title: Genetic and epigenetic variants contributing to clofarabine cytotoxicity.
abstract: 2-chloro-2-fluoro-deoxy-9-D-arabinofuranosyladenine (Clofarabine), a purine nucleoside analog, is used in the treatment of hematologic malignancies and as induction therapy for stem cell transplantation. The discovery of pharmacogenomic markers associated with chemotherapeutic efficacy and toxicity would greatly benefit the utility of this drug. Our objective was to identify genetic and epigenetic variants associated with clofarabine toxicity using an unbiased, whole genome approach. To this end, we employed International HapMap lymphoblastoid cell lines (190 LCLs) of European (CEU) or African (YRI) ancestry with known genetic information to evaluate cellular sensitivity to clofarabine. We measured modified cytosine levels to ascertain the contribution of genetic and epigenetic factors influencing clofarabine-mediated cytotoxicity. Association studies revealed 182 single nucleotide polymorphisms (SNPs) and 143 modified cytosines associated with cytotoxicity in both populations at the threshold P ≤ 0.0001. Correlation between cytotoxicity and baseline gene expression revealed 234 genes at P ≤ 3.98 × 10(-6). Six genes were implicated as: (i) their expression was directly correlated to cytotoxicity, (ii) they had a targeting SNP associated with cytotoxicity, and (iii) they had local modified cytosines associated with gene expression and cytotoxicity. We identified a set of three SNPs and three CpG sites targeting these six genes explaining 43.1% of the observed variation in phenotype. siRNA knockdown of the top three genes (SETBP1, BAG3, KLHL6) in LCLs revealed altered susceptibility to clofarabine, confirming relevance. As clofarabine's toxicity profile includes acute kidney injury, we examined the effect of siRNA knockdown in HEK293 cells. siSETBP1 led to a significant change in HEK293 cell susceptibility to clofarabine.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Eadon
authors.forename: Heather E
authors.initials: HE
authors.lastname: Wheeler
authors.forename: Amy L
authors.initials: AL
authors.lastname: Stark
authors.forename: Xu
authors.initials: X
authors.lastname: Zhang
authors.forename: Erika L
authors.initials: EL
authors.lastname: Moen
authors.forename: Shannon M
authors.initials: SM
authors.lastname: Delaney
authors.forename: Hae Kyung
authors.initials: HK
authors.lastname: Im
authors.forename: Patrick N
authors.initials: PN
authors.lastname: Cunningham
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.forename: M Eileen
authors.initials: ME
authors.lastname: Dolan
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics; D000227:Adenine Nucleotides / Q000627:therapeutic use / Q000633:toxicity*; D051017:Apoptosis Regulatory Proteins; D001087:Arabinonucleosides / Q000627:therapeutic use / Q000633:toxicity*; D044383:Black People / Q000235:genetics*; D002352:Carrier Proteins / Q000235:genetics; D002460:Cell Line; D000077866:Clofarabine; D003596:Cytosine / Q000378:metabolism*; D044127:Epigenesis, Genetic; D015870:Gene Expression; D005796:Genes; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D057809:HEK293 Cells; D060148:HapMap Project; D006801:Humans; D015810:Linkage Disequilibrium; D009687:Nuclear Proteins / Q000235:genetics; D010597:Pharmacogenetics; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D044465:White People / Q000235:genetics*
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D000227:Adenine Nucleotides; D051017:Apoptosis Regulatory Proteins; D001087:Arabinonucleosides; C414431:BAG3 protein, human; D002352:Carrier Proteins; C473356:KLHL6 protein, human; D009687:Nuclear Proteins; C425066:SETBP1 protein, human; D000077866:Clofarabine; D003596:Cytosine