Distinct phenotypic states and spatial distribution of CD8+ T cell clonotypes in human brain metastases

Cell Rep Med. 2022 May 17;3(5):100620. doi: 10.1016/j.xcrm.2022.100620. Epub 2022 Apr 27.


Metastatic disease in the brain is difficult to control and predicts poor prognosis. Here, we analyze human brain metastases and demonstrate their robust infiltration by CD8+ T cell subsets with distinct antigen specificities, phenotypic states, and spatial localization within the tumor microenvironment. Brain metastases are densely infiltrated by T cells; the majority of infiltrating CD8+ T cells express PD-1. Single-cell RNA sequencing shows significant clonal overlap between proliferating and exhausted CD8+ T cells, but these subsets have minimal clonal overlap with circulating and other tumor-infiltrating CD8+ T cells, including bystander CD8+ T cells specific for microbial antigens. Using spatial transcriptomics and spatial T cell receptor (TCR) sequencing, we show these clonally unrelated, phenotypically distinct CD8+ T cell populations occupy discrete niches within the brain metastasis tumor microenvironment. Together, our work identifies signaling pathways within CD8+ T cells and in their surrounding environment that may be targeted for immunotherapy of brain metastases.

Keywords: CD8(+) T cells; TCR-sequencing; brain metastases; bystander; exhaustion; spatial transcriptomics.

Publication types

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

MeSH terms

  • Brain Neoplasms* / metabolism
  • CD8-Positive T-Lymphocytes*
  • Humans
  • Receptors, Antigen, T-Cell / genetics
  • T-Lymphocyte Subsets
  • Tumor Microenvironment


  • Receptors, Antigen, T-Cell