Single-cell immune repertoire sequencing of B and T cells in murine models of infection and autoimmunity

Abstract

Adaptive immune repertoires are composed by the ensemble of B and T cell receptors (BCR, TCR) within an individual and reflect both past and current immune responses. Recent advances in single-cell sequencing enable recovery of the complete adaptive immune receptor sequences in addition to transcriptional information. Such high-dimensional datasets enable the molecular quantification of clonal selection of B and T cells across a wide variety of conditions such as infection and disease. Due to costs, time required for the analysis and current practices of academic publishing, small-scale sequencing studies are often not made publicly available, despite having informative potential to elucidate immunological principles and guide future-studies. Here, we performed single-cell sequencing of B and T cells to profile clonal selection across murine models of viral infection and autoimmune disease. Specifically, we recovered transcriptome and immune repertoire information for polyclonal T follicular helper cells following acute and chronic viral infection, CD8+ T cells with binding specificity restricted to two distinct peptides of lymphocytic choriomeningitis virus, and B and T cells isolated from the nervous system in the context of experimental autoimmune encephalomyelitis. We could relate repertoire features such as clonal expansion, germline gene usage, and clonal convergence to cell phenotypes spanning activation, memory, naive, antibody secretion, T cell inflation, and regulation. Together, this dataset provides a resource for experimental and computational immunologists that can be integrated with future single-cell immune repertoire and transcriptome sequencing datasets.

Persistent virus-specific and clonally expanded antibody secreting cells respond to induced self antigen in the CNS

“…Of note this subset of murine ASCs was entirely absent in the CNS of naive mice and in the widely used MOG 35-55 -and rMOG 1-125 -induced EAE mouse models (Yermanos, Neumeier, et al 2021;Shlesinger et al 2022). While minor clonal expansion of B cells was present in both naive and EAE conditions, the recovered B cells demonstrated either naive or memory B cell phenotypes and entirely lacked ASC gene signatures, class-switching, contemporary clonal variants, and expression of cell cycle and proliferation genes in contrast to MS patients as found in this study.…”

ePlatypus: an ecosystem for computational analysis of immunogenomics data

“…To demonstrate several use cases of the ePlatypus computational ecosystem, we integrated and analyzed multiple single-cell transcriptomes and immune receptor repertoires across different disease conditions, viral infections, and vaccination studies. We directly downloaded murine T cell repertoires from previously published datasets containing both CD4 and CD8 T cells from conditions such as acute and chronic viral infections (Khatun et al, 2021;Kuhn et al, 2022;Merkenschlager et al, 2021;Shlesinger et al, 2022), homeostatic aging and experimental autoimmune encephalomyelitis (Shlesinger et al, 2022) (Table S2). Following transcriptional integration with Harmony (Korsunsky et al, 2019), which aims to reduce batch effects across different datasets, we visualized all cells using uniform manifold approximation projection (UMAP) (Figure S11A,S11B).…”

“…Next, we used ePlatypus to investigate whether similar transcriptional heterogeneity could be detected for B cells present in the PlatypusDB. Multiple datasets derived from murine models of infection, immunization and autoimmune disease (Agrafiotis et al, 2021;Mathew et al, 2021b;Neumeier et al, 2021;Shlesinger et al, 2022;Yewdell et al, 2021) were integrated as previously described (Table S2). Transcriptional clustering suggested that common B cell clusters were present across multiple datasets (Figure S14A), which exhibited varying expression levels of markers relating to antibody secretion and B cell differentiation (e.g.…”