Temporal development of T cell receptor repertoires during childhood in health and disease

Abstract

T cell receptor (TCR) sequences are exceptionally diverse and can now be comprehensively measured with next generation sequencing technologies. However, a thorough investigation of longitudinal TCR repertoires throughout childhood in health and during development of a common childhood disease, type 1 diabetes (T1D), has not been undertaken. Here, we deep-sequenced the TCR beta chain (TCRβ) repertoires from longitudinal peripheral blood DNA samples at four time points beginning early in life (median age of 1.4 years) from children that progressed to T1D (n=29) and age/sex-matched islet autoantibody negative controls (n=25). From 53 million TCRβ sequences, we show that the repertoire is extraordinarily diverse early in life and narrows with age independent of disease. We demonstrate the ability to identify specific TCR sequences, including those known to recognize influenza A and separately those specific for insulin and its precursor, preproinsulin. Insulin-reactive TCRβ sequences are more common and frequent in number as the disease progressed in those who developed T1D compared to genetically at-risk non-diabetic children, which was not the case for influenza-reactive sequences. As an independent validation, we sequenced and analyzed TCRβ repertoires from a cohort of new-onset T1D patients (n=143), identifying the same preproinsulin-reactive TCRs. These results demonstrate an enrichment of preproinsulin-reactive TCR sequences during the progression to T1D, highlighting the importance of using disease-relevant TCR sequences as powerful biomarkers in autoimmune disorders.