Fig. 3: Differentially expressed pathways in partial responders.
From: Pilot study of bempegaldesleukin in combination with nivolumab in patients with metastatic sarcoma
A Volcano plot of differential expression between partial responders (n = 7 patients) and non-responders (n = 41 patients). Model included trial cohort, patient, purity, and sample time point as covariates. Points represent genes. Genes in Hallmark hedgehog pathway are highlighted in red. B Top 10 upregulated and all 5 downregulated Hallmark pathways between partial responders (n = 7 patients) and non-responders (n = 41 patients). Analysis performed using fgsea in R. All pathways are significantly enriched (BH adjusted p < 0.05). C Heatmap of ssGSEA scores of baseline (n = 41 patients) and on-treatment (n = 38 patients) expression in individual patients for top enriched pathways in (B) using the leading-edge genes from the fgsea analysis. D, E. Kaplan–Meier plot of progression-free survival of patients divided into four groups depending on the amount CD8 + T cells and ssGSEA score of hedgehog pathway enrichment across cohort (high versus low, split by median). Scores derived from expression at baseline in (D) and on-treatment samples in (E). Note, cross-validation analysis does not output p values. Source data are provided as a Source Data file.
