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London CA, Gardner H, Zhao S, Knapp DW, Utturkar SM, Duval DL, Chambers MR, Ostrander E, Trent JM, Kuffel G. Leading the pack: Best practices in comparative canine cancer genomics to inform human oncology. Vet Comp Oncol 2023; 21:565-577. [PMID: 37778398 DOI: 10.1111/vco.12935] [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: 05/10/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 10/03/2023]
Abstract
Pet dogs develop spontaneous cancers at a rate estimated to be five times higher than that of humans, providing a unique opportunity to study disease biology and evaluate novel therapeutic strategies in a model system that possesses an intact immune system and mirrors key aspects of human cancer biology. Despite decades of interest, effective utilization of pet dog cancers has been hindered by a limited repertoire of necessary cellular and molecular reagents for both in vitro and in vivo studies, as well as a dearth of information regarding the genomic landscape of these cancers. Recently, many of these critical gaps have been addressed through the generation of a highly annotated canine reference genome, the creation of several tools necessary for multi-omic analysis of canine tumours, and the development of a centralized repository for key genomic and associated clinical information from canine cancer patients, the Integrated Canine Data Commons. Together, these advances have catalysed multidisciplinary efforts designed to integrate the study of pet dog cancers more effectively into the translational continuum, with the ultimate goal of improving human outcomes. The current review summarizes this recent progress and provides a guide to resources and tools available for comparative study of pet dog cancers.
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Affiliation(s)
- Cheryl A London
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, USA
| | - Heather Gardner
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, USA
| | - Shaying Zhao
- University of Georgia Cancer Center, University of Georgia, Athens, Georgia, USA
| | - Deborah W Knapp
- College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
| | - Sagar M Utturkar
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Dawn L Duval
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | | | - Elaine Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Jeffrey M Trent
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Gina Kuffel
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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2
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Miyamae J, Okano M, Katakura F, Kulski JK, Moritomo T, Shiina T. Large-Scale Polymorphism Analysis of Dog Leukocyte Antigen Class I and Class II Genes ( DLA-88, DLA-12/88L and DLA-DRB1) and Comparison of the Haplotype Diversity between Breeds in Japan. Cells 2023; 12:cells12050809. [PMID: 36899945 PMCID: PMC10001263 DOI: 10.3390/cells12050809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/21/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Polymorphisms of canine leukocyte antigen (DLA) class I (DLA-88 and DLA-12/88L) and class II (DLA-DRB1) genes are important for disease susceptibility studies, but information on the genetic diversity among dog breeds is still lacking. To better elucidate the polymorphism and genetic diversity between breeds, we genotyped DLA-88, DLA-12/88L, and DLA-DRB1 loci using 829 dogs of 59 breeds in Japan. Genotyping by Sanger sequencing identified 89, 43, and 61 alleles in DLA-88, DLA-12/88L, and DLA-DRB1 loci, respectively, and a total of 131 DLA-88-DLA-12/88L-DLA-DRB1 haplotypes (88-12/88L-DRB1) were detected more than once. Of the 829 dogs, 198 were homozygotes for one of the 52 different 88-12/88L-DRB1 haplotypes (homozygosity rate: 23.8%). Statistical modeling suggests that 90% of the DLA homozygotes or heterozygotes with one or other of the 52 different 88-12/88L-DRB1 haplotypes within somatic stem cell lines would benefit graft outcome after 88-12/88L-DRB1-matched transplantation. As previously reported for DLA class II haplotypes, the diversity of 88-12/88L-DRB1 haplotypes varied remarkably between breeds but was relatively conserved within most breeds. Therefore, the genetic characteristics of high DLA homozygosity rate and poor DLA diversity within a breed are useful for transplantation therapy, but they may affect biological fitness as homozygosity progresses.
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Affiliation(s)
- Jiro Miyamae
- Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoino-oka, Imabari 794-8555, Japan
- Correspondence: ; Tel.: +81-898-52-9126
| | - Masaharu Okano
- Department of Legal Medicine, Nihon University School of Dentistry, 1-8-13 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
| | - Fumihiko Katakura
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan
| | - Jerzy K. Kulski
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara 259-1143, Japan
| | - Tadaaki Moritomo
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara 259-1143, Japan
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3
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Feng Y, Hess PR, Tompkins SM, Hildebrand WH, Zhao S. A Kmer-based paired-end read de novo assembler and genotyper for canine MHC class I genotyping. iScience 2023; 26:105996. [PMID: 36798440 PMCID: PMC9926114 DOI: 10.1016/j.isci.2023.105996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/28/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
The major histocompatibility complex class I (MHC-I) genes are highly polymorphic. MHC-I genotyping is required for determining the peptide epitopes available to an individual's T-cell repertoire. Current genotyping software tools do not work for the dog, due to very limited known canine alleles. To address this, we developed a Kmer-based paired-end read (KPR) de novo assembler and genotyper, which assemble paired-end RNA-seq reads from MHC-I regions into contigs, and then genotype each contig and estimate its expression level. KPR tools outperform other popular software examined in typing new alleles. We used KPR tools to successfully genotype152 dogs from a published dataset. The study discovers 33 putative new alleles, finds dominant alleles in 4 dog breeds, and builds allele diversity and expression landscapes among the 152 dogs. Our software meets a significant need in biomedical research.
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Affiliation(s)
- Yuan Feng
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Paul R. Hess
- Department of Clinical Sciences, North Carolina State University, College of Veterinary Medicine, Raleigh, NC 27607, USA
| | - Stephen M. Tompkins
- Center for Vaccines and Immunology, University of Georgia, UGA, Athens, GA 30602, USA
| | - William H. Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA,Corresponding author
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4
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Pyo C, Harkey MA, Torok‐Storb B, Storb R, Wang R, Thomas AS, Nelson WC, Geraghty DE. Genotyping of canine MHC gene DLA-88 by next-generation sequencing reveals high frequencies of new allele discovery and gene duplication. HLA 2022; 100:479-490. [PMID: 36227705 PMCID: PMC9563979 DOI: 10.1111/tan.14752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/12/2022] [Accepted: 07/31/2022] [Indexed: 01/05/2023]
Abstract
Dogs have served as one of the most reliable preclinical models for a variety of diseases and treatments, including stem/progenitor cell transplantation. At the genetic epicenter of dog transplantation models, polymorphic major histocompatibility complex (MHC) genes are most impactful on transplantation success. Among the canine class I and class II genes, DLA-88 has been best studied in transplantation matching and outcomes, with 129 DLA-88 alleles identified. In this study we developed and tested a next generation (NGS) sequencing protocol for rapid identification of DLA-88 genotypes in dogs and compared the workflow and data generated with an established DLA-88 Sanger sequencing protocol that has been in common prior use for clinical studies. By testing the NGS protocol on a random population of 382 dogs, it was possible to demonstrate superior efficacy based on laboratory execution and overall cost. In addition, NGS proved far more effective at discovering new alleles and detecting multiple alleles associated with gene duplication. A total of 51 new DLA-88 alleles are reported here. This rate of new allele discovery indicates that a large pool of yet un-discovered DLA-88 alleles exists in the domestic dog population. In addition, more than 46% of dogs carried three or more copies of DLA-88, further emphasizing the need for more sensitive and cost-effective DLA typing methodology for the dog clinical model.
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Affiliation(s)
- Chul‐Woo Pyo
- Division of Clinical ResearchFred Hutchinson Cancer CenterSeattleWashingtonUSA,Scisco Genetics Inc.SeattleWashingtonUSA
| | - Michael A. Harkey
- Division of Clinical ResearchFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Beverly Torok‐Storb
- Division of Clinical ResearchFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Rainer Storb
- Division of Clinical ResearchFred Hutchinson Cancer CenterSeattleWashingtonUSA,Department of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Ruihan Wang
- Division of Clinical ResearchFred Hutchinson Cancer CenterSeattleWashingtonUSA,Scisco Genetics Inc.SeattleWashingtonUSA
| | - Alexander S. Thomas
- Division of Clinical ResearchFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Wyatt C. Nelson
- Division of Clinical ResearchFred Hutchinson Cancer CenterSeattleWashingtonUSA,Scisco Genetics Inc.SeattleWashingtonUSA
| | - Daniel E. Geraghty
- Division of Clinical ResearchFred Hutchinson Cancer CenterSeattleWashingtonUSA,Scisco Genetics Inc.SeattleWashingtonUSA
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5
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Miyamae J, Okano M, Nishiya K, Katakura F, Kulski JK, Moritomo T, Shiina T. Haplotype structures and polymorphisms of dog leukocyte antigen (DLA) class I loci shaped by intralocus and interlocus recombination events. Immunogenetics 2022; 74:245-259. [PMID: 34993565 DOI: 10.1007/s00251-021-01234-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/10/2021] [Indexed: 11/26/2022]
Abstract
The dog leukocyte antigen (DLA) class I genomic region is located on chromosome 12, and the class I genomic region is composed of at least two distinct haplotypic gene structures, DLA-88-DLA-12 and DLA-88-DLA-88L. However, detailed information of the genomic differences among DLA-88, DLA-12, and DLA-88L are still lacking at the full-length gene level, and therefore, DLA allelic sequences classified for each of these loci are limited in number so far. In this study, we determined the DNA sequence of a 95-kb DLA class I genomic region including DLA-88, DLA-12/88L, and DLA-64 with three DLA homozygous dogs and of 37 full-length allelic gene sequences for DLA-88 and DLA-12/88L loci in 26 DLA class I homozygous dogs. Nucleotide diversity profiles of the 95-kb regions and sequence identity scores of the allelic sequences suggested that DLA-88L is a hybrid gene generated by interlocus and/or intralocus gene conversion between DLA-88 and DLA-12. The putative minimum conversion tract was estimated to be at least an 850-bp segment in length located from the 5´flanking untranslated region to the end of intron 2. In addition, at least one DLA-12 allele (DLA-12*004:01) was newly generated by interlocus gene conversion. In conclusion, the analysis for the occurrence of gene conversion within the dog DLA class I region revealed intralocus gene conversion tracts in 17 of 27 DLA-88 alleles and two of 10 DLA-12 alleles, suggesting that intralocus gene conversion has played an important role in expanding DLA allelic variations.
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Affiliation(s)
- Jiro Miyamae
- Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoino-oka, Imabari, Ehime, 794-8555, Japan.
| | - Masaharu Okano
- Department of Legal Medicine, Nihon University School of Dentistry, 1-8-13 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-8310, Japan
| | - Kohei Nishiya
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Fumihiko Katakura
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Jerzy K Kulski
- Discipline of Psychiatry, Medical School, The University of Western Australia, Crawley, WA, Australia
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1143, Japan
| | - Tadaaki Moritomo
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1143, Japan
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6
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Evolution of MHC class I genes in Japanese and Russian raccoon dogs, Nyctereutes procyonoides (Carnivora: Canidae). MAMMAL RES 2021; 66:371-383. [PMID: 33747753 PMCID: PMC7957040 DOI: 10.1007/s13364-021-00561-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/03/2021] [Indexed: 10/27/2022]
Abstract
Major histocompatibility complex (MHC) genes have been widely studied to assess the immunological fitness and evolutionary adaptation of animal populations. Among the Canidae, the raccoon dog's adventurous nature, omnivorous behavior, and high variability of intracellular pathogens make it ideal to study selection on MHC class I in a non-model canid species. Here, we examined allelic diversity and evolutionary patterns of MHC class I genes in the raccoon dog (Nyctereutes procyonoides). We identified 48 novel MHC class I alleles from 31 raccoon dogs from Japan and Russia. Some alleles were geographically restricted, whereas others were widely distributed across the species' range. The rate of non-synonymous substitutions was greater than that of synonymous substitutions for both exon 2 and exon 3 encoding α1 and α2 domains, respectively, in the α chain of the MHC class I protein. Positively selected sites at the amino acid level were evident in both the α1 and α2 domains, and a recombination breakpoint was found in exon 3. Bayesian phylogenetic trees showed no evidence of trans-species polymorphism (TSP) with alleles from carnivoran species in other families but did detect TSP between raccoon dogs and the domestic dog, Canis familiaris, indicative of long-term balancing selection in canids. Our results indicate that the extensive allelic diversity of MHC class I in Japanese and Russian raccoon dogs has been influenced and maintained by pathogen-driven positive selection, recombination, and long-term balancing selection. Supplementary Information The online version contains supplementary material available at 10.1007/s13364-021-00561-y.
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7
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Nemec PS, Holmes JC, Hess PR. Dog leukocyte antigen-88*034:01 presents nonamer peptides from canine distemper virus hemagglutinin, large polymerase, and matrix proteins. HLA 2021; 97:428-434. [PMID: 33527745 DOI: 10.1111/tan.14197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/30/2022]
Abstract
Canine spontaneous cancers may offer greater fidelity than rodent models in advancing clinical immunotherapies. Boxers in particular are distinguished as study subjects by their popularity, and high incidence of human-relevant cancers. Further, the MHC class I allele DLA-88*034:01, with a known motif, dominates the breed, facilitating discovery of shared CTL responses against mutation-origin neoepitopes by standard prediction methods. We experimentally confirmed the allomorph's binding motif by developing an MHC surface stabilization assay. The assay validated four DLA-88*034:01-presented peptides from canine distemper virus, ubiquitously administered in routine vaccines, for positive controls in future CTL studies. In turn, these viral peptides substantiated motif-based prediction for DLA-88*034:01. The study adds new tools for studying neoepitope-specific CTL in Boxers to foster canine comparative oncology.
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Affiliation(s)
- Paige S Nemec
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA.,Precision Biosciences, Durham, North Carolina, USA
| | - Jennifer C Holmes
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Paul R Hess
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA
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8
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Abstract
Comparative oncology clinical trials play an important and growing role in cancer research and drug development efforts. These trials, typically conducted in companion (pet) dogs, allow assessment of novel anticancer agents and combination therapies in a veterinary clinical setting that supports serial biologic sample collections and exploration of dose, schedule and corresponding pharmacokinetic/pharmacodynamic relationships. Further, an intact immune system and natural co-evolution of tumour and microenvironment support exploration of novel immunotherapeutic strategies. Substantial improvements in our collective understanding of the molecular landscape of canine cancers have occurred in the past 10 years, facilitating translational research and supporting the inclusion of comparative studies in drug development. The value of the approach is demonstrated in various clinical trial settings, including single-agent or combination response rates, inhibition of metastatic progression and randomized comparison of multiple agents in a head-to-head fashion. Such comparative oncology studies have been purposefully included in the developmental plan for several US FDA-approved and up-and-coming anticancer drugs. Challenges for this field include keeping pace with technology and data dissemination/harmonization, improving annotation of the canine genome and immune system, and generation of canine-specific validated reagents to support integration of correlative biology within clinical trial efforts.
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Affiliation(s)
- Amy K LeBlanc
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Christina N Mazcko
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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9
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Miyamae J, Yagi H, Sato K, Okano M, Nishiya K, Katakura F, Sakai M, Nakayama T, Moritomo T, Shiina T. Evaluation of alloreactive T cells based on the degree of MHC incompatibility using flow cytometric mixed lymphocyte reaction assay in dogs. Immunogenetics 2019; 71:635-645. [PMID: 31745606 DOI: 10.1007/s00251-019-01147-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 11/08/2019] [Indexed: 12/12/2022]
Abstract
It has become anticipated that regenerative medicine will extend into the field of veterinary medicine as new treatments for various disorders. Although the use of allogeneic stem cells for tissue regeneration is more attractive than that of autologous cells in emergencies, the therapeutic potential of allogeneic transplantation is often limited by allo-immune responses inducing graft rejection. Therefore, a methodology for quantifying and monitoring alloreactive T cells is necessary for evaluating allo-immune responses. The mixed lymphocyte reaction (MLR) is widely used to evaluate T cell alloreactivity. In human, flow cytometric MLR with carboxyfluorescein diacetate succinimidyl ester has been established and used as a more useful assay than conventional MLR with radioisotope labeling. However, the available information about alloreactivity based on the differences of dog major histocompatibility complex (MHC) (dog leukocyte antigen, DLA) is quite limited in dog. In this paper, we describe our established flow cytometric MLR method that can quantify the T cell alloreactivity while distinguishing cell phenotypes in dog, and T cell alloreactivity among DLA-type matched pairs was significantly lower than DLA-mismatched pairs, suggesting that our developed flow cytometric MLR method is useful for quantifying T cell alloreactivity. In addition, we demonstrated the advantage of DLA homozygous cells as a donor (stimulator) for allogeneic transplantation. We also elucidated that the frequency of alloreactive T cell precursors was almost the same as that of mouse and human (1-10%). To our knowledge, this is the first report to focus on the degree of allo-immune responses in dog based on the differences of DLA polymorphisms.
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Affiliation(s)
- Jiro Miyamae
- Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoino-oka, Imabari, Ehime, 794-8555, Japan.
| | - Hayato Yagi
- Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Keita Sato
- Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Masaharu Okano
- Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Kohei Nishiya
- Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Fumihiko Katakura
- Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Manabu Sakai
- Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Tomohiro Nakayama
- Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Tadaaki Moritomo
- Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Takashi Shiina
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1143, Japan
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10
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Overgaard NH, Fan TM, Schachtschneider KM, Principe DR, Schook LB, Jungersen G. Of Mice, Dogs, Pigs, and Men: Choosing the Appropriate Model for Immuno-Oncology Research. ILAR J 2019; 59:247-262. [PMID: 30476148 DOI: 10.1093/ilar/ily014] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 07/30/2018] [Indexed: 02/06/2023] Open
Abstract
The immune system plays dual roles in response to cancer. The host immune system protects against tumor formation via immunosurveillance; however, recognition of the tumor by immune cells also induces sculpting mechanisms leading to a Darwinian selection of tumor cell variants with reduced immunogenicity. Cancer immunoediting is the concept used to describe the complex interplay between tumor cells and the immune system. This concept, commonly referred to as the three E's, is encompassed by 3 distinct phases of elimination, equilibrium, and escape. Despite impressive results in the clinic, cancer immunotherapy still has room for improvement as many patients remain unresponsive to therapy. Moreover, many of the preclinical results obtained in the widely used mouse models of cancer are lost in translation to human patients. To improve the success rate of immuno-oncology research and preclinical testing of immune-based anticancer therapies, using alternative animal models more closely related to humans is a promising approach. Here, we describe 2 of the major alternative model systems: canine (spontaneous) and porcine (experimental) cancer models. Although dogs display a high rate of spontaneous tumor formation, an increased number of genetically modified porcine models exist. We suggest that the optimal immuno-oncology model may depend on the stage of cancer immunoediting in question. In particular, the spontaneous canine tumor models provide a unique platform for evaluating therapies aimed at the escape phase of cancer, while genetically engineered swine allow for elucidation of tumor-immune cell interactions especially during the phases of elimination and equilibrium.
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Affiliation(s)
- Nana H Overgaard
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Timothy M Fan
- Department of Veterinary Clinical Medicine, University of Illinois, Urbana-Champaign, Illinois
| | | | - Daniel R Principe
- Medical Scientist Training Program, University of Illinois College of Medicine, Chicago, Illinois
| | - Lawrence B Schook
- Department of Radiology, University of Illinois, Chicago, Illinois.,Department of Animal Sciences, University of Illinois, Urbana-Champaign, Illinois
| | - Gregers Jungersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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11
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Nemec PS, Kapatos A, Holmes JC, Stowe DM, Hess PR. Cancer-testis antigens in canine histiocytic sarcoma and other malignancies. Vet Comp Oncol 2019; 17:317-328. [PMID: 30854786 DOI: 10.1111/vco.12475] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 12/20/2022]
Abstract
Cancer-testis antigens (CTAs) are a category of self proteins aberrantly expressed in diverse malignancies, mostly solid tumours, due to epigenetic de-repression. Normally expressed only in fetal or gametogenic tissues, CTAs are tantalizing immunotherapy targets, since autoimmunity risks appear minimal. Few prevalent CTAs have been identified in human hematologic cancers, and just two in their veterinary counterparts. We sought to discover new CTAs in canine hematologic cancers such as histiocytic sarcoma (HS) and lymphoma to foster immunotherapy development. To accomplish this, the ligandome binding the dog leukocyte antigen (DLA)-88*508:01 class I allele overexpressed in an HS line was searched by mass spectrometry to identify possible CTA-derived peptides, which could serve as CD8+ T-cell epitopes. Twenty-two peptides mapped to 5 human CTAs and 12 additional proteins with CTA characteristics. Expression of five promising candidates was then evaluated in tumour and normal tissue by quantitative and end-point RT-PCR. The ortholog of an established CTA, IGF2BP3, had unexpectedly high expression in peripheral blood mononuclear cells (PBMCs). Four other testis-enhanced proteins were also assessed. AKR1E2, SPECC1 and TPX2 were expressed variably in HS and T-cell lymphoma biopsies, but also at high levels in critical tissues, including kidney, brain and marrow, diminishing their utility. A more tissue-restricted candidate, NT5C1B, was detected in T-cell lymphomas, but also at low levels in some normal dog tissues. These results illustrate the feasibility of discovering canine CTAs by a reverse approach, proceeding from identification of MHC class I-presented peptides to a comparative RNA expression survey of tumours and normal tissues.
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Affiliation(s)
- Paige S Nemec
- Department of Clinical Sciences, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina
| | - Alexander Kapatos
- Department of Clinical Sciences, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina
| | - Jennifer C Holmes
- Department of Clinical Sciences, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina
| | - Devorah M Stowe
- Department of Population, Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina
| | - Paul R Hess
- Department of Clinical Sciences, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina
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12
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Abduriyim S, Nishita Y, Kosintsev PA, Raichev E, Väinölä R, Kryukov AP, Abramov AV, Kaneko Y, Masuda R. Evolution of MHC class I genes in Eurasian badgers, genus Meles (Carnivora, Mustelidae). Heredity (Edinb) 2019; 122:205-218. [PMID: 29959426 PMCID: PMC6327056 DOI: 10.1038/s41437-018-0100-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 11/09/2022] Open
Abstract
Because of their role in immune defense against pathogens, major histocompatibility complex (MHC) genes are useful in evolutionary studies on how wild vertebrates adapt to their environments. We investigated the molecular evolution of MHC class I (MHCI) genes in four closely related species of Eurasian badgers, genus Meles. All four species of badgers showed similarly high variation in MHCI sequences compared to other Carnivora. We identified 7-21 putatively functional MHCI sequences in each of the badger species, and 2-7 sequences per individual, indicating the existence of 1-4 loci. MHCI exon 2 and 3 sequences encoding domains α1 and α2 exhibited different clade topologies in phylogenetic networks. Non-synonymous nucleotide substitutions at codons for antigen-binding sites exceeded synonymous substitutions for domain α1 but not for domain α2, suggesting that the domains α1 and α2 likely had different evolutionary histories in these species. Positive selection and recombination seem to have shaped the variation in domain α2, whereas positive selection was dominant in shaping the variation in domain α1. In the separate phylogenetic analyses for exon 2, exon 3, and intron 2, each showed three clades of Meles alleles, with rampant trans-species polymorphism, indicative of the long-term maintenance of ancestral MHCI polymorphism by balancing selection.
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Affiliation(s)
- Shamshidin Abduriyim
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yoshinori Nishita
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Pavel A Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Ekaterinburg, 620144, Russia
| | - Evgeniy Raichev
- Agricultural Faculty, Trakia University, 6000, Stara Zagora, Bulgaria
| | - Risto Väinölä
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, FI-00014, Helsinki, Finland
| | - Alexey P Kryukov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, 199034, Russia
| | - Yayoi Kaneko
- Carnivore Ecology and Conservation Research Group, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Ryuichi Masuda
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan.
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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13
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Nemec PS, Kapatos A, Holmes JC, Hess PR. The prevalent Boxer MHC class Ia allotype dog leukocyte antigen
(DLA)‐88*034:01
preferentially binds nonamer peptides with a defined motif. HLA 2018; 92:403-407. [DOI: 10.1111/tan.13398] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 09/13/2018] [Accepted: 09/17/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Paige S. Nemec
- Department of Clinical Sciences North Carolina State University College of Veterinary Medicine Raleigh North Carolina
| | - Alexander Kapatos
- Department of Clinical Sciences North Carolina State University College of Veterinary Medicine Raleigh North Carolina
| | - Jennifer C. Holmes
- Department of Clinical Sciences North Carolina State University College of Veterinary Medicine Raleigh North Carolina
| | - Paul R. Hess
- Department of Clinical Sciences North Carolina State University College of Veterinary Medicine Raleigh North Carolina
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14
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Cardiosphere-derived cells suppress allogeneic lymphocytes by production of PGE2 acting via the EP4 receptor. Sci Rep 2018; 8:13351. [PMID: 30190508 PMCID: PMC6127326 DOI: 10.1038/s41598-018-31569-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 08/07/2018] [Indexed: 12/17/2022] Open
Abstract
Cardiosphere-derived cells (CDCs) are a cardiac progenitor cell population, which have been shown to possess cardiac regenerative properties and can improve heart function in a variety of cardiac diseases. Studies in large animal models have predominantly focussed on using autologous cells for safety, however allogeneic cell banks would allow for a practical, cost-effective and efficient use in a clinical setting. The aim of this work was to determine the immunomodulatory status of these cells using CDCs and lymphocytes from 5 dogs. CDCs expressed MHC I but not MHC II molecules and in mixed lymphocyte reactions demonstrated a lack of lymphocyte proliferation in response to MHC-mismatched CDCs. Furthermore, MHC-mismatched CDCs suppressed lymphocyte proliferation and activation in response to Concanavalin A. Transwell experiments demonstrated that this was predominantly due to direct cell-cell contact in addition to soluble mediators whereby CDCs produced high levels of PGE2 under inflammatory conditions. This led to down-regulation of CD25 expression on lymphocytes via the EP4 receptor. Blocking prostaglandin synthesis restored both, proliferation and activation (measured via CD25 expression) of stimulated lymphocytes. We demonstrated for the first time in a large animal model that CDCs inhibit proliferation in allo-reactive lymphocytes and have potent immunosuppressive activity mediated via PGE2.
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15
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Ross P, Nemec PS, Kapatos A, Miller KR, Holmes JC, Suter SE, Buntzman AS, Soderblom EJ, Collins EJ, Hess PR. The canine MHC class Ia allele DLA-88*508:01 presents diverse self- and canine distemper virus-origin peptides of varying length that have a conserved binding motif. Vet Immunol Immunopathol 2018; 197:76-86. [PMID: 29475511 DOI: 10.1016/j.vetimm.2018.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/03/2018] [Accepted: 01/12/2018] [Indexed: 01/06/2023]
Abstract
Ideally, CD8+ T-cell responses against virally infected or malignant cells are defined at the level of the specific peptide and restricting MHC class I element, a determination not yet made in the dog. To advance the discovery of canine CTL epitopes, we sought to determine whether a putative classical MHC class Ia gene, Dog Leukocyte Antigen (DLA)-88, presents peptides from a viral pathogen, canine distemper virus (CDV). To investigate this possibility, DLA-88*508:01, an allele prevalent in Golden Retrievers, was expressed as a FLAG-tagged construct in canine histiocytic cells to allow affinity purification of peptide-DLA-88 complexes and subsequent elution of bound peptides. Pattern analysis of self peptide sequences, which were determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS), permitted binding preferences to be inferred. DLA-88*508:01 binds peptides that are 9-to-12 amino acids in length, with a modest preference for 9- and 11-mers. Hydrophobic residues are favored at positions 2 and 3, as are K, R or F residues at the C-terminus. Testing motif-matched and -unmatched synthetic peptides via peptide-MHC surface stabilization assay using a DLA-88*508:01-transfected, TAP-deficient RMA-S line supported these conclusions. With CDV infection, 22 viral peptides ranging from 9-to-12 residues in length were identified in DLA-88*508:01 eluates by LC-MS/MS. Combined motif analysis and surface stabilization assay data suggested that 11 of these 22 peptides, derived from CDV hemagglutinin, large polymerase, matrix, nucleocapsid, and V proteins, were processed and presented, and thus, potential targets of anti-viral CTL in DLA-88*508:01-bearing dogs. The presentation of diverse self and viral peptides indicates that DLA-88 is a classical MHC class Ia gene.
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Affiliation(s)
- Peter Ross
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, 27607, USA
| | - Paige S Nemec
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, 27607, USA
| | - Alexander Kapatos
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, 27607, USA
| | - Keith R Miller
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Jennifer C Holmes
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, 27607, USA
| | - Steven E Suter
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, 27607, USA
| | - Adam S Buntzman
- Department of Immunobiology, University of Arizona, Tucson, AZ, 85724, USA
| | - Erik J Soderblom
- Proteomics Core Facility, Institute for Genome Science and Policy, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Edward J Collins
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA; Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Paul R Hess
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, 27607, USA.
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16
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Harkey MA, Villagran AM, Venkataraman GM, Leisenring WM, Hullar MAJ, Torok-Storb BJ. Associations between gastric dilatation-volvulus in Great Danes and specific alleles of the canine immune-system genes DLA88, DRB1, and TLR5. Am J Vet Res 2017; 78:934-945. [PMID: 28738011 DOI: 10.2460/ajvr.78.8.934] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine whether specific alleles of candidate genes of the major histocompatibility complex (MHC) and innate immune system were associated with gastric dilatation-volvulus (GDV) in Great Danes. ANIMALS 42 healthy Great Danes (control group) and 39 Great Danes with ≥ 1 GDV episode. PROCEDURES Variable regions of the 2 most polymorphic MHC genes (DLA88 and DRB1) were amplified and sequenced from the dogs in each group. Similarly, regions of 3 genes associated with the innate immune system (TLR5, NOD2, and ATG16L1), which have been linked to inflammatory bowel disease, were amplified and sequenced. Alleles were evaluated for associations with GDV, controlling for age and dog family. RESULTS Specific alleles of genes DLA88, DRB1, and TLR5 were significantly associated with GDV. One allele of each gene had an OR > 2 in the unadjusted univariate analyses and retained a hazard ratio > 2 after controlling for temperament, age, and familial association in the multivariate analysis. CONCLUSIONS AND CLINICAL RELEVANCE The 3 GDV-associated alleles identified in this study may serve as diagnostic markers for identification of Great Danes at risk for GDV. Additional research is needed to determine whether other dog breeds have the same genetic associations. These findings also provided a new target for research into the etiology of, and potential treatments for, GDV in dogs.
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17
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Identification of novel polymorphisms and two distinct haplotype structures in dog leukocyte antigen class I genes: DLA-88, DLA-12 and DLA-64. Immunogenetics 2017; 70:237-255. [DOI: 10.1007/s00251-017-1031-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 09/19/2017] [Indexed: 12/14/2022]
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18
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Liu G, Zhang H, Sun G, Zhao C, Shang S, Gao X, Xia T, Yang X. Characterization of the peripheral blood transcriptome and adaptive evolution of the MHC I and TLR gene families in the wolf (Canis lupus). BMC Genomics 2017; 18:584. [PMID: 28784091 PMCID: PMC5545864 DOI: 10.1186/s12864-017-3983-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 08/01/2017] [Indexed: 01/25/2023] Open
Abstract
Background The wolf (Canis lupus) is one of the most widely distributed terrestrial mammals, because it is well adapted to various ecological niches and their corresponding pathogen environments. Immunological competence is a crucial factor involved in adapting to a changing environment and fighting pathogen infection in animals. In this study, the peripheral blood transcriptome of wolves was generated via RNA-seq to advance understanding of the wolf immunome, with a special focus on the major histocompatibility complex class I (MHC I) and toll-like receptor (TLR) gene families, which are involved in pathogen recognition and defense. Results The blood transcriptomic libraries of eight wolves originating from Tibet and Inner Mongolia were sequenced, and approximately 383 million reads were generated. Using a genome-guided assembly strategy, we obtained 123,851 unigenes, with a mean length of 845 bp and an N50 length of 1121 bp. On the basis of BLAST searches against the NCBI non-redundant protein database (Nr), a total of 36,192 (29.22%) unigenes were annotated. For functional classification, 24,663 unigenes were assigned to 13,016 Gene Ontology (GO) terms belonging to 51 sub-categories of the three main GO categories. Additionally, 7682 unigenes were classified into 6 Kyoto Encyclopedia of Genes and Genomes (KEGG) categories, in which the most represented functional sub-categories were signal transduction and the immune system, and 16,238 unigenes were functionally classified into 25 Eukaryotic Orthologous Groups (KOG) categories. We observed an overall higher ω (dN/dS) value at antigen-binding sites (ABSs) than at non-ABS regions as well as clear evidence of intergenic/intragenic recombination events at wolf MHC I loci. Additionally, our analysis revealed that carnivorous TLRs were dominated by purifying selection, with mean ω values at each TLR locus ranging from 0.173 to 0.527. However, we also found significant instances of positive selection that acted on several codons in pathogen recognition domains and were linked to species-specific differences in pathogen recognition. Conclusions This study represents the first attempt to characterize the blood transcriptome of the wolf and to highlight the value of investigating the immune system. Balancing selection and recombination have contributed to the historical evolution of wolf MHC I genes. Moreover, TLRs in carnivores have undergone adaptive evolution against the background of purifying selection, and a high level of adaptive evolution was detected in the wolf TLR system. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3983-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guangshuai Liu
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Honghai Zhang
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China.
| | - Guolei Sun
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Chao Zhao
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Shuai Shang
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Xiaodong Gao
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Tian Xia
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Xiufeng Yang
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
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19
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Venkataraman GM, Kennedy LJ, Little MTE, Graves SS, Harkey MA, Torok-Storb BJ, Storb R. Thirteen novel canine dog leukocyte antigen-88 alleles identified by sequence-based typing. HLA 2017; 90:165-170. [PMID: 28677267 DOI: 10.1111/tan.13077] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 04/25/2017] [Accepted: 06/09/2017] [Indexed: 11/29/2022]
Abstract
Major histocompatibility complex (MHC) genes in mammals include highly polymorphic class I and class II genes that are critical for donor-recipient matching for transplantation. Dogs have served as an effective, directly translatable model for stem/progenitor cell transplantation. Previous analyses of MHC class I genes in dogs point to a single highly polymorphic gene, dog leukocyte antigen (DLA)-88, as an important factor in the success or failure of hematopoietic stem cell transplants. Fifty-nine DLA-88 alleles have been identified and reported so far. Here, we extend this list by presenting 13 novel DLA-88 alleles found in domestic dogs.
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Affiliation(s)
- G M Venkataraman
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - L J Kennedy
- Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, UK
| | - M-T E Little
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - S S Graves
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington
| | - M A Harkey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - B J Torok-Storb
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - R Storb
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington
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20
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VanBelzen DJ, Malik AS, Henthorn PS, Kornegay JN, Stedman HH. Mechanism of Deletion Removing All Dystrophin Exons in a Canine Model for DMD Implicates Concerted Evolution of X Chromosome Pseudogenes. Mol Ther Methods Clin Dev 2017; 4:62-71. [PMID: 28344992 PMCID: PMC5363321 DOI: 10.1016/j.omtm.2016.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/07/2016] [Indexed: 01/19/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a lethal, X-linked, muscle-wasting disorder caused by mutations in the large, 2.4-Mb dystrophin gene. The majority of DMD-causing mutations are sporadic, multi-exon, frameshifting deletions, with the potential for variable immunological tolerance to the dystrophin protein from patient to patient. While systemic gene therapy holds promise in the treatment of DMD, immune responses to vectors and transgenes must first be rigorously evaluated in informative preclinical models to ensure patient safety. A widely used canine model for DMD, golden retriever muscular dystrophy, expresses detectable amounts of near full-length dystrophin due to alternative splicing around an intronic point mutation, thereby confounding the interpretation of immune responses to dystrophin-derived gene therapies. Here we characterize a naturally occurring deletion in a dystrophin-null canine, the German shorthaired pointer. The deletion spans 5.6 Mb of the X chromosome and encompasses all coding exons of the DMD and TMEM47 genes. The sequences surrounding the deletion breakpoints are virtually identical, suggesting that the deletion occurred through a homologous recombination event. Interestingly, the deletion breakpoints are within loci that are syntenically conserved among mammals, yet the high homology among this subset of ferritin-like loci is unique to the canine genome, suggesting lineage-specific concerted evolution of these atypical sequence elements.
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Affiliation(s)
- D. Jake VanBelzen
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alock S. Malik
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paula S. Henthorn
- Section of Medical Genetics, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Joe N. Kornegay
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Hansell H. Stedman
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael Crescenz Veterans Administration Medical Center, Philadelphia, PA 19104, USA
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21
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Barth SM, Schreitmüller CM, Proehl F, Oehl K, Lumpp LM, Kowalewski DJ, Di Marco M, Sturm T, Backert L, Schuster H, Stevanović S, Rammensee HG, Planz O. Characterization of the Canine MHC Class I DLA-88*50101 Peptide Binding Motif as a Prerequisite for Canine T Cell Immunotherapy. PLoS One 2016; 11:e0167017. [PMID: 27893789 PMCID: PMC5125661 DOI: 10.1371/journal.pone.0167017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/07/2016] [Indexed: 12/11/2022] Open
Abstract
There are limitations in pre-clinical settings using mice as a basis for clinical development in humans. In cancer, similarities exist between humans and dogs; thus, the dog patient can be a link in the transition from laboratory research on mouse models to clinical trials in humans. Knowledge of the peptides presented on MHC molecules is fundamental for the development of highly specific T cell-based immunotherapies. This information is available for human MHC molecules but is absent for the canine MHC. In the present study, we characterized the binding motif of dog leukocyte antigen (DLA) class I allele DLA-88*50101, using human C1R and K562 transfected cells expressing the DLA-88*50101 heavy chain. MHC class I immunoaffinity-purification revealed 3720 DLA-88*50101 derived peptides, which enabled the determination of major anchor positions. The characterized binding motif of DLA-88*50101 was similar to HLA-A*02:01. Peptide binding analyses on HLA-A*02:01 and DLA-88*50101 via flow cytometry showed weak binding of DLA-88*50101 derived peptides to HLA-A*02:01, and vice versa. Our results present for the first time a detailed peptide binding motif of the canine MHC class I allelic product DLA-88*50101. These data support the goal of establishing dogs as a suitable animal model for the evaluation and development of T cell-based cancer immunotherapies, benefiting both dog and human patients.
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Affiliation(s)
- Sharon M. Barth
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | | | - Franziska Proehl
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Kathrin Oehl
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
- Institute for Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Leonie M. Lumpp
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Daniel J. Kowalewski
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
- Immatics, Biotechnologies GmbH, Tuebingen, Germany
| | - Moreno Di Marco
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Theo Sturm
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Linus Backert
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
- Applied Bioinformatics, Center of Bioinformatics and Department of Computer Science, University of Tuebingen, Tuebingen, Germany
| | - Heiko Schuster
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
- Institute for Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Stefan Stevanović
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Oliver Planz
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
- * E-mail:
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22
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Xiao J, Xiang W, Chai Y, Haywood J, Qi J, Ba L, Qi P, Wang M, Liu J, Gao GF. Diversified Anchoring Features the Peptide Presentation of DLA-88*50801: First Structural Insight into Domestic Dog MHC Class I. THE JOURNAL OF IMMUNOLOGY 2016; 197:2306-15. [PMID: 27511732 DOI: 10.4049/jimmunol.1600887] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/08/2016] [Indexed: 11/19/2022]
Abstract
Canines represent a crucial animal model for studying human diseases and organ transplantation, as well as the evolution of domestic animals. MHCs, with a central role in cellular immunity, are commonly used in the study of dog population genetics and genome evolution. However, the molecular basis for the peptide presentation of dog MHC remains largely unknown. In this study, peptide presentation by canine MHC class I DLA-88*50801 was structurally determined, revealing diversified anchoring modes of the binding peptides. Flexible and large pockets composed of both hydrophobic and hydrophilic residues can accommodate pathogen-derived peptides with diverse anchor residues, as confirmed by thermostability measurements. Furthermore, DLA-88*50801 contains an unusual α2 helix with a large coil in the TCR contact region. These results further our understanding of canine T cell immunity through peptide presentation of MHC class I and shed light on the molecular basis for vaccine development for canine infectious diseases, for example, canine distemper virus.
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Affiliation(s)
- Jin Xiao
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd, Beijing 100095, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; China Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Wangzhen Xiang
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd, Beijing 100095, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yan Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Joel Haywood
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Limin Ba
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd, Beijing 100095, China
| | - Peng Qi
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd, Beijing 100095, China
| | - Ming Wang
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd, Beijing 100095, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jun Liu
- College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China; and National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - George F Gao
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; China Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China; and National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
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23
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Holmes JC, Holmer SG, Ross P, Buntzman AS, Frelinger JA, Hess PR. Polymorphisms and tissue expression of the feline leukocyte antigen class I loci FLAI-E, FLAI-H, and FLAI-K. Immunogenetics 2013; 65:675-89. [PMID: 23812210 PMCID: PMC3777221 DOI: 10.1007/s00251-013-0711-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 05/18/2013] [Indexed: 01/14/2023]
Abstract
Cytotoxic CD8+ T-cell immunosurveillance for intracellular pathogens, such as viruses, is controlled by classical major histocompatibility complex (MHC) class Ia molecules, and ideally, these antiviral T-cell populations are defined by the specific peptide and restricting MHC allele. Surprisingly, despite the utility of the cat in modeling human viral immunity, little is known about the feline leukocyte antigen class I complex (FLAI). Only a few coding sequences with uncertain locus origin and expression patterns have been reported. Of 19 class I genes, three loci--FLAI-E, FLAI-H, and FLAI-K--are predicted to encode classical molecules, and our objective was to evaluate their status by analyzing polymorphisms and tissue expression. Using locus-specific, PCR-based genotyping, we amplified 33 FLAI-E, FLAI-H, and FLAI-K alleles from 12 cats of various breeds, identifying, for the first time, alleles across three distinct loci in a feline species. Alleles shared the expected polymorphic and invariant sites in the α1/α2 domains, and full-length cDNA clones possessed all characteristic class Ia exons. Alleles could be assigned to a specific locus with reasonable confidence, although there was evidence of potentially confounding interlocus recombination between FLAI-E and FLAI-K. Only FLAI-E, FLAI-H, and FLAI-K origin alleles were amplified from cDNAs of multiple tissue types. We also defined hypervariable regions across these genes, which permitted the assignment of names to both novel and established alleles. As predicted, FLAI-E, FLAI-H, and FLAI-K fulfill the major criteria of class Ia genes. These data represent a necessary prerequisite for studying epitope-specific antiviral CD8+ T-cell responses in cats.
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Affiliation(s)
- Jennifer C. Holmes
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Savannah G. Holmer
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Peter Ross
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Adam S. Buntzman
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Jeffrey A. Frelinger
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Paul R. Hess
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
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Tsai KL, Starr-Moss AN, Venkataraman GM, Robinson C, Kennedy LJ, Steiner JM, Clark LA. Alleles of the major histocompatibility complex play a role in the pathogenesis of pancreatic acinar atrophy in dogs. Immunogenetics 2013; 65:501-9. [PMID: 23604463 DOI: 10.1007/s00251-013-0704-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/05/2013] [Indexed: 11/30/2022]
Abstract
Exocrine pancreatic insufficiency (EPI) is a disease wherein pancreatic acinar cells fail to synthesize and secrete sufficient amounts of digestive enzymes for normal digestion of food. EPI affects many dog breeds, with a dramatically higher prevalence in the German shepherd dog (GSD) population. In this breed and perhaps others, EPI most often results from degeneration of the acinar cells of the pancreas, a hereditary disorder termed pancreatic acinar atrophy (PAA). Evidence of lymphocytic infiltration indicates that PAA is an autoimmune disease, but the genetic etiology remains unclear. Data from global gene expression and single nucleotide polymorphism profiles in the GSD suggest the involvement of the major histocompatibility complex [MHC; dog leukocyte antigen (DLA)]. To determine if alleles of the MHC influence development of EPI, genotyping of polymorphic class I (DLA-88) and II loci (DLA-DRB1, DLA-DQA1, and DLA-DQB1) was carried out for 70 affected and 63 control GSDs, and four-locus haplotypes were determined. One haplotype containing a novel allele of DLA-88 is very highly associated with EPI (OR > 17; P = 0.000125), while two haplotypes were found to confer protection from EPI (P = 0.00087 and 0.0115). Described herein is the genotyping of MHC class I and II loci in a GSD cohort, establishment of four-locus haplotypes, and association of alleles/haplotypes with EPI.
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Affiliation(s)
- Kate L Tsai
- Department of Genetics and Biochemistry, College of Agriculture, Forestry and Life Sciences, Clemson University, 154 Poole Agricultural Center, 130 McGinty Ct, Clemson, SC 29634, USA
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Ross P, Holmes JC, Gojanovich GS, Hess PR. A cell-based MHC stabilization assay for the detection of peptide binding to the canine classical class I molecule, DLA-88. Vet Immunol Immunopathol 2012; 150:206-12. [PMID: 23062801 PMCID: PMC3494747 DOI: 10.1016/j.vetimm.2012.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 08/10/2012] [Indexed: 11/19/2022]
Abstract
Identifying immunodominant CTL epitopes is essential for studying CD8+ T-cell responses in populations, but remains difficult, as peptides within antigens typically are too numerous for all to be synthesized and screened. Instead, to facilitate discovery, in silico scanning of proteins for sequences that match the motif, or binding preferences, of the restricting MHC class I allele - the largest determinant of immunodominance - can be used to predict likely candidates. The high false positive rate with this analysis ideally requires binding confirmation, which is obtained routinely by an assay using cell lines such as RMA-S that have defective transporter associated with antigen processing (TAP) machinery, and consequently, few surface class I molecules. The stabilization and resultant increased life-span of peptide-MHC complexes on the cell surface by the addition of true binders validates their identity. To determine whether a similar assay could be developed for dogs, we transfected a prevalent class I allele, DLA-88*50801, into RMA-S. In the BARC3 clone, the recombinant heavy chain was associated with murine β2-microglobulin, and importantly, could differentiate motif-matched and -mismatched peptides by surface MHC stabilization. This work demonstrates the potential to use RMA-S cells transfected with canine alleles as a tool for CTL epitope discovery in this species.
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Affiliation(s)
- Peter Ross
- Immunology Program, Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA 27607
| | - Jennifer C. Holmes
- Immunology Program, Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA 27607
| | - Gregory S. Gojanovich
- Immunology Program, Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA 27607
| | - Paul R. Hess
- Immunology Program, Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA 27607
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Hammond JA, Guethlein LA, Norman PJ, Parham P. Natural selection on marine carnivores elaborated a diverse family of classical MHC class I genes exhibiting haplotypic gene content variation and allelic polymorphism. Immunogenetics 2012; 64:915-33. [PMID: 23001684 DOI: 10.1007/s00251-012-0651-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 09/07/2012] [Indexed: 12/12/2022]
Abstract
Pinnipeds, marine carnivores, diverged from terrestrial carnivores ~45 million years ago, before their adaptation to marine environments. This lifestyle change exposed pinnipeds to different microbiota and pathogens, with probable impact on their MHC class I genes. Investigating this question, genomic sequences were determined for 71 MHC class I variants: 27 from harbor seal and 44 from gray seal. These variants form three MHC class I gene lineages, one comprising a pseudogene. The second, a candidate nonclassical MHC class I gene, comprises a nonpolymorphic transcribed gene related to dog DLA-79 and giant panda Aime-1906. The third is the diversity lineage, which includes 62 of the 71 seal MHC class I variants. All are transcribed, and they minimally represent six harbor and 12 gray seal MHC class I genes. Besides species-specific differences in gene number, seal MHC class I haplotypes exhibit gene content variation and allelic polymorphism. Patterns of sequence variation, and of positions for positively selected sites, indicate the diversity lineage genes are the seals' classical MHC class I genes. Evidence that expansion of diversity lineage genes began before gray and harbor seals diverged is the presence in both species of two distinctive sublineages of diversity lineage genes. Pointing to further expansion following the divergence are the presence of species-specific genes and greater MHC class I diversity in gray seals than harbor seals. The elaboration of a complex variable family of classical MHC class I genes in pinnipeds contrasts with the single, highly polymorphic classical MHC class I gene of dog and giant panda, terrestrial carnivores.
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Affiliation(s)
- John A Hammond
- Department of Structural Biology, Stanford University School of Medicine, Fairchild D-159 299 Campus Drive West, Stanford, CA 94305, USA.
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