TCGA Kidney Renal Clear Cell Carcinoma (KIRC)

Overview

The TCGA KIRC dataset comprises 491 clear cell renal cell carcinoma (ccRCC) samples and is one of the primary anchor cohorts in large-scale multi-cohort ccRCC studies. It includes bulk RNA-seq, DNA-seq, and clinical outcome data. TCGA-KIRC has been extensively used as a reference for molecular subtyping, survival analysis, and immunotherapy biomarker discovery in ccRCC.

Composition

  • Cancer type: clear cell renal cell carcinoma (CCRCC), n = 491.
  • Assays: bulk rna-seq, DNA-seq (NGS).
  • Used as one of 14 public cohorts (n = 3,621 ccRCC samples total) in the HiTME meta-analysis PMID:22138691.

Assays / panels (linked)

Papers using this cohort

  • PMID:22138691 — HiTME ccRCC molecular subtyping and IO biomarker study (meta-cohort including TCGA-KIRC as anchor).
  • PMID:23792563 — TCGA Research Network 2013, “Comprehensive molecular characterization of clear cell renal cell carcinoma,” Nature.
  • PMID:23797736 — Lima et al. 2025, mouse scRNA-seq HIF1A/HIF2A isoform study (TCGA-KIRC used as human validation dataset).

Notable findings derived from this cohort

  • Five HiTME immune tumor microenvironment subtypes (IE, IE/M, F, V, D) were defined using harmonized transcriptomic data from 14 cohorts including TCGA-KIRC; fibrotic subtypes IE/M and F had worst overall survival in the TCGA-KIRC cohort PMID:22138691.
  • BAP1, SETD2, and PBRM1 mutations were associated with distinct HiTME subtypes and differential ICI/TKI response profiles PMID:22138691.
  • MTOR-activating mutations associated with ICI non-response (15/16 patients resistant) in the meta-cohort anchored on TCGA-KIRC PMID:22138691.
  • TCGA multi-platform molecular characterization of 446 primary ccRCC tumors identified 19 significantly mutated genes (VHL, PBRM1, SETD2, BAP1, KDM5C, PTEN, MTOR, TP53) and chromosome 3p loss in 91% of samples; PI3K/AKT/mTOR pathway altered in ~28%; metabolic Warburg shift correlated with worse survival PMID:23792563
  • Human ccRCC TCGA expression data used as secondary validation for HIF1A/HIF2A isoform-specific transcriptional gene programs identified in a conditional mouse Vhl-knockout scRNA-seq study; both early and adaptive HIF2A-driven programs were significantly active in human ccRCC vs. normal kidney PMID:23797736

Sources

This page was processed by crosslinker on 2026-05-09. - PMID:23797736

This page was processed by crosslinker on 2026-05-09.