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Single-nucleotide polymorphism profiling by multimodal-targeted next-generation sequencing in methotrexate-resistant
Chiara Casotti1,2, Claudia Maria Hattinger1, Maria Pia Patrizio3
1Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.
Frontiers in Pharmacology
|December 11, 2023
Summary
This study investigated genetic changes in high-grade osteosarcoma (HGOS) cell lines resistant to methotrexate (MTX). It found specific genetic variations and gene expression changes linked to MTX resistance, offering insights into treatment resistance mechanisms.
Area of Science:
- Pharmacogenomics
- Cancer Genetics
- Molecular Biology
Background:
- Methotrexate (MTX) is a key drug for high-grade osteosarcoma (HGOS).
- Genetic factors influencing MTX resistance in HGOS are not fully understood.
- Pharmacogenetic studies have explored polymorphisms related to MTX response and toxicity.
Purpose of the Study:
- To investigate single nucleotide polymorphisms (SNPs) and their role in MTX resistance in HGOS.
- To explore genetic variations at both DNA and RNA levels in MTX-resistant HGOS cell lines.
- To identify potential genetic markers associated with MTX resistance development.
Main Methods:
- Utilized a custom multimodal-targeted next-generation sequencing (mmNGS) approach.
- Analyzed 22 SNPs in folate metabolism, MTX transporter genes, and TP53 in 8 MTX-resistant and 12 MTX-sensitive HGOS cell lines.
- Validated findings using TaqMan genotyping assays.
Main Results:
- Observed high instability of TP53 rs1642785 in MTX-resistant variants.
- Identified allele changes in SLC19A1 rs1051266 in MTX-resistant Saos-2 cell lines at both DNA and RNA levels.
- Detected allele changes in MTHFR rs1801133 (RNA-derived) and altered expression of DHFR (upregulated) and SLC19A1 (downregulated) in highly resistant U2OS variants.
- Discovered a DHFR-MSH3 fusion transcript in highly MTX-resistant U2OS variants.
Conclusions:
- The mmNGS approach effectively identified genetic alterations at DNA and RNA levels simultaneously.
- Evidence suggests functional involvement of allele changes in the development of MTX resistance in HGOS.
- Findings provide a basis for understanding and potentially overcoming MTX resistance in HGOS treatment.
