Fig. 2. MCL-PDLS transcriptome recapitulates lymph node hallmarks.

A Volcano plot representing the differentially expressed genes (DEG) comparing PDLS after 7 days of culture with the original MCL peripheral blood (MCL-PB) sample. DEG were obtained by a paired (n = 4) DESeq2 analysis (FDR < 0.1 and absolute log₂FC > 0.5). B Heatmap of DEG for the individual patients (n = 4). C Signature score of MCL hallmark pathways as described by Saba and Rosenwald [12, 34]. Values were calculated as the geometric mean of the normalized counts for the genes involved in each pathway. For each significantly upregulated gene set, the leading genes are represented in a heatmap. D Bubble plot representing the most significant and representative GSEA pathways upregulated in MCL-PDLS compared to MCL-PB.