Methylenetetrahydrofolate reductase (MTHFR) polymorphisms, particularly C677T and A1298C, are established regulators of homocysteine (Hcy) metabolism and one-carbon homeostasis. While their role in recurrent spontaneous abortion (RSA) is well recognized via hyperhomocysteinemia (HHcy), their contribution to immune dysregulation, clinical heterogeneity, and therapeutic outcomes in rheumatic diseases—particularly axial spondyloarthritis (axSpA) and systemic lupus erythematosus (SLE)-associated conditions—remains poorly integrated.To address this gap, this study aims to: (1) characterize the multi-omics landscape of MTHFR 677TT-associated RSA beyond the classic HHcy paradigm; (2) delineate the  impact of MTHFR risk alleles on disease severity, immune profiles, and treatment response in axSpA; and (3) synthesize these findings into a unified framework linking MTHFR polymorphisms to rheumatic disease pathogenesis, thereby informing precision management strategies.

We conducted a multi-component study integrating: (1) a cross-sectional analysis of 180 axSpA patients stratified by MTHFR C677T/A1298C risk allele burden, assessing radiographic damage (mSASSS), serum Hcy, liver enzymes, CD4⁺ T cell subsets (flow cytometry), and TNF inhibitor (TNFi) response in a subset of 50 patients; (2) a cross-sectional multi-omics analysis of 196 RSA patients stratified by MTHFR C677T genotype (CC/CT/TT = 66/64/66), integrating immunophenotyping, serum metabolomics (UPLC-MS), and genome-wide DNA methylation analysis (RRBS); and (3) a systematic review synthesizing evidence on MTHFR polymorphisms in eight autoimmune disorders, focusing on inflammatory responses, immune imbalance, epigenetic modifications, and pharmacogenomics.

In axSpA, C677T risk allele carriers exhibited a dose-dependent phenotype: higher cumulative allele burden correlated with increased Hcy, liver enzymes (GGT, ALP), severe spinal damage (mSASSS: 20.50 vs. 13.50, p=0.009), and Th17 polarization (elevated Th17/Treg and Th17/Th2 ratios, all p<0.05). Notably, TNFi response was stratified by genetic burden—CRP reduction was significant in patients with 0–1 risk alleles (p=0.001) but not in those with 2 risk alleles (p=0.188). In RSA, the MTHFR 677TT genotype defined a distinct subgroup with: (1) a clinical-metabolic triad of HHcy, elevated estrogen, and reduced androgens; (2) pronounced Th17/Th1-skewed immunity; (3) widespread downregulation of 12 serum bile acids; and (4) genome-wide promoter hypomethylation, with hypomethylated regions enriched in Th17/Th2 differentiation genes. Our systematic review further identified convergent mechanisms across eight autoimmune disorders—HHcy-induced endothelial dysfunction, epigenetic instability, and pro-inflammatory T-cell skewing—with pharmacogenomic implications.

MTHFR polymorphisms define a unifying genetic node linking folate metabolism to rheumatic disease pathogenesis. Across axSpA and MTHFR-associated RSA, risk alleles converge on a shared pathogenic triad: HHcy, Th17-skewed immunity, and epigenetic dysregulation, with additional metabolic (bile acid deficiency) and clinical (attenuated TNFi response) dimensions. These findings establish MTHFR genotyping as a potential biomarker for risk stratification and provide a mechanistic rationale for precision management—combining folate optimization with bile acid modulation or targeted Th17 pathway intervention—across MTHFR-associated rheumatic conditions.