Co-evolution of human influenza A and Epstein Barr virus-specific CD8 ex vivo memory T cell receptor BV repertoires with increasing age

Abstract

CD8 memory T cells are generated during primary infection with intracellular pathogens, such as viruses. These cells play an important role in the protection of the host upon re-infection with the same pathogen. In this study, we compare CD8 memory T cell receptor (TCR) beta repertoires directly ex vivo for two common human viruses, influenza A virus (IAV), an RNA virus that frequently re-infects due to a high rate of genetic mutation, and Epstein-Barr virus (EBV), a DNA virus, which persists in B cells for life, in the 95% of people that become infected. In cross-sectional and longitudinal studies of EBV seropositive, HLA-A2+, young (18-22 years), middle age (25-59 years), and older (>60 years) donors, we demonstrate that CD8 memory TCR repertoires to three immunodominant epitopes, known to have cross-reactive responses, IAV-M158-66 (M1), EBV-BMLF1280-288 (BM), and EBV-BRLF109-117 (BR) co-evolve as individuals age. Cross-sectional studies showed that IAV-M1- and both EBV-specific repertoires narrowed their TRBV usage with increasing age manifesting to different degrees for each epitope. In fact, narrowing of EBV-BM and EBV-BR-specific TRBV family usage correlated with increasing age. IAV-M1-specific TRBV usage was significantly narrowed by middle-age. There was evidence that TRBV usage was changing with increasing age. For instance, IAV-M1-specific dominant BV19 usage appeared to become bimodal showing either high or low frequency of usage in the older age group, while BV30 usage frequency directly correlated with age. For the EBV epitope-specific responses there was preferential usage of particular TRBV and changes in the hierarchy of BV family usage in the different age groups. There appeared to be focusing of the TRBV repertoire by all 3 epitopes to three common BV in the older donors, which would be consistent with retention of cross-reactive TCR suggesting co-evolution. Longitudinal studies tracking two donors over 14-15 years (middle age to older) showed that there were continuous modulations in the TCR repertoire of IAV-M1, EBV-BM and EBV-BR-specific responses over time. There was evidence that acute IAV infection could contribute to these changes in TCR repertoire. This could be occurring by the TCR cross-reactivity that is known to exist between these 3 epitopes, and which appeared to be enhanced during acute IAV infection based on increased usage of common shared TRBV. These studies suggest that virus-specific TCR repertoires change over time as individuals age leading to narrowing of the repertoire favoring retention of potentially cross-reactive TCR.

Cross-reactivity influences changes in human influenza A virus and Epstein Barr virus specific CD8 memory T cell receptor alpha and beta repertoires between young and old

“…Interestingly, for IAV-M1 responses, TRBV19 was highly dominant in both groups as has been previously reported for older and middle aged donors (6,37,38). These changes in TRBV usage, particularly in the EBV-specific responses are consistent with our ex vivo findings (36) and are highly suggestive that TRBV repertoire does evolve and change with increasing age.…”

“…We have previously determined the CD8 memory T cell frequencies and TRBV repertoires by mAb staining to IAV-M1, EBV-BM and EBV-BR epitope-specific responses ex vivo in these same individuals in a cross-sectional study (36). Here, we will examine in more detail the differences in both TRBV and TRAV usage in these two age groups by high throughput sequencing and single cell sequencing of tetramer positive cells.…”

“…Thus, we would predict that being infected with two viruses at the same time would greatly enhance selection of CD8 T cells that are cross-reactive during acute IAV infection. We have evidence that not only IAV-M1, but also EBV-BM and EBV-BR tetramer frequencies increase during acute asymptomatic IAV with changes in their TCR repertoire (36). Here, we dissected IAV-M1, EBV-BM and EBV-BR TCRab repertoires in the two age groups, young and older donors, all persistently infected with EBV and previously exposed to IAV.…”