Background Although genetic factors have been identified in the pathogenesis of rheumatoid arthritis (RA), the concordance rate in monozygotic (MZ) twins is low, suggesting that other features contribute to disease development. Further, the relative contribution of such non-genetic elements in identical twins have not been characterized. Here, we aimed to measure differentiating host and microbial biomarkers of RA by studying MZ twins discordant for disease using a multi-omics approach. Methods Eight pairs of MZ twins discordant for RA (n=16) were enrolled. Gut microbiome was assessed using shotgun metagenomic sequencing. Autoantibodies, cytokines, and other plasma proteins were measured in both plasma and feces. Levels of short and medium-chain fatty acids from serum and feces were quantified using gas chromatography mass spectrometry (GC-MS). Results While overall microbiome diversity and composition did not significantly differ between twins, we observed a decrease in Blautia faecis in affected twins. Affected twins had higher concentrations of both fecal and plasma citrullinated and non-citrullinated autoantibodies, as well as significantly lower concentrations of fecal butyrate and propionate. Conclusion Multi-omics biomarkers differentiate MZ twins discordant for RA. Blautia faecis, which is associated with reduced inflammatory cytokine expression, was decreased in RA twins. Similarly, short-chain fatty acids, known to have immune modulatory effects, were decreased in affected twins, suggesting further bi-directional interactions between inflammation at the gut barrier and disease state. If confirmed in other cohorts, exhaustive multi-omics approaches may improve our understanding of RA pathogenesis and potentially contribute to novel diagnostics and co-adjuvant therapies.

RBB, KB, WC, IC, AH, RH, RRN, JH, AC, JL, JS, LL, CU, JCC, have no conflicts to declare. JUS has served as a consultant for Janssen, Novartis, Pfizer, Sanofi, Amgen, UCB, BMS, and AbbVie; and has received funding for investigator-initiated studies from Janssen and Pfizer.

This work was supported by NIH/NIAMS UC2AR081034 (J.U.S., PI; J.C.C., MPI; R.B.B.) NIH/NIAMS R01AR074500 (J.U.S, PI; J.C.C; R.N.), R03 AR072182 (J.U.S., PI), National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, through Grant Award Number UL1TR001445 (R.B. trainee); NIH/NIAMS T32AR069515 (J.U.S., MPI; R.B. trainee); NYU Judith and Stewart Colton Center for Autoimmunity (J.U.S.)

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