Sjogren's International Collaborative Clinical Alliance Next Generation Studies (SICCA-NextGen) - ABSTRACT Through the NIDCR-funded Sjögren’s International Collaborative Clinical Alliance (SICCA), our team established a unique biorepository/registry involving 3,514 participants enabling key insights into Sjögren’s disease (SjD)’s phenotype, and leading to the validation of classification criteria approved by the American College of Rheumatology (ACR) and the European League Against Rheumatism (EULAR). A Genome-Wide Association Study highlighted the genetic heterogeneity of SjD according to ancestry, and established a unique genetic repository for SjD available for public use through dbGAP. We characterized epigenetic changes in labial salivary glands (LSG) from SICCA participants, and a genome-wide LSG DNA methylation study identified two major clusters of SjD cases with distinct phenotypic features. In 2020, NIDCR funded SICCA-NextGen expanding our SjD research into transcriptomics and epigenetics at cellular and blood/tissue levels. Our team performed single cell RNA-sequencing (scRNA-seq) on 472 PBMC samples from 370 participants, generating a massive dataset with over 16,000 genes and BCR/TCR sequencing for 1.5M cells. Among the 370 individuals, we also performed single nuclei (sn)RNA-seq on 100 LSG, and DNA methylation and bulkRNA-seq on 271 LSG. An epigenetics and exome sequencing project involving more than 1300 LSG is also ongoing as part of a SICCA dissemination plan project. Key findings of our scRNA-seq on PBMCs include significant differences in gene expression (GE) associated with anti-SSA antibodies, primarily driven by interferon-stimulated genes. Anti-SSA positivity correlated with altered immune cell distribution, particularly an expansion of transitional B cells with restricted antigen recognition. Loss of B cell diversity was inversely proportional to the IFN score, highlighting a crucial IFN-I and B cell maturation interplay. Notably, the lack of GE differences between SSA-SjD and non-SjD participants raises the question of whether SSA-SjD represents a distinct disease entity. This renewal proposes to further explore and define SjD’s molecular and phenotypic heterogeneity through multimodal integration, and mechanistic approaches through an expanded dissemination plan. Further, we aim to investigate SjD’s multifactorial etiology and potential therapeutic targets by assessing metabolic pathways and environmental exposures, through high-resolution metabolomics and exposomics, and their impact on gene regulation via DNA methylation. Thus, leveraging the wealth of SICCA-NextGen data and the SICCA repository, our specific aims are to 1) Apply high resolution metabolomics and exposomics to identify endogenous metabolites (from LSGs/saliva/serum) and novel exogenous chemicals (from serum), assessing their association/correlation with SjD phenotypes and IFN activity, using both untargeted and targeted approaches; 2) Employ multimodal integration combining existing genetic, transcriptomic, and epigenetic data, and new high resolution metabolomics and exposomics data, to assess the impact of the methylome, transcriptome, metabolome, and exposome (i.e., the “multiome”) on SjD and its phenotypic features of disease severity; and 3) Expand the SICCA Dissemination Plan to facilitate mechanistic and machine-learning studies, enabling scientists worldwide to refine and test hypotheses generated by our multiomic analyses.
