Background Rheumatoid arthritis (RA) is a complex autoimmune disease characterized by clinical and molecular heterogeneity, notably in the presence of anti-cyclic citrullinated peptide antibodies (CCP). CCP positivity in RA patients is associated with more severe disease progression and distinct responses to treatment compared to CCP-patients. Although previous studies have investigated cellular and molecular differences between these RA subtypes, there has been limited exploration of their genetic differences at a systems scale, taking into account underlying molecular networks.

Methods Here, we use a novel multi-scale framework that couples a network-based genome-wide association study (GWAS) to functional genomic data to uncover network modules distinguishing CCP+ and CCP-RA.

Findings We utilized the RACER (Rheumatoid Arthritis Comparative Effectiveness Research) cohort, comprising 555 CCP+/RF+ and 384 CCP-/RF+ RA patients, and uncovered significant differences in heritability between these two disease groups. This was followed by a network-based GWAS which uncovered 14 putative gene modules that explained genetic differences between CCP+/RF+ and CCP-/RF+ RA. Interestingly, these included many genes outside the HLA locus. Further validation through heritability partitioning and multivariate expression analyses underscored the significance of specific modules, highlighting novel genetic loci driving heterogeneity in antibody prevalence in RA. The identified modules were validated in a completely orthogonal cohort from the All of Us program. Functional analysis revealed that these modules captured critical molecular programs that not only relate to serological variation but also underlie broader functional heterogeneity in RA, including differences in synovial cell-type abundance phenotypes and variation in treatment response.

Interpretation Our findings demonstrate the utility of network-based approaches in elucidating the complex genetic landscape of RA, offering new insights into the differential genetic risk factors underlying CCP+/RF+ and CCP-/RF+ RA, and paving the way for more personalized therapeutic strategies.

The authors have declared no competing interest.

supported in part by NIAID DP2AI164325 and a pilot grant from the Pittsburgh Autoimmunity Center for Excellence in Rheumatology

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

The ethics committee/IRB of the University of Pittsburgh gave ethical approval for this work

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Yes

I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes

I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

Yes

The individual genotype data is not available to the public. Summary statistics and validation data are available upon request.