Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines

Liang Li, Brooke L. Fridley, Krishna R Kalari, Nifang Niu, Gregory Jenkins, Anthony Batzler, Ryan P. Abo, Daniel J Schaid, Liewei M Wang

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Background: Two cytidine analogues, gemcitabine and cytosine arabinoside (AraC), are widely used in the treatment of a variety of cancers with a large individual variation in response. To identify potential genetic biomarkers associated with response to these two drugs, we used a human lymphoblastoid cell line (LCL) model system with extensive genomic data, including 1.3 million SNPs and 54,000 basal expression probesets to perform genome-wide association studies (GWAS) with gemcitabine and AraC IC50 values.Results: We identified 11 and 27 SNP loci significantly associated with gemcitabine and AraC IC50 values, respectively. Eleven candidate genes were functionally validated using siRNA knockdown approach in multiple cancer cell lines. We also characterized the potential mechanisms of genes by determining their influence on the activity of 10 cancer-related signaling pathways using reporter gene assays. Most SNPs regulated gene expression in a trans manner, except 7 SNPs in the PIGB gene that were significantly associated with both the expression of PIGB and gemcitabine cytotoxicity.Conclusion: These results suggest that genetic variation might contribute to drug response via either cis- or trans- regulation of gene expression. GWAS analysis followed by functional pharmacogenomics studies might help identify novel biomarkers contributing to variation in response to these two drugs and enhance our understanding of underlying mechanisms of drug action.

Original languageEnglish (US)
Article number93
JournalBMC Genomics
Volume15
Issue number1
DOIs
StatePublished - Feb 1 2014

Fingerprint

gemcitabine
Cytidine
Single Nucleotide Polymorphism
Genome-Wide Association Study
Biomarkers
Cell Line
Pharmaceutical Preparations
Inhibitory Concentration 50
Genes
Neoplasms
Cytarabine
Gene Expression Regulation
Reporter Genes
Small Interfering RNA
Gene Expression

Keywords

  • Cytidine analogues
  • Cytosine arabinoside
  • Expression array
  • Functional genomics
  • Gemcitabine
  • Genome-wide association study
  • Genome-wide SNPs
  • Lymphoblastoid cell lines
  • Translational research

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Medicine(all)

Cite this

Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines. / Li, Liang; Fridley, Brooke L.; Kalari, Krishna R; Niu, Nifang; Jenkins, Gregory; Batzler, Anthony; Abo, Ryan P.; Schaid, Daniel J; Wang, Liewei M.

In: BMC Genomics, Vol. 15, No. 1, 93, 01.02.2014.

Research output: Contribution to journalArticle

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