Fig 2: Investigation of immunoglobulin characteristics of FcRL4+ and FcRL4- B cells. (A). Ig heavy chain variable (VH) genes of individually sorted FcRL4+ and FcRL4- B cells were sequenced and analyzed by IgBLAST and IMGT/V-QUEST for gene segment repertoire usage. (B) Characteristics of IgH complementarity determining region 3 (CDR3) amino acid composition: average length of CDR3s in amino acids, and the mean number of positively and negatively charged amino acids in the CDR3 regions. P values were calculated by χ2 test and corrected for multiple comparisons by the method of false discovery rates.

Fig 3: LCL subsets exhibit co-expression of genes associated with distinct GC phenotypes. (A) Gene module scores for mantle zone (MZ), dark zone (DZ), DZ cycling, light zone (LZ), plasmablast (PB), and antibody-secreting cell (ASC) states across tonsils and LCLs. Trajectories depict the path starting at the MZ phenotype and progressing through DZ, DZ cycling, LZ, post GC PB, and Late ASC. Blue trajectories depict the core GC and red trajectories represent exits from this dynamic. [MZ module = CCR6, CD22, CD69, FCRL4, FCRL5, BANK1, MARCH1; DZ module = AICDA, FOXO1, CXCR4, AURKC, IL2RB; DZ cycling module = TCF3, EZH2, CCND3, E2F2, TP53, PLK4, BRCA1; LZ module = NFKB1, NFKB2, CD80, CD83, CD86, BCL2A1, EBI3, CD40, CR2, MIR155HG, ACKR3, MYO1C, MYC; PB module = PRDM1, XBP1, MZB1, TNFRSF17, CD27, CD38; Late ASC = SDC1] (B) Detailed example of a GC-like cell paths in GM12878. Violin plots depicting key gene expression are presented to highlight the core GC dynamic (blue trajectory and box) as well as terminal differentiation to Late ASCs (red trajectory and box). The bifurcation point between ASC and GC re-entry trajectories is associated with cluster-resolved expression of IRF4 and PRDM1, with lower expression of these genes associated with perpetual GC re-entry and higher expression associated with Late ASCs.

Fig 4: Expression levels of genes previously described as over- or under-expressed in synovial fluid and tonsillar FcRL4+ B cells. (<5% FDR, DESeq2) A) overexpressed in FcRL4+ B) underexpressed in FcRL4+ B cells.

Fig 5: Synovial fluid FcRL4+ and FcRL4- B cells differ in their gene expression profiles. FcRL4+ and FcRL4- B cells were sorted from RA patients' synovial fluid. Their gene expression profile was determined by RNAseq. Scatter plots show the expression of individual Ig segments (A) and further differentially expressed genes at the genome-wide level (<5% FDR, DESeq2) after Benjamini-Hochberg correction (B) for the two groups of B cells. The RNA-seq data has been deposited at Gene Expression Omnibus with accession number GSE94897.