Checkpoint inhibitors produce durable responses in numerous metastatic cancers, but immune-related adverse events (irAEs) complicate and limit their benefit. IrAEs may affect any organ system in an idiosyncratic fashion; presentations range from mild and self-limited to fulminant and fatal. The molecular mechanisms underlying these irAEs are not well understood. Here, we report a case of fatal encephalitis arising during anti-PD-1 therapy. Histopathologic analysis of affected brain tissue revealed a robust T-cell infiltration and prominent PD-L1 expression. To assess the scope and impact of checkpoint inhibitor-associated encephalitis, we searched global pharmacovigilance databases and identified 209 reported cases of encephalitis associated with anti-PD-1 and/or anti-CTLA-4 regimens. Cases occurred across cancer types and had a 19% fatality rate, demonstrating the recurrent and often fulminant nature of these irAEs. Further analyses were performed from the index case and two additional cases.

Multidimensional protein and transcriptomic analyses pinpointed memory activated CD4+ T cell phenotypes as highly enriched in the inflamed region. T cell receptor (TCR) sequencing identified a highly oligoclonal T cell repertoire, with one clone representing nearly 20% of detected T cells. The clonal TCR bore striking resemblance to a known CD8+ TCR with Epstein-Barr virus (EBV) reactivity, and several other highly represented clones were identical to known TCRβs recognizing EBV. Dual immunohistochemistry (IHC)/RNA in situ analysis localized this clone to memory activated cytotoxic (CD45RO+GZMB+) CD4 cells. Staining of neural tissue for EBER transcripts identified EBV+ lymphocytes in the cortex and meninges of the affected region. Collectively, this study suggests that latent EBV+ lymphocytes infiltrating the CNS may contribute to neural inflammation after release from peripheral tolerance by anti-PD-1 therapy and identifies cytotoxic CD4+ and CD8+ T cells as culprits of checkpoint inhibitor-associated immune encephalitis.

Sample Information

Sample ID Case Series Sample Type Analysis Type Tissue Type Species Sequencing ID
S13-11593-1A ENCEPHALITIS Non-ICI encephalitis RNAseq FFPE Human JB-2809-01
N15-264-2A ENCEPHALITIS Non-ICI encephalitis RNAseq FFPE Human JB-2809-02
N15-63-6B ENCEPHALITIS Non-ICI encephalitis RNAseq FFPE Human JB-2809-03
V17-67-2C ENCEPHALITIS Normal temporal lobe control RNAseq FFPE Human JB-2809-04
V16-26-2C ENCEPHALITIS ICI-encephalitis (affected region) RNAseq FFPE Human 505-JB-1
V16-26-2I ENCEPHALITIS ICI-encephalitis (unaffected region) RNAseq FFPE Human 505-JB-2

Data are available on reasonable request by sending email to Justin M. Balko.


  1. Douglas B. Johnson, Wyatt J. McDonnell, Paula I. Ericsson-Gonzalez, Rami Al-Rohil, Bret C. Mobley, Joe-Elie Salem, Daniel Y. Wang, Violeta Sanchez, Yu Wang, Cody A. Chastain, Kristi Barker, Yan Liang, Sarah Warren, Joseph Beechem, Alexander M. Menzies, Martin Tio, Georgina V. Long, Justine V. Cohen, Amanda C. Guidon, Méabh O’Hare, Sunandana Chandra, Akansha Chowdhary, Benedicte Lebrun-Vignes, Simone Goldinger, Elisabeth Rushing, Elizabeth Buchbinder, Simon A. Mallal, Chanjuan Shi, Yaomin Xu, Javid J. Moslehi, Melinda E. Sanders, Jeffrey A. Sosman, and Justin M. Balko. A case report of clonal EBV-like memory CD4+ T cell activation in fatal checkpoint inhibitor-induced encephalitis. Nature Medicine. 2019. accepted.