Thiopurine Pharmacogenomics: Association of Snps with Clinical Response and Functional Validation of Candidate Genes

Abstract

Aim: We investigated candidate genes associated with thiopurine metabolism and clinical response in childhood acute lymphoblastic leukemia. Materials & methods: We performed genome-wide SNP association studies of 6-thioguanine and 6-mercaptopurine cytotoxicity using lymphoblastoid cell lines. We then genotyped the top SNPs associated with lymphoblastoid cell line cytotoxicity, together with tagSNPs for genes in the ‘thiopurine pathway‘ (686 total SNPs), in DNA from 589 Caucasian UK ALL97 patients. Functional validation studies were performed by siRNA knockdown in cancer cell lines. Results: SNPs in the thiopurine pathway genes ABCC4, ABCC5, IMPDH1, ITPA, SLC28A3 and XDH, and SNPs located within or near ATP6AP2, FRMD4B, GNG2, KCNMA1 and NME1, were associated with clinical response and measures of thiopurine metabolism. Functional validation showed shifts in cytotoxicity for these genes. Conclusion: The clinical response to thiopurines may be regulated by variation in known thiopurine pathway genes and additional novel genes outside of the thiopurine pathway.

Original submitted 31 July 2013; Revision submitted 4 November 2013

KEYWORDS::

• 6-mercaptopurine
• 6-thioguanine
• childhood acute lymphoblastic leukemia
• single nucleotide polymorphisms
• thiopurine pharmacogenomics

Acknowledgements

The authors wish to thank all the clinicians who entered patients into UK ALL97 and the participating children and their families. The authors thank the Clinical Trials Service Unit, University of Oxford, for patient outcome and demographic data and the UK Medical Research Council funded UK Childhood Leukaemia Working Party, which oversaw recruitment to the trial and enabled the thiopurine studies. The authors thank L Wussow for her assistance with the preparation of this manuscript.

Financial & competing interests disclosure

This work was supported in part by NIH grants R01 GM28157, R01 CA132780, R01 CA138461, R21 GM86689, U01 HG005137 and U19 GM61388 (R Weinshilboum and L Wang: The Pharmacogenomics Research Network). The UK ALL Thiopurine Studies were supported by Leukaemia and Lymphoma Research (LLR), London, UK (LL: LLR grants 96/40, 99/05, 09/027). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

This work was supported in part by NIH National Institutes of Health grants R01 GM28157, R01 CA132780, R01 CA138461, R21 GM86689, U01 HG005137 and U19 GM61388 (R Weinshilboum and L Wang: The Pharmacogenomics Research Network). The UK ALL Thiopurine Studies were supported by Leukaemia and Lymphoma Research (LLR), London, UK (LL: LLR grants 96/40, 99/05, 09/027). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.