title: Integrative analysis of epigenetic modulation in melanoma cell response to decitabine: clinical implications.
abstract: Decitabine, an epigenetic modifier that reactivates genes otherwise suppressed by DNA promoter methylation, is effective for some, but not all cancer patients, especially those with solid tumors. It is commonly recognized that to overcome resistance and improve outcome, treatment should be guided by tumor biology, which includes genotype, epigenotype, and gene expression profile. We therefore took an integrative approach to better understand melanoma cell response to clinically relevant dose of decitabine and identify complementary targets for combined therapy. We employed eight different melanoma cell strains, determined their growth, apoptotic and DNA damage responses to increasing doses of decitabine, and chose a low, clinically relevant drug dose to perform whole-genome differential gene expression, bioinformatic analysis, and protein validation studies. The data ruled out the DNA damage response, demonstrated the involvement of p21(Cip1) in a p53-independent manner, identified the TGFbeta pathway genes CLU and TGFBI as markers of sensitivity to decitabine and revealed an effect on histone modification as part of decitabine-induced gene expression. Mutation analysis and knockdown by siRNA implicated activated beta-catenin/MITF, but not BRAF, NRAS or PTEN mutations as a source for resistance. The importance of protein stability predicted from the results was validated by the synergistic effect of Bortezomib, a proteasome inhibitor, in enhancing the growth arrest of decitabine in otherwise resistant melanoma cells. Our integrative analysis show that improved therapy can be achieved by comprehensive analysis of cancer cells, identified biomarkers for patient's selection and monitoring response, as well as targets for improved combination therapy.
authors.affiliation: Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, United States of America. ruth.halaban@yale.edu
authors.forename: Ruth
authors.initials: R
authors.lastname: Halaban
authors.forename: Michael
authors.initials: M
authors.lastname: Krauthammer
authors.forename: Mattia
authors.initials: M
authors.lastname: Pelizzola
authors.forename: Elaine
authors.initials: E
authors.lastname: Cheng
authors.forename: Daniela
authors.initials: D
authors.lastname: Kovacs
authors.forename: Mario
authors.initials: M
authors.lastname: Sznol
authors.forename: Stephan
authors.initials: S
authors.lastname: Ariyan
authors.forename: Deepak
authors.initials: D
authors.lastname: Narayan
authors.forename: Antonella
authors.initials: A
authors.lastname: Bacchiocchi
authors.forename: Annette
authors.initials: A
authors.lastname: Molinaro
authors.forename: Yuval
authors.initials: Y
authors.lastname: Kluger
authors.forename: Min
authors.initials: M
authors.lastname: Deng
authors.forename: Nam
authors.initials: N
authors.lastname: Tran
authors.forename: Wengeng
authors.initials: W
authors.lastname: Zhang
authors.forename: Mauro
authors.initials: M
authors.lastname: Picardo
authors.forename: Jan J
authors.initials: JJ
authors.lastname: Enghild
mesh_terms: D017209:Apoptosis; D001374:Azacitidine / Q000031:analogs & derivatives* / Q000494:pharmacology / Q000627:therapeutic use; D014408:Biomarkers, Tumor; D045744:Cell Line, Tumor; D049109:Cell Proliferation; D019295:Computational Biology; D004249:DNA Damage; D000077209:Decitabine; D019008:Drug Resistance, Neoplasm / Q000235:genetics; D044127:Epigenesis, Genetic / Q000187:drug effects*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects*; D006801:Humans; D008545:Melanoma / Q000188:drug therapy / Q000235:genetics* / Q000473:pathology*
chemical_list: D014408:Biomarkers, Tumor; D000077209:Decitabine; D001374:Azacitidine