Fig. 3: Immune cell type-specific gene transcription associated with response to cryoablation therapy.
A UMAP of T cell subclustering with cluster annotations. B Box plots displaying the frequency of T cells belonging to a specific subcluster per patient comparing PD (n = 9), SD (n = 2), and PR (n = 2). Horizontal line indicates median. C Plots of DESeq2-normalized counts for highlighted genes differentially expressed by T cells between categories of best response post-cryoablation for pre-treatment samples (n = 13). FDR-adjusted p-values are for two-sided DESeq2 Wald test differential expression results; pbenefit denotes grouping SD + PR. D Gene set enrichment analysis (GSEA) for the differentially expressed T cell genes from C). Bar lengths correspond to normalized enrichment score (NES). Positive NES values indicate enrichment in SD + PR and negative values indicate enrichment in PD. Asterisks denote significance as defined in the figure. E UMAP of myeloid cell subclustering with cluster annotations. F Box plots displaying the frequency of myeloid cells belonging to a specific subcluster per patient comparing PD (n = 9), SD (n = 2), and PR (n = 2). Horizontal line indicates median. G Plots of DESeq2-normalized counts for highlighted genes differentially expressed by myeloid cells between categories of best response post-cryoablation (n = 13). FDR-adjusted p-values are for two-sided DESeq2 Wald test differential expression results; pbenefit denotes grouping SD + PR. H Timeline summary of patient course for patients with available pre- and post-cryoablation biopsies. I Box plots displaying the percent of immune cells in each lineage per sample, with lines connecting pre- and post-treatment samples from the same patient (n = 4). Box plots indicate interquartile range, with horizontal line indicating median, and whiskers extending to maxima and minima excluding outliers (>1.5 * IQR). PD progressive disease, SD stable disease, PR partial response. Source data for Fig are provided as a Source Data file.
