Fig. 2: FL-PDLS transcriptome recapitulates the LN signaling.

A Volcano plots representing the differentially expressed genes (DEG) comparing LN with the original FL peripheral blood (PB) sample (upper panel), or FL-PDLS after 7 days of culture with PB sample (lower panel). DEG was obtained by a paired (n = 2) DESeq2 analysis (FDR < 0.1 and absolute log₂ Fold change (FC) > 0.5). Heatmaps of DEG for the individual patients (n = 2). NS non-significant, Down Downregulated, Up upregulated. B Scatter plot of RNA-seq comparison of LN versus PB (y-axis) in log₂(fold change), and PDLS versus PB (y-axis), for all protein-coding genes. Heatmaps of the top-20 genes commonly upregulated (right) and downregulated (left) genes are displayed (log₂FC > 2 or log₂FC < −2). C Enrichment plot of LN signatures comparing PDLS vs PB by GSEA. D Venn diagrams of all significant gene set from LN vs PB and PDLS vs PB comparatives by GSEA analysis (upper left panel). Bubble plots representing the most significant and representative GSEA pathways upregulated in LN or PDLS compared to PB (lower left panel). For a selection of significantly enriched gene sets (*), GSEA plots of LN or PDLS compared to PB and a heatmap of the leading genes are represented (lower right panel).