Fig. 3: Identification and characterization of B subpopulations by scRNA-seq.

a A total of ten major B subsets with distinct canonical markers are presented on the tSNE plot. b Representative markers for functionally unique B subsets are presented in the dot plot. c GSEA reveals differentially enriched immune-associated signatures across the subsets and the groups. CLEC1⁺CD1C⁺ B cells (Cluster 6) in cSjD preferentially upregulated gene sets associated with autoimmune antibodies. d Hex density enrichment plot reveals B cell homeostasis and immunity signatures in Cluster 6 across the groups. Note that the B cells in patients with cSjD and, to a lesser extent, non-cSjD show substantial skewness toward both types of signatures. The numbers in red and blue on each quadrant illustrate upward and downward trends, respectively, compared to HC. e The volcano plot reveals that the CLEC1⁺CD1C⁺ B subset significantly upregulates TBX21, IRF7, TRBC2, and HLA-DQA2 involved in B cell immunity signature in cSjD compared to HC. Genes that are specific for cSjD but not identified in aSjD, are highlighted with the box. f Dot plot indicating the upregulation of TBX21, IRF7, and TRBC2, which is remarkably specific to cSjD (Cluster 6). g Immunoglobulin genes upregulated in plasma cells of cSjD and BxRP, compared to HC. h PLD4⁺NEIL1⁺ naïve B cells (Cluster 4) shows upregulation of DEGs such as Ro60. i Gene ontology analysis reveals significant enrichment of gene sets associated with antigen presentation of endogenous peptide antigens in Cluster 6 of cSjD compared to HC. Dot or gene colored by blue and red refers to down and up-regulated DEGs, respectively, and a grey-colored dot refers to a gene that has no statistical significance in the differential expression (e–h). HC healthy control, cSjD childhood Sjögren’s disease, BX biopsy-positive non-cSjD without RP, BXRP biopsy-positive non-cSjD with RP.