Distinct waves of CD8 T cell affinity during demyelinating disease progression

Abstract The animal model of Multiple Sclerosis, Experimental Autoimmune Encephalomyelitis (EAE), requires CD4 T cells to induce demyelinating disease. However, CD8 T cells are ever present during EAE and have been hypothesized to have both effector and suppressor functions. To understand autoimmune disease progression, we analyzed the affinity and genetic profile of the CD4 and CD8 T cell response over time. Affinity analysis of CD8 T cells during the autoimmune disease course revealed the greatest affinity for myelin at peak disease (d21-23), whereas affinities were significantly lower at onset (d14) and chronic (d36-38) timepoints. Conversely, affinity analysis of CD4 T cells revealed no significant changes at the same time points. Additionally, CD8 T cells displayed a smaller, 10-fold range in affinity, suggestive of a restricted TCR clonal response. CD4 affinities covered a much wider 10,000-fold range, consisting of low and high affinity clones. To further understand the dynamics of the T cell population during disease, we performed single cell RNA-sequencing. Heterogenous populations of CD4 and CD8 T cells were observed at peak EAE disease, including a genetically distinct population of FoxP3+, CD25+ CD8 T cells which accounted for 3.33% the total CD8 population. These genomic data paired with the known associations between affinity and T cell fate suggest phenotypically and functionally distinct waves of CD8 T cells with limited clonality infiltrate the CNS during EAE progression.