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Zuleger CL, Schwartz RW, Ong IM, Newton MA, Vail DM, Albertini MR. Development of a next-generation sequencing protocol for the canine T cell receptor beta chain repertoire. Vet Immunol Immunopathol 2024; 268:110702. [PMID: 38183837 PMCID: PMC10872364 DOI: 10.1016/j.vetimm.2023.110702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 01/08/2024]
Abstract
Profiling the T cell receptor (TCR) repertoire using next-generation sequencing has become common in both human and translational research. Companion dogs with spontaneous tumors, including canine melanoma, share several features, e.g., natural occurrence, shared environmental exposures, natural outbred population, and immunocompetence. T cells play an important role in the adaptive immune system by recognizing specific antigens via a surface TCR. As such, understanding the canine T cell response to vaccines, cancer, immunotherapies, and infectious diseases is critically important for both dog and human health. Off-the-shelf commercial reagents, kits and services are readily available for human, non-human primate, and mouse in this context. However, these resources are limited for the canine. In this study, we present a cost-effective protocol for analysis of canine TCR beta chain genes. Workflow can be accomplished in 1-2 days starting with total RNA and resulting in libraries ready for sequencing on Illumina platforms.
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Affiliation(s)
- Cindy L Zuleger
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Rene Welch Schwartz
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Irene M Ong
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States; Department of Obstetrics and Gynecology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Michael A Newton
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - David M Vail
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Mark R Albertini
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States; Department of Dermatology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States; The Medical Service, William S. Middleton Memorial Veterans Hospital, Madison, WI, United States.
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Sanz CR, Sevane N, Pérez-Alenza MD, Valero-Lorenzo M, Dunner S. Polymorphisms in canine immunoglobulin heavy chain gene cluster: a double-edged sword for diabetes mellitus in the dog. Anim Genet 2021; 52:333-341. [PMID: 33621396 DOI: 10.1111/age.13047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2021] [Indexed: 02/06/2023]
Abstract
Insulin deficiency diabetes (IDD) in dogs is an endocrine disease similar to human type 1 diabetes. There are breeds more commonly affected, such as Yorkshire Terrier and Samoyed, suggesting an underlying genetic component. However, the genetic basis for canine diabetes mellitus (DM) is not fully established. We conducted both whole-genome scans for selection signatures and GWASs to compare the genomes of 136 dogs belonging to 29 breeds previously described at low or high risk for developing DM. Candidate variants were tested in dogs with a diagnosis of IDD and controls attending the Complutense Veterinary Teaching Hospital. The only genomic region under selection (CFA8:72 700 000-74 600 000; CanFam3.1) retrieved by our analyses is included in the immunoglobulin heavy chain gene cluster, which has already been related to human human type 1 diabetes susceptibility. This region contains two non-synonymous variants, rs852072969 and rs851728071, showing significant associations with high or low risk for IDD, respectively. The first variant, rs852072969, alters a protein poorly characterised in the dog. In contrast, rs851728071 was predicted to block the synthesis of an immunoglobulin variable (V) domain in breeds at low risk for DM. Although a large and diverse V gene repertoire is thought to offer a fitness advantage, we suggest that rs851728071 prevents the formation of an auto-reactive immunoglobulin V domain probably involved in the pathophysiology of IDD and, thus, decreases the risk for the disease. These results should be interpreted with caution until the functional roles of the proposed variants have been proved in larger studies.
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Affiliation(s)
- C R Sanz
- Department of Animal Production, Veterinary Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - N Sevane
- Department of Animal Production, Veterinary Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - M D Pérez-Alenza
- Department of Animal Medicine, Surgery and Pathology, Veterinary Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - M Valero-Lorenzo
- Department of Animal Production, Veterinary Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - S Dunner
- Department of Animal Production, Veterinary Faculty, Complutense University of Madrid, Madrid, 28040, Spain
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Holder A, Mirczuk SM, Fowkes RC, Palmer DB, Aspinall R, Catchpole B. Perturbation of the T cell receptor repertoire occurs with increasing age in dogs. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 79:150-157. [PMID: 29103899 PMCID: PMC5711257 DOI: 10.1016/j.dci.2017.10.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/27/2017] [Accepted: 10/27/2017] [Indexed: 05/16/2023]
Abstract
Immunosenescence is the gradual deterioration in immune system function associated with ageing. This decline is partly due to involution of the thymus, which leads to a reduction in the output of naive T cells into the circulating lymphocyte pool. Expansion of existing naive and memory T cell populations, to compensate for the reduction in thymic output, can lead to reduced diversity in the T cell repertoire with increasing age, resulting in impairment of immune responses to novel antigenic challenges, such as during infection and vaccination. Since associations between T cell repertoire and age have only been examined in a limited number of species, to gain further insights into this relationship, we have investigated age-related changes in the canine T cell receptor (TCR) repertoire. Blood samples were obtained from Labrador retriever dogs of varying ages and variation in the complementary determining region 3 (CDR3) of the T cell receptor beta (TCRB) chain was investigated. CDR3 size spectratyping was employed to evaluate clonal expansion/deletion in the T cell repertoire, allowing identification of profiles within individual variable (V) region families that skewed away from a Gaussian distribution. Older dogs (10-13 years) were found to have an increased number of TCRB V gene spectratypes that demonstrated a skewed distribution, compared with young dogs (≤3 years). Additionally, there was a reduction in the number of clonal peaks present in the spectratypes of old dogs, compared with those of young dogs. The study findings suggest that there is an age-associated disturbance in the diversity of the T cell receptor repertoire in dogs.
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Affiliation(s)
- Angela Holder
- Department of Pathobiology and Population Sciences, Royal Veterinary College, North Mymms, Hertfordshire, UK
| | - Samantha M Mirczuk
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, UK
| | - Robert C Fowkes
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, UK
| | - Donald B Palmer
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, UK
| | - Richard Aspinall
- Health and Wellbeing Academy, Postgraduate Medical Institute, Anglia Ruskin University, Chelmsford, Essex, UK
| | - Brian Catchpole
- Department of Pathobiology and Population Sciences, Royal Veterinary College, North Mymms, Hertfordshire, UK.
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Martin J, Ponstingl H, Lefranc MP, Archer J, Sargan D, Bradley A. Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci. Immunogenetics 2017; 70:223-236. [PMID: 28924718 PMCID: PMC5871656 DOI: 10.1007/s00251-017-1028-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/12/2017] [Indexed: 12/11/2022]
Abstract
Dogs are an excellent model for human disease. For example, the treatment of canine lymphoma has been predictive of the human response to that treatment. However, an incomplete picture of canine (Canis lupus familiaris) immunoglobulin (IG) and T cell receptor (TR)-or antigen receptor (AR)-gene loci has restricted their utility. This work advances the annotation of the canine AR loci and looks into breed-specific features of the loci. Bioinformatic analysis of unbiased RNA sequence data was used to complete the annotation of the canine AR genes. This annotation was used to query 107 whole genome sequences from 19 breeds and identified over 5500 alleles across the 550 genes of the seven AR loci: the IG heavy, kappa, and lambda loci; and the TR alpha, beta, gamma, and delta loci. Of note was the discovery that half of the IGK variable (V) genes were located downstream of, and inverted with respect to, the rest of the locus. Analysis of the germline sequences of all the AR V genes identified greater conservation between dog and human than mouse with either. This work brings our understanding of the genetic diversity and expression of AR in dogs to the same completeness as that of mice and men, making it the third species to have all AR loci comprehensively and accurately annotated. The large number of germline sequences serves as a reference for future studies, and has allowed statistically powerful conclusions to be drawn on the pressures that have shaped these loci.
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Affiliation(s)
- Jolyon Martin
- Wellcome Trust Sanger Institute, Hinxton, UK.
- University of Cambridge, Cambridge, UK.
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