Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy

Cancer Cell. 2021 May 10;39(5):662-677.e6. doi: 10.1016/j.ccell.2021.03.007. Epub 2021 Apr 15.


Clear cell renal cell carcinomas (ccRCCs) are highly immune infiltrated, but the effect of immune heterogeneity on clinical outcome in ccRCC has not been fully characterized. Here we perform paired single-cell RNA (scRNA) and T cell receptor (TCR) sequencing of 167,283 cells from multiple tumor regions, lymph node, normal kidney, and peripheral blood of two immune checkpoint blockade (ICB)-naïve and four ICB-treated patients to map the ccRCC immune landscape. We detect extensive heterogeneity within and between patients, with enrichment of CD8A+ tissue-resident T cells in a patient responsive to ICB and tumor-associated macrophages (TAMs) in a resistant patient. A TCR trajectory framework suggests distinct T cell differentiation pathways between patients responding and resistant to ICB. Finally, scRNA-derived signatures of tissue-resident T cells and TAMs are associated with response to ICB and targeted therapies across multiple independent cohorts. Our study establishes a multimodal interrogation of the cellular programs underlying therapeutic efficacy in ccRCC.

Keywords: TCR sequencing; immunotherapy; pathology; renal cell carcinoma; single-cell RNA-sequencing; tissue-resident; tumor-associated macrophages; tyrosine kinase inhibitors.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carcinoma, Renal Cell / genetics*
  • Humans
  • Kidney Neoplasms / genetics*
  • Kidney Neoplasms / immunology
  • Lymphocyte Activation / genetics
  • Lymphocyte Activation / immunology*
  • Programmed Cell Death 1 Receptor / genetics
  • Receptors, Antigen, T-Cell / genetics
  • Receptors, Antigen, T-Cell / immunology
  • T-Lymphocytes / immunology*


  • Programmed Cell Death 1 Receptor
  • Receptors, Antigen, T-Cell