Practical considerations such as the necessary cost and time required to generate and analyze each single-cell sequencing sample has been a limitation to performing large-scale experiments (i.e., with many samples). In recent years, a number of studies have employed single-cell immune repertoire sequencing to dissect the heterogeneity and differentiation of T and B cells in contexts such as infection, disease, and vaccination. This now enables investigation of how parameters such as clonal expansion relate to gene expression phenotypes, thereby providing novel insights not accessible by bulk sequencing (e.g., BCR variable heavy chain, TCR variable beta chain) methodologies. The development of standardized protocols, reagents and dedicated commercial platforms (e.g., 10x Genomics) has made it possible to perform single-cell immune repertoire sequencing that simultaneously recovers gene expression (whole transcriptome) and immune repertoire (full-length, paired chains of BCRs (heavy and light chains) and TCRs (alpha and beta chains)) information. While this selection and differentiation of lymphocytes is heavily regulated under healthy conditions, dysfunctional clonal selection can contribute to autoimmunity and host pathology. Following the resolution of immune challenges, and thereby the diminishing presence of cognate antigens, B and T cells contract and preferentially adopt heterogenous memory phenotypes characterized by expression of certain gene signatures. B cells expressing high-affinity BCRs are selected for by T follicular helper (Tfh) cells, which are characterized by their expression of CD4, PD-1, CXCR5, and BCL6, and provide the required selection signals for B cell differentiation. B cells further engage in germinal center (GC) reactions, where they undergo diversification through class-switch recombination and somatic hypermutation, hence increasing the range of effector functions and molecular recognition. Upon primary antigen exposure, B and T cells rapidly undergo clonal expansion and can adopt a diverse set of cellular phenotypes with corresponding effector functions. Together, this dataset provides a resource for immunologists that can be integrated with future single-cell immune repertoire and transcriptome sequencing datasets.ī and T cells play a central role in orchestrating the immune response by recognizing foreign antigens through their B cell receptor (BCR secreted version: antibodies) and T cell receptor (TCR), respectively. ![]() We could relate clonal expansion, germline gene usage, and clonal convergence to cell phenotypes spanning activation, memory, naive, antibody secretion, T-cell inflation, and regulation. Here, we recovered transcriptome and immune repertoire information for polyclonal T follicular helper cells following lymphocytic choriomeningitis virus (LCMV) infection, CD8+ T cells with binding specificity restricted to two distinct LCMV peptides, and B and T cells isolated from the nervous system in the context of experimental autoimmune encephalomyelitis. Recent advances in single-cell sequencing enable recovery of the complete adaptive immune receptor sequences in addition to transcriptional information. Adaptive immune repertoires are composed by the ensemble of B and T-cell receptors within an individual, reflecting both past and current immune responses.
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