Identification of molecular mechanisms for cellular drug resistance by combining drug activity and gene expression profiles

Acquired drug resistance is a major problem in cancer treatment. To explore the genes involved in chemosensitivity and resistance, 10 human tumour cell lines, including parental cells and resistant subtypes selected for resistance against doxorubicin, melphalan, teniposide and vincristine, were profiled for mRNA expression of 7400 genes using cDNA microarray technology. The drug activity of 66 cancer agents was evaluated on the cell lines, and correlations between drug activity and gene expression were calculated and ranked. Hierarchical clustering of drugs based on their drug–gene correlations yielded clusters of drugs with similar mechanism of action. Genes correlated with drug sensitivity and resistance were imported into the PathwayAssist software to identify putative molecular pathways involved. A substantial number of both proapoptotic and antiapoptotic genes such as signal transducer and activator of transcription 1, mitogen-activated protein kinase 1 and focal adhesion kinase were found to be associated to drug resistance, whereas genes linked to cell cycle control and proliferation, such as cell division cycle 25A and signal transducer of activator of transcription 5A, were associated to general drug sensitivity. The results indicate that combined information from drug activity and gene expression in a resistance-based cell line panel may provide new knowledge of the genes involved in anticancer drug resistance and become a useful tool in drug development.

[1]  T. Hsieh,et al.  Mutations of human topoisomerase IIα affecting multidrug resistance and sensitivity , 1999 .

[2]  K. Nilsson,et al.  Development of vincristine resistance and increased sensitivity to cyclosporin A and verapamil in the human U‐937 lymphoma cell line without overexpression of the 170‐KDa P‐glycoprotein , 1994, International journal of cancer.

[3]  J. Trent,et al.  Development and characterization of a melphalan-resistant human multiple myeloma cell line. , 1991, Cancer research.

[4]  C. Beam,et al.  Genotypic and phenotypic comparisons of de novo and acquired melphalan resistance in an isogenic multiple myeloma cell line model. , 2003, Cancer research.

[5]  R. Scully,et al.  Molecular Functions of BRCA1 in the DNA Damage Response , 2004, Cancer biology & therapy.

[6]  D. Alberts,et al.  Characterization of a new drug-resistant human myeloma cell line that expresses P-glycoprotein. , 1986, Cancer research.

[7]  K. Luthman,et al.  Antitumor activity of the alkylating oligopeptides J1 (L-melphalanyl-p-L-fluorophenylalanine ethyl ester) and P2 (L-prolyl-m-L-sarcolysyl-p-L-fluorophenylalanine ethyl ester): comparison with melphalan , 2003, Anti-cancer drugs.

[8]  R. Mulcahy,et al.  Up-regulation of γ-glutamylcysteine synthetase activity in melphalan-resistant human multiple myeloma cells expressing increased glutathione levels , 2004, Cancer Chemotherapy and Pharmacology.

[9]  D. Geschwind,et al.  An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis. , 2002, Nucleic acids research.

[10]  J. Mesirov,et al.  Chemosensitivity prediction by transcriptional profiling , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[11]  D A Scudiero,et al.  Display and analysis of patterns of differential activity of drugs against human tumor cell lines: development of mean graph and COMPARE algorithm. , 1989, Journal of the National Cancer Institute.

[12]  G. S. Johnson,et al.  An Information-Intensive Approach to the Molecular Pharmacology of Cancer , 1997, Science.

[13]  Qiuping Guo,et al.  A new class of homogeneous nucleic acid probes based on specific displacement hybridization. , 2002, Nucleic acids research.

[14]  W. T. Beck,et al.  Atypical multiple drug resistance in a human leukemic cell line selected for resistance to teniposide (VM-26). , 1987, Cancer research.

[15]  PETER ALEXANDER,et al.  Cancer Chemotherapy , 1968, Nature.

[16]  S. Dudoit,et al.  Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. , 2002, Nucleic acids research.

[17]  K. Nilsson,et al.  Anti-cancer drug characterisation using a human cell line panel representing defined types of drug resistance. , 1996, British Journal of Cancer.

[18]  Rolf Larsson,et al.  Multiparametric evaluation of apoptosis: effects of standard cytotoxic agents and the cyanoguanidine CHS 828. , 2004, Molecular cancer therapeutics.

[19]  D. Botstein,et al.  A gene expression database for the molecular pharmacology of cancer , 2000, Nature Genetics.

[20]  M. Slovak,et al.  Localization of a novel multidrug resistance-associated gene in the HT1080/DR4 and H69AR human tumor cell lines. , 1993, Cancer research.

[21]  A. Veerman,et al.  Cell proliferation is related to in vitro drug resistance in childhood acute leukaemia , 2003, British Journal of Cancer.

[22]  M. Blagosklonny.  Prospective strategies to enforce selectively cell death in cancer cells , 2004, Oncogene.

[23]  Yusuke Nakamura,et al.  An integrated database of chemosensitivity to 55 anticancer drugs and gene expression profiles of 39 human cancer cell lines. , 2002, Cancer research.

[24]  J. Briones,et al.  Role of the STAT1 pathway in apoptosis induced by fludarabine and JAK kinase inhibitors in B-cell chronic lymphocytic leukemia , 2005, Leukemia & lymphoma.

[25]  Bernard Roizman,et al.  STAT1 is overexpressed in tumors selected for radioresistance and confers protection from radiation in transduced sensitive cells. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[26]  D. Suttle,et al.  Altered catalytic activity of and DNA cleavage by DNA topoisomerase II from human leukemic cells selected for resistance to VM-26. , 1988, Biochemistry.

[27]  P B Laub,et al.  Identification of genes associated with platinum drug sensitivity and resistance in human ovarian cancer cells , 2005, British Journal of Cancer.

[28]  J N Weinstein,et al.  Neural computing in cancer drug development: predicting mechanism of action. , 1992, Science.

[29]  Mitsutoshi Nakamura,et al.  Contributions of mitogen‐activated protein kinase and nuclear factor kappa B to N‐(4‐hydroxyphenyl)retinamide–induced apoptosis in prostate cancer cells , 2002, Molecular carcinogenesis.

[30]  M. Boyd,et al.  Some practical considerations and applications of the national cancer institute in vitro anticancer drug discovery screen , 1995 .

[31]  L. V. van Putten,et al.  Proliferation-dependent cytotoxicity of anticancer agents: a review. , 1975, Cancer research.

[32]  R. Larsson,et al.  Differential in vitro sensitivity of human tumor and normal cells to chemotherapeutic agents and resistance modulators , 1991, International Journal of Cancer.

[33]  R. Larsson,et al.  Chemotherapeutic drug sensitivity testing of human leukemia cells in vitro using a semiautomated fluorometric assay. , 1990, Leukemia.

[34]  C. Yu,et al.  Mutations of human topoisomerase II alpha affecting multidrug resistance and sensitivity. , 1999, Biochemistry.

[35]  P. Brown,et al.  Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Nicola Gebbia,et al.  STAT proteins: From normal control of cellular events to tumorigenesis , 2003, Journal of cellular physiology.

[37]  A. Duncan,et al.  Overexpression of a transporter gene in a multidrug-resistant human lung cancer cell line. , 1992, Science.

[38]  S. Mirski,et al.  Multidrug resistance in a human small cell lung cancer cell line selected in adriamycin. , 1987, Cancer research.

[39]  J. Marie.  Drug resistance in hematologic malignancies , 2001, Current opinion in oncology.

[40]  S. Hanks,et al.  Focal Adhesion Kinase Suppresses Apoptosis by Binding to the Death Domain of Receptor-Interacting Protein , 2004, Molecular and Cellular Biology.

[41]  Yves Pommier,et al.  Apoptosis defects and chemotherapy resistance: molecular interaction maps and networks , 2004, Oncogene.