Profiling virus-specific Tcf1+ T cell repertoires during acute and chronic viral infection

Abstract

CD8 T cells play a crucial role in providing protection from viral infections. It has recently been established that a subset of CD8 T cells expressing Tcf1 are responsible for sustaining exhausted T cells during chronic lymphocytic choriomeningitis virus (LCMV) infection. Many of these studies, however, have been performed using T cell receptor (TCR) transgenic mice, in which CD8 T cells express a monoclonal TCR specific for the LCMV glycoprotein. To investigate whether the Tcf1+ and Tcf1-repertoires are naturally composed of similar or different clones in wild-type mice exposed to acute or chronic LCMV infection, we performed TCR repertoire sequencing of virus-specific CD8 T cells, including Tcf1+ and Tcf1populations. Our analysis revealed that the Tcf1+ TCR repertoire is maintained at an equal or higher degree of clonal diversity despite harboring fewer cells. Additionally, within the same animal, there was extensive clonal overlap between the Tcf1+ and Tcf1-repertoires in both chronic and acute LCMV infection. We could further detect these virus-specific clones in longitudinal blood samples earlier in the infection. With respect to common repertoire parameters (clonal overlap, germline gene usage, and clonal expansion), we found minor differences between the virus-specific TCR repertoire of acute and chronic LCMV infection 40 days post infection. Overall, our results indicate that the Tcf1+ population emerging during chronic LCMV infection is not clonally distinct from the Tcf1-population, supporting the notion that the Tcf1+ pool is indeed a fuel for the more exhausted Tcf1-population within the heterogenous repertoire of LCMV-specific CD8 T cells.Yermanos et al.

Clonally expanded virus-specific CD8 T cells acquire diverse transcriptional phenotypes during acute, chronic, and latent infections

“…In contrast to our previous findings (Yermanos, Sandu, et al 2020; Welten et al 2020), the virus-specific CD8+ TCR repertoires were extremely personalized, with minor clonal overlap between mice. This was true for both expanded and unexpanded clones, suggesting a stochasticity underlying the selection and expansion of virus-specific clones.…”

“…The number of unique clones reported by both studies were comparable to the number of GP33-specific CD8+ T cells found in naive CD8+ T cells of uninfected C57BL/6 mice (Malhotra et al 2020; Obar, Khanna, and Lefrançois 2008; Kotturi et al 2008). Importantly, both TRB studies demonstrated high clonal overlap between the TCF1+ and TCF1-CD8+ T cell repertoires (Yermanos, Sandu, et al 2020; Chang et al 2020), which together supports a previously proposed model in which TCF1+ CD8+ T cells feed into the TCF1-CD8+ T cell subset (Utzschneider et al 2016; Siddiqui et al 2019). Similarly, a high degree of clonal overlap between the TCF1+ and TCF1-repertoires was observed in the context of inflationary T cells following MCMV infection (Welten et al 2020).…”

“…After observing the low degree of sequence similarity across all mice, we determined if stereotypical patterns of germline gene usage could be observed in any of the infection conditions, as previous repertoire sequencing experiments investigating virus-specific T cells in the context of LCMV or MCMV infection have demonstrated preferential germline use (Welten et al 2020; Yermanos, Sandu, et al 2020). Leveraging the ability of our single-cell immune repertoire profiling, we could investigate the variable (V) gene usage for both TRB and TRA chains, in addition to quantifying how often certain pairings occured.…”

“…Previous experiments characterizing the endogenous GP33-specific TCR repertoire in the context of LCMV infection have demonstrated varying degrees of polyclonality (Yermanos, Sandu, et al 2020; Chang et al 2020). Leveraging TRB repertoire sequencing, both studies recovered multiple distinct clones, ranging from 40 to hundreds of unique GP33-specific CD8+ T cell clones following chronic and acute LCMV infection.…”

“…While recent studies have leveraged bulk sequencing of the TCR beta (TRB) chain during acute, chronic, and latent murine infections (Welten et al 2020; Yermanos, Sandu, et al 2020; Chang et al 2020), these methodologies are inherently limited by the inability to accurately access clonal expansion and further relate transcriptional profiles to those expanded TRB clones. Recent advances in single-cell immune repertoire sequencing can link the complete TCR beta and alpha sequence (VDJ) to gene expression (GEX) at the single-cell resolution (Yermanos, Neumeier, et al 2021; Yermanos, Agrafiotis, et al 2021; Horns, Dekker, and Quake 2020).…”