FIGURE 3 from Transcriptome Deconvolution Reveals Absence of Cancer Cell Expression Signature in Immune Checkpoint Blockade Response

Validation and characterization of stromal DEGs with scRNA-seq and immune cell deconvolution analysis. A, Dotplot showing the percentage of stromal (nonmalignant) cells expressing each gene for each response category. Color represents the average scaled expression of the gene in stromal cells (PD, progressive disease; SD, stable disease; PR, partial response). B, Cell-type specific expression of the top stromal biomarkers in ICB responders (PR) and nonresponders (PD/SD). C, Heat map of the association between immune cell types and ICB response. Abundance of immune cell types of each tumor is estimated using CIBERSORTx. Heat map is colored by the signed −log10(P-value) of the difference in CIBERSORTx scores between responders (MSI) and nonresponders (MSS). Cell types with no significant difference in abundance between ICB responders and nonresponders (P-value >0.1) were colored gray. D, Consensus correlations between the abundance of immune cell types and expression of the top stromal biomarkers. Mean Pearson correlation coefficients across the seven discovery cohorts were plotted for each cell type-gene pair. Positive correlations were colored red, negative correlations were colored blue, and tiles with Pearson correlation coefficient