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Pharmacogenomics Applied to Acute Leukemias: Identifying Clinically Relevant Genetic Variants.

Flávia Melo Cunha de Pinho Pessoa1, Isabelle Magalhães Farias1, Beatriz Maria Dias Nogueira1

  • 1Clinical Genetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil.

Biomedicines
|November 27, 2025
PubMed
Summary

Pharmacogenomic variants significantly impact chemotherapy effectiveness and toxicity in acute leukemias (AML and ALL). Identifying key genetic markers like ABCB1, TPMT, and NUDT15 can personalize treatment and reduce adverse events for better patient outcomes.

Keywords:
acute lymphoblastic leukemiaacute myeloid leukemiadrug toxicitypharmacogenomic variantspharmacogenomics

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Area of Science:

  • Hematology
  • Pharmacogenomics
  • Oncology

Background:

  • Acute leukemias (AML and ALL) require intensive chemotherapy, but drug toxicity limits treatment success.
  • Pharmacogenomics, by analyzing genetic variants, offers a strategy to optimize chemotherapy efficacy and minimize toxicity.
  • Single-nucleotide variants (SNVs) can influence drug metabolism, response, and adverse events in leukemia patients.

Purpose of the Study:

  • To identify and analyze clinically relevant genetic variants affecting chemotherapy response and toxicity in Acute Myeloid Leukemia (AML) and Acute Lymphoblastic Leukemia (ALL).
  • To evaluate the frequency and clinical significance of specific variants, including those in ABCB1, TPMT, and NUDT15, within leukemia patient cohorts.

Main Methods:

  • Utilized the ClinPGx/PharmGKB database for curated, clinically annotated genetic variants.
  • Analyzed variant data for AML and ALL, categorizing them by type (synonymous, nonsynonymous, intronic) and clinical significance.
  • Focused on variants associated with drug metabolism, efficacy, and toxicity, including those in ABCB1, TPMT, NUDT15, ABCC1, SLC28A3, and RARG.

Main Results:

  • Curated 24 variants for AML and 57 for ALL, with nonsynonymous variants more frequent in ALL and synonymous in AML.
  • Identified clinically significant variants in ABCB1 in 12.5% of AML and 10.5% of ALL cases, suggesting a role in chemotherapy resistance.
  • Associated variants in TPMT, NUDT15, ABCC1, SLC28A3, and RARG with severe adverse events like myelotoxicity, mucositis, cardiotoxicity, and hepatotoxicity.

Conclusions:

  • Genetic variants play a crucial role in modulating chemotherapy response and toxicity in acute leukemias.
  • ABCB1 variants may serve as resistance markers, while pre-treatment genotyping of TPMT and NUDT15 is recommended to prevent severe toxicities.
  • Consolidating pharmacogenetic data and prospective validation are essential for integrating precision medicine into routine acute leukemia management.