Creating a bovine C-type lectin receptor atlas and identification of their ligands

Lead Research Organisation: Royal Veterinary College
Department Name: Pathology and Pathogen Biology

Abstract

The innate immune system is the first line of defence against invading pathogens. Cells of the innate immune system, such as macrophages and dendritic cells express a variety of receptors that bind to sugar (glycan) targets. These receptors, known as lectins, perform a dual function: under non-infectious conditions, they support the normal function of the immune system through enhancing the interaction of macrophages/dendritic cells with T cells. Under infectious conditions, they aide the recognition of pathogens that express specific glycan motifs in case of an infection. Distinguishing host cells from pathogens by these receptors derives from their ability to bind pathogen-specific surface sugars.
Recently, the idea of using glycan structures as vaccine adjuvants/vaccine delivery systems to target specific innate immune cell subsets through the sugar-binding receptors has been explored. Using this approach robust humoral and cellular immune responses have been induced in mice. Thus, in addition to providing an understanding of innate immune cell - T cell interaction in farm animals in more detail, the proposed work will provide a basis for exploiting adjuvant-like properties of glycans themselves resulting from their ability to activate both inflammatory and phagocytic receptors expressed on antigen-presenting cells. Our preliminary data demonstrate that there are substantial differences between the glycan-receptors expressed in different mammalian species, and the ligands that they recognise. This observation has important implications for vaccine design for farm animals, specifically ruminants as studied here, as it means that vaccine adjuvants designed and tested in the human and/or murine system may not work in other mammalian species, a fact supported by the recent failure of mycobacterial vaccines in the appropriate host. Thus, identifying the glycan (lectin) receptors in the bovine genome and understanding their function may provide new avenues to understand the first steps in host pathogen interaction. As the key way of reducing antibiotic dependence, and thus the reduction of AMR is to improve current vaccine strategies, the gained knowledge may also provide the basis for the development of more host-specific adjuvant/vaccine-delivery systems.

Technical Summary

In the work proposed here, we will identify genes encoding C-type lectin receptors (CLRs) within the bovine genome and characterise the ligand-binding spectrum of selected CLRs. This knowledge will be subsequently used to investigate the functions of the selected CLRs in normal immune system homoeostasis as well as to assess their roles in binding and uptake of specific (and sometimes zoonotic) pathogens. We will build on preliminary studies performed in the laboratories of the two Principal Investigators to validate differences in ligand-binding of bovine CLRs compared to their human/murine counterparts, and to assess the immune response of antigen-presenting cell subsets to antigens delivered by CLR ligands. The test systems developed within this proposal will use state-of-the art lectin arrays to identify the ligand-binding spectrum of bovine CLRs. Given the existing knowledge of human CRL binding to specific pathogens, we will subsequently assess the importance of identified CLRs in the binding/uptake of Mycobacterium bovis, Listeria monocytogenes and bovine viral diarrhoea virus. All of these diseases are endemic in UK livestock and pose major animal/public health concerns with significant impacts on food security, food safety and economic productivity. We will investigate which pathogens are recognised and which glycans mediate the recognition by bovine CLRs, to identify new intervention strategies. Major outputs will include an on-line atlas of CLRs encoded in the bovine genome including, where possible, annotation of their specific chromosomal locations; documentation of the ligand-binding spectrum of these CLRs using glycan arrays; and demonstration of the functions of the CLRs in normal antigen-presenting cell - T cell interactions. A further key outcome will be an assessment of the importance of specific CLRs in the binding and uptake of (zoonotic) pathogens, with the ultimate aim of bridging the gap between tool development and practical use.

Planned Impact

This research contributes to the BBSRC strategic plan Strategic Research Priority 1 - Agriculture and Food Security, specifically under the aspects of Animal Health and Welfare and Development of Next Generation Vaccines. It will underpin long term commercial aims for improved therapeutic and preventative methods to reduce infectious disease in cattle by identifying new ways to deal with increased AMR. Through comparing the function of CLR in rodents, human and ruminants, this project will also fall under the priority of functional and comparative genomics. Outcomes will assist in increasing UK competitiveness in the global animal production market, improving animal welfare and helping to guarantee a secure supply of safe, healthy food. The following stakeholders will benefit from this work.
1. The cattle industry
Cattle production and welfare benefit from many vaccines with various efficacies. Identification of new vaccine targets/vaccine adjuvants based on sugar-motifs recognised by appropriate receptors can potentially revolutionise how infectious diseases are treated, thus increasing production, improving economic performance, welfare and life-span of animals. Our close relationships with industry representatives can fast track the results into field use. Findings will be relevant to vaccines targeting other pathogens in cattle, as well as pigs and chicken.
2. The animal health industry
Whereas carbohydrate-based vaccines are already used in human medicine (S. pneunomiae, N. meningitides, H. influenza), their development is still in its infancy in veterinary medicine, due to lack of understanding of presence and functionality of these receptors in farm animals. Being able to develop such carbohydrate-based vaccine would potentially provide means of replacing anti-microbial therapies for bacterial infections, for which there are constantly increasing risks of resistance development, such as Mycobacteria spp., E. coli, Salmonella spp, and Staphylococci. These diseases do not only provide potential zoonotic problems, but are also considered to be the main agents for some of the most economically important diseases for the cattle industry in the UK, causing mastitis and bTB.
3. Animal welfare
The expectation today is that all farm livestock should have "a life worth living - from their point of view" (Farm Animal Welfare Council, 2009). Welfare would benefit if health status is improved. This proposal may provide the basis for development of carbohydrate-based vaccines in ruminants and, if successful, encourage farmers to potentially change their approach in treating specific infectious diseases, reducing their reliance on antimicrobial drug therapy.
4. General public and the environment
Increased efficiency in cattle production will raise cattle product availability at a lower cost for the consumer, contributing to improved food security. Consequences of improved pathogen control include a reduction in the requirement for chemoprophylaxis/anti-microbial treatment, reducing drug consumption, the risk of contamination to the food chain and the environment, and selection for drug resistance. All investigators are actively engaged in public dissemination of UK research. Students at all levels of education can benefit from the principles established in this work.
5. Skills, knowledge and training
The multidisciplinary nature of this project will provide opportunities for broad training to all staff, in addition to other members and students of each host institution, strengthening the research community in the areas of disease control and vaccine development. Broader impact can be achieved using avenues such as the UK Veterinary Vaccines Network.
6. International development
Infectious diseases impose serious costs on animal production in developing counties. Translating high quality, innovative, strategic research within UK universities into cheap, efficacious vaccines can improve economic income and alleviate poverty.
 
Description Bovine orthologues to human and mouse CLR genes were identified in a new, as yet unpublished, bovine genome (ARS-UCDv0.1) using the Basic Local Alignment Search Tool
(BLAST). The bovine genome was found to contain orthologues of most human and mouse CLR genes. As in humans and mice, bovine CLR genes were found to cluster in regions
on a small number of chromosomes, however the distribution of the genes on the chromosomes varies between the different species. The
majority of bovine genes appear to occur as a single copy, unlike some mouse genes (e.g. CLEC4A) where multiple paralogues exist.
Exploitation Route Identification of bovine pathogen specific recognition by bovine CLRs may help develop new vaccines
Sectors Pharmaceuticals and Medical Biotechnology

 
Description Commercialisation of produced antibodies is in signing stage
First Year Of Impact 2023
Sector Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description IDENTIFICATION OF CARBOHYDRATE STRUCTURES EXPRESSED BY MYCOPLASMA HYOPNEUNOMIAE AND M.HYORHINIS AS POTENTIAL VACCINE ANTIGENS
Amount € 80,000 (EUR)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2020 
End 09/2024
 
Description Investigation of the Theileria parva sporozoite surface glycan repertoire and binding C-type lectin receptors
Amount £80,000 (GBP)
Organisation GALVmed 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2019 
End 09/2022
 
Title Bovine CTLR specific antibodies 
Description As a result of the absence of cross-reactive antibodies, we generated 5 bovine specific CTLR antibodies 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? Yes  
Impact none as yet 
 
Title Brown Swiss Genome 
Description Brown Swiss Genome Assembly and QC Four lanes of 10x Genomics data were generated using an Illumina HiSeq. This provided ~1200 million reads with a 150bp read length. The data was assembled de novo using the 10x Genomics assembly tool Supernova v2.0.1, using the option to output a phased genome, which generates two homologous assemblies where each scaffold in the assembly has one of the paternal or maternal haplotypes (48). Using one of the haplotypes, we used RepeatMasker, using 'bovidae' as the repeat library to soft-mask repeat regions in the assembly. We tested the assembly for completeness using several quality control metrics. First, BUSCO (v5.0.0) was used to identify the number of mammalian single-copy orthologs present in the genome (using the database mammalia_odb10) . Using the Kmer Analysis Toolkit, we examined the content and distribution of kmers in the assembly to that of the reads using the tool 'kat comp', ignoring the first 16 bases of each R1 read in order to omit 10x barcodes from the analyses. We then visualised the distribution of kmers using the tool 'kat plot'. 
Type Of Material Biological samples 
Year Produced 2021 
Provided To Others? Yes  
Impact Brown Swiss Genome Annotation and Gene Expansion The LiftOff tool was used to lift over the B. taurus genome annotation (ARS-UCD1.2.103) to that of the Brown Swiss, noting any genes that were unmapped in Brown Swiss. We then identified genes in the Brown Swiss genome annotation that were present in multiple copies (compared to B. taurus ARS-UCD1.2.103) and downloaded the functional information for these genes using ENSEMBL BioMart database. For genes annotated as being duplicated three or more times and where a gene name or description was missing, we downloaded the coding sequence for that gene and used megablast to search the NCBI nr database and noted the highest scoring hit (with 100% query coverage and an E-value equal to 0), that contained functional information about the gene (i.e., disregarding hits for clones, BACs, isolates, etc.). The Brown Swiss genome assembly, along with the associated raw read data are available from the European Nucleotide Archive under study accession PRJEB47135. 
 
Title Updated version of Animal LEctin Database currently in process 
Description Te database provides a summary of the known lectin families, and an overview of the subcellular location and ligand binding specificities and evolution of the different families. The links below provide more detailed information on the structure, sugar-binding activity, biological function and evolution of proteins in each of the lectin families as well as annotated sequence alignments. 
Type Of Material Database/Collection of data 
Year Produced 2014 
Provided To Others? Yes  
Impact Provides evidence of clear differences between ruminant, murine and human lectins, which are impacting on vaccine (adjuvant) design 
URL http://www.imperial.ac.uk/research/animallectins/default.html
 
Description C-type lectins in farm animals 
Organisation U.S. Department of Agriculture USDA
Department Beltsville Agricultural Research Center
Country United States 
Sector Academic/University 
PI Contribution Allowed us to identify other CTLRs in porcine, avian and fisg genomes
Collaborator Contribution Enhanced genetic analysis by granting access to genomes
Impact Multi-disciplinary research, manuscript in preparation
Start Year 2021
 
Description Conference Poster 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Presented poster at British Society for Immunology Annual Conference in Brighton, 4-7 Dec 2017
Year(s) Of Engagement Activity 2017
 
Description Poster presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact 6th European Veterinary Immunology Workshop, Utrecht, The Netherlands, September 5-7, 2018
Year(s) Of Engagement Activity 2018