Preferential use of public T cell receptors during autoimmune encephalomyelitis determined by high resolution saturating sequencing

How the TCR repertoire, in concert with risk-associated MHC, imposes susceptibility for autoimmune diseases is incompletely resolved. Due largely to recombinatorial biases, a small fraction of TCR ? or ? chains are shared by most individuals, or public. If public TCR chains modulate a TCR?? heterodimer's likelihood of productively engaging autoantigen, because they are pervasive and often high frequency, they could also broadly influence disease risk and progression. Prior data, using low resolution techniques, have identified the heavy use of select public TCR in some autoimmune models. Here we assess public repertoire representation in mice with experimental autoimmune encephalomyelitis (EAE) at high resolution. Saturation sequencing was used to identify >18x106 TCR? sequences from the central nervous systems, periphery, and thymi of mice at different stages of autoimmune encephalomyelitis and healthy controls. Analyses indicated the prominent representation of a highly diverse public TCR? repertoire in the disease response. Preferential formation of public TCR implicated in autoimmunity was identified in pre-selection thymocytes and, consistently, public, disease-associated TCR? were observed to be commonly oligoclonal. Increased TCR sharing and a focusing of the public TCR response was seen with disease progression. Critically, comparisons of peripheral and CNS repertoires and repertoires from pre-immune and diseased mice demonstrated that public TCR were preferentially deployed relative to non-shared, or private, sequences. Our findings implicate public TCR in skewing repertoire response during autoimmunity, and suggest that subsets of public TCR sequences may serve as disease-specific biomarkers or influence disease susceptibility or progression.