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. Author manuscript; available in PMC: 2022 Feb 2.
Published in final edited form as: Nat Cancer. 2021 Aug 2;2:978–993. doi: 10.1038/s43018-021-00237-1

Extended Data Fig. 7. Transcriptomic analysis of Myc-CaP tumors treated with ESK981 in combination with anti-PD-1 immunotherapy in FVB mice.

Extended Data Fig. 7.

(a) Principal Component Analysis (PCA) of individual Myc-CaP tumors from indicated treatment groups based on variance-stabilizing transformation (vst) of read-count data. The vehicle and ESK981+anti-PD-1 combination groups form a relatively distinct cluster based on the first two principal components.

(b) Volcano plot of differential gene expression analysis for groups treated with ESK981+anti-PD-1 versus vehicle. The horizontal dashed line corresponds to the FDR = 0.05. The vertical dashed lines correspond to log2FC >= 1 (up-regulation) or log2FC <= −1 (down-regulation).

(c) Mouse Gene Set Enrichment Analysis (GSEA) with biological process gene ontology for groups treated with ESK981+anti-PD-1 versus vehicle. Top 10 gene sets are ordered by normalized enrichment score (NES). The top enriched categories are relevant to immune responses and inflammation.

(d) Heatmap representation of top differentially expressed genes in groups treated with ESK981+anti-PD-1 versus vehicle (FDR <= 0.01, up or down-regulated by at least 2-fold).

(e) Fragments per kilobase of exon model per million reads mapped (FPKM) of indicated targets from individual Myc-CaP tumors treated with vehicle (n=10 tumors), ESK981 (n=8 tumors), anti-PD-1 (n=7 tumors), or ESK981+anti-PD-1 (n=8 tumors). Data were analyzed by two-tailed unpaired t test and presented as mean ± SEM. P-value indicated.