Analysis of Gene Expression from Systemic Lupus Erythematosus Synovium Reveals a Profile of Activated Immune Cells and Inflammatory Pathways

Abstract

Arthritis is a common manifestation of systemic lupus erythematosus (SLE) yetunderstanding of the underlying pathogenic mechanisms remains incomplete. We, therefore, interrogated gene expression profiles of SLE synovium to gain insight into the nature of lupus arthritis (LA), using osteoarthritis (OA) and rheumatoid arthritis (RA) as comparators. Knee synovia from SLE, OA, and RA patients were analyzed for differentially expressed genes (DEGs) and also by Weighted Gene Co-expression Network Analysis (WGCNA) to identify modules of highly co-expressed genes. Genes upregulated and/or co-expressed in LA revealed numerous immune/inflammatory cells dominated by a myeloid phenotype, whereas OA was characteristic of fibroblasts and RA of T-and B-cells. Upstream regulator analysis identified CD40L and inflammatory cytokines as drivers of the LA gene expression profile. Genes governing trafficking of immune cells into the synovium by chemokines were identified, but not in situ generation of germinal centers. GSVA confirmed activation of specific myeloid and lymphoid cell types in LA. Numerous therapies were predicted to target LA, including TNF, NFκB, MAPK, and CDK inhibitors. Detailed gene expression analysis identified a unique pattern of cellular components and physiologic pathways operative in LA, as well as drugs potentially able to target this common manifestation of SLE. 4 approach, we provide an expanded view of SLE synovitis that might serve as the basis to identify new targeted therapies. RESULTS Bioinformatic and Pathway Analysis of LA and OA Gene ExpressionDifferential expression (DE) analysis demonstrated 6,496 differentially expressed genes (DEGs) in LA versus OA (Fig. 1a), of which 2,477 transcripts were upregulated whereas 4,019 transcripts were downregulated. The upregulated DEGs included 243 immune cell-specific transcripts (odds ratio of 2.84, p<2.2e-16, Fisher's Exact Test), indicating a significant immune/inflammatory cell infiltrate. There was considerable enrichment of T-cell, B-cell, plasma-cell, and myeloid-cell transcripts among the upregulated DEGs (Fig. 1b), whereas fibroblast-associated genes were increased in OA. Immune signaling and immune cell surface markers, as well as the interferon transcriptional program, pattern recognition receptors (PRRs), and MHC Class I and II were enriched in LA, along with intracellular signaling, apoptosis, the proteasome, and processing/packaging material inside cells.Of the 4,019 downregulated DEGs, only 17 were immune cell transcripts and thus downregulated genes did not reflect a change in hematopoietic cells (odds ratio of 0.0749, p=1).Notably, however, the fibroblast gene signature was downregulated (Fig. 1c). Functional analysis identified several molecular processes that were decreased in LA, most of which related to transcriptional activity/nuclear processes and cytoskeletal and integrin pathway changes. A list of genes significantly up-and downregulated in LA can be found in Supplementary Data S1 online.Ingenuity Pathway Analysis (IPA) identified predo...