Genetic and epigenetic variants contributing to clofarabine cytotoxicity

Michael Eadon, Heather E. Wheeler, Amy L. Stark, Xu Zhang, Erika L. Moen, Shannon M. Delaney, Hae Kyung Im, Patrick N. Cunningham, Wei Zhang, Eileen E. Dolan

Research output: Contribution to journalArticle

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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.

Original languageEnglish (US)
Pages (from-to)4007-4020
Number of pages14
JournalHuman Molecular Genetics
Volume22
Issue number19
DOIs
StatePublished - Oct 2013
Externally publishedYes

Fingerprint

Epigenomics
Cytosine
Single Nucleotide Polymorphism
HEK293 Cells
Small Interfering RNA
Vidarabine
HapMap Project
Genes
Purine Nucleosides
Gene Expression
Gene Targeting
Pharmacogenetics
Stem Cell Transplantation
Hematologic Neoplasms
Acute Kidney Injury
clofarabine
Genome
Phenotype
Cell Line
Therapeutics

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)
  • Molecular Biology

Cite this

Eadon, M., Wheeler, H. E., Stark, A. L., Zhang, X., Moen, E. L., Delaney, S. M., ... Dolan, E. E. (2013). Genetic and epigenetic variants contributing to clofarabine cytotoxicity. Human Molecular Genetics, 22(19), 4007-4020. https://doi.org/10.1093/hmg/ddt240

Genetic and epigenetic variants contributing to clofarabine cytotoxicity. / Eadon, Michael; Wheeler, Heather E.; Stark, Amy L.; Zhang, Xu; Moen, Erika L.; Delaney, Shannon M.; Im, Hae Kyung; Cunningham, Patrick N.; Zhang, Wei; Dolan, Eileen E.

In: Human Molecular Genetics, Vol. 22, No. 19, 10.2013, p. 4007-4020.

Research output: Contribution to journalArticle

Eadon, M, Wheeler, HE, Stark, AL, Zhang, X, Moen, EL, Delaney, SM, Im, HK, Cunningham, PN, Zhang, W & Dolan, EE 2013, 'Genetic and epigenetic variants contributing to clofarabine cytotoxicity', Human Molecular Genetics, vol. 22, no. 19, pp. 4007-4020. https://doi.org/10.1093/hmg/ddt240
Eadon, Michael ; Wheeler, Heather E. ; Stark, Amy L. ; Zhang, Xu ; Moen, Erika L. ; Delaney, Shannon M. ; Im, Hae Kyung ; Cunningham, Patrick N. ; Zhang, Wei ; Dolan, Eileen E. / Genetic and epigenetic variants contributing to clofarabine cytotoxicity. In: Human Molecular Genetics. 2013 ; Vol. 22, No. 19. pp. 4007-4020.
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AU - Delaney, Shannon M.

AU - Im, Hae Kyung

AU - Cunningham, Patrick N.

AU - Zhang, Wei

AU - Dolan, Eileen E.

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AB - 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.

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