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Open Access Research article

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

Liang Li1, Brooke L Fridley23, Krishna Kalari2, Nifang Niu1, Gregory Jenkins2, Anthony Batzler2, Ryan P Abo1, Daniel Schaid2 and Liewei Wang2*

Author Affiliations

1 Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA

2 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA

3 Current affiliation: Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas, USA

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BMC Genomics 2014, 15:93  doi:10.1186/1471-2164-15-93

Published: 1 February 2014

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.

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