Fig. 3: Tumor features correlated with iCCA prognosis and GOLP response. | Nature Communications

Fig. 3: Tumor features correlated with iCCA prognosis and GOLP response.

From: Macro CD5L+ deteriorates CD8+T cells exhaustion and impairs combination of Gemcitabine-Oxaliplatin-Lenvatinib-anti-PD1 therapy in intrahepatic cholangiocarcinoma

Fig. 3

A Bar plot showing the top enriched pathways of differentially expressed genes between pre- and post-GOLP tumor cells (N = 18 samples). A hypergeometric test was used. A Benjamini–Hochberg adjusted P < 0.05 (two-sided) was used as a significance cutoff. B Correlation between gene features of tumor cells before GOLP treatment and tumor shrinkage (N = 8 patients). Gene features above zero were favorably associated with tumor shrinkage (P < 0.05: red); gene features below zero were unfavorably associated with tumor shrinkage (P < 0.05: blue); Pearson’s correlation test (two-sided); exact P values were listed in Supplementary Data 3. C GSEA showed that PD1 signaling, positive regulation of vasculature development and signaling by KIT in disease were enriched in the pre-GOLP tumor cells in samples with a good response. Empirical phenotype-based permutation test (one-sided). D UMAP plot showing the expression profiles of tumor cells from the 18 samples (N = 14,411 cells). E Heatmap showing the 4 meta-clusters (C1-C4) of tumor cells identified using consensus non-negative matrix factorization (cNMF). The terms on the left represent the pathways enriched in each meta-cluster. F Dot plot showing the average expression levels of representative effector genes in the 4 meta-clusters between the PR and SD groups (N = 8 patients). The dot size indicates the fraction of cells expressing the specific gene in the group, and the dot color represents the average gene expression level in the group. G Pi values of the 4 meta-clusters (C1-C4). N = 8 patients. The dot size represents the significance evaluated as -log10 (P value). *: P < 0.05. Wald test, two-sided. P values of C1, C2, C3, and C4 are 0.0011, 0.57, 0.27 and 0.9, respectively. (H) Heatmap showing the expression profiles of the 4 meta-clusters in the large GOLP treatment-naive iCCA cohort (FU-iCCA, N = 262) with bulk RNA-seq data. The representative genes of each meta-cluster are highlighted on the right. Source data are provided as a Source Data file.

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