Gene expression profiling of nonneoplastic mucosa may predict clinical outcome of colon cancer patients

Diseases of the Colon and Rectum

Volumn 48, Issue 12, 2005, Pages 2238-2248

  Barrier, Alain ^a,b,c   Boelle, Pierre Yves ^b   Lemoine, Antoinette ^b   Tse, Chantal ^a   Brault, Didier ^a   Chiappini, Franck ^b   Lacaine, François ^a   Houry, Sidney ^a   Huguier, Michel ^a   Flahault, Antoine ^b   Dudoit, Sandrine ^c  

^a SORBONNE UNIVERSITÉ   (France)

^b INSERM   (France)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Colon cancer; Functional genomics; Nonneoplastic mucosa; Prognosis prediction

Indexed keywords

FLUOROURACIL; FOLINIC ACID; MESSENGER RNA;

ADULT; AGED; ARTICLE; CANCER ADJUVANT THERAPY; CANCER PATIENT; CANCER STAGING; CANCER SURGERY; CLINICAL ARTICLE; CLINICAL TRIAL; COLON ADENOCARCINOMA; COLON MUCOSA; COMPUTER ASSISTED TOMOGRAPHY; CONTROLLED CLINICAL TRIAL; CONTROLLED STUDY; DNA MICROARRAY; EXPERIENCE; FEMALE; FREQUENCY ANALYSIS; GENE EXPRESSION PROFILING; HUMAN; HUMAN TISSUE; LIVER METASTASIS; LUNG METASTASIS; LYMPH NODE METASTASIS; MALE; MEDICAL INFORMATION; MITOCHONDRIAL RESPIRATION; PHOSPHORYLATION; PREDICTION; PROGNOSIS; RECURRENT CANCER; RISK ASSESSMENT; SAMPLE SIZE; SENSITIVITY ANALYSIS; SIGNAL TRANSDUCTION; THORAX RADIOGRAPHY; TIME SERIES ANALYSIS; TREATMENT FAILURE; ULTRASOUND; VALIDATION PROCESS;

EID: 30444436907     PISSN: 00123706     EISSN: 15300358     Source Type: Journal    
DOI: 10.1007/s10350-005-0175-9     Document Type: Article

References (60)

1. Fleming ID, Cooper JS, Henson DE, et al. AJCC: cancer staging manual. 5th ed. Philadelphia: Lippincott-Raven, 1997
2. CG Moertel TR Fleming JS [tmp] MacDonald 1990 Levamisole and fluorouracil as adjuvant therapy of resected colon carcinoma N Engl J Med 322 352 8
3. N Wolmark H Rockette B Fisher 1993 The benefit of leucovorin-modulated fluorouracil as postoperative adjuvant therapy for primary colon cancer: results from National Surgical Adjuvant Breast and Bowel Project protocol C-03 J Clin Oncol 11 1879 87
4. International Multicentre Pooled Analysis of Colon Cancer Trials (IMPACT) Investigators. Efficacy of adjuvant fluorouracil and folinic acid in colon cancer. Lancet 1995;345:939-44.
5. MJ O'Connell JA Mailliard MJ Kahn 1997 Controlled trial of fluorouracil and low-dose leucovorin given for 6 months as postoperative adjuvant therapy for colon cancer J Clin Oncol 15 246 50
6. N Wolmark H Rockette E Mamounas 1999 Clinical trial to assess the relative efficacy of fluorouracil and leucovorin, fluorouracil and levamisole, and fluorouracil, leucovorin, and levamisole in patients with Dukes' B and C carcinoma of the colon. Results from National Surgical Adjuvant Breast and Bowel Project C-04 J Clin Oncol 17 3553 9
7. MJ O'Connell JA Laurie M Kahn 1998 Prospectively randomized trial of postoperative adjuvant chemotherapy in patients with high-risk colon cancer J Clin Oncol 16 295 300
8. HC Moore DG Haller 1999 Adjuvant therapy of colon cancer Semin Oncol 26 545 55
9. A Zaniboni 1997 Adjuvant chemotherapy in colorectal cancer with high-dose leucovorin and fluorouracil: impact on disease-free survival and overall survival J Clin Oncol 15 2432 41
10. T Andre C Boni L Mounedji-Boudiaf 2004 Oxaliplatin, fluorouracil, and leucovorin as adjuvant treatment for colon cancer N Engl J Med 350 2343 51
11. International Multicenter Pooled Analysis of B2 Colon Cancer Trials (IMPACT B2) Investigators. Efficacy of adjuvant fluorouracil and folinic acid in B2 colon cancer. J Clin Oncol 1999;17:1356-63
12. E Mamounas S Wieand N Wolmark 1999 Comparative efficacy of adjuvant chemotherapy in patients with Dukes' B versus Dukes' C colon cancer. Results from four National Surgical Adjuvant Breast and Bowel Project adjuvant studies (C-01, C-02, C-03, and C-04) J Clin Oncol 17 1349 55
13. S Gill CL Loprinzi DJ Sargent 2004 Pooled analysis of fluorouracil-based adjuvant therapy for stage II and III colon cancer: who benefits and by how much? J Clin Oncol 22 1797 806
14. KC Halling AJ French SK [tmp] McDonnell 1999 Microsatellite instability and 8p allelic imbalance in stage B2 and C colorectal cancers J Natl Cancer Inst 91 1295 303
15. R Gryfe H Kim ET Hsieh 2000 Tumor satellite instability and clinical outcome in young patients with colorectal cancer N Engl J Med 342 69 77
16. N Hawkins M Norrie K Cheong 2002 CpG island methylation in sporadic colorectal cancers and its relationship to microsatellite instability Gastroenterology 122 1376 87
17. C Wang M van Rijnsoever F Grieu 2003 Prognostic significance of microsatellite instability and Ki-ras mutation type in stage II colorectal cancer Oncology 64 259 65
18. TE Witzig CL Loprinzi NJ Gonchoroff 1991 DNA ploidy and cell kinetic measurements as predictors of recurrence and survival in stages B2 and C colorectal adenocarcinoma Cancer 68 879 88
19. MA Chapman JD Hardcastle NC Armitage 1995 Five-year prospective study of DNA tumor ploidy and colorectal cancer survival Cancer 76 383 7
20. E Martinez-Lopez A Abad A Font 1998 Allelic loss on chromosome 18q as a prognostic marker in stage II colorectal cancer Gastroenterology 114 1180 7
21. W Zhou SN Goodman G Galizia 2002 Counting alleles to predict recurrence of early-stage colorectal cancers Lancet 359 219 25
22. HL [tmp] McLeod GI Murray 1999 Tumor markers of prognosis in colorectal cancer Br J Cancer 79 191 203
23. D Shibata MA Reale P Lavin 1996 The DCC protein and prognosis in colorectal cancer N Engl J Med 335 1727 32
24. OA Ogunbiyi PJ Goodfellow K Herfarth 1998 Confirmation that chromosome 18q allelic loss in colon cancer is a prognostic indicator J Clin Oncol 16 427 33
25. XF Sun S Rutten H Zhang 1999 Expression of the deleted in colorectal cancer gene is related to prognosis in DNA diploid and low proliferative colorectal adenocarcinoma J Clin Oncol 17 1745 50
26. W Zhou G Galizia E Lieto 2001 Counting alleles reveals a connection between chromosome 18q loss and vascular invasion Nat Biotechnol 19 78 81
27. LJ Vant Veer H Dai MJ Van de Vijver 2002 Gene expression profiling predicts clinical outcome of breast cancer Nature 415 530 6
28. MJ Van de Vijver DH Yudong LJ Vant Veer 2002 A gene-expression signature as a predictor of survival in breast cancer N Engl J Med 347 1999 2009
29. DG Beer SLR Kardia C Huang 2002 Gene expression profiles predict survival of patients with lung adenocarcinoma Nat Med 8 816 24
30. A Bhattacharjee WG Richards J Staunton 2001 Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses Proc Natl Acad Sci USA 98 13790 5
31. MA Shipp KN Ross P Tamayo 2002 Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning Nat Med 8 68 74
32. A Rosenwald G Wright WC Chan 2002 The use of molecular profiling to predict survival after chemotherapy for diffuse large B-cell lymphoma N Engl J Med 346 1937 47
33. CM Fredericksen S Knudsen S Laurberg TF Orntoft 2003 Classification of Dukes' B and C colorectal cancers using expression arrays J Cancer Res Clin Oncol 129 263 71
34. K Birkenkamp-Demtroder LL Christensen SH Olesen 2002 Gene expression in colorectal cancer Cancer Res 62 4352 63
35. F Bertucci S Salas S Eysterier 2004 Gene expression profiling of colon cancer and correlation with histoclinical parameters Oncogene 23 1377 91
36. B Iacopetta 2002 Are there two sides to colorectal cancer? Int J Cancer 101 403 8
37. U Alon N Barkai DA Notterman 1999 Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays Proc Natl Acad Sci USA 96 6745 50
38. S Backert M Gelos U Kobalz 1999 Differential gene expression in colon carcinoma cells and tissues detected with a cDNA array Int J Cancer 82 868 74
39. P Hedge R Qi R Gaspard 2001 Identification of tumor markers in models of human colorectal cancer using a 19,200-element complementary DNA microarray Cancer Res 61 7792 7
40. O Kitahara Y Furukawa T Tanaka 2001 Alterations of gene expression during colorectal carcinogenesis revealed by cDNA microarrays after laser-capture microdissection of tumor tissues and normal epithelia Cancer Res 61 3544 9
41. DA Notterman U Alon AJ Sierk AJ Levine 2001 Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma and normal tissue examined by oligonucleotide arrays Cancer Res 61 3124 30
42. D Agrawal T Chen R Irby 2002 Osteopontin identified as lead marker of colon cancer progression, using pooled sample expression profiling J Natl Cancer Inst 94 513 21
43. YM Lin Y Furukawa T Tsunoda CT Yue KC Yang Y Nakamura 2002 Molecular diagnosis of colorectal tumors by expression profiles of 50 genes expressed differentially in adenomas and carcinomas Oncogene 21 4120 8
44. TT Zou FM Selaru Y Xu 2002 Application of cDNA microarrays to generate a molecular taxonomy capable of distinguishing between colon cancer and normal colon Oncogene 21 4855 62
45. O Tureci J Ding H Hilton 2003 Computational dissection of tissue contamination for identification of colon cancer-specific expression profiles FASEB J 17 376 85
46. NS Williams RB Gaynor S Scoggin 2003 Identification and validation of genes involved in the pathogenesis of colorectal cancer using cDNA microarrays and RNA interference Clin Cancer Res 9 931 46
47. Y Wang T Jatkoe Y Zhang 2004 Gene expression profiles and molecular markers to predict recurrence of Dukes' B colon cancer J Clin Oncol 27 1564 71
48. RA Irizarry B Hobbs F Collin 2003 Exploration, normalization, and summaries of high density oligonucleotide array probe level data Biostatistics 4 249 64
49. BM Bolstad RA Irizarry M Astrand TP Speed 2003 A comparison of normalization methods for high density oligonucleotide array based on variance and bias Bioinformatics 19 185 93
50. Westfall PH, Young SS. Resampling-based multiple testing: examples and methods for p-value adjustment. New York: John Wiley £ Sons, 1993
51. MJ Van der Laan S Dudoit KS Pollard 2004 Multiple testing. Part II. Step-down procedures for control of the family-wise error rate Stat Appl Genet Mol Biol 3 14
52. S Dudoit JP Shaffer JC Boldrick 2003 Multiple hypothesis testing in microarray experiments Stat Sci 18 71 103
53. Dudoit S, Fridlyand J. Classification in microarray experiments. In: Speed T, ed. Statistical analysis of gene expression microarray data. Boca Raton: Chapman £ Hall/CRC, 2003:93-158
54. L Breiman 1996 Heuristics of instability and stabilization in model selection Ann Stat 24 2350 83
55. M West C Blanchette H Dressman 2001 Predicting the clinical status of human breast cancer by using gene expression profiles Proc Natl Acad Sci USA 98 11462 7
56. C Ambroise GJ [tmp] McLachlan 2002 Selection bias in gene extraction on the basis of microarray gene-expression data Proc Natl Acad Sci USA 99 6562 6
57. MM Mueller NE Fusenig 2004 Friends or foes-bipolar effects of the tumour stroma in cancer Nat Rev Cancer 4 839 49
58. MD Sternlicht A Lochter CJ Sympson 1999 The stromal proteinase MMP3/stromelysin-1 promotes mammary carcinogenesis Cell 98 137 46
59. NA Bhowmick A Chytil D Plieth 2004 TGF-beta signaling in fibroblasts modulates the oncogenic potential of adjacent epithelia Science 303 848 51
60. LC Chen CY Hao YS Chiu 2004 Alteration of gene expression in normal-appearing colon mucosa of APC(min) mice and human cancer patients Cancer Res 64 3694 700