Single-cell immune repertoire sequencing of B and T cells in murine models of infection and autoimmunity
Danielle Shlesinger, Kai‐Lin Hong, Ghazal Shammas, Nicolas Pagé, Ioana Sandu, Andreas Agrafiotis, Victor Kreiner, Nicolas Fonta, Ilena Vincenti, Ingrid Wagner, Margot Piccinno, Alexandre Mariotte, Bogna Klimek, Raphael Dizerens, Marcos Manero-Carranza, Raphael Kuhn, Roy A. Ehling, Lester Frei, Keywan Khodaverdi, Camilla Panetti, Nicole Joller, Annette Oxenius, Doron Merkler, Sai T. Reddy, Alexander Yermanos
Abstract
Adaptive immune repertoires are composed by the ensemble of B and T-cell receptors within an individual, reflecting 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. 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. 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. Together, this dataset provides a resource for immunologists that can be integrated with future single-cell immune repertoire and transcriptome sequencing datasets.