Fig. 3: Comparative transcriptome atlas of a variety of renal tumors delineates molecular characteristics of histologically rare RCC and may define features of unclassified RCC.

a The upper heatmap created from an unsupervised clustering based on expression profiles shows a variety of molecular characteristics of histologically rare RCC and unclassified RCC. The lower heatmap created from single-sample GSEA (ssGSEA) displays the top 10 upregulated ssGSEA pathways in each cluster. Sarcomatoid: renal tumors with sarcomatoid variant. Systemic ther. systemic therapy, BOR best overall response. Inherited: hereditary kidney cancer. Subtype: Expression subtypes based on expressions of FOXI1 or L1CAM²⁴. Chen’s class.: Subtypes based on Chen’s classification²⁵. Immune subtype: Classification based on a condensed Thorsson immune subtype classification^26,27,28,29. IO immuno-oncology drug, TKI tyrosine kinase inhibitor, MTSCC mucinous tubular spindle cell carcinoma, PGL/PCC hereditary paraganglioma-pheochromocytoma syndrome, HOCT hybrid oncocytic chromophobe tumor, Other oncocytic other oncocytic tumors of the kidney, ChRCC chromophobe RCC, ACD-RCC acquired cystic disease-associated RCC, HLRCC FH-deficient RCC, CDC collecting duct carcinoma, MTSCC mucinous tubular and spindle cell carcinoma, TFE3-RCC TFE3-rearranged RCC, tcRCC tubulocystic RCC, pRCC papillary RCC, ccRCC clear cell RCC, Onco oncocytoma, MCRN multilocular cystic renal neoplasm, Other other rare subtypes, uRCC unclassified RCC. b t-distributed Stochastic Neighbor Embedding (t-SNE) plot is shown. Black dots indicate unclassified RCC cases. Expressions of CA9, FOXI1, AKR1B10, and VEGFA are shown in the lower panels. c t-SNE plot highlighted with the Jaccard index is shown. Source data are provided in the Source data file.