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Fig. 1 | Genome Biology

Fig. 1

From: Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures

Fig. 1

In vitro validation of the immune cell scoring method. a Immune cell populations were sorted from ccRCC patient specimens, and profiled for RNA-Seq gene expression. ssGSEA scores were computed for each sample using Bindea et al. signatures. Each ssGSEA score was the highest for the corresponding tumor-associated immune cell population and also had a significant difference from the other sorted populations (p values are provided above each figure). b Principal component analysis (PCA) of sorted tumor-associated immune cell populations. PCs were computed as a linear combination of 29 immune microenvironment variables (Additional file 2: Table S3). c Immunofluorescence (IF) validation of ssGSEA scores in an MSKCC cohort. The top left panel shows the unsupervised clustering of ssGSEA scores for NK, CD8+ T, and Treg cells in the 10 patients. IF staining for two samples at the opposite ends of the heatmap is shown in the bottom left panel (CD56, CD8, and FOXP3 antibodies respectively). The association of the immune infiltrate levels inferred by these two orthogonal methods (ssGSEA and IF) is shown in the right panel. The IF score (y-axis) represents the ratio of CD56, CD8, and FOXP3 positive cells versus total cells (DAPI-stained) for a given sample and was determined as the average across three representative regions on the slide

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