Author ORCID Identifier
https://orcid.org/0000-0003-0867-5830
Date of Award
Spring 4-22-2026
Document Type
Thesis (Ph.D.)
Department or Program
Microbiology and Immunology
First Advisor
Pamela C. Rosato
Abstract
The central nervous system (CNS) is now recognized as an immunologically active site. However, whether peripheral viral infections generate long-term antigen-specific CD8+ T cell memory within brain tissue remains unclear. Two complementary studies were conducted to address this question. First, we developed and validated a multiplexed bead-based assay for peptide-MHC class I tetramer quality control. This enabled reliable detection of rare virus-specific CD8+ T cells from limited human tissue samples. Applied to paired blood and adenotonsillar tissue from pediatric donors with prior SARS-CoV-2 infection, we found that EBV- and influenza-specific CD8+ T cells established tissue residency in adenotonsillar tissue. In contrast, SARS-CoV-2-specific populations were consistently less abundant and showed minimal expression of residency markers. In the second study, we used single-cell RNA and paired TCR sequencing to characterize CD8+ T cell residency across multiple CNS compartments in two independent cohorts. CNS CD8+ T cells expressed canonical tissue-resident transcriptional programs with consistent regional organization. Meningeal populations were enriched for effector cytokine transcripts, while parenchymal populations were comparatively quiescent. Expanded clonotypes were distributed across CNS compartments but adopted region-specific transcriptional states. This suggests residency commitment is stable at the clonal level while effector programming is controlled by the local microenvironment. Using HLA-A*02:01 tetramers and TCR database matching, we directly identified virus-specific CD8+ T cells in CNS tissue for EBV, CMV, influenza, and SARS-CoV-2. All donors showed multi-pathogen specificity. Each viral specificity was associated with a distinct clonal architecture showing its persistence mode. EBV-specific populations were oligoclonal and broadly distributed, while influenza-specific populations were polyclonal and tissue-restricted. SARS-CoV-2-specific populations included a prominent brain-restricted clone absent from peripheral blood. This represents the first characterization of this population in non-neurological donors. Together, these data show that peripheral viral exposures leave lasting antigen-specific imprints on CNS immunity. These are shaped by both viral biology and local tissue environment. This work provides a baseline for comparison with disease-associated changes in multiple sclerosis, long COVID, and neurodegeneration.
Recommended Citation
Degefu, Hanna Negash, "Virus-Specific CD8+ T Cell Residency Across Distinct Human Tissue Compartments" (2026). Dartmouth College Ph.D Dissertations. 494.
https://digitalcommons.dartmouth.edu/dissertations/494
