Biology subjects

Driver, J. P.

Publications and source records attributed to Driver, J. P..

4 recordsLinked to original sources

bioRxiv2025

Pigs lacking Natural Killer T cells have altered cellular responses to influenza

It is increasingly recognized that innate T cells such as natural killer T (NKT) cells, mucosal associated invariant T (MAIT) cells, and {gamma}{delta} T cells play an important role in shaping adaptive immune responses following influenza infection or vaccination. This is largely through the multiple cytokines these cells release upon activation, which have downstream effects on the scope and magnitude of virus-specific T and B cells, and antibodies which form. Here, we examined the contribution of NKT cells using pigs, which are considered a highly translational model of human influenza A infection. CD1D-expressing and CD1D-deficient pigs that respectively possess and lack NKT cells were infected with the swine influenza virus H3N2 A/Swine/Colorado/23619/1999 (CO99), with or without prior mucosal immunization with a recombinant H3N2 A/Swine/Texas/4199-2/1998 (TX98) modified live vaccine encoding a truncated NS1 protein (TX98 NS1{Delta}126). Vaccination reduced virus load and pulmonary pathology by similar amounts in both genotypes. However, NKT cells status had a significant impact on the underlying immune response: Unlike following vaccination, virus-specific T cell expansion after infection was greater in CD1D-deficient than -intact pigs, indicating that NKT cells play opposing roles in different phases of the immune response. NKT cell-deficient pigs also had reduced T cells cuffing around airways and higher numbers of expanded T and B cell clones according to single-cell {beta} T cell receptor (TCR) and B cell receptor (BCR) sequencing. Using our newly developed porcine-specific {gamma} and {delta} chain primers, we characterized the pulmonary {gamma}{delta} TCR repertoire. This revealed a high frequency of expanded clones, especially within the CD2- subset, and a tendency for larger expansion in NKT cell-expressing pigs. Overall, our results indicate a homeostatic role for NKT cells on several important features of the influenza immune response, including the dynamics of T cell expansion and contraction.

immunology↗

bioRxiv2024

Single-Cell Antigen Receptor Sequencing in Pigs with Influenza

Understanding the pulmonary adaptive immune system of pigs is important 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 T cell receptor (TCR) and {beta} chains as well as B cell receptor (BCR) heavy and light chains to interrogate their repertoires has not to our knowledge been demonstrated for pigs. Here, we developed primers to enrich porcine TCR and {beta} chains along with BCR {kappa} and {lambda} light chains and IgM, IgA, and IgG heavy 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) to examine whether natural killer T (NKT) cells alter pulmonary TCR and BCR repertoire selection. We also performed paired single-cell RNA and receptor 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.

immunology↗

bioRxiv2024

A single-nucleus census of immune and non-immune cell types for the major immune organ systems of chicken.

In the avian host, comprehensively cataloging immune cell types, their transcriptome profiles, and varying molecular responses to pathogen challenges are necessary steps toward a better understanding of the interplay between genetics and disease resilience. We present a first nuclei atlas of immune cell types derived from the three main immune organs of layer chickens, including spleen, bursa, and thymus. In bursa we also present, an accounting of cell type activation with the bacterial toxin lipopolysaccharide (LPS). Our analysis includes 36,370 total nuclei and 16, 12, and 12 transcriptionally distinct clusters for spleen, bursa, and thymus, respectively. We discover nuclei molecular profiles that uniquely distinguish states of the transcriptome within cell type that could serve as new means to characterize avian immune subtypes. We further subcluster refined immune cell type classifications, specifically highlighting the transcriptomic diversity of B and T cell subtypes. In the bursa, inferred intercellular communication and signaling pathway enrichment analyses across immune and non-immune cell types demonstrate the unappreciated complexity of the B cell repertoire in a model mimicking systemic bacterial infection. This census of all cell types in both primary and one major secondary avian immune organ system, although preliminary, provides a first review of how nuclei transcribe numerous genes, known and unknown, a critical prerequisite for the study avian immunogenetics by cell type.

immunology↗

bioRxiv2024

Single cell sequencing of pig lungs reveals immune responses underlying influenza infection and oseltamivir therapy

Despite pigs being an important species in influenza A virus (IAV) epidemiology and a reliable model of human IAV infections, many aspects of the porcine pulmonary immune system remain poorly understood. Here, we characterized the single cell landscape of lung leukocytes of healthy pigs and then compared them to pigs infected with 2009 pandemic H1N1 IAV with or without oseltamivir antiviral therapy. Our data show conserved features as well as species-specific differences in cell types and cell states compared to human and mouse lung leukocytes. IAV infection induced a robust antiviral transcriptional response in multiple lymphoid and myeloid cell types, as well as distinct patterns of cell-cell cross talk. Oseltamivir treatment reduced these responses. Together our findings describe key events in the pulmonary anti-IAV response of pigs that open new avenues to develop IAV vaccines and therapies. They should also enable the better use of pigs as a model for human IAV infection and immunity.

immunology↗