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Pharmacogenetic determinants of thiopurines in an Indian cohort

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Abstract

Background

Several genetic variants of thiopurine metabolic pathway are associated with 6-thiopurine-mediated leucopenia. A population-based evaluation of these variants lays the foundation for Pharmacogenetic-guided thiopurine therapy.

Methods

A total of 2000 subjects were screened for the pharmacogenetic determinants using the infinium global screening array (GSA). The functional relevance of these variants was deduced using SNAP2, SIFT, Provean, Mutalyzer, Mutation Taster, Phyre2, SwissDock, AGGRESCAN, and CUPSAT.

Results

The minor allele frequencies of NUDT15*3, NUDT15*5, TPMT*3C, TPMT*3B variant alleles were 6.78%, 0.11%, 1.98% and 0.69%, respectively. TPMT*3A genotype was observed in 0.35% subjects. No gender-based differences were observed in the incidence of these variants. Data from studies of the Indian population showed that 92.86% subjects heterozygous for NUDT15*3 and 60% subjects heterozygous for TPMT*3C exhibit thiopurine-mediated hematological toxicity. NUDT15 variants have no impact on the binding of ‘dGTP’ to the NUDT protein. NUDT15*3 variant increases aggregation ‘hot spot’ region and induces unfavourable torsion in the protein. NUDT15*5 destabilizes the protein and impairs Mg/Mn binding. TPMT*3A, TPMT*3B and TPMT*3C variants lower binding affinity to 6-mercaptopurine compared to the wild protein. TPMT*3C variant destabilizes the TPMT protein in the thermal experiment. Compared to the data of European and African/African American populations, NUDT15*3 frequency is higher and TPMT*3C frequency is lower in our population.

Conclusions

TPMT variants were less frequent in Indian population, while NUDT15*3 is more frequent compared to European and African/African American populations. NUDT15*3 increases aggregation ‘hot spot’ and induces unfavourable torsion in the protein. NUDT15*5 and TPMT*3C destabilize the respective proteins. TPMT*3A, TPMT*3B and TPMT*3C are associated with a lower binding affinity towards 6-mercaptopurine.

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Abbreviations

ALFA:

Aggregate allele and genotype frequencies computed from non-sensitive dbGaP studies

ALL:

Acute lymphoblastic leukemia

AZT:

Azathioprine

DNA-TG:

DNA-incorporated thioguanine

GSA:

Global Screening array

IBD:

Inflammatory bowel disease

MAF:

Minor allele frequency

MP:

Mercaptopurine

NUDT15:

Nudix hydrolase 15

PCNA:

Proliferating cell nuclear antigen

SAM:

S-Adenosyl methionine

SIFT:

Sorting intolerant from tolerant

TGN:

Thioguanine

TPMT:

Thiopurine S-methyltransferase

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Acknowledgements

The study was funded by intramural Grants of Sandor Speciality Diagnostics Pvt Ltd, Hyderabad, India. The authors are grateful to the Deanship of Scientific Research, King Saud University for funding through Vice Deanship of Scientific Research Chairs.

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Authors and Affiliations

  1. Department of Biochemical Genetics and Pharmacogenomics, Sandor Speciality Diagnostics Pvt Ltd, Banjara Hills, Road No 3, Hyderabad, 500034, India

    Shaik Mohammad Naushad

  2. School of Chemical and Biotechnology, SASTRA University, Thanjavur, India

    Mekala Janaki Ramaiah

  3. Department of Clinical Pharmacology and Therapeutics, Nizam’s Institute of Medical Sciences, Hyderabad, India

    Vijay Kumar Kutala

  4. Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia

    Tajamul Hussain

  5. Biochemistry Department, College of Science, Research Chair for Biomedical Applications of Nanomaterials, King Saud University, Riyadh, 11451, Saudi Arabia

    Tajamul Hussain & Salman A. Alrokayan

  6. Biochemistry Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia

    Salman A. Alrokayan

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  1. Shaik Mohammad Naushad
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  2. Mekala Janaki Ramaiah
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Contributions

The study was conceived and designed by SMN and VKK. The recruitment of subjects, extraction of DNA, GSA analysis, and genoty** were performed by SMN, MJR, VKK, TA, and SAA. The data analysis and bioinformatics analysis were performed by SMN, MJR, and TA. The manuscript was drafted by SMN and MJR. The manuscript was revised for the critical content by TA and SAA. The final version of the manuscript was approved by all the authors.

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Correspondence to Shaik Mohammad Naushad.

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Naushad, S.M., Janaki Ramaiah, M., Kutala, V.K. et al. Pharmacogenetic determinants of thiopurines in an Indian cohort. Pharmacol. Rep 73, 278–287 (2021). https://doi.org/10.1007/s43440-020-00158-3

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  • DOI: https://doi.org/10.1007/s43440-020-00158-3

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