A single non-coding SNP in FPGS modulates folate drug efficacy in acute lymphoblastic leukemia: data-driven exploration and experimental validation

作者：Wenliang Yu, Chenyang Li, Yuning Meng, Qiang Li, Mengyue Gao, Wei Tang, Yao Li, Ziyi Tan, Xiaoran Zhou, Zeyang Liu, Yang Xu, Zichun Hua · 发表于：Molecular Biomedicine · 年份：2025 · DOI：10.1186/s43556-025-00353-9 · 被引用次数：2 · 研究领域：Acute Lymphoblastic Leukemia research、Folate and B Vitamins Research、Acute Myeloid Leukemia Research

For over 70 years, methotrexate (MTX) has remained a first-line chemotherapeutic agent for acute lymphoblastic leukemia (ALL), playing a pivotal role in maintenance therapy. Understanding the genetic determinants of MTX efficacy is therefore essential for improving clinical outcomes. However, studies on MTX efficacy-related polymorphisms remain limited, particularly for non-coding variants, for which most evidence is based on statistical associations. Here, through integrative bioinformatics analysis and systematic meta-analysis, we identified rs1544105, a non-coding SNP in the folylpoly-γ-glutamate synthetase (FPGS) gene, as closely associated with MTX efficacy. Compared with the GG genotype, the AA genotype increased disease progression risk (OR: 2.23; 95% CI: 1.16-4.30; p = 0.017) and elevated plasma MTX concentration-to-dose ratios at 24 h (WMD: 2.27; 95% CI: 1.04-4.40; p = 0.002) and 40 h (WMC: 0.02; 95% CI: 0.00-0.04; p = 0.033). Using prime editing, we generated homozygous mutant (GG) 293T cells, demonstrating that rs1544105 A > G increased FPGS expression (~ 1.5-fold, p < 0.05) and intracellular MTX retention (p < 0.05). Moreover, both cell-based and animal experiments confirmed that rs1544105 A > G markedly improved MTX efficacy. Mechanistically, dual-luciferase reporter and electrophoretic mobility shift assays revealed that rs1544105 A > G enhanced the binding affinity of the SNP-containing sequence for the transcription factor CREB1, thereby increasing FPGS transc...