Brown, Rachel L; (2025) Understanding T cell immunity in anti-NMDAR encephalitis: Developing therapeutic tools for neurological autoimmunity. Doctoral thesis (Ph.D), UCL (University College London).

Text Brown, Rachel_Rachel_Brown_PhD_Thesis.pdf - Accepted Version Access restricted to UCL open access staff until 1 February 2026. Download (48MB)

Abstract

Background: Anti-NMDA receptor antibody associated encephalitis is a relatively recently described neurological disease primarily of young women which results in significant morbidity including prolonged intensive care and hospital admissions. Many patients are refractory to currently available first- and second-line therapies. Understanding the complete immunopathogenesis of this syndrome will help identify new targets for treatment and broaden and improve therapeutic opportunities. Whilst the humoral aspects of the disease are implicit in the name, the role of T cells has not yet been explored. Materials and Methods: Peripheral blood mononuclear cells derived from patients and healthy volunteers underwent three rounds of stimulation with peptide pools derived from the NR1 subunit of the NMDA receptor, that spanned the length of the NR1 protein. At each round of peptide stimulation, an aliquot of cells was taken to assess for NR1-specific CD4+ and CD8+ T cell responses by flow cytometry. Culture supernatants analysed using ELISA or multiplex assays for specific cytokine production. Where responses were identified to NR1 peptide pools, a peptide matrix was used to identify individual immunogenic 15mer peptides from the relevant peptide pool. HLA binding prediction platforms NetMHCpan 4.1 and NetMHCIIpan-4.0 were used to predict HLA molecules on which identified immunogenic peptides might be presented. Patient and healthy volunteers demonstrating NR1-specific responses then underwent three further rounds of peptide stimulation with single immunogenic NR1 peptides. An aliquot of cells was taken at each round of stimulation for RNA extraction and bulk TCR sequencing analysis. Finally, to explore whether T cells may be relevant in other antibody-associated autoimmune encephalitis syndromes, the same peptide stimulation experiments were completed using PBMCs from patients with LGI1 encephalitis and healthy volunteers and using an overlapping LGI1 peptide library. Results: NR1-specific CD4+ and CD8+ T cells were identified in both patients and healthy volunteers, but more frequently in patients. These cells often appeared earlier in patients, usually after just one or two rounds of stimulation before disappearing; however other responses to NR1-derived peptide pools could be expanded after a third round of peptide stimulation. NR1-specific CD8+ T cells were identified more frequently than NR1 specific CD4+ T cells. Although both NR1-specific CD4+ and CD8+ T cell responses recognised peptide sequences spanning the whole NR1 protein, CD4+ T cell responses were most often seen in response to a limited library of NR1-pool 4 peptides, whereas CD8+ T cell responses were most often seen to NR1 pools 6 or 8. Using a matrix method, ten regions of the NR1 protein were identified as being especially immunogenic, often containing one or more overlapping immunogenic peptides. Bulk TCR sequencing data demonstrated enrichment of specific T cell clonotypes over three rounds of stimulation with single immunogenic NR1 peptides in patient and healthy volunteer samples suggesting antigen-specific selection had occurred. Experiments in patients with LGI1 encephalitis and healthy volunteers yielded similar results, with earlier and more frequent LGI1-specific T cell responses in patients compared with healthy volunteers. Conclusions: NR1-specific CD4+ and CD8+ T cells can be identified in both patients and healthy volunteers. Different patterns of responses suggest there may be disease specific changes in the T cell repertoire, and a potential role for these cells in disease pathogenesis. Further work is required to better characterise these responses and explore their implications for novel therapeutic approaches in this disease.

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