Metformin Treatment Potentially Modifies Genetically Driven Metabolite-HbA1c Associations: A Gene–Environment Interaction Mendelian Randomization Study

Introduction/Background: Metformin is the first-line therapy for type 2 diabetes (T2D); however, a considerable inter-individual variability in glycemic response is observed among patients. This heterogeneity suggests that metformin’s effects depend not only on drug exposure but also on the underlying metabolic and genetic factors. Methods: We applied a Gene–Environment interaction Mendelian Randomization (MR-G×E) in a cohort of 2743 individuals to investigate whether genetically influenced metabolite-HbA1c associations differ by metformin use. Metabolites associated with metformin response were used to establish metabolite-specific polygenic risk scores (PRSs) using metabolome-wide association study (mGWAS) variants. Generated PRS were used as genetic instruments within a one-sample, modified two-stage least squares model. An interaction term between PRS and metformin use was included to assess treatment-dependent genetic effects, adjusting for age, sex, body mass index, and genetic ancestry (principal components). Results: Metformin use significantly modified genetically influenced associations between 18 metabolites and HbA1c. Positive and negative PRS-metformin interaction effects indicated attenuation, strengthening or reversal of baseline genetic associations under treatment. Several amino acid metabolites, palmitoyl sphingomyelin (d18:1/16:0), and carbohydrate-related metabolite 1,5-anhydroglucitol showed specific patterns under metformin use. Interestingly, several metabolites (creatinine, gamma glutamylcitrulline, N-acetylthreonine, 3-methyl-2-oxovalerate, glycerol-3-phosphate, 1-(1-enyl-palmitoyl)-GPC (P-16:0), 1-(1-enyl-palmitoyl)-2-linoleoyl-GPC (P-16:0/18:2), sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1), fructose, and methyl-glucopyranoside (alpha + beta)) showed no basal causal association with HbA1c but exhibited significant interaction effect with metformin use, suggesting metabolic association only in the presence of metformin. Conclusions: These findings indicate that metformin modifies the genetically influenced metabolite-HbA1c relationships, exhibiting treatment-dependent metabolic effects that are not detectable with standard MR approaches. Incorporating pharmacological context into causal inference provides new insights into the metabolic basis for the variable metformin response and helps inform precision strategies for T2D management.