Single-Cell Antigen Receptor Sequencing in Pigs with Influenza

ABSTRACT: Understanding the pulmonary adaptive immune system of pigs is of importance as respiratory pathogens present a major challenge for swine producers and pigs are increasingly used to model human pulmonary diseases. Single-cell RNA sequencing (scRNAseq) has accelerated the characterization of cellular phenotypes in the pig respiratory tract under both healthy and diseased conditions. However, combining scRNAseq with recovery of paired VJ and VDJ T cell receptor (TCR) as well as heavy (IGH) and light (IGL) chains of B cell receptors (BCR) to interrogate receptor repertoires has not to our knowledge been demonstrated for pigs. Here, we developed primers to enrich porcine TCR and BCR chains that are compatible with the 10x Genomics VDJ sequencing protocol. Using these pig-specific assays, we sequenced the T and B cell receptors of cryopreserved lung cells from CD1D-expressing and -deficient pigs after one or two infections with influenza A virus (IAV), a major swine and human respiratory pathogen, to examine whether natural killer T (NKT) cells alter pulmonary TCR and BCR repertoire selection. We also performed paired single-cell RNA and TCR sequencing of FACS-sorted T cells longitudinally sampled from the lungs of IAV-vaccinated and -infected pigs to track clonal expansion in response to IAV exposure. All pigs presented highly diverse repertoires. Pigs re-exposed to influenza antigens from either vaccination or infection exhibited higher numbers of expanded CD4 and CD8 T cell clonotypes with activated phenotypes, suggesting potential IAV reactive T cell populations. Our results demonstrate the utility of high throughput single-cell TCR and BCR sequencing in pigs.

ORGANISM(S): Sus scrofa

PROVIDER: GSE277475 | GEO | 2024/12/05

REPOSITORIES: GEO