Gene expression-based chemical genomics identifies potential therapeutic drugs in hepatocellular carcinoma

PLoS ONE

Volumn 6, Issue 11, 2011, Pages

  Chen, Ming Huang ^a   Yang, Wu Lung R ^b   Lin, Kuan Ting ^a,c   Liu, Chia Hung ^b,c   Liu, Yu Wen ^a   Huang, Kai Wen ^d   Chang, Peter Mu Hsin ^a   Lai, Jin Mei ^e   Hsu, Chun Nan ^c,f   Chao, Kun Mao ^b   Kao, Cheng Yan ^b   Huang, Chi Ying F ^a  

^a NATIONAL YANG MING UNIVERSITY   (Taiwan)

^b NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^c INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^d NATIONAL TAIWAN UNIVERSITY HOSPITAL   (Taiwan)

^e FU JEN CATHOLIC UNIVERSITY   (Taiwan)

^f UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

17ALPHA ESTRADIOL; 2 MORPHOLINO 8 PHENYLCHROMONE; 3 (4,5 DIMETHYL 2 THIAZOLYL) 2,5 DIPHENYLTETRAZOLIUM BROMIDE; 8 AZAGUANINE; ALSTERPAULLONE; APIGENIN; BISACODYL; CHLORPROMAZINE; DIPYRIDAMOLE; DOXORUBICIN; ENTINOSTAT; LUTEOLIN; MEBENDAZOLE; METICRANE; NEUROLEPTIC AGENT; OXAPROZIN; PHENOXYBENZAMINE; PRONETALOL; REPAGLINIDE; ROTTLERIN; SULCONAZOLE; TANESPIMYCIN; THIOGUANOSINE; THIORIDAZINE; TRICHOSTATIN A; TRIFLUOPERAZINE; TRIOXYSALEN; UNINDEXED DRUG; VORINOSTAT; WITHAFERIN A; DOPAMINE RECEPTOR BLOCKING AGENT;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ANTINEOPLASTIC ACTIVITY; ARTICLE; CANCER CELL CULTURE; CANCER CHEMOTHERAPY; CANCER INHIBITION; CELL VIABILITY; CLONOGENIC ASSAY; CONCENTRATION RESPONSE; CONTROLLED STUDY; DOWN REGULATION; DRUG DETERMINATION; DRUG EFFICACY; FUNCTIONAL GENOMICS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE OVEREXPRESSION; GENETIC SELECTION; LIVER CELL CARCINOMA; MOUSE; NONHUMAN; SIGNAL TRANSDUCTION; TUMOR GENE; UPREGULATION; VALIDATION PROCESS; ANIMAL; CELL PROLIFERATION; DRUG DEVELOPMENT; DRUG EFFECT; DRUG SCREENING; GENETICS; HUMAN; INFORMATION PROCESSING; LIVER TUMOR; METHODOLOGY; NUCLEIC ACID DATABASE; PROCEDURES; VALIDATION STUDY;

MUS;

ANIMALS; CARCINOMA, HEPATOCELLULAR; CELL PROLIFERATION; CHLORPROMAZINE; DATA COLLECTION; DATABASES, NUCLEIC ACID; DOPAMINE ANTAGONISTS; DRUG DISCOVERY; DRUG EVALUATION, PRECLINICAL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LIVER NEOPLASMS; METHODS; MICE; TRIFLUOPERAZINE;

EID: 80455158366     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0027186     Document Type: Article

References (40)

1. Investigators TCotLIP (1998) A new prognostic system for hepatocellular carcinoma: A retrospective study of 435 patients. Hepatology 28: 751-755.
2. Cheng A-L, Kang Y-K, Chen Z, Tsao C-J, Qin S, et al. (2009) Efficacy and safety of sorafenib in patients in the Asia-Pacific region with advanced hepatocellular carcinoma: a phase III randomised, double-blind, placebo-controlled trial. The Lancet Oncology 10: 25-34.
3. Galle PR, (2008) Sorafenib in advanced hepatocellular carcinoma- We have won a battle not the war. Journal of Hepatology 49: 871-873.
4. Finn RS, (2010) Development of molecularly targeted therapies in hepatocellular carcinoma: where do we go now? Clinical cancer research: an official journal of the American Association for Cancer Research 16: 390-397.
5. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
6. Stegmaier K, Ross KN, Colavito SA, O'Malley S, Stockwell BR, et al. (2004) Gene expression-based high-throughput screening(GE-HTS) and application to leukemia differentiation. Nat Genet 36: 257-263.
7. Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, et al. (2006) The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313: 1929-1935.
8. Wei G, Twomey D, Lamb J, Schlis K, Agarwal J, et al. (2006) Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL1 and glucocorticoid resistance. Cancer Cell 10: 331-342.
9. Hieronymus H, Lamb J, Ross KN, Peng XP, Clement C, et al. (2006) Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators. Cancer Cell 10: 321-330.
10. de Thé H, Chen Z, (2010) Acute promyelocytic leukaemia: novel insights into the mechanisms of cure. Nat Rev Cancer 10: 775-783.
11. Duensing S, Duensing A, (2010) Targeted therapies of gastrointestinal stromal tumors (GIST)-The next frontiers. Biochemical Pharmacology 80: 575-583.
12. Neo SY, Leow CK, Vega VB, Long PM, Islam AF, et al. (2004) Identification of discriminators of hepatoma by gene expression profiling using a minimal dataset approach. Hepatology 39: 944-953.
13. Kim J, Ye Q, Forgues M, Chen Y, Budhu A, et al. (2004) Cancer-associated molecular signature in the tissue samples of patients with cirrhosis. Hepatology 39: 518-527.
14. Lee J, Thorgeirsson S, (2002) Functional and genomic implications of global gene expression profiles in cell lines from human hepatocellular cancer. Hepatology 35: 1134-1143.
15. Shirota Y, Kaneko S, Honda M, Kawai H, Kobayashi K, (2001) Identification of differentially expressed genes in hepatocellular carcinoma with cDNA microarrays. Hepatology 33: 832-840.
16. Hsu C, Chang C, Siek H, Lu J, Chiou J, (2003) Reconfigurable web wrapper agents for web information integration. Proceedings of IJCAI-2003 Workshop on Information Integration on the Web.
17. Hsu CN, Lai JM, Liu CH, Tseng HH, Lin CY, et al. (2007) Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online). BMC bioinformatics 8: 66.
18. Liu C-H, Lin K-T, Huang C-YF, Shann Y-J, Lin Y-S, et al. (2011) Genome-Wide Detection of Putative Oncofetal Genes in Human Hepatocellular Carcinoma by Splicing Pattern Comparison. iConcept Transaction on Computational Intelligence in Bioinformatics (TCIB).
19. Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, et al. (2010) STITCH 2: an interaction network database for small molecules and proteins. Nucleic acids research 38: D552-556.
20. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
21. Lee SA, Chan CH, Chen TC, Yang CY, Huang KC, et al. (2009) POINeT: protein interactome with sub-network analysis and hub prioritization. BMC Bioinformatics 10: 114.
22. Hoshida Y, Toffanin S, Lachenmayer A, Villanueva A, Minguez B, et al. (2010) Molecular classification and novel targets in hepatocellular carcinoma: recent advancements. Semin Liver Dis 30: 35-51.
23. Chen T-C, Lee S-A, Chan C-H, Juang Y-L, Hong Y-R, et al. (2009) Cliques in mitotic spindle network bring kinetochore-associated complexes to form dependence pathway. Proteomics 9: 4048-4062.
24. Braconi C, Meng F, Swenson E, Khrapenko L, Huang N, et al. (2009) Candidate therapeutic agents for hepatocellular cancer can be identified from phenotype-associated gene expression signatures. Cancer 115: 3738-3748.
25. Platta C, Greenblatt D, Kunnimalaiyaan M, Chen H, (2007) The HDAC inhibitor trichostatin A inhibits growth of small cell lung cancer cells. Journal of Surgical Research 142: 219-226.
26. Weichert W, Roske A, Gekeler V, Beckers T, Ebert M, et al. (2008) Association of patterns of class I histone deacetylase expression with patient prognosis in gastric cancer: a retrospective analysis. Lancet Oncology 9: 139-148.
27. Weiss JW, Pitot HC, (1974) Inhibition of ribosomal RNA maturation in Novikoff hepatoma cells by toyocamycin, tubercidin, and 6-thioguanosine. Cancer Res 34: 581-587.
28. Creighton CJ, Casa A, Lazard Z, Huang S, Tsimelzon A, et al. (2008) Insulin-like growth factor-I activates gene transcription programs strongly associated with poor breast cancer prognosis. J Clin Oncol 26: 4078-4085.
29. Garman KS, Acharya CR, Edelman E, Grade M, Gaedcke J, et al. (2008) A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities. Proc Natl Acad Sci U S A 105: 19432-19437.
30. Setlur SR, Mertz KD, Hoshida Y, Demichelis F, Lupien M, et al. (2008) Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer. J Natl Cancer Inst 100: 815-825.
31. Lan MY, Chen CL, Lin KT, Lee SA, Yang WL, et al. (2010) From NPC therapeutic target identification to potential treatment strategy. Mol Cancer Ther 9: 2511-2523.
32. Gray SG, Kytola S, Lui WO, Larsson C, Ekstrom TJ, (2000) Modulating IGFBP-3 expression by trichostatin A: potential therapeutic role in the treatment of hepatocellular carcinoma. Int J Mol Med 5: 33-41.
33. Vlahos CJ, Matter WF, Hui KY, Brown RF, (1994) A specific inhibitor of phosphatidylinositol 3-kinase,2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one (LY294002). J Biol Chem 269: 5241-5248.
34. Shin SY, Kim CG, Kim SH, Kim YS, Lim Y, et al. (2010) Chlorpromazine activates p21Waf1/Cip1 gene transcription via early growth response-1 (Egr-1) in C6 glioma cells. Exp Mol Med 42: 395-405.
35. Wiklund ED, Catts VS, Catts SV, Ng TF, Whitaker NJ, et al. (2010) Cytotoxic effects of antipsychotic drugs implicate cholesterol homeostasis as a novel chemotherapeutic target. Int J Cancer 126: 28-40.
36. Lee MS, Johansen L, Zhang Y, Wilson A, Keegan M, et al. (2007) The novel combination of chlorpromazine and pentamidine exerts synergistic antiproliferative effects through dual mitotic action. Cancer Res 67: 11359-11367.
37. Gil-Ad I, Shtaif B, Levkovitz Y, Nordenberg J, Taler M, et al. (2006) Phenothiazines induce apoptosis in a B16 mouse melanoma cell line and attenuate in vivo melanoma tumor growth. Oncol Rep 15: 107-112.
38. Kast RE, Altschuler EL, (2007) Consideration of use of phenothiazines in particular trifluorperazine for epidermal growth factor receptor associated cancers. Medical Hypotheses 69: 1074-1075.
39. Yoo DR, Jang YH, Jeon YK, Kim JY, Jeon W, et al. (2009) Proteomic identification of anti-cancer proteins in luteolin-treated human hepatoma Huh-7 cells. Cancer Lett 282: 48-54.
40. Dourado M, Sarmento AB, Pereira SV, Alves V, Silva T, et al. (2007) CD26/DPPIV expression and 8-azaguanine response in T-acute lymphoblastic leukaemia cell lines in culture. Pathophysiology 14: 3-10.