Genetic Regulation and Therapeutic Targeting of MTMR3 Reshape TLR9-Mediated IgA Responses

Background: Genome-wide association studies (GWAS) have identified rs4823074, a noncoding variant within the MTMR3–HORMAD2 locus, as strongly associated with IgA nephropathy and serum IgA levels. Yet the mechanistic basis of this association and its downstream immunological effects remain elusive. Methods: Luciferase assays, EMSA, and ChIP-qPCR were used for regulatory analysis; mRFP-GFP-LC3 imaging for autophagy and localization; Immunoprecipitation, RNA-sequencing, ELISA, mass spectrometry, Co-IP, and Malachite Green assays for signaling and enzymatic studies. Results: Carriers of the rs4823074 risk allele exhibited elevated MTMR3 expression (p=0.01) and higher serum IgA levels (p=0.08). Dual-luciferase assays revealed increased transcriptional activity driven by the risk allele (p<0.001), while EMSA demonstrated stronger protein–DNA complex. SP1 was confirmed as the binding factor via super-shift. ChIP-seq and ChIP-qPCR further validated SP1 binding at both rs4823074 locus and MTMR3 promoter (~33.85% and ~18.72% of input). The regulatory effect of the risk allele on MTMR3 prompted investigation of its downstream function. Upon TLR9 stimulation, MTMR3 translocated from the cytoplasm to the nucleus, in parallel with autophagy induction, suggesting a spatially regulated inhibitory role. MTMR3 overexpression reduced TLR9-induced autophagic flux, increased the expression of TRAF3 (p<0.001) and promoted its K63-linked ubiquitination, leading to elevated IFN-β production. Recombinant IFN-β augmented IgA secretion from cultured splenocytes (p<0.001), implicating an MTMR3–TRAF3–IFN-β axis in modulating TLR9-driven humoral responses. To evaluate MTMR3 as a therapeutic target, we assessed AUTEN-67, which inhibited MTMR3 enzymatic activity at 100μM and reduced CpG-induced IgA by 34% (p=0.002). To gain an insight into the post-translational regulation, we performed mass spectrometry and Co-IP and identified PARP1 as a key binding partner of MTMR3. PARP1 inhibitor reduced MTMR3-PARylation and suppressed CpG-induced IgA production (p=0.012). These results highlight MTMR3 as a promising immunoregulatory target. Conclusion: We identify rs4823074 as a functional variant that enhances SP1 binding and upregulates MTMR3 transcription, which in turn modulates the TLR9–TRAF3–IFN-β axis and positions MTMR3 as a promising therapeutic target for reducing IgA production. Funding: Government Support – Non-U.S.