Extended Data Fig. 3: scRNA-seq analysis of tumour-associated B cells.

a, Box plots of gene-expression scores, based on different B cell developmental states in 812 B cells from 27 tumours from a previous study¹⁸. b, Heat map of selected genes across all 812 B cells. IGLL5and CD69 were two of the five genes with highest expression variation across all B cells. The heat map is sorted on IGLL5 and CD69 expression, excluding the cells that displayed increased expression of the plasma-cell signature. Genes showing a Pearson correlation >0.4 to IGLL5 or CD69 expression are also indicated. SDC1 and PRDM1 mark plasma cells, BCL6 and AICDA mark germinal centres, HLA-DRA mark MHC-II and HLA-A, HLA-B and HLA-C mark MHC-I. TLS-hallmark genes, germinal-centre-related genes and other B cell genes are also indicated. c, Extracting the single B cell RNA-seq data from a previous study¹⁷ using pretreatment samples (n = 16). The fraction of CD69⁺ B cells was higher in responders to ICB than in nonresponders (n = 8), but the fraction of IGLL5⁺ B cells was not. The fraction of IGLL5⁻ CD69⁺ cells was also higher in responders. Plots of fraction of IGHD⁺ and IGHG⁺ B cells in relation to response to ICB therapy. P values from two-sided Wilcoxon test. In a, the centre lines in the box plot represent the median, the box limits represent the lower and upper quartiles, and the whiskers extend to the most extreme values within 1.5× IQR. d, Pearson correlation between expression of CD69 and germinal centre genes (CD83 and CXCR4) in data from a previous study¹⁸. Pie charts display the fact that the fraction of CD83⁺ and CXCR4⁺ B cells is increased among CD69⁺ B cells. Expression > 1 was used as a cut-off for being present. Seven hundred and fifty-three B cells without a present plasma-cell signature were analysed. P value from two-sided Fisher’s exact test. e, f, Heat map of gene-expression values corresponding to our TLS signature (e) and TLS-hallmark genes from the literature (f). Blue corresponds to increased expression. Mal., malignant cells. In e, f, single cells from the seven cell types on the left are from ref. ¹⁸, and from the four cell types on the right are from ref. ¹⁷.