Extended Data Fig. 4: High TLS density is associated with increased T and B cell activation.

a, Principal component analysis of bulk RNA sequencing data from HCC tumors resected after neoadjuvant ICB (n = 12) assigned to high (n = 5) and low (n = 7) TLS density groups. b, Heatmap showing differentially expressed genes (DEGs) with a log2 fold change (log₂FC) > 1 and adjusted P value < 0.05 between tumors with TLS high and low groups. Annotation rows indicate TLS density group, HCC etiology, neoadjuvant treatment, pathologic response, relapse status, and TLS density. Annotation columns at right identify DEGs belonging to Gene Oncology Biological Pathways gene sets for T cell activation, B cell activation, Cytokine production, and Dendritic Cell Antigen Processing and Presentation. c, Volcano plot showing differentially expressed genes between tumors with high and low TLS density. Vertical dotted lines represent log₂FC greater than or less than 1. Horizontal dotted line indicates adjusted P value of 0.05. 4 outlier genes with the lowest log₂FC are excluded from the plot for the purposes of visualization. d, Gene set enrichment analysis showing differentially enriched gene sets from the HALLMARK database between tumors with high and low TLS density. e, Heatmap showing expression of the 12-chemokine TLS gene signature in TLS high and low tumors.