Conserved Brain-Associated CD8+ T Cell Programs and Their Regulation by the Brain Microenvironment

Abstract

CD8+ T cells are increasingly recognized as components of the healthy brain, yet whether their specialized functional characteristics are conserved across species and how the brain microenvironment regulates their effector programs remain poorly understood. Here, we characterized brain-associated CD8+ T cells in the common marmoset and investigated their regulation by brain-derived signals. Flow cytometric analysis revealed a substantial population of CD8+ T cells in the healthy marmoset brain parenchyma that exhibited high IFN-{gamma} competence but minimal granzyme B (GzmB) expression, resembling the functional phenotype previously identified in mice. Single-cell transcriptomic analyses of mouse and marmoset CD8+ T cells revealed tissue-associated transcriptional heterogeneity and distinct differentiation- and effector-associated programs. To investigate how the brain microenvironment shapes these characteristics, we exposed activated mouse CD8+ T cells to brain lysate and performed targeted CRISPR interference screening of 107 cell-surface receptor genes coupled with single-cell RNA sequencing. Brain lysate selectively reduced Gzmb and Ifng expression while increasing Tnf and Xcl1, indicating differential regulation of cytotoxic and inflammatory effector programs. Receptor perturbations revealed heterogeneous transcriptional responses and identified candidate pathways potentially involved in sensing brain-derived signals. Together, these findings identify shared functional characteristics of brain-associated CD8+ T cells across rodents and nonhuman primates and establish a framework for understanding how the neural microenvironment shapes adaptive immune function.