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Nielsen SCA, Boyd SD. Human adaptive immune receptor repertoire analysis-Past, present, and future. Immunol Rev 2019; 284:9-23. [PMID: 29944765 DOI: 10.1111/imr.12667] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The genes encoding adaptive immune antigen receptors, namely the immunoglobulins expressed in membrane-bound or secreted forms by B cells, and the cell surface T cell receptors, are unique in human biology because they are generated by combinatorial rearrangement of the genomic DNA. The diversity of receptors so generated in populations of lymphocytes enables the human immune system to recognize antigens expressed by pathogens, but also underlies the pathological specificity of autoimmune diseases and the mistargeted immunity in allergies. Several recent technological developments, foremost among them the invention of high-throughput DNA sequencing instruments, have enabled much deeper and thorough evaluation of clones of human B cells and T cells and the antigen receptors they express during physiological and pathogenic immune responses. The evolutionary struggles between host adaptive immune responses and populations of pathogens are now open to greater scrutiny, elucidation of the underlying reasons for successful or failed immunity, and potential predictive modeling, than ever before. Here we give an overview of the foundations, recent progress, and future prospects in this dynamic area of research.
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Affiliation(s)
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA, USA
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2
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Luo S, Yu JA, Li H, Song YS. Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humans. Life Sci Alliance 2019; 2:2/2/e201800221. [PMID: 30808649 PMCID: PMC6391684 DOI: 10.26508/lsa.201800221] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/14/2019] [Accepted: 02/14/2019] [Indexed: 12/31/2022] Open
Abstract
This article presents a comprehensive study of the IGHV and TRBV gene families in a globally diverse sample of humans and shows that the two gene families exhibit starkly different patterns of variation. The immunoglobulin heavy variable (IGHV) and T cell beta variable (TRBV) loci are among the most complex and variable regions in the human genome. Generated through a process of gene duplication/deletion and diversification, these loci can vary extensively between individuals in copy number and contain genes that are highly similar, making their analysis technically challenging. Here, we present a comprehensive study of the functional gene segments in the IGHV and TRBV loci, quantifying their copy number and single-nucleotide variation in a globally diverse sample of 109 (IGHV) and 286 (TRBV) humans from over a 100 populations. We find that the IGHV and TRBV gene families exhibit starkly different patterns of variation. In addition to providing insight into the different evolutionary paths of the IGHV and TRBV loci, our results are also important to the adaptive immune repertoire sequencing community, where the lack of frequencies of common alleles and copy number variants is hampering existing analytical pipelines.
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Affiliation(s)
- Shishi Luo
- Computer Science Division, University of California, Berkeley, Berkeley, CA, USA.,Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Jane A Yu
- Computer Science Division, University of California, Berkeley, Berkeley, CA, USA
| | - Heng Li
- Department of Biostatistics, Harvard Medical School, Boston, MA, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, Berkeley, CA, USA .,Department of Statistics, University of California, Berkeley, Berkeley, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
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3
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Huth A, Liang X, Krebs S, Blum H, Moosmann A. Antigen-Specific TCR Signatures of Cytomegalovirus Infection. THE JOURNAL OF IMMUNOLOGY 2018; 202:979-990. [PMID: 30587531 DOI: 10.4049/jimmunol.1801401] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/19/2018] [Indexed: 11/19/2022]
Abstract
CMV is a prevalent human pathogen. The virus cannot be eliminated from the body, but is kept in check by CMV-specific T cells. Patients with an insufficient T cell response, such as transplant recipients, are at high risk of developing CMV disease. However, the CMV-specific T cell repertoire is complex, and it is not yet clear which T cells protect best against virus reactivation and disease. In this study, we present a highly resolved characterization of CMV-specific human CD8+ T cells based on enrichment by specific peptide stimulation and mRNA sequencing of their TCR β-chains (TCRβ). Our analysis included recently identified T cell epitopes restricted through HLA-C, whose presentation is resistant to viral immunomodulation, and well-studied HLA-B-restricted epitopes. In eight healthy virus carriers, we identified a total of 1052 CMV-specific TCRβ sequences. HLA-C-restricted, CMV-specific TCRβ clonotypes dominated the ex vivo T cell response and contributed the highest-frequency clonotype of the entire repertoire in two of eight donors. We analyzed sharing and similarity of CMV-specific TCRβ sequences and identified 63 public or related sequences belonging to 17 public TCRβ families. In our cohort, and in an independent cohort of 352 donors, the cumulative frequency of these public TCRβ family members was a highly discriminatory indicator of carrying both CMV infection and the relevant HLA type. Based on these findings, we propose CMV-specific TCRβ signatures as a biomarker for an antiviral T cell response to identify patients in need of treatment and to guide future development of immunotherapy.
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Affiliation(s)
- Alina Huth
- German Center for Infection Research Group Host Control of Viral Latency and Reactivation, Research Unit Gene Vectors, Helmholtz Center Munich, 81377 Munich, Germany.,Deutsches Zentrum für Infektionsforschung, 81377 Munich, Germany; and
| | - Xiaoling Liang
- German Center for Infection Research Group Host Control of Viral Latency and Reactivation, Research Unit Gene Vectors, Helmholtz Center Munich, 81377 Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Andreas Moosmann
- German Center for Infection Research Group Host Control of Viral Latency and Reactivation, Research Unit Gene Vectors, Helmholtz Center Munich, 81377 Munich, Germany; .,Deutsches Zentrum für Infektionsforschung, 81377 Munich, Germany; and
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Watson CT, Matsen FA, Jackson KJL, Bashir A, Smith ML, Glanville J, Breden F, Kleinstein SH, Collins AM, Busse CE. Comment on “A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data”. THE JOURNAL OF IMMUNOLOGY 2017; 198:3371-3373. [DOI: 10.4049/jimmunol.1700306] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Ferjeni Z, Bouzid D, Fourati H, Stayoussef M, Abida O, Kammoun T, Hachicha M, Penha-Gonçalves C, Masmoudi H. Association of TCR/CD3, PTPN22, CD28 and ZAP70 gene polymorphisms with type 1 diabetes risk in Tunisian population: family based association study. Immunol Lett 2014; 163:1-7. [PMID: 25448703 DOI: 10.1016/j.imlet.2014.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/30/2014] [Accepted: 11/10/2014] [Indexed: 11/28/2022]
Abstract
Type 1 diabetes (T1D) is caused by an immune-mediated destruction of the insulin-producing β-cells. Several studies support the involvement of T cell activation molecules in the pathogenesis of T1D. In order to underline the role of the genes involved in this activation pathway, we investigated, using the Sequenom MassARRAY platform, 45 single-nucleotide polymorphisms (SNPs) belonging to TCR/CD3, CD28, ZAP70, and PTPN22 genes in 59 T1D Tunisian families. In the current study, we identified an association with rs706 (Z score=2.782; p=0.005) of TCRβ gene. We also demonstrated that rs10918706 in the intron of the CD3z gene was associated with increased risk of T1D (Z score 2.137; p=0.032). In the same region, rs2949655 (Z score=2.101; p=0.035) and rs1214611 (Z score=4.036; p=0.00005) showed a genotype association with the risk of T1D. When haplotypes were constructed, GAA haplotype displayed significant association with T1D (Z score=2.135; p=0.032), while GGA haplotype (Z score=-1.988; p=0.046) was negatively associated with the disease. We also identified an association with rs3181096 (Z score=2.177; p=0.029), rs17695937 (Z score =2.111; p=0.034) and rs2488457 (Z score=2.219; p=0.026), respectively of CD28, ZAP70 and PTPN22 genes. In addition, our results suggest a significant effect on T1D susceptibility for AC (Z score=2.30; p=0.02) and CTGGC (Z score=2.309, p=0.02) haplotypes of ZAP70 and PTPN22 genes, respectively. While, the GTCT (Z score=-2.114, p=0.034) and CTAGG (Z score=-2.121, p=0.033) haplotypes of CD28 and PTPN22 genes, may confer protection against T1D. These findings confirm the role of PTPN22 and CD28 involved in the T cell activation pathway in the development of T1D in Tunisian families. Interestingly, ZAP70 and TCRβ/CD3z seem to contribute to the susceptibility to the disease in our population. However, this finding has to be confirmed in further studies.
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Affiliation(s)
- Zouidi Ferjeni
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia.
| | - D Bouzid
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - H Fourati
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - M Stayoussef
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - O Abida
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - T Kammoun
- Pediatric Department, Hedi Chaker Hospital, University of Sfax, Sfax, Tunisia
| | - M Hachicha
- Pediatric Department, Hedi Chaker Hospital, University of Sfax, Sfax, Tunisia
| | | | - H Masmoudi
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
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Thorborn G, Young GR, Kassiotis G. Effective T helper cell responses against retroviruses: are all clonotypes equal? J Leukoc Biol 2014; 96:27-37. [PMID: 24737804 DOI: 10.1189/jlb.2ri0613-347r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The critical importance of CD4(+) T cells in coordinating innate and adaptive immune responses is evidenced by the susceptibility to various pathogenic and opportunistic infections that arises from primary or acquired CD4(+) T cell immunodeficiency, such as following HIV-1 infection. However, despite the clearly defined roles of cytotoxic CD8(+) T cells and antibodies in host protection from retroviruses, the ability of CD4(+) T cells to exert a similar function remains unclear. Recent studies in various settings have drawn attention to the complexity of the T cell response within and between individuals. Distinct TCR clonotypes within an individual differ substantially in their response to the same epitope. Functionally similar, "public" TCR clonotypes can also dominate the response of different individuals. TCR affinity for antigen directly influences expansion and differentiation of responding T cells, also likely affecting their ultimate protective capacity. With this increasing understanding of the parameters that determine the magnitude and effector type of the T cell response, we are now better equipped to address the protective capacity against retroviruses of CD4(+) T cell clonotypes induced by natural infection or vaccination.
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Affiliation(s)
| | - George R Young
- Divisions of Immunoregulation and Virology, Medical Research Council National Institute for Medical Research, The Ridgeway, London, United Kingdom; and
| | - George Kassiotis
- Divisions of Immunoregulation and Department of Medicine, Faculty of Medicine, Imperial College London, United Kingdom
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7
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Brennan RM, Burrows JM, Elliott T, Neller MA, Gras S, Rossjohn J, Miles JJ, Burrows SR. Missense single nucleotide polymorphisms in the human T cell receptor loci control variable gene usage in the T cell repertoire. Br J Haematol 2014; 166:148-52. [PMID: 24646048 DOI: 10.1111/bjh.12830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rebekah M Brennan
- QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia.
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8
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Burrows SR, Miles JJ. Immune parameters to consider when choosing T-cell receptors for therapy. Front Immunol 2013; 4:229. [PMID: 23935599 PMCID: PMC3733007 DOI: 10.3389/fimmu.2013.00229] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 07/22/2013] [Indexed: 11/13/2022] Open
Abstract
T-cell receptor (TCR) therapy has arrived as a realistic treatment option for many human diseases. TCR gene therapy allows for the mass redirection of T-cells against a defined antigen while high affinity TCR engineering allows for the creation of a new class of soluble drugs. However, deciding which TCR blueprint to take forward for gene therapy or engineering is difficult. More than one quintillion TCR combinations can be generated by somatic recombination and we are only now beginning to appreciate that not all are functionally equal. TCRs can exhibit high or low degrees of HLA-restricted cross-reactivity and alloreact against one or a combination of HLA alleles. Identifying TCR candidates with high specificity and minimal cross-reactivity/alloreactivity footprints before engineering is obviously highly desirable. Here we will summarize what we currently know about TCR biology with regard to immunoengineering.
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Affiliation(s)
- Scott R Burrows
- Human Immunity Laboratory and Cellular Immunology Laboratory, Queensland Institute of Medical Research , Brisbane, QLD , Australia ; School of Medicine, The University of Queensland , Brisbane, QLD , Australia
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Tzifi F, Kanariou M, Tzanoudaki M, Mihas C, Paschali E, Chrousos G, Kanaka-Gantenbein C. Flow cytometric analysis of the CD4+ TCR Vβ repertoire in the peripheral blood of children with type 1 diabetes mellitus, systemic lupus erythematosus and age-matched healthy controls. BMC Immunol 2013; 14:33. [PMID: 23915345 PMCID: PMC3750582 DOI: 10.1186/1471-2172-14-33] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 07/31/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Data regarding the quantitative expression of TCR Vβ subpopulations in children with autoimmune diseases provided interesting and sometimes conflicting results. The aim of the present study was to assess by comparative flow cytometric analysis the peripheral blood CD4+ TCR Vβ repertoire of children with an organ-specific autoimmune disorder, such as type 1 diabetes mellitus (T1DM), in comparison to children with a systemic autoimmune disease, such as Systemic Lupus Erythematosus (SLE) in comparison to healthy age-matched controls of the same ethnic origin. The CD4+ TCR Vβ repertoire was analysed by flow cytometry in three groups of participants: a) fifteen newly diagnosed children with T1DM (mean age: 9.2 ± 4.78 years old), b) nine newly diagnosed children with SLE, positive for ANA and anti-dsDNA, prior to treatment (mean age: 12.8 ±1.76 years old) and c) 31 healthy age-matched controls (mean age: 6.58 ± 3.65 years old), all of Hellenic origin. RESULTS CD4 + TCR Vβ abnormalities (± 3SD of controls) were observed mainly in SLE patients. Statistical analysis revealed that the CD4 + Vβ4 chain was significantly increased in patients with T1DM (p < 0.001), whereas CD4 + Vβ16 one was significantly increased in SLE patients (p < 0.001) compared to controls. CONCLUSIONS CD4 + Vβ4 and CD4 + Vβ16 chains could be possibly involved in the cascade of events precipitating the pathogenesis of T1DM and SLE in children, respectively.
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Gras S, Burrows SR, Turner SJ, Sewell AK, McCluskey J, Rossjohn J. A structural voyage toward an understanding of the MHC-I-restricted immune response: lessons learned and much to be learned. Immunol Rev 2012; 250:61-81. [DOI: 10.1111/j.1600-065x.2012.01159.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stephanie Gras
- Department of Biochemistry and Molecular Biology; School of Biomedical Sciences; Monash University; Clayton; Australia
| | - Scott R. Burrows
- Queensland Institute of Medical Research and Australian Centre for Vaccine Development; Brisbane; Australia
| | - Stephen J. Turner
- Department of Microbiology and Immunology; University of Melbourne; Parkville; Australia
| | - Andrew K. Sewell
- Institute of Infection and Immunity; Cardiff University School of Medicine; Cardiff; UK
| | - James McCluskey
- Department of Microbiology and Immunology; University of Melbourne; Parkville; Australia
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11
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Brennan RM, Petersen J, Neller MA, Miles JJ, Burrows JM, Smith C, McCluskey J, Khanna R, Rossjohn J, Burrows SR. The Impact of a Large and Frequent Deletion in the Human TCR β Locus on Antiviral Immunity. THE JOURNAL OF IMMUNOLOGY 2012; 188:2742-8. [DOI: 10.4049/jimmunol.1102675] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Melenhorst JJ, Lay MDH, Price DA, Adams SD, Zeilah J, Sosa E, Hensel NF, Follmann D, Douek DC, Davenport MP, Barrett AJ. Contribution of TCR-beta locus and HLA to the shape of the mature human Vbeta repertoire. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2008; 180:6484-9. [PMID: 18453566 DOI: 10.4049/jimmunol.180.10.6484] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
T cells that survive thymic selection express a diverse array of unique heterodimeric alphabeta TCRs that mediate peptide-MHC Ag recognition. The proportion of the total T cell repertoire that expresses a particular Vbeta protein may be determined by a variety of factors: 1) germline preference for use of particular Vbeta genes; 2) allelic effects on the expression of different Vbeta genes; and 3) HLA effects on the expression of different Vbeta genes (acting via thymic selection and/or peripheral mechanisms). In this study, we show that Vbeta usage by human CD4(+) and CD8(+) T cells in neonatal and adult donors is highly correlated between unrelated individuals, suggesting that a large proportion of the observed pattern of Vbeta expression is determined by factors intrinsic to the TCR-beta locus. The presence of identical TCR alleles (within an individual) leads to a significantly better correlation between CD4(+) and CD8(+) T cells with respect to Vbeta expression; these effects are, however, relatively minor. The sharing of HLA alleles between individuals also leads to an increased correlation between their Vbeta expression patterns, although this did not reach statistical significance. We therefore conclude that the correlation in Vbeta expression patterns between CD4(+) and CD8(+) T cells can be explained predominantly by germline TCR-beta locus factors and not TCR-beta allelic or HLA effects.
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Affiliation(s)
- J Joseph Melenhorst
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Tripputi P, Bianchi S, Fedele L. A possible mechanism for non-replication of allelic association between a single nucleotide polymorphism of the human beta T-cell receptor and autoimmune diseases. Int J Immunogenet 2008; 35:141-4. [PMID: 18279372 DOI: 10.1111/j.1744-313x.2008.00751.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gene polymorphisms, in particular single nucleotide polymorphisms (SNPs), have been associated to multifactorial diseases such as cancer, inflammation and autoimmunity. Indeed for some autoimmune diseases, it has been possible to identify critical residues that play a major role in susceptibility to diseases. The association of a common T/C polymorphism in the promoter region of the beta 2 constant chain of the T-cell receptor with autoimmune diseases, such as insulin-dependent diabetes, autoimmune hepatitis, IgA nephropathy, membranous nephropathy, Graves' disease and Hashimoto's thyroiditis, was described in the 1990 s. These reports have not been confirmed in the last few years. We also failed in a previous study to detect any difference between 70 normal subjects and 70 patients with primary biliary cirrhosis; however, we found a difference in allelic frequency between males and females. This finding led us to make an allele frequency study of this single nucleotide polymorphism between sexes in a new series of patients. We studied 165 subjects, 80 males and 85 females, and we found a significant difference between sexes especially for the CC homozygous genotype: 34% of females vs. 14% of males (P = 0.008). If the higher frequency of CC homozygous genotype (that is associated with an increased risk of autoimmune diseases) in females would be confirmed in normal population, this could be an explanation of the controversial results obtained by association studies made between this SNP and autoimmune diseases.
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Affiliation(s)
- P Tripputi
- Department of Medicine, Surgery and Dentistry, University of Milan, Milan, Italy.
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14
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Bonfigli S, Fozza C, Contini S, Buzzetti R, Cucca F, Longinotti M. High frequency of the TCRBV20S1 null allele in the Sardinian population. Hum Immunol 2007; 68:426-9. [PMID: 17462510 DOI: 10.1016/j.humimm.2007.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 01/16/2007] [Accepted: 01/17/2007] [Indexed: 11/26/2022]
Abstract
Single nucleotide polymorphisms (SNPs) in the T-cell receptor (TCR) gene segments might play a role in shaping the TCR repertoire. Three polymorphisms have been described for the TCRBV20S1 gene segment, one of which is responsible for a nucleotide substitution at position 524, resulting in the introduction of a stop codon. Individuals homozygous for this inactivating polymorphism ("null allele") are unable to express TCRBV20 gene products. Using DNA restriction digestion analysis, we investigated the frequency of this polymorphism in 111 healthy Sardinian subjects. Inhabitants of the Mediterranean island of Sardinia are considered to represent a genetically isolated population. Our analyses revealed an incidence of 19.8% of homozygosity for the null allele, corresponding to an allele frequency of 0.45. Such an incidence, significantly higher than the one detected in 83 non-Sardinian Caucasians (6%), is the most elevated so far reported in the literature. BV20 is a single member subfamily and the null allele produces a gap in the potential TCR repertoire. Therefore, it is possible that an undetermined selective pressure could have played a role in determining the high frequency of this inactivating polymorphism in Sardinians. Alternatively, this finding could be related to a founder effect in this ancient island population.
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Mackelprang R, Livingston RJ, Eberle MA, Carlson CS, Yi Q, Akey JM, Nickerson DA. Sequence diversity, natural selection and linkage disequilibrium in the human T cell receptor alpha/delta locus. Hum Genet 2006; 119:255-66. [PMID: 16425038 DOI: 10.1007/s00439-005-0111-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2005] [Accepted: 11/16/2005] [Indexed: 12/22/2022]
Abstract
T cell receptors (TR), through their interaction with the major histocompatibility complex, play a central role in immune responsiveness and potentially immune-related disorders. We resequenced all 57 variable (V) genes in the human T cell receptor alpha and delta (TRA/TRD) locus in 40 individuals of Northern European, Mexican, African-American and Chinese descent. Two hundred and eighty-four single nucleotide polymorphisms (SNPs) were identified. The distribution of SNPs between V genes was heterogeneous, with an average of five SNPs per gene and a range of zero to 15. We describe the patterns of linkage disequilibrium for these newly discovered SNPs and compare these patterns with other emerging large-scale datasets (e.g. Perlegen and HapMap projects) to place our findings into a framework for future analysis of genotype-phenotype associations across this locus. Furthermore, we explore signatures of natural selection across V genes. We find evidence of strong directional selection at this locus as evidenced by unusually high values of Fst.
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Affiliation(s)
- Rachel Mackelprang
- Department of Genome Sciences, University of Washington, 357730, Seattle, WA, 98195-7730, USA.
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