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. 2021 Sep 6;12:5262. doi: 10.1038/s41467-021-25618-z

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — A A volcano plot representing differentially expressed genes between the tumors and paired adjacent normal tissues. Significantly upregulated genes are colored in red, whereas significantly downregulated genes are colored in blue. The q values (-log10 p) were calculated using paired two-sided moderated Student’s t test. B Kyoto Encyclopedia of Genes and Genomes enrichment analysis of differentially expressed genes. Enrichment q values (-log10 p) are calculated by hypergeometric test. C GSEA enrichment scores of PI3K-AKT-mTOR, P53, G2M Checkpoint, and E2F targets pathways in TFE3-tRCC versus normal tissues. D Unsupervised clustering of samples from the TCGA RCC and our TFE3-tRCC cohorts (n = 63) using ssGSEA scores from 25 immune cell types, IIS and TIS. KICH (n = 65), KIRC (n = 539), KIRP (n = 289). E Comparing the expression of 25 immune cell types, IIS and TIS between TCGA-KIRC (n = 539) and our TFE3-tRCC cohorts (n = 63). (F) Bar chart depicts the prevalence of CD8 expression by immunohistochemistry. G Representative immunofluorescence demonstrating the presence of overall CD8 ⁺T-cell, tumor-associated macrophage (CD68 and HLA-DR), and NK cell (CD56) infiltration in three selected samples (TFE3-32, TFE3-38, and TFE3-37) in our cohort. Ten random high-power fields of tumor parenchyma were checked for CD8, CD68, HLA-DR, and CD56 positive expression. Magnification × 400. Scale bar = 100 μm. H Bar chart depicts the prevalence of PD-L1 expression by immunohistochemistry. P-values were determined by Pearson’s chi-square test. I) Heatmap shows the immune features among TFE3-tRCCs (n = 63). Each column represents an individual tumor. Patients were separated into eight groups: those with ASPSCR1-TFE3 (n = 13), with SFPQ-TFE3 (n = 15), with NONO-TFE3 (n = 8), with MED15-TFE3 (n = 8), with PRCC-TFE3 (n = 6), with RBM10-TFE3 fusions (n = 4), with rare TFE3-associated gene fusions (n = 3, including FUBP1-TFE3, SETD1B-TFE3, and ZC3H4-TFE3), and unknow partners (n = 6). The top panel shows fusion partners and isoforms. The bottom panel shows immune features, including TIS, IIS, PD-L, CD8, and TIME type. TFE3-tRCC TFE3-translocation renal cell carcinoma, TCGA The Cancer Genome Atlas. KICH chromophobe renal cell carcinoma, KIRC renal clear cell carcinoma, KIRP renal papillary cell carcinoma, IIS immune infiltration score, TIS T-cell infiltration score, IHC immunohistochemistry, TIME tumor immune microenvironment.