Fig. 1

Chronic kidney injury and B cell immunity in human allografts. a Heatmap showing the gene expression correlation of the 120 most variably expressed genes across kidney biopsies collected at 3 and 12 months after transplantation (N = 80). The names of the genes included in the cluster in the bottom right corner are shown. b, c RPKM values of MS4A1 (CD20) and IGKC over time in human kidney allograft biopsies. BL: baseline. N = 39–42 for each time point. Wilcoxon matched-pairs signed rank test, ****P < 0.0001, **P < 0.01, *P < 0.05. d Semi-quantitative evaluation of immune cell infiltrates in the kidney at different time points after transplantation as determined by CIBERSORT analysis on RNAseq data. N = 39–42 for each time point. Wilcoxon matched-pairs signed rank test, **P < 0.01. e Cluster analysis based on the expression of B cell-associated genes including kidney biopsies collected at 12 months after transplantation (N = 39). Patients classified in the CKI group are indicated on the left. f t-SNE analysis on RNAseq data from kidney biopsies collected 12 months after transplantation defining the classification of patients in the CKI group. The boundary was determined by visual examination of the t-SNE plot. N = 39. g RPKM values of COL1A1 and MMP2 shown as examples of genes differentially expressed in CKI and non-CKI. Mean value and standard error (SE) are shown. Mann–Whitney test, ****P < 0.0001. h Gene enrichment analysis including genes differentially expressed in the CKI group compared to non-CKI, P values adjusted according to Benjamini–Hochberg