Selection of personalized patient therapy through the use of knowledge-based computational models that identify tumor-driving signal transduction pathways

Cancer Research

Volumn 74, Issue 11, 2014, Pages 2936-2945

  Verhaegh, Wim ^a   Van Ooijen, Henk ^a   Inda, Márcia A ^a   Hatzis, Pantelis ^e   Versteeg, Rogier ^c   Smid, Marcel ^d   Martens, John ^d   Foekens, John ^d   Van De Wiel, Paul ^a   Clevers, Hans ^b   Van De Stolpe, Anja ^a  

^a PHILIPS RESEARCH LABORATORIES   (Netherlands)

^b HUBRECHT INSTITUTE   (Netherlands)

^c ACADEMIC MEDICAL CENTER   (Netherlands)

^d ERASMUS MEDICAL CENTER   (Netherlands)

^e BIOMEDICAL SCIENCES RESEARCH CENTER ALEXANDER FLEMING   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

BETA CATENIN; ESTROGEN RECEPTOR; PROGESTERONE RECEPTOR; TAMOXIFEN; WNT PROTEIN; ANTINEOPLASTIC AGENT; TRANSCRIPTOME;

ARTICLE; BAYES THEOREM; BAYESIAN COMPUTATIONAL MODEL; BETA CATENIN GENE; BREAST CANCER; CANCER CELL LINE; CANCER PROGNOSIS; CANCER SURVIVAL; CONTROLLED STUDY; DISEASE FREE SURVIVAL; GENE MUTATION; HUMAN; HUMAN CELL; HUMAN TISSUE; LIVER CANCER; MAJOR CLINICAL STUDY; MATHEMATICAL MODEL; MEDULLOBLASTOMA; PERSONALIZED MEDICINE; PREDICTION; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; TREATMENT RESPONSE; TUMOR GROWTH; WNT SIGNALING PATHWAY; BIOLOGICAL MODEL; COMPUTER SIMULATION; DRUG EFFECTS; METABOLISM; NEOPLASMS; PROCEDURES; STATISTICAL MODEL;

ANTINEOPLASTIC AGENTS; BAYES THEOREM; COMPUTER SIMULATION; HUMANS; INDIVIDUALIZED MEDICINE; MODELS, BIOLOGICAL; MODELS, STATISTICAL; NEOPLASMS; SIGNAL TRANSDUCTION; TRANSCRIPTOME;

EID: 84901711204     PISSN: 00085472     EISSN: 15387445     Source Type: Journal    
DOI: 10.1158/0008-5472.CAN-13-2515     Document Type: Article

References (57)

1. Hanahan D, Weinberg RA. Hallmarks of cancer: The next generation. Cell 2011;144:646-74.
2. Pharmaceutical Research and Manufacturers of America. Medicines in development for cancer: more than 900 medicines and vaccines in clinical testing offer new hope in the fight against cancer, PhRMA, Washington, DC, 2012 [monograph on the Internet]. Available from: http://www.phrma.org/sites/default/ files/pdf/phrmamedicinesindevelopmentcancer2012.pdf.
3. Hamburg MA., Collins FS. The path to personalized medicine. N Engl J Med 2010;363:301-4.
4. Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 2012;483:570-5.
5. DeVita VT, Lawrence TS, Rosenberg SA. Cancer: principles and practice of oncology. Philadelphia: Wolters Kluwer; 2011.
6. Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, et al. The genomic and transcriptomic architecture of 2, 000 breast tumours reveals novel subgroups. Nature 2012;486:346-52.
7. Hanahan D, Coussens LM. Accessories to the crime: functions of cells recruited to the tumor microenvironment. Cancer Cell 2012; 21:309-22.
8. Shmelkov E, Tang Z, Aifantis I, Statnikov A. Assessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale. Biol Direct 2011;6:15.
9. Van de Wetering M, Sancho E, Verweij C, DeLau W, Oving I, Hurlstone A, et al. The beta-catenin/TCF-4 complex imposes a crypt progenitor phenotype on colorectal cancer cells. Cell 2002;111:241-50.
10. Van der Flier LG, Sabates-Bellver J, Oving I, Haegebarth A, De Palo M, Anti M, et al. The intestinal Wnt/TCF signature. Gastroenterology 2007;132:628-32.
11. Sabates-Bellver J, Van der Flier LG, de Palo M, Cattaneo E, Maake C, Rehrauer H, et al. Transcriptome profile of human colorectal adenomas. Mol Cancer Res 2007;5:1263-75.
12. Hatzis P, van der Flier LG, van Driel MA, Guryev V, Nielsen F, Denissov S, et al. Genome-wide pattern of TCF7L2/TCF4 chromatin occupancy in colorectal cancer cells. Mol Cell Biol 2008;28:2732-44.
13. R Development Core Team. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2008.
14. Mokry M, Hatzis P, Schuijers J, Lansu N, Ruzius FP, Clevers H, et al. Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes. Nucleic Acids Res 2012;40:148-58.
15. Barker N, Ridgway RA, Van Es JH, Van de Wetering M, Begthel H, Van den Born M, et al. Crypt stem cells as the cells-of-origin of intestinal cancer. Nature 2009;457:608-11.
16. Skrzypczak M, Goryca K, Rubel T, Paziewska A, Mikula M, Jarosz D, et al. Modeling oncogenic signaling in colon tumors by multidirectional analyses of microarray data directed for maximization of analytical reliability. PLoS ONE 2010;5. pii:e13091.
17. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, et al. Tumour evolution inferred by single-cell sequencing. Nature 2011;472: 90-4.
18. De Sousa E, Melo F, Colak S, Buikhuisen J, Koster J, Cameron K, De Jong JH, et al. Methylation of cancer-stem-cell-associated Wnt target genes predicts poor prognosis in colorectal cancer patients. Cell Stem Cell 2011;9:476-85.
19. Koch A, Denkhaus D, Albrecht S, Leuschner I, von Schweinitz D, Pietsch T. Childhood hepatoblastomas frequently carry a mutateddegradation targeting box of the beta-catenin gene. Cancer Res 1999;59:269-73.
20. Guichard C, Amaddeo G, Imbeaud S, Ladeiro Y, Pelletier L, Maad IB, et al. Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma. Nat Genet 2012;44:694-8.
21. Provost E, McCabe A, Stern J, Lizardi I, D'Aquila TG, Rimm DL. Functional correlates of mutation of the Asp32 and Gly34 residues of beta-catenin. Oncogene 2005;24:2667-76.
22. Chiang DY, Villanueva A, Hoshida Y, Peix J, Newell P, Minguez B, et al. Focal gains of VEGFA and molecular classification of hepatocellular carcinoma. Cancer Res 2008;68:6779-88.
23. Wurmbach E, Chen YB, Khitrov G, Zhang W, Roayaie S, Schwartz M, et al. Genome-wide molecular profiles of HCV-induced dysplasia and hepatocellular carcinoma. Hepatology 2007;45:938-47.
24. Kool M, Koster J, Bunt J, Hasselt NE, Lakeman A, Van Sluis P, et al. Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features. PLoS ONE 2008;3:e3088.
25. Fattet S, Haberler C, Legoix P, Varlet P, Lellouch-Tubiana A, Lair S, et al. Beta-catenin status in paediatric medulloblastomas: correlation of immunohistochemical expression with mutational status, genetic profiles, and clinical characteristics. J Pathol 2009;218:86-94.
26. Hayes MJ, Thomas D, Emmons A, Giordano TJ, Kleer CG. Genetic changes of WNT pathway genes are common events in metaplastic carcinomas of the breast. Clin Cancer Res 2008;14:4038-44.
27. Lehmann BD, Bauer JA, Chen X, Sanders ME, Chakravarthy AB, Shyr Y, et al. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J Clin Invest 2011;121:2750-67.
28. Bos PD, Zhang XH, Nadal C, Shu W, Gomis RR, Nguyen DX, et al. Genes that mediate breast cancer metastasis to the brain. Nature 2009;459:1005-9.
29. Sabatier R, Finetti P, Cervera N, Lambaudie E, Esterni B, Mamessier E, et al. A gene expression signature identifies two prognostic subgroups of basal breast cancer. Breast Cancer Res Treat 2011; 126:407-20.
30. Desmedt C, Haibe-Kains B, Wirapati P, Buyse M, Larsimont D, Bontempi G, et al. Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clin Cancer Res 2008;14:5158-65.
31. Hu Z, Fan C, Oh DS, Marron JS, He X, Qaqish BF, et al. The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics 2006;7:96.
32. Bourdeau V, Deschenes J, Laperriere D, AidM, White JH, Mader S. Mechanisms of primary and secondary estrogen target gene regulation in breast cancer cells. Nucleic Acids Res 2008;36: 76-93.
33. Van Landeghem AA, Poortman J, Nabuurs M, Thijssen JH. Endogenous concentration and subcellular distribution of androgens in normal and malignant human breast tissue. Cancer Res 1985:45: 2907-12.
34. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012;483:603-7.
35. Krupp M, Itzel T, Maass T, Hildebrandt A, Falle PR, Teufel A. CellLineNavigator: A workbench for cancer cell line analysis. Nucleic Acids Res 2013;41:D942-8.
36. Barry WT, Kernagis DN, Dressman HK, Griffis RJ, Hunter JD, Olson JA, et al. Intratumor heterogeneity and precision of microarray-based predictors of breast cancer biology and clinical outcome. J Clin Oncol 2010;28:2198-206.
37. Oyama M, Nagashima T, Suzuki T, Kozuka-Hata H, Yumoto N, Shiraishi Y, et al. Integrated quantitative analysis of the phosphoproteome and transcriptome in tamoxifen-resistant breast cancer. J Biol Chem 2011;286:818-29.
38. Loi S, Haibe-Kains B, Desmedt C, Lallemand F, Tutt AM, Gillet C, et al. Definition of clinically distinct molecular subtypes in estrogen receptor- positive breast carcinomas through genomic grade. J Clin Oncol 2007;25:1239-46.
39. Loi S, Haibe-Kains B, Desmedt C, Wirapati P, Lallemand F, Tutt AM, et al. Predicting prognosis using molecular profiling in estrogen receptor- positive breast cancer treated with tamoxifen. BMC Genomics 2008;9:239.
40. Papadopoulos N, Kinzler KW, Vogelstein B. The role of companion diagnostics in the development and use of mutation-targeted cancer therapies. Nat Biotechnol 2006;24:985-95.
41. Tsimberidou AM, Iskander NG, Hong DS, Wheler JJ, Falchook GS, Fu S, et al. Personalized medicine in a phase I clinical trials program: The MD Anderson Cancer Center initiative. Clin Cancer Res 2012;18: 6373-83.
42. White BD, Chien AJ, Dawson DW. Dysregulation of Wnt/b-catenin signaling in gastrointestinal cancers. Gastroenterology 2012;142: 219-32.
43. Geyer FC, Lacroix-Triki M, Savage K, Arnedos M, Lambros MB, MacKay A, et al. b-Catenin pathway activation in breast cancer is associated with triple-negative phenotype but not with CTNNB1 mutation. Mod Pathol 2011;24:209-31.
44. King TD, Suto MJ, Li Y.The Wnt/b-catenin signaling pathway: A potential therapeutic target in the treatment of triple negative breast cancer. J Cell Biochem 2012;113:13-8.
45. Schade B, Lesurf R, Sanguin-Gendreau V, Bui T, Deblois G, O'Toole SA, et al. b-catenin signaling is a critical event in ErbB2-mediated mammary tumor progression. Cancer Res 2013;73:4474-87.
46. Taniguchi K, Roberts LR, Aderca IN, Dong X, Qian C, Murphy LM, et al. Mutational spectrum of beta-catenin, AXIN1, and AXIN2 in hepatocellular carcinomas and hepatoblastomas. Oncogene 2002;21:4863-71.
47. Malanchi I, Santamaria-Martínez A, Susanto E, Peng H, Lehr HA, Delaloye JF, et al. oInteractions between cancer stem cells and their niche govern metastatic colonizatin. Nature 2011;481:85-9.
48. Green JL, La J, Yum KW, Desai P, Rodewald LW, Zhang X, et al. Paracrine Wnt signaling both promotes and inhibits human breast tumor growth. Proc Natl Acad Sci U S A 2013;110:6991-6.
49. O'Toole SA, Beith JM, Millar EK, West R, McLean A, Cazet A, et al. Therapeutic targets in triple negative breast cancer. J Clin Pathol 2013;66:530-42.
50. Khalil S, Tan GA, Giri DD, Zhou XK, Howe LR. Activation status of Wnt/b-catenin signaling in normal and neoplastic breast tissues: relationship to HER2/neu expression in human and mouse. PLoS ONE 2012;7: e33421.
51. Incassati A, Chandramouli A, Eelkema R, Cowin P. Key signaling nodes in mammary gland development and cancer: b-catenin. Breast Cancer Res 2010;12:213.
52. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005;102:15545-50.
53. Symmans WF, Hatzis C, Sotiriou C, Andre F, Peintinger F, Regitnig P, et al. Genomic index of sensitivity to endocrine therapy for breast cancer. J Clin Oncol 2010;28:4111-9.
54. Rieger ME, Sims AH, Coats ER, Clarke RB, Briegel KJ. The embryonic transcription cofactor LBH is a direct target of the Wnt signaling pathway in epithelial development and in aggressive basal subtype breast cancers. Mol Cell Biol 2010;30:4267-79.
55. Hui M, Cazet A, Nair R, Watkins DN, O'Toole SA, Swarbrick A. The Hedgehog signalling pathway in breast development, carcinogenesis and cancer therapy. Breast Cancer Res 2013;15:203.
56. Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, et al. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst 2006;98:262-72.
57. Hammond ME, Hayes DF, Dowsett M, Allred DC, Hagerty KL, Badve S, et al. American Society of Clinical Oncology/College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer (unabridged version). Arch Pathol Lab Med 2010;134:48-72.