Single-cell immune repertoire and transcriptome sequencing reveals that clonally expanded and transcriptionally distinct lymphocytes populate the aged central nervous system in mice

Abstract

Neuroinflammation plays a crucial role during ageing and various neurological conditions, including Alzheimer's disease, multiple sclerosis and infection. Technical limitations, however, have prevented an integrative analysis of how lymphocyte immune receptor repertoires and their accompanying transcriptional states change with age in the central nervous system. Here, we leveraged single-cell sequencing to simultaneously profile B cell receptor and T cell receptor repertoires and accompanying gene expression profiles in young and old mouse brains. We observed the presence of clonally expanded B and T cells in the central nervous system of aged male mice. Furthermore, many of these B cells were of the IgM and IgD isotypes, and had low levels of somatic hypermutation. Integrating gene expression information additionally revealed distinct transcriptional profiles of these clonally expanded lymphocytes. Our findings implicate that clonally related T and B cells in the CNS of elderly mice may contribute to neuroinflammation accompanying homeostatic ageing.

Generation of a single-cell B cell atlas of antibody repertoires and transcriptomes to identify signatures associated with antigen-specificity

“…Surprisingly, we observed minor transcriptional differences between these two populations of cells when performing unsupervised clustering and differential gene expression analysis. Transcriptional differences were however observed in IgM-, IgA-and IgG-expressing B cells, which was consistent with previous results (Neumeier et al, 2021a), as well as expansion-specific transcriptional clustering (Kuhn et al, 2021;Yermanos et al, 2021a).…”

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

“…We lastly questioned whether including repertoires lacking specificity to GP33 could provide contrast for how similar the 6 repertoires were following acute, chronic, and latent infection. Including publicly available data from either naive PBMCs (10x genomics) or CNS-resident T cells (Yermanos, Neumeier, et al 2021) demonstrated clear separation between the repertoires of GP33-specific T cells and naive T cells (Figure 4C), further supporting the notion that the GP33-specific repertoire has stereotypic germline gene usage irrespective of the infection condition.…”

“…We next integrated TCR sequence with transcriptomes at single-cell resolution. It has been previously demonstrated that highly expanded clones upregulate effector molecules such as Nkg7 , Ccl5 , and granzymes (Yermanos, Agrafiotis, et al 2021; Yermanos, Neumeier, et al 2021). Therefore, we first focused our analysis on the 30 most expanded clones for each infection by quantifying the fraction of cells present in each transcriptional cluster (Figure 5A).…”

“…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). This technology has recently demonstrated dynamic clonal and transcriptional profiles for virus-specific CD4+ T cells in the context of acute LCMV infection (Khatun et al 2021), however, it remains unknown how previously described memory, effector, exhaustion, and inflationary phenotypes of virus-specific CD8+ T cells relate to antigen-driven clonal selection.…”

Echidna: integrated simulations of single-cell immune receptor repertoires and transcriptomes

“…The advent of singlecell sequencing (scSeq) has revolutionized the resolution at which clonal selection of immune repertoires can be quantified (Friedensohn et al, 2017). For example, scSeq workflows have been established that enable the simultaneous recovery of both full-length, paired BCR or TCR sequence (VDJ), and full transcriptome [gene expression (GEX)] information, thereby providing a crucial link between clonal selection and expansion with a high-dimensional transcriptional cell phenotype (Horns et al, 2020;Khatun et al, 2021;Yermanos, Neumeier, et al, 2021;Mathew et al, 2021;Lindeman et al, 2018;Stubbington et al, 2016). Interpreting such datasets, however, remains challenging as the accompanying computational pipelines and software are still in their infancy (Yermanos, Agrafiotis, et al, 2021b;Borcherding et al, 2020;Sturm et al, 2020).…”