Fig 2: Increased number of F4/80+ KMO+ cells in the colon exacerbates TNBS-induced colitis. Mice were treated with either TNBS or vehicle, and colons were collected three days after treatment. A: Histological scores determined based on a histological grading as described in Materials and Methods. B: Representative images of H&E-stained colons of the said mice. C, D: The KMO+ cells in the colons of the said mice were counted using immunohistochemical staining for KMO. E: KMO mRNA expression in the colon was determined by quantitative PCR. F: The colons of TNBS-treated mice were stained for F4/80, CD19, CD11c, KMO, and DAPI (nuclei) using immunofluorescence staining. The negative controls for F4/80, CD19, CD11c, and KMO were not stained (Supplementary Figure 2 and 3). aP < 0.05 vs Vehicle group, bP < 0.01 vs Vehicle group, cP < 0.05 vs TNBS-treated KMO+/+ mice group. KMO: Kynurenine 3-monooxygenase; TNBS: Trinitrobenzene sulfonic acid.

Fig 3: (A) CD19-positive B lymphocyte in the modiolus. The cell also expresses MHCII. (B) CD4 and CD8-positive T cells in the peripheral region of the RC. (C) A CD8-positive lymphocyte and an MHCII-expressing cell in Rosenthal's canal. (D) A CD8 cell is seen to physically interact with an IBA1-positive macrophage.

Fig 4: Intrarenal B cells have an innate-like gene signature.a A volcano plot showing DEGs between Ig class-switched intrarenal and tonsil B cells. Genes expressed higher in intrarenal B cells are shown on the right side of the plot. b A violin plot demonstrating RNA expression of AHNAK. c Staining images of AHNAK with nuclei (Hoechst) and a B-cell marker CD19 in rejected renal allograft and tonsil. The high-magnification panel corresponds to the yellow square on the merged panel. Scale bars indicate 50 μm or 25 μm (high-magnification panel). Staining has been tested on tissues from two patients and a representative result is shown. d Expression of 333 murine genes that correlate with Ahnak in Immgen. The mean value of the 333 Ahnak-covariant genes (including Ahnak itself) is shown as the black line with the gray shade indicating standard deviation. Expression of Ahnak is the red line. T: transitional, Fo: follicular, GC: germinal center, MZ: marginal zone, Sp: spleen, and PC: peritoneal cavity. e Enrichment of GO terms and KEGG pathways in the 293 AHNAK-covariant genes. At most 10 most significantly enriched pathways are shown. f Enrichment of the AHNAK-covariant genes in each gene cluster from Fig. 2d. g A heatmap showing DGE scores, a sum of scaled expression levels of each gene cluster within each murine B cell subset in Immgen data. Each row and column represents the gene clusters found in Fig. 2d and the murine B cell subpopulations. DEG scores were scaled by row to obtain Z-scores.

Fig 5: Sorting and scRNA-seq of activated B cells in renal allograft and tonsil.a Gating scheme for single-cell sorting of CD19+ CD38+ activated B cells in renal allograft and tonsil samples. b A t-SNE plot of scRNA-seq. Color and shape respectively indicate patients and tissue sources from which cells were derived.