Applications of genomic tools to colorectal cancer therapeutics

Current Opinion in Molecular Therapeutics

Volumn 10, Issue 6, 2008, Pages 548-554

  Auman, J T ^a   McLeod, H L ^a  

^a University of North Carolina   (United States)

Author keywords

Chemotherapy; Colorectal cancer; Gene expression profiling; Microarray; Pharmacogenomics

Indexed keywords

CAPECITABINE; FLUOROURACIL; FOLINIC ACID; IRINOTECAN; OXALIPLATIN;

CANCER ADJUVANT THERAPY; CANCER CHEMOTHERAPY; CANCER RADIOTHERAPY; CANCER RECURRENCE; CANCER RISK; CANCER STAGING; CANCER SURGERY; CANCER SURVIVAL; COLORECTAL CANCER; COMBINATION CHEMOTHERAPY; DRUG EFFECT; DRUG MECHANISM; DRUG SENSITIVITY; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE MUTATION; GENETIC POLYMORPHISM; GENETIC SCREENING; HISTOPATHOLOGY; HUMAN; LYMPH NODE METASTASIS; METASTASIS; PHARMACOGENETICS; PROGNOSIS; RADIATION DOSE; RECTUM CANCER; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; SENSITIVITY AND SPECIFICITY; TREATMENT RESPONSE;

COLORECTAL NEOPLASMS; GENE EXPRESSION PROFILING; GENOME, HUMAN; GENOMICS; HUMANS; PHARMACOGENETICS;

EID: 57349199077     PISSN: 14648431     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (45)

1. Cancer facts and figures 2007: American Cancer Society, Atlanta, GA, USA (2007). http://www.cancer.org/downloads/STT/BCFF-Final.pdf
2. Chen JJ, Wang SJ, Tsai CA, Lin CJ: Selection of differentially expressed genes in microarray data analysis. Pharmacogenomics J (2006) 7(3):212-220.
3. Sotiriou C, Piccart MJ: Taking gene-expression profiling to the clinic: When will molecular signatures become relevant to patient care? Nat Rev Cancer (2007) 7(7):545-553.
4. Nevins JR, Potti A: Mining gene expression profiles: Expression signatures as cancer phenotypes. Nat Rev Genet (2007) 8(8):601-609.
5. th Edition. New York Springer-Verlag, New York, NY, USA (2002).
6. Efficacy of adjuvant fluorouracil and folinic acid in B2 colon cancer. International multicentre pooled analysis of B2 colon cancer trials (IMPACT B2) investigators. J Clin Oncol (1999) 17(5):1356-1363.
7. Wang Y, Jatkoe T, Zhang Y, Mutch MG, Talantov D, Jiang J, McLeod HL, Atkins D: Gene expression profiles and molecular markers to predict recurrence of Dukes' B colon cancer. J Clin Oncol (2004) 22(9):1564-1571.
8. Eschrich S, Yang I, Bloom G, Kwong KY, Boulware D, Cantor A, Coppola D, Kruhoffer M, Aaltonen L, Orntoft TF, Quackenbush J, Yeatman TJ: Molecular staging for survival prediction of colorectal cancer patients. J Clin Oncol (2005) 23(15):3526-3535.
9. Detailed guide: Colon and rectum cancer: American Cancer Society, Atlanta, USA (2008). http://www.cancer.org/docroot/CRI/CRI_2_3x.asp?rnav= cridg&dt=10
10. Barrier A, Boelle P-Y, Roser F, Gregg J, Tse C, Brault D, Lacaine F, Houry S, Huguier M, Franc B, Flahault A et al: Stage II colon cancer prognosis prediction by tumor gene expression profiling. J Clin Oncol (2006) 24(29):4685-4691.
11. Barrier A, Lemoine A, Boelle P-Y, Tse C, Brault D, Chiappini F, Breittschneider J, Lacaine F, Houry S, Huguier M, Van der Laan MJ et al: Colon cancer prognosis prediction by gene expression profiling. Oncogene (2005) 24(40):6155-6164.
12. Barrier A, Roser F, Boelle PY, Franc B, Tse C, Brault D, Lacaine F, Houry S, Callard P, Penna C, Debuire B et al: Prognosis of stage II colon cancer by non-neoplastic mucosa gene expression profiling. Oncogene (2007) 26(18):2642-2648.
13. Compton CC: Optimal pathologic staging: Defining stage II disease. Clin Cancer Res (2007) 13(22 Pt 2):6862s-6870s.
14. Groene J, Mansmann U, Meister R, Staub E, Roepcke S, Heinze M, Klaman I, Brümmendorf T, Hermann K, Loddenkemper C, Pilarsky C et al: Transcriptional census of 36 microdissected colorectal cancers yields a gene signature to distinguish UICC II and III. Int J Cancer (2006) 119(8):1829-1836.
15. Croner RS, Peters A, Brueckl WM, Matzel KE, Klein-Hitpass L, Brabletz T, Papadopoulos T, Hohenberger W, Reingruber B, Lausen B: Microarray versus conventional prediction of lymph node metastasis in colorectal carcinoma. Cancer (2005) 104(2):395-404.
16. Grade M, Hormann P, Becker S, Hummon AB, Wangsa D, Varma S, Simon R, Liersch T, Becker H, Difilippantonio MJ, Ghadimi BM, Ried T: Gene expression profiling reveals a massive, aneuploidy-dependent transcriptional deregulation and distinct differences between lymph node-negative and lymph node-positive colon carcinomas. Cancer Res (2007) 67(1):41-56.
17. Lin Y-H, Friederichs J, Black MA, Mages J, Rosenberg R, Guilford PJ, Phillips V, Thompson-Fawcett M, Kasabov N, Toro T, Merrie AE et al: Multiple gene expression classifiers from different array platforms predict poor prognosis of colorectal cancer. Clin Cancer Res (2007) 13(2 Pt 1):498-507. • Gene expression predictors were compared with clinical and histopathological predictors in two different patient cohorts.
18. De Angelis PM, Svendsrud DH, Kravik K, Stokke T: Cellular response to 5-fluorouracil (5-FU) in 5-FU-resistant colon cancer cell lines during treatment and recovery. Mol Cancer (2006) 5:20.
19. Maxwell PJ, Longley DB, Latif T, Boyer J, Allen W, Lynch M, McDermott U, Harkin DP, Allegra CJ, Johnston PG: Identification of 5-fluorouracilinducible target genes using cDNA microarray profiling. Cancer Res (2003) 63(15):4602-4606.
20. Boyer J, Allen WL, McLean EG, Wilson PM, McCulla A, Moore S, Longley DB, Caldas C, Johnston PG: Pharmacogenomic identification of novel determinants of response to chemotherapy in colon cancer. Cancer Res (2006) 66(5):2765-2777.
21. Souza V, Dong YB, Zhou HS, Zacharias W, McMasters KM: SW-620 cells treated with topoisomerase I inhibitor SN-38: Gene expression profiling. J Transl Med (2005) 3:44.
22. Voland C, Bord A, Peleraux A, Penarier G, Carriere D, Galiegue S, Cvitkovic E, Jbilo O, Casellas P: Repression of cell cycle-related proteins by oxaliplatin but not cisplatin in human colon cancer cells. Mol Cancer Ther (2006) 5(9):2149-2157.
23. Arango D, Wilson AJ, Shi Q, Corner GA, Aranes MJ, Nicholas C, Lesser M, Mariadason JM, Augenlicht LH: Molecular mechanisms of action and prediction of response to oxaliplatin in colorectal cancer cells. Br J Cancer (2004) 91(11):1931-1946.
24. Watanabe T, Komuro Y, Kiyomatsu T, Kanazawa T, Kazama Y, Tanaka J, Tanaka T, Yamamoto Y, Shirane M, Muto T, Nagawa H: Prediction of sensitivity of rectal cancer cells in response to preoperative radiotherapy by DNA microarray analysis of gene expression profiles. Cancer Res (2006) 66(7):3370-3374.
25. Kim I-J, Lim S-B, Kang H, Chang H, Ahn S-A, Park H-W, Jang S-G, Park J-H, Kim D, Jung K, Choi H et al: Microarray gene expression profiling for predicting complete response to preoperative chemoradiotherapy in patients with advanced rectal cancer. Dis Colon Rectum (2007) 50(9):1342- 1353.
26. Del Rio M, Molina F, Bascoul-Mollevi C, Copois V, Bibeau F, Chalbos P, Bareil C, Kramar A, Salvetat N, Fraslon C, Conseiller E et al: Gene expression signature in advanced colorectal cancer patients select drugs and response for the use of leucovorin, fluorouracil, and irinotecan. J Clin Oncol (2007) 25(7):773-780.
27. Ruzzo A, Graziano F, Loupakis F, Santini D, Catalano V, Bisonni R, Ficarelli R, Fontana A, Andreoni F, Falcone A, Canestrari E et al: Pharmacogenetic profiling in patients with advanced colorectal cancer treated with first-line FOLFIRI chemotherapy. Pharmacogenomics J (2008) 8(4):278-288.
28. Mandola MV, Stoehlmacher J, Zhang W, Groshen S, Yu MC, Iqbal S, Lenz HJ, Ladner RD: A 6 bp polymorphism in the thymidylate synthase gene causes message instability and is associated with decreased intratumoral TS mRNA levels. Pharmacogenetics (2004) 14(5):319-327.
29. Popat S, Matakidou A, Houlston RS: Thymidylate synthase expression and prognosis in colorectal cancer: A systematic review and meta-analysis. J Clin Oncol (2004) 22(3):529-536.
30. Pierce AJ, Johnson RD, Thompson LH, Jasin M: XRCC3 promotes homology-directed repair of DNA damage in mammalian cells. Genes Dev (1999) 13(20):2633-2638.
31. Rothenberg ML: Topoisomerase I inhibitors: Review and update. Ann Oncol (1997) 8(9):837-855.
32. Graudens E, Boulanger V, Mollard C, Mariage-Samson R, Barlet X, Grémy G, Couillault C, Lajémi M, Piatier-Tonneau D, Zaborski P, Eveno E et al: Deciphering cellular states of innate tumor drug responses. Genome Biol (2006) 7(3):R19. • A systems biology strategy toward interrogating innate colorectal cancer resistance to the FOLFIRI chemotherapeutic regimen was investigated in this study.
33. Shimizu D, Ishikawa T, Ichikawa Y, Togo S, Hayasizaki Y, Okazaki Y, Danenberg PV, Shimada H: Prediction of chemosensitivity of colorectal cancer to 5-fluorouracil by gene expression profiling with cDNA microarrays. Int J Oncol (2005) 27(2):371-376.
34. Matsuyama R, Togo S, Shimizu D, Momiyama N, Ishikawa T, Ichikawa Y, Endo I, Kunisaki C, Suzuki H, Hayasizaki Y, Shimada H: Predicting 5-fluorouracil chemosensitivity of liver metastases from colorectal cancer using primary tumor specimens: Three-gene expression model predicts clinical response. Int J Cancer (2006) 119(2):406-413.
35. Miquel C, Jacob S, Grandjouan S, Aime A, Viguier J, Sabourin JC, Sarasin A, Duval A, Praz F: Frequent alteration of DNA damage signalling and repair pathways in human colorectal cancers with microsatellite instability. Oncogene (2007) 26(40):5919-5926.
36. Thomas RK, Baker AC, DeBiasi RM, Winckler W, LaFramboise T, Lin WM, Wang M, Feng W, Zander T, MacConnaill LE, Lee JC et al: High-throughput oncogene mutation profiling in human cancer. Nat Genet (2007) 39(3):347-351.
37. Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C, Edkins S et al: Patterns of somatic mutation in human cancer genomes. Nature (2007) 446(7132):153-158.
38. Sjöblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S et al: The consensus coding sequences of human breast and colorectal cancers. Science (2006) 314(5797):268-274. •• The most comprehensive and rigorous mutation screen completed to date in colorectal cancer.
39. CCDS database: National Center for Biotechnology Information, Bethesda, MD, USA (2008). http://www.ncbi.nlm.nih.gov/CCDS
40. Lin J, Gan CM, Zhang X, Jones S, Sjöblom T, Wood LD, Parsons DW, Papadopoulos N, Kinzler KW, Vogelstein B, Parmigiani G, Velculescu VE: A multidimensional analysis of genes mutated in breast and colorectal cancers. Genome Res (2007) 17(9):1304-1318. •• A systems biology strategy toward identifying the significantly altered pathways putatively involved in carcinogenesis was utilized.
41. Broderick P, Carvajal-Carmona L, Pittman AM, Webb E, Howarth K, Rowan A, Lubbe S, Spain S, Sullivan K, Fielding S, Jaeger E et al: A genome-wide association study shows that common alleles of SMAD7 influence colorectal cancer risk. Nat Genet (2007) 39(11):1315-1317.
42. Haiman CA, Le Marchand L, Yamamato J, Stram DO, Sheng X, Kolonel LN, Wu AH, Reich D, Henderson BE: A common genetic risk factor for colorectal and prostate cancer. Nat Genet (2007) 39(8):954-956.
43. Tomlinson I, Webb E, Carvajal-Carmona L, Broderick P, Kemp Z, Spain S, Penegar S, Chandler I, Gorman M, Wood W, Barclay E et al: A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21. Nat Genet (2007) 39(8):984-988.
44. Zanke BW, Greenwood CMT, Rangrej J, Kustra R, Tenesa A, Farrington SM, Prendergast J, Olschwang S, Chiang T, Crowdy E, Ferretti V et al: Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24. Nat Genet (2007) 39(8):989-994.
45. Wellcome Trust Case Control Consortium: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature (2007) 447(7145):661-678. • This study presented data obtained through collaborations across multiple institutes to attain sufficient clinical samples for rigorous testing of genome-wide associations.