Gene Expression-Based Chemical Genomics Identifies Potential Therapeutic Drugs in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is an aggressive tumor with a poor prognosis. Currently, only sorafenib is approved by the FDA for advanced HCC treatment; therefore, there is an urgent need to discover candidate therapeutic drugs for HCC. We hypothesized that if a drug signature could reverse, at least in part, the gene expression signature of HCC, it might have the potential to inhibit HCC-related pathways and thereby treat HCC. To test this hypothesis, we first built an integrative platform, the “Encyclopedia of Hepatocellular Carcinoma genes Online 2”, dubbed EHCO2, to systematically collect, organize and compare the publicly available data from HCC studies. The resulting collection includes a total of 4,020 genes. To systematically query the Connectivity Map (CMap), which includes 6,100 drug-mediated expression profiles, we further designed various gene signature selection and enrichment methods, including a randomization technique, majority vote, and clique analysis. Subsequently, 28 out of 50 prioritized drugs, including tanespimycin, trichostatin A, thioguanosine, and several anti-psychotic drugs with anti-tumor activities, were validated via MTT cell viability assays and clonogenic assays in HCC cell lines. To accelerate their future clinical use, possibly through drug-repurposing, we selected two well-established drugs to test in mice, chlorpromazine and trifluoperazine. Both drugs inhibited orthotopic liver tumor growth. In conclusion, we successfully discovered and validated existing drugs for potential HCC therapeutic use with the pipeline of Connectivity Map analysis and lab verification, thereby suggesting the usefulness of this procedure to accelerate drug repurposing for HCC treatment.

[1]  T. Golub,et al.  Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL1 and glucocorticoid resistance. , 2006, Cancer cell.

[2]  P. Galle.  Sorafenib in advanced hepatocellular carcinoma - We have won a battle not the war. , 2008, Journal of hepatology.

[3]  S. Thorgeirsson,et al.  Functional and genomic implications of global gene expression profiles in cell lines from human hepatocellular cancer , 2002, Hepatology.

[4]  Zhu Chen,et al.  Acute promyelocytic leukaemia: novel insights into the mechanisms of cure , 2010, Nature Reviews Cancer.

[5]  R. Finn.  Development of Molecularly Targeted Therapies in Hepatocellular Carcinoma: Where Do We Go Now? , 2010, Clinical Cancer Research.

[6]  Yoon-Koo Kang,et al.  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. , 2009, The Lancet. Oncology.

[7]  M. Honda,et al.  Identification of differentially expressed genes in hepatocellular carcinoma with cDNA microarrays , 2001, Hepatology.

[8]  C. Keith,et al.  The novel combination of chlorpromazine and pentamidine exerts synergistic antiproliferative effects through dual mitotic action. , 2007, Cancer research.

[9]  Abraham Weizman,et al.  Phenothiazines induce apoptosis in a B16 mouse melanoma cell line and attenuate in vivo melanoma tumor growth. , 2006, Oncology reports.

[10]  Tushar Patel,et al.  Candidate therapeutic agents for hepatocellular cancer can be identified from phenotype‐associated gene expression signatures , 2009, Cancer.

[11]  Philip M. Long,et al.  Identification of discriminators of hepatoma by gene expression profiling using a minimal dataset approach , 2004, Hepatology.

[12]  Todd R Golub,et al.  Gene expression–based high-throughput screening(GE-HTS) and application to leukemia differentiation , 2004, Nature Genetics.

[13]  Elena Edelman,et al.  A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities , 2008, Proceedings of the National Academy of Sciences.

[14]  Chia-Hui Chang,et al.  Reconfigurable Web Wrapper Agents for Web Information Integration , 2003, IIWeb.

[15]  Chia-Hung Liu,et al.  Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online) , 2007, BMC Bioinformatics.

[16]  S. Duensing,et al.  Targeted therapies of gastrointestinal stromal tumors (GIST)--the next frontiers. , 2010, Biochemical pharmacology.

[17]  Paul A Clemons,et al.  The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease , 2006, Science.

[18]  Carsten Denkert,et al.  Association of patterns of class I histone deacetylase expression with patient prognosis in gastric cancer: a retrospective analysis. , 2008, The Lancet. Oncology.

[19]  Herb Chen,et al.  The HDAC inhibitor trichostatin A inhibits growth of small cell lung cancer cells. , 2007, The Journal of surgical research.

[20]  Chi-Ying F. Huang,et al.  From NPC Therapeutic Target Identification to Potential Treatment Strategy , 2010, Molecular Cancer Therapeutics.

[21]  M. S. Rosa,et al.  CD26/DPPIV expression and 8-azaguanine response in T-acute lymphoblastic leukaemia cell lines in culture. , 2007, Pathophysiology : the official journal of the International Society for Pathophysiology.

[22]  Damian Szklarczyk,et al.  STITCH 2: an interaction network database for small molecules and proteins , 2009, Nucleic Acids Res..

[23]  S. Catts,et al.  Cytotoxic effects of antipsychotic drugs implicate cholesterol homeostasis as a novel chemotherapeutic target , 2010, International journal of cancer.

[24]  Tzu-Chi Chen,et al.  POINeT: protein interactome with sub-network analysis and hub prioritization , 2009, BMC Bioinformatics.

[25]  X. Wang,et al.  Cancer‐associated molecular signature in the tissue samples of patients with cirrhosis , 2004, Hepatology.

[26]  H. Pitot,et al.  Inhibition of ribosomal RNA maturation in Novikoff hepatoma cells by toyocamycin, tubercidin, and 6-thioguanosine. , 1974, Cancer research.

[27]  T. Golub,et al.  Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer. , 2008, Journal of the National Cancer Institute.

[28]  Yudong D. He,et al.  Functional Discovery via a Compendium of Expression Profiles , 2000, Cell.

[29]  J. Llovet,et al.  Molecular classification and novel targets in hepatocellular carcinoma: recent advancements. , 2010, Seminars in liver disease.

[30]  K Y Hui,et al.  A specific inhibitor of phosphatidylinositol 3-kinase, 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one (LY294002). , 1994, The Journal of biological chemistry.

[31]  Cheng-Yan Kao,et al.  Genome-Wide Detection of Putative Oncofetal Genes in Human Hepatocellular Carcinoma by Splicing Pattern Comparison , 2010 .

[32]  Yun Ho Jang,et al.  Proteomic identification of anti-cancer proteins in luteolin-treated human hepatoma Huh-7 cells. , 2009, Cancer letters.

[33]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[34]  F. Izzo,et al.  A new prognostic system for hepatocellular carcinoma: A retrospective study of 435 patients , 1998, Hepatology.

[35]  Tzu-Chi Chen,et al.  Cliques in mitotic spindle network bring kinetochore‐associated complexes to form dependence pathway , 2009, Proteomics.

[36]  E. Altschuler,et al.  Consideration of use of phenothiazines in particular trifluorperazine for epidermal growth factor receptor associated cancers. , 2007, Medical Hypotheses.

[37]  Adrian V. Lee,et al.  Insulin-like growth factor-I activates gene transcription programs strongly associated with poor breast cancer prognosis. , 2008, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[38]  T. Golub,et al.  Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators. , 2006, Cancer cell.

[39]  C. Larsson,et al.  Modulating IGFBP-3 expression by trichostatin A: potential therapeutic role in the treatment of hepatocellular carcinoma. , 2000, International Journal of Molecular Medicine.

[40]  Chang Gun Kim,et al.  Chlorpromazine activates p21Waf1/Cip1 gene transcription via early growth response-1 (Egr-1) in C6 glioma cells , 2010, Experimental & Molecular Medicine.