Regulatory Roles of Long Non-Coding RNAs in Methotrexate Pharmacology: Mechanistic and Translational Insights

BACKGROUND: Methotrexate (MTX) remains a cornerstone therapy in autoimmune diseases and oncology; however, substantial interindividual variability in efficacy and toxicity persists. While variability in MTX pharmacokinetics (PK) and pharmacodynamics (PD) has been linked to transporters, folate-cycle enzymes, and intracellular polyglutamate accumulation, the contribution of long non-coding RNAs (lncRNAs) as regulatory modifiers of these processes is not yet systematically defined. OBJECTIVE: To synthesize current evidence on lncRNA-mediated regulation of MTX response and to organize these interactions within a pharmacology-centered mechanistic framework. METHODS: A narrative, mechanism-oriented review was conducted integrating preclinical, translational, and computational studies evaluating lncRNA involvement in MTX-related pathways across immune-mediated diseases and cancer. RESULTS: lncRNAs were found to intersect with MTX pharmacology across four principal mechanistic nodes: (1) regulation of drug transport and intracellular retention (e.g., modulation of ABC transporters); (2) control of folate-axis targets and compensatory metabolic pathways (e.g., DHFR and TYMS regulation); (3) modulation of adenosine-mediated immunoregulation and NF-κB signaling, with lincRNA-p21 representing the most mechanistically supported example in rheumatoid arthritis; and (4) orchestration of stress-adaptive and survival pathways influencing antifolate resistance (e.g., PI3K-AKT-mTOR and apoptosis networks). However, most evidence derives from in vitro or computational studies, with limited integration of lncRNA perturbation and quantitative PK metrics such as intracellular MTX-polyglutamate levels. CONCLUSIONS: lncRNAs function as context-dependent modulators of MTX PK/PD processes rather than primary drug targets. Current evidence is heterogeneous, future studies integrating functional genomics, PK measurements, and prospective clinical validation are required to establish lncRNAs as predictive biomarkers or therapeutic targets in MTX precision pharmacology.