Novel modeling of cancer cell signaling pathways enables systematic drug repositioning for distinct breast cancer metastases

Cancer Research

Volumn 73, Issue 20, 2013, Pages 6149-6163

  Zhao, Hong ^a,b   Jin, Guangxu ^a,b   Cui, Kemi ^a   Ren, Ding ^a,f   Liu, Timothy ^a   Chen, Peikai ^a,g   Wong, Solomon ^e   Li, Fuhai ^a,b   Fan, Yubo ^a   Rodriguez, Angel ^c   Chang, Jenny ^b,c   Wong, Stephen T C ^a,b,c,d  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

^b HOUSTON METHODIST RESEARCH INSTITUTE   (United States)

^c Texas and the Task Force on the ACGME Competencies   (United States)

^d BAYLOR COLLEGE OF MEDICINE   (United States)

^e UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^f No 85 Hospital of PLA   (China)

^g UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

DASATINIB; ESTROGEN RECEPTOR; HISTONE DEACETYLASE 1; HISTONE DEACETYLASE 2; KI 67 ANTIGEN; NUCLEIC ACID BINDING PROTEIN; PROTEIN KINASE FYN; PROTEIN RET; SUNITINIB; VASCULOTROPIN RECEPTOR 2;

ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BLOOD BRAIN BARRIER; BONE METASTASIS; BRAIN METASTASIS; BREAST CANCER; CANCER SIGNALING BRIDGE; CANCER SURVIVAL; CONTROLLED STUDY; CORRELATIONAL STUDY; DRUG EFFECT; DRUG MECHANISM; DRUG MEGADOSE; DRUG REPOSITIONING; DRUG TARGETING; FEMALE; FYN GENE; GENE OVEREXPRESSION; GENE SILENCING; HIGH CONFIDENCE DOWNSTREAM SIGNALING PATHWAY; HUMAN; HUMAN CELL; IN VITRO STUDY; IN VIVO STUDY; INTRACELLULAR SIGNALING; LOW DRUG DOSE; LUNG METASTASIS; MATHEMATICAL MODEL; METASTASIS FREE SURVIVAL; METASTASIS INHIBITION; MICROMETASTASIS; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTO ONCOGENE; RET GENE; VALIDATION STUDY; WESTERN BLOTTING;

BONE NEOPLASMS; BRAIN NEOPLASMS; BREAST NEOPLASMS; DRUG REPOSITIONING; FEMALE; HUMANS; KAPLAN-MEIER ESTIMATE; LUNG NEOPLASMS; MICROARRAY ANALYSIS; MODELS, BIOLOGICAL; NEOPLASM METASTASIS; SIGNAL TRANSDUCTION;

EID: 84885979840     PISSN: 00085472     EISSN: 15387445     Source Type: Journal    
DOI: 10.1158/0008-5472.CAN-12-4617     Document Type: Article

References (48)

1. Jin G, Fu C, Zhao H., Cui K, Chang J, Wong ST A novel method of transcriptional response analysis to facilitate drug repositioning for cancer therapy. Cancer Res 2012; 72:33-44.
2. Schaefer CF, Anthony K, Krupa S., Buchoff J, Day M, Hannay T., et al PID: the Pathway Interaction Database. Nucleic Acids Res 2009; 37: D674-9.
3. Zou S, Chang J, LaFever L., Tang W, Johnson EL, Hu J, et al Identification of dAven, a Drosophila melanogaster ortholog of the cell cycle regulator Aven. Cell Cycle 2011; 10:989-98.
4. Kanehisa M, Goto S, Kawashima S., Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004; 32: D277-80.
5. Hamosh A, Scott AF, Amberger J.S., Bocchini CA, McKusick VA Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005; 33: D514-7.
6. Yildirim MA, Goh KI, Cusick M.E., Barabasi AL, Vidal M. Drug-target network. Nat Biotechnol 2007; 25:1119-26.
7. Milo R, Shen-Orr S, Itzkovitz S., Kashtan N, Chklovskii D, Alon U. Network motifs: simple building blocks of complex networks. Science 2002; 298:824-7.
8. Iorio F, Bosotti R, Scacheri E., Belcastro V, Mithbaokar P, Ferriero R., et al Discovery of drug mode of action and drug repositioning from transcriptional responses. Proc Natl Acad Sci U S A 2011; 107: 14621-6.
9. Shats I, Gatza ML, Chang J.T., Mori S., Wang J, Rich J, et al Using a stem cell-based signature to guide therapeutic selection in cancer. Cancer Res 2011; 71:1772-80.
10. Sirota M, Dudley JT, Kim J, Chiang A.P., Morgan AA, Sweet-Cordero A, et al Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med 2011; 3: 96ra77.
11. Thomson Reuters. White paper. Knowledge-based drug repositioning to drive R&D productivity. September 2012. http://thomsonreuters.com/business-unit/ science/subsector/pdf/knowledge-based-drugrepositioning-to-drive-rd- productivity.pdf.
12. Chindelevitch L, Ziemek D, Enayetallah A., Randhawa R, Sidders B, Brockel C., et al Causal reasoning on biological networks: interpreting transcriptional changes. Bioinformatics 2012; 28: 1114-21.
13. Li Y, Agarwal P. Apathway-based view of human diseases and disease relationships. PLoS ONE 2009; 4:e4346.
14. Croft D, O'Kelly G, Wu G, Haw R., Gillespie M, Matthews L, et al Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 2011; 39:D691-7.
15. Chang JC, Wooten EC, Tsimelzon A, Hilsenbeck S.G., Gutierrez MC, Elledge R, et al Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer. Lancet 2003; 362:362-9.
16. 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.
17. Wang Y, Klijn JG, Zhang Y, Sieuwerts A.M., Look MP, Yang F, et al Gene-expression profiles to predict distant metastasis of lymph-nodenegative primary breast cancer. Lancet 2005; 365:671-9.
18. Minn AJ, Gupta GP, Siegel P.M., Bos PD, Shu W, Giri DD, et al Genes that mediate breast cancer metastasis to lung. Nature 2005; 436: 518-24.
19. Jin G, Zhou X, Wang H., Zhao H, Cui K, Zhang X.S., et al The knowledge integrated network biomarkers discovery for major adverse cardiac events. J Proteome Res 2008; 7:4013-21.
20. Fu C, Jin G, Gao J., Zhu R, Ballesteros-villagrana E, Wong STC. DrugMap Central (DMC), an on-line query and visualization tool to facilitate drug repositioning studies. Bioinformatics 2013; 29:1834-6.
21. Rodriguez AA, Makris A, Wu M.F., Rimawi M., Froehlich A, Dave B, et al DNA repair signature is associated with anthracycline response in triple negative breast cancer patients. Breast Cancer Res Treat 2011; 123:189-96.
22. Andersen JN, Sathyanarayanan S, Di Bacco A, Chi A, Zhang T., Chen AH, et al Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors. Sci Transl Med 2010; 2:43ra55.
23. Yoneda T, Williams PJ, Hiraga T, Niewolna M., Nishimura R. A boneseeking clone exhibits different biological properties from the MDAMB-231 parental human breast cancer cells and a brain-seeking clone in vivo and in vitro. J Bone Miner Res 2001; 16:1486-95.
24. Zhao H, Cui K, Nie F., Wang L, Brandl MB, Jin G, et al The effect of mTOR inhibition alone or combined with MEK inhibitors on brain metastasis: an in vivo analysis in triple-negative breast cancer models. Breast Cancer Res Treat 2011; 131:425-36.
25. Pajouhesh H, Lenz GR Medicinal chemical properties of successful central nervous system drugs. NeuroRx 2005; 2:541-53.
26. Palmieri D, Lockman PR, Thomas F.C., Hua E., Herring J, Hargrave E, et al Vorinostat inhibits brain metastatic colonization in a model of triple-negative breast cancer and induces DNA double-strand breaks. Clin Cancer Res 2009; 15:6148-57.
27. + breast cancer brain metastasis. Clin Cancer Res 2011; 17:142-53.
28. Gordon MS, Vogelzang NJ, Schoffski P, Daud A., Spira AI, O'Keefe BA, et al Activity of cabozantinib (XL184) in soft tissue and bone: results of a phase II randomized discontinuation trial (RDT) in patients (pts) with advanced solid tumors. J Clin Oncol 2011; 29:3010.
29. Hwu WJ, Lis E, Menell J.H., Panageas KS, Lamb LA, Merrell J, et al Temozolomide plus thalidomide in patients with brain metastases from melanoma: a phase II study. Cancer 2005; 103:2590-7.
30. Hwu WJ, Krown SE, Menell J.H., Panageas KS, Merrell J, Lamb LA, et al Phase II study of temozolomide plus thalidomide for the treatment of metastatic melanoma. J Clin Oncol 2003; 21:3351-6.
31. Kan Z, Jaiswal BS, Stinson J, Janakiraman V., Bhatt D, Stern HM, et al Diverse somatic mutation patterns and pathway alterations in human cancers. Nature 2010; 466:869-73.
32. Saito YD, Jensen AR, Salgia R, Posadas EM Fyn: a novel molecular target in cancer. Cancer 2010; 116:1629-37.
33. Ban K, Gao Y, Amin H.M., Howard A., Miller C, Lin Q, et al BCR-ABL1 mediates up-regulation of Fyn in chronic myelogenous leukemia. Blood 2008; 111:2904-8.
34. Yadav V, Denning MF Fyn is induced by Ras/PI3K/Akt signaling and is required for enhanced invasion/migration. Mol Carcinog 2011; 50:346-52.
35. Beroukhim R, Mermel CH, Porter D, Wei G., Raychaudhuri S, Donovan J, et al The landscape of somatic copy-number alteration across human cancers. Nature 2010; 463:899-905.
36. Kang Y, Siegel PM, Shu W, Drobnjak M., Kakonen SM, Cordon-Cardo C, et al A multigenic program mediating breast cancer metastasis to bone. Cancer Cell 2003; 3:537-49.
37. Reddy KB, Nabha SM, Atanaskova N. Role of MAP kinase in tumor progression and invasion. Cancer Metastasis Rev 2003; 22:395-403.
38. Fukai I, Hussey RE, Sunder-Plassmann R, Reinherz EL A critical role for p59(fyn) in CD2-based signal transduction. Eur J Immunol 2000; 30:3507-15.
39. Venteo S, Bourane S, Mechaly I., Sar C, Abdel Samad O, Puech S, et al Regulation of the Na, K-ATPase gamma-subunit FXYD2 by Runx1 and Ret signaling in normal and injured non-peptidergic nociceptive sensory neurons. PLoS ONE 2012; 7:e29852.
40. Nie F, Yang J, Wen S., An YL, Ding J, Ju SH, et al Involvement of epidermal growth factor receptor overexpression in the promotion of breast cancer brain metastasis. Cancer 2012; 118: 5198-209.
41. Carmeliet P, Jain RK Principles and mechanisms of vessel normalization for cancer and other angiogenic diseases. Nat Rev 2011; 10: 417-27.
42. Finn RS, Dering J, Ginther C., Wilson CA, Glaspy P, Tchekmedyian N, et al Dasatinib, an orally active small molecule inhibitor of both the src and abl kinases, selectively inhibits growth of basal-type/"triple-negative" breast cancer cell lines growing in vitro. Breast Cancer Res Treat 2007; 105:319-26.
43. Reagan-Shaw S., Nihal M, Ahmad N. Dose translation from animal to human studies revisited. FASEB J 2008; 22:659-61.
44. Porkka K, Koskenvesa P, Lundan T., Rimpilainen J, Mustjoki S, Smykla R., et al Dasatinib crosses the blood-brain barrier and is an efficient therapy for central nervous system Philadelphia chromosome-positive leukemia. Blood 2008; 112:1005-12.
45. Gore ME, Szczylik C, Porta C., Bracarda S, Bjarnason GA, Oudard S, et al Safety and efficacy of sunitinib for metastatic renalcell carcinoma: an expanded-access trial. Lancet Oncol 2009; 10: 757-63.
46. Buti S, Donini M, Lazzarelli S., Passalacqua R. A new modified schedule of sunitinib for metastatic renal cell carcinoma: a retrospective analysis. Acta Biomed 2012; 83:88-94.
47. Barsky A, Gardy JL, Hancock R.E., Munzner T. Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics 2007; 23: 1040-2.
48. Vandesompele J, De Preter K, Pattyn F, Poppe B., Van Roy N, De Paepe A, et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002; 3:RESEARCH0034.