CMV and natural killer cells: shaping the response to vaccination.

Cytomegaloviruses (CMVs) are highly prevalent, persistent human pathogens that not only evade but also shape our immune responses. Natural killer (NK) cells play an important role in the control of CMV and CMVs have in turn developed a plethora of immunoevasion mechanisms targeting NK cells. This complex interplay can leave a long-lasting imprint on the immune system in general and affect responses toward other pathogens and vaccines. This review aims to provide an overview of NK cell biology and development, the manipulation of NK cells by CMVs and the potential impact of these evasion strategies on responses to vaccination

Determination of the genetic mechanisms responsible for generating diversity in the cattle NK cell receptor repertoire

Cattle have expanded the KIR gene repertoire, a polymorphic and polygenic im- munoglobulin family that encode Natural Killer cell receptors specific to MHC class I ligands. In humans, KIR are important mediators of innate immunity to viral pathogens such as HCV and HIV, and there is potential for exploiting cattle KIR diversity as a means of improving animal health. Cattle KIR expansion has occurred independently to humans, the result is a cattle KIR haplotype (CKH) with a completely different gene content. Successful sequencing and assembly of the CKH using whole genome techniques has failed. To interrogate cattle KIR, their function and comparative evolution, the content of a CKH must be estab- lished, then the extent of polymorphism and gene presence/absence variation can be studied. In this project the first CKH has been sequenced and assembled using second generation sequencing of BAC clones. This has provided a reference sequence for whole genome sequence data to be aligned revealing the KIR content of different Bovidae species, including the aurochs, the ancestor to all domesticated cattle. Furthermore genome capture and enrichment was performed to determine polymorphic and polygenic KIR variation within 24 different cattle genomes. The sheep KIR haplotype (SKH) was sequenced using PacBio of BAC clones to enable comparative analysis with cattle. The CKH has expanded through block duplications resulting in 16 discrete KIR loci. The haplotype is dominated by functional inhibitory receptor genes and the attenuated remains of activating KIR. Predicted similarity between au- rochs and modern CKH suggests KIR blocks expanded through natural selection and not artificial selection generated through centuries of domestication. Com- parative analysis of the SKH and CKH reveals that sheep have independently expanded at least five of the shared KIR that cattle have expanded. Cattle KIR are extremely polymorphic, with diversity focused within the Ig domains, regions predicted to interact with ligand.Open Acces

Understanding the evolution of immune genes in jawed vertebrates

Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into—and generate evolutionary hypotheses on—the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.Biotechnology and Biological Sciences Research CouncilGrant/Award Number: BB/K004468/1, BB/M011224/1, BB/ N023803/1 and BB/V000756/1Department for Environment, Food and Rural AffairsUK Government, Grant/ Award Number: OD0221Deutsche Forschungsgemeinschaft, Grant/ Award Number: 437857095Grantová Agentura České Republiky, Grant/Award Number: 19-20152YGrantová Agentura, Univerzita Karlova, Grant/Award Number: 646119H2020 European Research Council, Grant/Award Number: ERC-2019- StG- 853272- PALAEOFARMUniversity of Oxford, Grant/Award Number: 0005172; Ministerstvo Školství, Mládeže a TělovýchovyGrant/Award Number: SVV 260684/2023; Ministerstvo Zemědělství, Grant/Award Number: MZE-RO0723National Institutes of Health, Grant/Award Number: 1R01AI123659-01A1; Univerzita Karlova v PrazeGrant/Award Number: START/SCI/113 with reg. no. CZ.02.2.69/0.0/0.0/19_; Vetenskapsrådet, Grant/Award Number: 2020-0428

Understanding the evolution of immune genes in jawed vertebrates

Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations

Studies of Immunogenetic Variation in Cattle

Genetic selection for animal health and disease resistance has been limited, likely due to the challenges of performing controlled studies with an industry relevant phenotype. Studies in large populations of animals of unknown relationship pose challenges for genome wide association studies of disease resistance. The aims of this project were to characterize variation in the bovine major histocompatibility complex (BoLA), a specific region of the bovine genome known be critical for development of immune response, and then investigate individual variation in host immunity to a specific viral pathogen of cattle, bovine viral diarrhea virus (BVDV). Cattle “homozygous” for BoLA were identified from approximately 2,000 head of Holstein calves in large genome wide association studies. Cattle were genotyped on the Illumina BovineHD SNP chip and PHASED for the characterization of BoLA haplotypes. Among 160 “homozygous” animals, we identified 38 different haplotype groups. The 38 haplotype groups maintained the structure predicted by earlier studies that identified 50K SNP haplotypes, but demonstrated that more diversity is present among these 38 BoLA haplotype groups than was indicated by the 50K haplotypes. Among the 1,221 SNPs genotyped on the HD chip were 230 SNPs with no calls in at least one of the 160 homozygous animals. The no call SNPs are located predominately in regions predicted to contain copy number variation, and no call SNPs appear to likely mark regions of polymorphic structural variation otherwise undetected in the SNP defined haplotypes. This structural variation may be important for future genome association studies. Cattle diseases are often difficult to diagnose due to presentation with different disease phenotypes, ranging from subclinical to lethal. Likewise, immune response to vaccination is also variable and may be related to individual differences in disease susceptibilities. To evaluate individualized response to BVDV vaccination, we evaluated protection afforded by commercial vaccines against a BVDV challenge. The results from the BVDV challenge study indicate that measuring antibody titer as a response to BVDV vaccination may not be predictive of a protective immune response. Rectal temperature alone for health classification missed up to 50% of animals with subclinical disease. Variation in host immunity appears to underlie the response to pathogens and likely to vaccination as well. Host differences in immunity between Bos indicus and Bos taurus cattle were evaluated subsequent to BVDV vaccination. Differences in baseline immune cell counts were observed. Indicine cattle had higher white blood cell counts primarily influenced by the 2-fold higher neutrophil levels. Response to vaccination was primarily observed as an innate immune response with an increase in neutrophils. The largest change was in neutrophil response observed in the taurine calves. Immunosuppression from the modified live vaccination was greater in the indicine calves compared to taurine calves. However, a combination of vaccination protocols appear to mitigate the immunosuppression observed in the indicine cattle

Determinants of long-lived memory B cells for antiviral immunity

The protection offered by B cell responses after viral infection or vaccination features neutralising antibodies produced by plasmablasts and memory B cells (MBCs) which can provide long lasting immunity against reinfection. Hence understanding the factors associated with MBC persistence is crucial for vaccine design. Murine and human studies have implicated initial antigen affinity, bystander activation, activation-induced cytidine deaminase (AID) expression, and chemokine levels as being associated with persistence of antigen-specific MBCs, but detailed understanding of the genesis of long-lived MBCs in humans is lacking. During the initial phase of COVID-19 pandemic there were multiple studies characterising natural immune responses against SARS-CoV-2 infection, but then the interest shifted towards understanding vaccine-induced immunity. With the spread of variants of concern and breakthrough infections in vaccinees, understanding the longevity of natural immunity is essential to design improved vaccines. The primary objective of this thesis was to develop a highly specific tetramer for flow cytometry-based isolation of SARS-CoV-2 specific MBCs, evaluate their longevity, and identify biomarkers and transcriptomic signatures present early after infection that associate with durable MBCs. The samples used in this thesis were selected from the COVID-19 Outbreak Samples in NSW (COSIN) cohort, an ongoing prospective cohort evaluating the natural history of the SARS-CoV-2 infection in NSW. This thesis observed that at one year post infection, despite declining antibody titers, maintenance of neutralisation breadth and a variant specific protection (45% - 76%) against symptomatic disease. Encouragingly 80% of participants who had SARS-CoV-2 specific MBCs during early convalescence had detectable MBCs at one year. Based on MBC persistence, the cohort was divided into two groups – “Maintained” and “Dropped”. Early antigen specific CD4+ T cell responses was associated with maintenance of antibody neutralisation breadth and MBC durability. Smart-seq2 analysis of the MBCs identified ongoing maturation of the B cell receptor in both grand transcriptomic differences between the two groups. The transcriptomic analysis revealed that an enhanced activation profile of mature, proliferating MBCs was associated with persistence at one year. These findings provide initial identification of biomarkers that can be used to predict the durability of vaccine induced immunity

Virus Encoded MHC-Like Decoys Diversify the Inhibitory KIR Repertoire

<div><p>Natural killer (NK) cells are circulating lymphocytes that play an important role in the control of viral infections and tumors. Their functions are regulated by several activating and inhibitory receptors. A subset of these receptors in human NK cells are the killer immunoglobulin-like receptors (KIRs), which interact with the highly polymorphic MHC class I molecules. One important function of NK cells is to detect cells that have down-regulated MHC expression (missing-self). Because MHC molecules have non polymorphic regions, their expression could have been monitored with a limited set of monomorphic receptors. Surprisingly, the KIR family has a remarkable genetic diversity, the function of which remains poorly understood. The mouse cytomegalovirus (MCMV) is able to evade NK cell responses by coding “decoy” molecules that mimic MHC class I. This interaction was suggested to have driven the evolution of novel NK cell receptors. Inspired by the MCMV system, we develop an agent-based model of a host population infected with viruses that are able to evolve MHC down-regulation and decoy molecules. Our simulations show that specific recognition of MHC class I molecules by inhibitory KIRs provides excellent protection against viruses evolving decoys, and that the diversity of inhibitory KIRs will subsequently evolve as a result of the required discrimination between host MHC molecules and decoy molecules.</p></div