Fig. 1: Impact of neoadjuvant chemotherapy ± Pembrolizumab on the HGSC microenvironment using bulk RNAseq. | Nature Communications

Fig. 1: Impact of neoadjuvant chemotherapy ± Pembrolizumab on the HGSC microenvironment using bulk RNAseq.

From: Immunomic longitudinal profiling of the NeoPembrOv trial identifies drivers of immunoresistance in high-grade ovarian carcinoma

Fig. 1

A Heatmap depicting the expression level of selected individual genes, gene signatures (MCPcounter and quanTIseq) and gene ratios inferred from bulk RNAseq data of tumors collected before (orange) or after treatment (purple) from patients of the NeoPembrOv trial receiving NACT (blue) or NACT + P (red). Red and Blue colors represent a high and low expression score, respectively. Statistically significant unadjusted p-values from two-sided Wilcoxon signed rank test between pre- and post-treatment samples are indicated on the left for the control arm and on the right for the experimental arm. Patients (x-axis) are ordered according to increasing PTPRC (CD45) expression before treatment and are listed in the same order for post-treatment samples. B Box and dotplots depicting the MCP counter gene signature expression scores in pre- and post-treatment samples for each patient in the NACT arm (left, N = 21 patients) and the NACT + P arm (right, N = 31 patients). The centerline of boxes depicts the median values; the bottom and top box edges correspond to the first and third quartiles. Statistical significance was evaluated using two-sided Wilcoxon signed-rank tests and unadjP values are reported for NACT arm: EPCAM = 0.016; CD8B/FOXP3 = 0.038; JCHAIN = 0.008; IGHA1-2 = 0.004 and NACT + P arm: PTPRC (CD45) = 0.027; EPCAM = 8.66e-05; CD8 T cells = 0.001; CD8B/FOXP3 = 0.001; JCHAIN = 0.001; IGHA1-2 = 0.002; Cytotoxic lymphocytes = 0.027. C Graphs depicting the top 10 pathways (GO BP) enriched in the differentially expressed genes between post- and pre-treatment samples for each treatment arms (upregulated pathways are in the top and down regulated are in the bottom part of the figure). Pathways highlighted in blue are common to both arms (NACT and NACT + P). Pathways highlighted in red are specific to the NACT + P arm. Only genes with a fold-change > 1.5 and an adjusted p-value < 0.05 were considered. Gene ratio represents the percentage of differentially expressed genes (DEG) identified in the pathway, dot size (Count) is representative of the number of DEG considered for pathway analysis and adjusted p-values (adjust.p) were obtained from one-sided Fisher exact test. Source data are provided as a Source Data file.

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