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Liang C, Sun L, Zhu Y, Wu J, Zhao A, Huang T, Yan F, He K. Local chicken breeds exhibit abundant TCR-V segments but similar repertoire diversity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 157:105196. [PMID: 38762097 DOI: 10.1016/j.dci.2024.105196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/22/2024] [Accepted: 05/16/2024] [Indexed: 05/20/2024]
Abstract
The thymus-derived lymphocytes of jawed vertebrates have four T-cell receptor (TCR) chains that play a significant role in immunity. As chickens have commercial value, their immune systems require a great deal of attention. Local chicken breeds are an essential part of poultry genetic resources in China. Here, we used high-throughput sequencing to analyze the TCRα and TCRβ repertoires and their relative expression levels in the native chicken breeds Baier Buff, Longyou Partridge, Xiaoshan, and Xianju. We found that TCR Vα and TCR Vβ were expressed and included 17, 19, 17, and six segments of the Vα2, Vα3, Vβ1, and Vβ2 subgroups, respectively. V-J pairing was biased; Jα11 was utilized by nearly all Vα segments and was the most commonly used. Breed-specific V segments and V-J pairings were detected as well. The results of the principal coordinate analysis (PCoA) as well as the V-J pairing and CDR3 diversity analyses suggested that the four local chicken breeds did not significantly differ in terms of TCR diversity. Hence, they expressed not significant differentiation, and they are rich genetic resources for the development and utilization of immune-related poultry breeding.
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Affiliation(s)
- Chunhong Liang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Lin Sun
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Jianqing Wu
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Ayong Zhao
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Tao Huang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Feifei Yan
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China.
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Früh SP, Früh MA, Kaufer BB, Göbel TW. Unraveling the chicken T cell repertoire with enhanced genome annotation. Front Immunol 2024; 15:1359169. [PMID: 38550579 PMCID: PMC10972964 DOI: 10.3389/fimmu.2024.1359169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/23/2024] [Indexed: 04/02/2024] Open
Abstract
T cell receptor (TCR) repertoire sequencing has emerged as a powerful tool for understanding the diversity and functionality of T cells within the host immune system. Yet, the chicken TCR repertoire remains poorly understood due to incomplete genome annotation of the TCR loci, despite the importance of chickens in agriculture and as an immunological model. Here, we addressed this critical issue by employing 5' rapid amplification of complementary DNA ends (5'RACE) TCR repertoire sequencing with molecular barcoding of complementary DNA (cDNA) molecules. Simultaneously, we enhanced the genome annotation of TCR Variable (V), Diversity (D, only present in β and δ loci) and Joining (J) genes in the chicken genome. To enhance the efficiency of TCR annotations, we developed VJ-gene-finder, an algorithm designed to extract VJ gene candidates from deoxyribonucleic acid (DNA) sequences. Using this tool, we achieved a comprehensive annotation of all known chicken TCR loci, including the α/δ locus on chromosome 27. Evolutionary analysis revealed that each locus evolved separately by duplication of long homology units. To define the baseline TCR diversity in healthy chickens and to demonstrate the feasibility of the approach, we characterized the splenic α/β/γ/δ TCR repertoire. Analysis of the repertoires revealed preferential usage of specific V and J combinations in all chains, while the overall features were characteristic of unbiased repertoires. We observed moderate levels of shared complementarity-determining region 3 (CDR3) clonotypes among individual birds within the α and γ chain repertoires, including the most frequently occurring clonotypes. However, the β and δ repertoires were predominantly unique to each bird. Taken together, our TCR repertoire analysis allowed us to decipher the composition, diversity, and functionality of T cells in chickens. This work not only represents a significant step towards understanding avian T cell biology, but will also shed light on host-pathogen interactions, vaccine development, and the evolutionary history of avian immunology.
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Affiliation(s)
- Simon P. Früh
- Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | | | | | - Thomas W. Göbel
- Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
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Linti AE, Göbel TW, Früh SP. Chicken γδ T cells proliferate upon IL-2 and IL-12 treatment and show a restricted receptor repertoire in cell culture. Front Immunol 2024; 15:1325024. [PMID: 38420118 PMCID: PMC10900522 DOI: 10.3389/fimmu.2024.1325024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 03/02/2024] Open
Abstract
In chickens, γδ T cells represent a large fraction of peripheral T cells; however, their function remains largely unknown. Here, we describe the selective in vitro expansion of γδ T cells from total splenocytes by stimulation with the cytokines IL-2 and IL-12. Under these conditions, γδ T cells proliferated preferentially and reached frequencies of >95% within three weeks. Although IL-2 alone also triggered proliferation, an increased proliferation rate was observed in combination with IL-12. Most of the expanded cells were γδ TCR and CD8 double-positive. Splenocytes sorted into TCR1+CD8+, TCR1highCD8-, and TCR1lowCD8- subsets proliferated well upon dual stimulation with IL-2/IL-12, indicating that none of the three γδ T cell subsets require bystander activation for proliferation. TCR1+CD8+ cells maintained CD8 surface expression during stimulation, whereas CD8- subpopulations showed varied levels of CD8 upregulation, with the highest upregulation observed in the TCR1high subset. Changes in the γδ T-cell receptor repertoire during cell culture from day 0 to day 21 were analyzed by next-generation sequencing of the γδ variable regions. Overall, long-term culture led to a restricted γ and δ chain repertoire, characterized by a reduced number of unique variable region clonotypes, and specific V genes were enriched at day 21. On day 0, the δ chain repertoire was highly diverse, and the predominant clonotypes differed between animals, while the most frequent γ-chain clonotypes were shared between animals. However, on day 21, the most frequent clonotypes in both the γ and δ chain repertoires were different between animals, indicating that selective expansion of dominant clonotypes during stimulation seems to be an individual outcome. In conclusion, IL-2 and IL-12 were sufficient to stimulate the in vitro outgrowth of γδ T cells. Analyses of the TCR repertoire indicate that the culture leads to an expansion of individual T cell clones, which may reflect previous in vivo activation. This system will be instrumental in studying γδ T cell function.
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Affiliation(s)
- Antonia E. Linti
- Department of Veterinary Immunology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thomas W. Göbel
- Department of Veterinary Immunology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Simon P. Früh
- Department of Veterinary Immunology, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Veterinary Medicine, Institute of Virology, Freie Universität Berlin, Berlin, Germany
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Liang C, Sun L, Zhu Y, Zhao A, Liu H, He K. Macroevolution of avian T cell receptor C segments using genomic data. Immunogenetics 2023; 75:531-541. [PMID: 37804321 DOI: 10.1007/s00251-023-01322-8] [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: 08/07/2023] [Accepted: 09/26/2023] [Indexed: 10/09/2023]
Abstract
All jawed vertebrates have four T cell receptor (TCR) chains expressed by thymus-derived lymphocytes that play a significant role in animal immune defense. However, avian TCR studies have been limited to a few species, although their co-functional major histocompatibility complexes (MHCs) have been studied for decades, showing various copy numbers and polymorphisms. Here, using public genome data, we characterized the copy numbers, the phylogenic relationship and selection of T cell receptor complex (TCR-C) segments, and the genomic organization of TCR loci across birds. Various numbers of C segments were found in the TCRα/TCRδ, TCRβ, and TCRγ loci, and phylogenetic analysis reflected both ancient gene duplication events (two Cβ segments and Cδ segments divergent into CδI and CδII) and contemporary evolution (lineage-specific and species-specific characteristics). Most passerines lack CδII segments and a second TRD locus, except Meliphagidae and Maluridae. A relatively stable structure was verified in four TCR loci of birds, except for the arrangement of V segment groups. In this study, we explored the phylogenetic relationships of TCR-C segments across avians for the first time. We inferred gene duplication and loss events during the evolution process. The finding of diverse TCR germline repertoires provides a better understanding of the immune systems of birds.
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Affiliation(s)
- Chunhong Liang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Lin Sun
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Ayong Zhao
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Hongyi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China.
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Zhang T, Li Q, Li X, Kang L, Jiang Y, Sun Y. Correction to: Characterization of the chicken T cell receptor γ repertoire by high-throughput sequencing. BMC Genomics 2021; 22:859. [PMID: 34844555 PMCID: PMC8628409 DOI: 10.1186/s12864-021-08136-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Tongtong Zhang
- Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Shandong Province, 271018, Taian City, People's Republic of China
| | - Qian Li
- Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Shandong Province, 271018, Taian City, People's Republic of China
| | - Xiaoqing Li
- Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Shandong Province, 271018, Taian City, People's Republic of China
| | - Li Kang
- Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Shandong Province, 271018, Taian City, People's Republic of China
| | - Yunliang Jiang
- Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Shandong Province, 271018, Taian City, People's Republic of China.
| | - Yi Sun
- Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Shandong Province, 271018, Taian City, People's Republic of China.
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