukuchi M., Nakajima M., Fukai Y., et al. Increased expression of c-Ski as a co-repressor in transforming growth factor-beta signaling correlates with progression of esophageal squamous cell carcinoma. Int J Cancer 2004;108:818-824 (Pubitemid 38112608)
27. Parsons D.W., Wang T.L., Samuels Y., et al. Colorectal cancer: Mutations in a signalling pathway. Nature 2005;436:792. (Pubitemid 41160630)
28. Ferby I., Reschke M., Kudlacek O., et al. Mig6 is a negative regulator of EGF receptor-mediated skin morphogenesis and tumor formation. Nat med 2006;12:568-573
29. Takeda K., Kinoshita I., Shimizu Y., et al. Clinicopathological significance of expression of p-c-Jun, TCF4 and beta-Catenin in colorectal tumors. BMC Cancer 2008;8:328.
30. Kim R.H., Peters M., Jang Y., et al. DJ-1, a novel regulator of the tumor suppressor PTEN. Cancer cell 2005;7:263-273 (Pubitemid 40568685)
31. Pasello G., Agata S., Bonaldi L., et al. DNA copy number alterations correlate with survival of esophageal adenocarcinoma patients. Mod Pathol 2009;22:58-65.
32. Ginestier C., Charafe-Jauffret E., Penault-Llorca F., et al. Comparative multimethodological measurement of ERBB2 status in breast cancer. J Pathol 2004;202:286-298 (Pubitemid 38325237)
33. Wang K.L., Wu T.T., Choi I.S., et al. Expression of epidermal growth factor receptor in esophageal and esophagogastric junction adenocarcinomas: Association with poor outcome. Cancer 2007;109:658-667 (Pubitemid 46233226)
34. Niksic M., Slight J., Sanford J.R., et al. The Wilms' tumour protein (WT1) shuttles between nucleus and cytoplasm and is present in functional polysomes. Hum Mol Genet 2004;13:463-471 (Pubitemid 38239797)
35. Han Y., San-Marina S., Liu J., et al. Transcriptional activation of c-myc proto-oncogene by WT1 protein. Oncogene 2004;23:6933-6941 (Pubitemid 39279994)
36. Fraizer G., Leahy R., Priyadarshini S., et al. Suppression of prostate tumor cell growth in vivo by WT1, the Wilms' tumor suppressor gene. Int J Oncol 2004;24:461-471
37. Gross I., Morrison D.J., Hyink D.P., et al. The receptor tyrosine kinase regulator Sprouty1 is a target of the tumor suppressor WT1 and important for kidney development. J Biol Chem 2003;278:41420-41430 (Pubitemid 37280971)
38. Lee S.B., Huang K., Palmer R., et al. The Wilms tumor suppressor WT1 encodes a transcriptional activator of amphiregulin. Cell 1999;98:663-673 (Pubitemid 29418957)
39. Rodriguez E., Rao P.H., Ladanyi M., et al. 11p13-15 is a specific region of chromosomal rearrangement in gastric and esophageal adenocarcinomas. Cancer Res 1990;50:6410-6416 (Pubitemid 20323707)
40. Hazra T.K., Izumi T., Boldogh I., et al. Identification and characterization of a human DNA glycosylase for repair of modified bases in oxidatively damaged DNA. Proc Natl Acad Sci U S A 2002;99:3523-3528 (Pubitemid 34252141)
41. Mochizuki Y., Majerus P.W. Characterization of myotubularin-related protein 7 and its binding partner, myotubularin-related protein 9. Proc Natl Acad Sci U S A 2003;100:9768-9773 (Pubitemid 37087016)
42. Zou J., Chang S.C., Marjanovic J., et al. MTMR9 increases MTMR6 enzyme activity, stability, and role in apoptosis. J Biol Chem 2009;284:2064-2071
43. Schoorlemmer J., Goldfarb M. Fibroblast growth factor homologous factors and the islet brain-2 scaffold protein regulate activation of a stress-activated protein kinase. J Biol Chem 2002;277:49111-49119 (Pubitemid 36014339)
44. Vantaggiato C., Redaelli F., Falcone S., et al. A novel CLN8 mutation in late-infantile-onset neuronal ceroid lipofuscinosis (LINCL) reveals aspects of CLN8 neurobiological function. Hum mut 2009;30:1104-16.