Spatial Transcriptomics reveals a T cell-mediated microglial activation axis of neurodegeneration following immune checkpoint inhibition

Immune checkpoint inhibitor (ICI) combinations that block cytotoxic T-lymphocyte–associated protein 4 (CTLA-4) and programmed cell death protein 1 (PD-1) signaling have revolutionized cancer care but also exert a range of immune-related adverse events (irAE) in various tissues, including the brain. Our understanding of the mechanisms of irAE in the brain is still evolving, and we recently demonstrated that ICI (blockade of CTLA-4 and PD-1) perturbs hippocampal-dependent memory function by derailing neuro-immune homeostasis and compromising synaptic integrity. However, the spatial patterns and the cell–type–specific molecular mechanisms underlying ICI-related brain dysfunction remain not well-defined. To address this gap, we performed spatial transcriptomic profiling of the hippocampal region using multiplexed error-robust fluorescence in situ hybridization (MERFISH) to map gene expression at single-cell resolution. By integrating spatial single-cell data with bulk RNA-seq, we define the distribution of microglia, astrocytes, synaptic, and neuroinflammatory markers, and determine how ICI reshapes hippocampal cellular composition in a syngeneic murine melanoma model. MERFISH revealed upregulation of microglial, astrocytic, oligodendrocytic, and T cell markers post-ICI treatment, revealing unique pathways driving neuroinflammation, synaptic function, and cellular signaling. Furthermore, immunofluorescence analysis of postmortem brains from patients treated with ICI corroborates our findings of ICI-related immune activation of microglia. Finally, using a conditional deletion model, we show that T cells are indispensable for ICI-driven microglial activation. Altogether, our study provides a high-resolution spatial framework for understanding irAEs in brain function and a T cell-microglia crosstalk axis as a driving mechanism of dysregulated neuro-immune homeostasis during ICI.