Integrated Transcriptomic and Single-Cell Analysis Reveals Shared Macrophage-Associated Inflammatory Signatures in MASLD/NAFLD and Rheumatoid Arthritis

Metabolic dysfunction-associated steatotic liver disease/nonalcoholic fatty liver disease (MASLD/NAFLD) and rheumatoid arthritis (RA) may share inflammatory mechanisms, although their common cellular basis remains unclear. We integrated bulk transcriptomic datasets (GSE66676 and GSE55235), single-cell RNA-sequencing datasets from murine RA synovium (GSE192504) and NASH liver (GSE129516), disease-association analysis, molecular docking, and in vitro experiments in LPS-stimulated RAW264.7 macrophages. Bulk transcriptomic analysis identified 630 shared differentially expressed genes, including 344 concordantly upregulated genes enriched in immune response, cytokine and chemokine signaling, phagosome, Toll-like receptor signaling, and Fc receptor-mediated phagocytosis; a strict dual-dataset intersection further defined 18 core genes significantly upregulated in both diseases. Immune-signature analysis indicated altered myeloid cell-associated inflammatory activity in both diseases, and several shared genes, including S100A8, S100A9, FCER1G, FCGR3A, LYZ, and MS4A7, correlated positively with monocyte/macrophage-related signatures. Single-cell analysis identified macrophage subsets with high S100a9 expression and elevated shared myeloid inflammatory signature scores in both RA synovium and NASH liver. Triptolide showed favorable predicted binding to the S100A8/A9 complex and reduced LPS-induced inflammatory cytokine secretion and expression of the six-gene signature in RAW264.7 cells, supporting the hypothesis that S100A9-associated inflammatory macrophage activation represents a candidate target for further investigation. These findings support a shared S100A9-positive inflammatory macrophage-associated program in MASLD/NAFLD and RA, and support the hypothesis that the S100A8/A9 complex represents a candidate target for further investigation.