Versatile pathway-centric approach based on high-throughput sequencing to anticancer drug discovery

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 12, 2012, Pages 4609-4614

  Li, Hairi ^a   Zhou, Hongyan ^b   Wang, Dong ^a   Qiu, Jinsong ^a   Zhou, Yu ^a   Li, Xiangqiang ^c   Rosenfeld, Michael G ^d,e   Ding, Sheng ^b   Fu, Xiang Dong ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b GLADSTONE INSTITUTE OF CARDIOVASCULAR DISEASE   (United States)

^c Signosis Inc   (United States)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^e UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Chemical screening; Gene signature

Indexed keywords

ANDROGEN; ANTINEOPLASTIC AGENT; PERUVOSIDE;

ARTICLE; CANCER CELL CULTURE; CYTOTOXICITY; DRUG ACTIVITY; DRUG SCREENING; GENE EXPRESSION; GENE SEQUENCE; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; PHENOTYPE; PRIORITY JOURNAL; PROSTATE CANCER;

ANDROGENS; ANTIGENS; ANTINEOPLASTIC AGENTS; APOPTOSIS; CARDENOLIDES; CELL LINE, TUMOR; CHEMISTRY, PHARMACEUTICAL; DRUG DESIGN; DRUG SCREENING ASSAYS, ANTITUMOR; GENOMICS; GLYCOSIDES; HUMANS; PHENOTYPE; PROTEASOME ENDOPEPTIDASE COMPLEX; RNA INTERFERENCE;

EID: 84863376218     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1200305109     Document Type: Article

References (35)

1. Flordellis CS, Manolis AS, Paris H, Karabinis A (2006) Rethinking target discovery in polygenic diseases. Curr Top Med Chem 6:1791-1798. (Pubitemid 44323063)
2. Swinney DC, Anthony J (2011) How were new medicines discovered? Nat Rev Drug Discov 10:507-519.
3. Imming P, Sinning C, Meyer A (2006) Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov 5:821-834. (Pubitemid 44480536)
4. Paul SM, et al. (2010) How to improve R&D productivity: The pharmaceutical industry's grand challenge. Nat Rev Drug Discov 9:203-214.
5. Stegmaier K, et al. (2004) Gene expression-based high-throughput screening (GE-HTS) and application to leukemia differentiation. Nat Genet 36:257-263. (Pubitemid 38282750)
6. Hieronymus H, et al. (2006) Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators. Cancer Cell 10:321-330. (Pubitemid 44512193)
7. Corsello SM, et al. (2009) Identification of AML1-ETO modulators by chemical genomics. Blood 113:6193-6205.
8. Chen CD, et al. (2004) Molecular determinants of resistance to antiandrogen therapy. Nat Med 10:33-39. (Pubitemid 38524696)
9. Niu Y, et al. (2010) Differential androgen receptor signals in different cells explain why androgen-deprivation therapy of prostate cancer fails. Oncogene 29:3593-3604.
10. Goldin AG, Safa AR (1984) Digitalis and cancer. Lancet 1:1134.
11. Prassas I, Diamandis EP (2008) Novel therapeutic applications of cardiac glycosides. Nat Rev Drug Discov 7:926-935.
12. Platz EA, et al. (2011) A novel two-stage, transdisciplinary study identifies digoxin as a possible drug for prostate cancer treatment. Cancer Discov 2011:68-77.
13. Yeakley JM, et al. (2002) Profiling alternative splicing on fiber-optic arrays. Nat Biotechnol 20:353-358. (Pubitemid 34286328)
14. Li HR, et al. (2006) Two-dimensional transcriptome profiling: Identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimens. Cancer Res 66:4079-4088.
15. Fan JB, et al. (2004) A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res 14:878-885.
16. Mashima T, Okabe S, Seimiya H (2010) Pharmacological targeting of constitutively active truncated androgen receptor by nigericin and suppression of hormone-refractory prostate cancer cell growth. Mol Pharmacol 78:846-854.
17. Li H, et al. (2008) Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci USA 105:20179-20184.
18. Covell DG, et al. (2005) Linking tumor cell cytotoxicity to mechanism of drug action: An integrated analysis of gene expression, small-molecule screening and structural databases. Proteins 59:403-433. (Pubitemid 40594287)
19. Reid P, Kantoff P, Oh W (1999) Antiandrogens in prostate cancer. Invest New Drugs 17:271-284. (Pubitemid 30037959)
20. McPherson SJ, et al. (2007) Essential role for estrogen receptor beta in stromal-epithelial regulation of prostatic hyperplasia. Endocrinology 148:566-574. (Pubitemid 46143161)
21. Jones JO, et al. (2009) Non-competitive androgen receptor inhibition in vitro and in vivo. Proc Natl Acad Sci USA 106:7233-7238.
22. Jones JO, Diamond MI (2008) A cellular conformation-based screen for androgen receptor inhibitors. ACS Chem Biol 3:412-418.
23. Gupta PB, et al. (2009) Identification of selective inhibitors of cancer stem cells by high-throughput screening. Cell 138:645-659.
24. Yeh JY, Huang WJ, Kan SF, Wang PS (2003) Effects of bufalin and cinobufagin on the proliferation of androgen dependent and independent prostate cancer cells. Prostate 54:112-124. (Pubitemid 36120327)
25. McConkey DJ, Lin Y, Nutt LK, Ozel HZ, Newman RA (2000) Cardiac glycosides stimulate Ca2+ increases and apoptosis in androgen-independent, metastatic human prostate adenocarcinoma cells. Cancer Res 60:3807-3812. (Pubitemid 32204572)
26. Zhang H, et al. (2008) Digoxin and other cardiac glycosides inhibit HIF-1alpha synthesis and block tumor growth. Proc Natl Acad Sci USA 105:19579-19586.
27. Huh JR, Jr., et al. (2011) Digoxin and its derivatives suppress TH17 cell differentiation by antagonizing ROR?t activity. Nature 472:486-490.
28. Wang Q, et al. (2009) Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell 138:245-256.
29. Fox-Walsh K, Davis-Turak J, Zhou Y, Li H, Fu XD (2011) A multiplex RNA-seq strategy to profile poly(A+) RNA: Application to analysis of transcription response and 3′ end formation. Genomics 98:266-271.
30. Ye J, Chen S, Maniatis T (2011) Cardiac glycosides are potent inhibitors of interferon-β gene expression. Nat Chem Biol 7:25-33.
31. Libertini SJ, et al. (2007) Evidence for calpain-mediated androgen receptor cleavage as a mechanism for androgen independence. Cancer Res 67:9001-9005. (Pubitemid 47535881)
32. Guo Z, et al. (2009) A novel androgen receptor splice variant is up-regulated during prostate cancer progression and promotes androgen depletion-resistant growth. Cancer Res 69:2305-2313.
33. Amit I, et al. (2009) Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 326:257-263.
34. Wang D, et al. (2011) Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474:390-394.
35. Li H, Qiu J, Fu X-D (2011) RASL-seq for massive parallel and quantitative analysis of gene expression. Curr Protoc Mol Biol, in press.