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Eisenblätter R, Seifert F, Schürmann P, Beckhaus T, Hanel P, Jentschke M, Böhmer G, Strauß HG, Hirchenhain C, Schmidmayr M, Müller F, Hein A, Stuebs F, Koch M, Ruebner M, Beckmann MW, Fasching PA, Luyten A, Häfner N, Hillemanns P, Dörk T, Ramachandran D. Validation and functional follow-up of cervical cancer risk variants at the HLA locus. HLA 2024; 104:e15597. [PMID: 39101335 DOI: 10.1111/tan.15597] [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: 04/17/2024] [Revised: 06/19/2024] [Accepted: 07/02/2024] [Indexed: 08/06/2024]
Abstract
Cervical cancer is the fourth most common cancer in females. Genome-wide association studies (GWASs) have proposed cervical cancer susceptibility variants at the HLA locus on chromosome 6p21. To corroborate these findings and investigate their functional impact in cervical tissues and cell lines, we genotyped nine variants from cervical cancer GWASs (rs17190106, rs535777, rs1056429, rs2763979, rs143954678, rs113937848, rs3117027, rs3130214, and rs9477610) in a German hospital-based series of 1122 invasive cervical cancers, 1408 dysplasias, and 1196 healthy controls. rs17190106, rs1056429 and rs143954678/rs113937848 associated with cervical malignancies overall, while rs17190106 and rs535777 associated specifically with invasive cancer (OR = 0.69, 95% CI = 0.55-0.86, p = 0.001) or adenocarcinomas (OR = 1.63, 95%CI = 1.17-2.27, p = 0.004), respectively. We tested these and one previously genotyped GWAS variant, rs9272117, for potential eQTL effects on 36 gene transcripts at the HLA locus in 280 cervical epithelial tissues. The strongest eQTL pairs were rs9272117 and HLA-DRB6 (p = 1.9x10E-5), rs1056429 and HLA-DRB5 (p = 2.5x10E-4), and rs535777 and HLA-DRB1 (p = 2.7x10E-4). We also identified transcripts that were specifically upregulated (DDX39B, HCP5, HLA-B, LTB, NFKBIL1) or downregulated (HLA-C, HLA-DPB2) in HPV+ or HPV16+ samples. In comparison, treating cervical epithelial cells with proinflammatory cytokine γ-IFN led to a dose-dependent induction of HCP5, HLA-B, HLA-C, HLA-DQB1, HLA-DRB1, HLA-DRB6, and repression of HSPA1L. Taken together, these results identify relevant genes from both the MHC class I and II regions that are inflammation-responsive in cervical epithelium and associate with HPV (HCP5, HLA-B, HLA-C) and/or with genomic cervical cancer risk variants (HLA-DRB1, HLA-DRB6). They may thus constitute important contributors to the immune escape of precancerous cells after HPV-infection.
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Affiliation(s)
- Rieke Eisenblätter
- Department of Gynaecology, Comprehensive Cancer Center, Hannover Medical School, Hannover, Germany
| | - Finja Seifert
- Department of Gynaecology, Comprehensive Cancer Center, Hannover Medical School, Hannover, Germany
| | - Peter Schürmann
- Department of Gynaecology, Comprehensive Cancer Center, Hannover Medical School, Hannover, Germany
| | - Theresa Beckhaus
- Department of Gynaecology, Comprehensive Cancer Center, Hannover Medical School, Hannover, Germany
| | - Patricia Hanel
- Department of Gynaecology, Comprehensive Cancer Center, Hannover Medical School, Hannover, Germany
| | - Matthias Jentschke
- Department of Gynaecology, Comprehensive Cancer Center, Hannover Medical School, Hannover, Germany
| | | | - Hans-Georg Strauß
- Department of Gynaecology, University Clinics, Martin-Luther University, Halle-Wittenberg, Germany
| | - Christine Hirchenhain
- Department of Gynaecology, Clinics Carl Gustav Carus, University of Dresden, Dresden, Germany
| | - Monika Schmidmayr
- Department of Gynaecology, Technische Universität München, Munich, Germany
| | - Florian Müller
- Martin-Luther Hospital, Charite University, Berlin, Germany
| | - Alexander Hein
- Department of Gynaecology and Obstetrics, Klinikum Esslingen, Esslingen am Neckar, Germany
| | - Frederik Stuebs
- Department of Gynaecology and Obstetrics, Erlangen University Hospital, Comprehensive Cancer Center Erlangen-EMN, Friedrich Alexander, University of Erlangen-Nuremberg (FAU), Erlangen, Germany
- Institute of Human Genetics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Martin Koch
- Department of Gynaecology and Obstetrics, Erlangen University Hospital, Comprehensive Cancer Center Erlangen-EMN, Friedrich Alexander, University of Erlangen-Nuremberg (FAU), Erlangen, Germany
- Institute of Human Genetics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Matthias Ruebner
- Department of Gynaecology and Obstetrics, Erlangen University Hospital, Comprehensive Cancer Center Erlangen-EMN, Friedrich Alexander, University of Erlangen-Nuremberg (FAU), Erlangen, Germany
- Institute of Human Genetics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Matthias W Beckmann
- Department of Gynaecology and Obstetrics, Erlangen University Hospital, Comprehensive Cancer Center Erlangen-EMN, Friedrich Alexander, University of Erlangen-Nuremberg (FAU), Erlangen, Germany
- Institute of Human Genetics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Peter A Fasching
- Department of Gynaecology and Obstetrics, Erlangen University Hospital, Comprehensive Cancer Center Erlangen-EMN, Friedrich Alexander, University of Erlangen-Nuremberg (FAU), Erlangen, Germany
- Institute of Human Genetics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Alexander Luyten
- Dysplasia Unit, Department of Gynecology and Obstetrics, Mare Klinikum, Kronshagen, Germany
- Department of Gynaecology, Wolfsburg Hospital, Wolfsburg, Germany
| | - Norman Häfner
- Department of Gynaecology, Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany
| | - Peter Hillemanns
- Department of Gynaecology, Comprehensive Cancer Center, Hannover Medical School, Hannover, Germany
| | - Thilo Dörk
- Department of Gynaecology, Comprehensive Cancer Center, Hannover Medical School, Hannover, Germany
| | - Dhanya Ramachandran
- Department of Gynaecology, Comprehensive Cancer Center, Hannover Medical School, Hannover, Germany
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2
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Simpson CL, Kimble DC, Chandrasekharappa SC, Alqosayer K, Holzinger E, Carrington B, McElderry J, Sood R, Al‐Souqi G, Albacha‐Hejazi H, Bailey‐Wilson JE. A novel de novo TP63 mutation in whole-exome sequencing of a Syrian family with Oral cleft and ectrodactyly. Mol Genet Genomic Med 2023; 11:e2179. [PMID: 37070724 PMCID: PMC10422068 DOI: 10.1002/mgg3.2179] [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: 03/03/2022] [Revised: 03/06/2023] [Accepted: 03/20/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Oral clefts and ectrodactyly are common, heterogeneous birth defects. We performed whole-exome sequencing (WES) analysis in a Syrian family. The proband presented with both orofacial clefting and ectrodactyly but not ectodermal dysplasia as typically seen in ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome-3. A paternal uncle with only an oral cleft was deceased and unavailable for analysis. METHODS Variant annotation, Mendelian inconsistencies, and novel variants in known cleft genes were examined. Candidate variants were validated using Sanger sequencing, and pathogenicity assessed by knocking out the tp63 gene in zebrafish to evaluate its role during zebrafish development. RESULTS Twenty-eight candidate de novo events were identified, one of which is in a known oral cleft and ectrodactyly gene, TP63 (c.956G > T, p.Arg319Leu), and confirmed by Sanger sequencing. CONCLUSION TP63 mutations are associated with multiple autosomal dominant orofacial clefting and limb malformation disorders. The p.Arg319Leu mutation seen in this patient is de novo but also novel. Two known mutations in the same codon (c.956G > A, p.(Arg319His; rs121908839, c.955C > T), p.Arg319Cys) cause ectrodactyly, providing evidence that mutating this codon is deleterious. While this TP63 mutation is the best candidate for the patient's clinical presentation, whether it is responsible for the entire phenotype is unclear. Generation and characterization of tp63 knockout zebrafish showed necrosis and rupture of the head at 3 days post-fertilization (dpf). The embryonic phenotype could not be rescued by injection of zebrafish or human messenger RNA (mRNA). Further functional analysis is needed to determine what proportion of the phenotype is due to this mutation.
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Affiliation(s)
- Claire L. Simpson
- Computational and Statistical Genomics Branch, National Human Genome Research InstituteNational Institutes of HealthBaltimoreMaryland21224USA
- Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisTennessee38163USA
| | - Danielle C. Kimble
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research InstituteNational Institutes of HealthBethesdaMaryland20814USA
| | - Settara C. Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research InstituteNational Institutes of HealthBethesdaMaryland20814USA
| | | | | | - Emily Holzinger
- Computational and Statistical Genomics Branch, National Human Genome Research InstituteNational Institutes of HealthBaltimoreMaryland21224USA
| | - Blake Carrington
- Zebrafish Core, National Human Genome Research InstituteNational Institutes of HealthBethesdaMaryland20892USA
| | - John McElderry
- Zebrafish Core, National Human Genome Research InstituteNational Institutes of HealthBethesdaMaryland20892USA
| | - Raman Sood
- Zebrafish Core, National Human Genome Research InstituteNational Institutes of HealthBethesdaMaryland20892USA
| | | | | | - Joan E. Bailey‐Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research InstituteNational Institutes of HealthBaltimoreMaryland21224USA
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3
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Lukacs M, Nymo IH, Madslien K, Våge J, Veiberg V, Rolandsen CM, Bøe CA, Sundaram AYM, Grimholt U. Functional immune diversity in reindeer reveals a high Arctic population at risk. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.1058674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Climate changes the geographic range of both species as well as pathogens, causing a potential increase in the vulnerability of populations or species with limited genetic diversity. With advances in high throughput sequencing (HTS) technologies, we can now define functional expressed genetic diversity of wild species at a larger scale and identify populations at risk. Previous studies have used genomic DNA to define major histocompatibility complex (MHC) class II diversity in reindeer. Varying numbers of expressed genes found in many ungulates strongly argues for using cDNA in MHC typing strategies to ensure that diversity estimates relate to functional genes. We have used available reindeer genomes to identify candidate genes and established an HTS approach to define expressed MHC class I and class II diversity. To capture a broad diversity we included samples from wild reindeer from Southern Norway, semi-domesticated reindeer from Northern Norway and reindeer from the high Artic archipelago Svalbard. Our data show a medium MHC diversity in semi-domesticated and wild Norwegian mainland reindeer, and low MHC diversity reindeer in Svalbard reindeer. The low immune diversity in Svalbard reindeer provides a potential risk if the pathogenic pressure changes in response to altered environmental conditions due to climate change, or increased human-related activity.
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4
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Vangenot C, Nunes JM, Doxiadis GM, Poloni ES, Bontrop RE, de Groot NG, Sanchez-Mazas A. Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans indicate highly conserved mechanisms of MHC molecular evolution. BMC Evol Biol 2020; 20:119. [PMID: 32933484 PMCID: PMC7491122 DOI: 10.1186/s12862-020-01669-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 08/06/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Many species are threatened with extinction as their population sizes decrease with changing environments or face novel pathogenic threats. A reduction of genetic diversity at major histocompatibility complex (MHC) genes may have dramatic effects on populations' survival, as these genes play a key role in adaptive immunity. This might be the case for chimpanzees, the MHC genes of which reveal signatures of an ancient selective sweep likely due to a viral epidemic that reduced their population size a few million years ago. To better assess how this past event affected MHC variation in chimpanzees compared to humans, we analysed several indexes of genetic diversity and linkage disequilibrium across seven MHC genes on four cohorts of chimpanzees and we compared them to those estimated at orthologous HLA genes in a large set of human populations. RESULTS Interestingly, the analyses uncovered similar patterns of both molecular diversity and linkage disequilibrium across the seven MHC genes in chimpanzees and humans. Indeed, in both species the greatest allelic richness and heterozygosity were found at loci A, B, C and DRB1, the greatest nucleotide diversity at loci DRB1, DQA1 and DQB1, and both significant global linkage disequilibrium and the greatest proportions of haplotypes in linkage disequilibrium were observed at pairs DQA1 ~ DQB1, DQA1 ~ DRB1, DQB1 ~ DRB1 and B ~ C. Our results also showed that, despite some differences among loci, the levels of genetic diversity and linkage disequilibrium observed in contemporary chimpanzees were globally similar to those estimated in small isolated human populations, in contrast to significant differences compared to large populations. CONCLUSIONS We conclude, first, that highly conserved mechanisms shaped the diversity of orthologous MHC genes in chimpanzees and humans. Furthermore, our findings support the hypothesis that an ancient demographic decline affecting the chimpanzee populations - like that ascribed to a viral epidemic - exerted a substantial effect on the molecular diversity of their MHC genes, albeit not more pronounced than that experienced by HLA genes in human populations that underwent rapid genetic drift during humans' peopling history. We thus propose a model where chimpanzees' MHC genes regenerated molecular variation through recombination/gene conversion and/or balancing selection after the selective sweep.
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Affiliation(s)
- Christelle Vangenot
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - José Manuel Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Gaby M Doxiadis
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288, GJ, Rijswijk, The Netherlands
| | - Estella S Poloni
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288, GJ, Rijswijk, The Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288, GJ, Rijswijk, The Netherlands
| | - Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland. .,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.
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5
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Zhang X, Zhang R, Yu J. New Understanding of the Relevant Role of LINE-1 Retrotransposition in Human Disease and Immune Modulation. Front Cell Dev Biol 2020; 8:657. [PMID: 32850797 PMCID: PMC7426637 DOI: 10.3389/fcell.2020.00657] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/01/2020] [Indexed: 12/21/2022] Open
Abstract
Long interspersed nuclear element-1 (LINE-1) retrotransposition is a major hallmark of cancer accompanied by global chromosomal instability, genomic instability, and genetic heterogeneity and has become one indicator for the occurrence, development, and poor prognosis of many diseases. LINE-1 also modulates the immune system and affects the immune microenvironment in a variety of ways. Aberrant expression of LINE-1 retrotransposon can provide strong stimuli for an innate immune response, activate the immune system, and induce autoimmunity and inflammation. Therefore, inhibition the activity of LINE-1 has become a potential treatment strategy for various diseases. In this review, we discussed the components and regulatory mechanisms involved with LINE-1, its correlations with disease and immunity, and multiple inhibitors of LINE-1, providing a new understanding of LINE-1.
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Affiliation(s)
- Xiao Zhang
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Rui Zhang
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jinpu Yu
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
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6
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Matern BM, Olieslagers TI, Voorter CEM, Groeneweg M, Tilanus MGJ. Insights into the polymorphism in HLA-DRA and its evolutionary relationship with HLA haplotypes. HLA 2019; 95:117-127. [PMID: 31617688 DOI: 10.1111/tan.13730] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/07/2019] [Accepted: 10/12/2019] [Indexed: 01/05/2023]
Abstract
HLA-DRA encodes the alpha chain of the HLA-DR protein, one of the classical HLA class II molecules. Reported polymorphism within HLA-DRA is currently limited compared with other HLA genes, as only a single polymorphism encodes an amino acid difference in the translated protein. Since this SNP (rs7192, HLA00662.1:g.4276G>T p.Val217Leu) lies within exon 4, in the region encoding the cytoplasmic tail, the resulting protein is effectively monomorphic. For this reason, in-depth studies on HLA-DRA and its function have been limited. However, analysis of sequences from the 1000 Genomes Project and preliminary data from our lab reveals unrepresented polymorphism within HLA-DRA, suggesting a more complex role within the MHC than previously assumed. This study focuses on elucidating the extent of HLA-DRA polymorphism, and extending our understanding of the gene's role in HLA-DR~HLA-DQ haplotypes. Ninety-eight samples were sequenced for full-length HLA-DRA, and from this analysis, we identified 20 novel SNP positions in the intronic sequences within the 5711 bp region represented in IPD-IMGT/HLA. This polymorphism gives rise to at least 22 novel HLA-DRA alleles, and the patterns of intronic and 3' UTR polymorphism correspond to HLA-DRA~HLA-DRB345~HLA-DRB1~HLA-DQB1 haplotypes. The current understanding of the organization of the genes within the HLA-DR region assumes a single lineage for the HLA-DRA gene, as opposed to multiple gene lineages, such as in HLA-DRB. This study suggests that the intron and 3' UTR polymorphism of HLA-DRA indicates different lineages, and represents the HLA-DRA~HLA-DRB345~HLA-DRB1~HLA-DQB1 haplotypes.
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Affiliation(s)
- Ben M Matern
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Timo I Olieslagers
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Christina E M Voorter
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Mathijs Groeneweg
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Marcel G J Tilanus
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
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7
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Barsakis K, Babrzadeh F, Chi A, Mallempati K, Pickle W, Mindrinos M, Fernández-Viña MA. Complete nucleotide sequence characterization of DRB5 alleles reveals a homogeneous allele group that is distinct from other DRB genes. Hum Immunol 2019; 80:437-448. [PMID: 30954494 PMCID: PMC6622178 DOI: 10.1016/j.humimm.2019.04.001] [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: 02/04/2019] [Revised: 03/23/2019] [Accepted: 04/01/2019] [Indexed: 01/28/2023]
Abstract
Next Generation Sequencing allows for testing and typing of entire genes of the HLA region. A better and comprehensive sequence assessment can be achieved by the inclusion of full gene sequences of all the common alleles at a given locus. The common alleles of DRB5 are under-characterized with the full exon-intron sequence of two alleles available. In the present study the DRB5 genes from 18 subjects alleles were cloned and sequenced; haplotype analysis showed that 17 of them had a single copy of DRB5 and one consanguineous subject was homozygous at all HLA loci. Methodological approaches including robust and efficient long-range PCR amplification, molecular cloning, nucleotide sequencing and de novo sequence assembly were combined to characterize DRB5 alleles. DRB5 sequences covering from 5'UTR to the end of intron 5 were obtained for DRB5*01:01, 01:02 and 02:02; partial coverage including a segment spanning exon 2 to exon 6 was obtained for DRB5*01:03, 01:08N and 02:03. Phylogenetic analysis of the generated sequences showed that the DRB5 alleles group together and have distinctive differences with other DRB loci. Novel intron variants of DRB5*01:01:01, 01:02 and 02:02 were identified. The newly characterized DRB5 intron variants of each DRB5 allele were found in subjects harboring distinct associations with alleles of DRB1, B and/or ethnicity. The new information provided by this study provides reference sequences for HLA typing methodologies. Extending sequence coverage may lead to identify the disease susceptibility factors of DRB5 containing haplotypes while the unexpected intron variations may shed light on understanding of the evolution of the DRB region.
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Affiliation(s)
- Konstantinos Barsakis
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Biology, University of Crete, Heraklion, Crete 71003, Greece
| | - Farbod Babrzadeh
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Anjo Chi
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Kalyan Mallempati
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - William Pickle
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Michael Mindrinos
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
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8
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Ferreira SN, Leite MDM, Silveira MSLD, Santos EFD, Silva ALSD, Santos EJMD. MicroRNA layer of MHC in infectious diseases. Hum Immunol 2019; 80:243-247. [PMID: 30769034 DOI: 10.1016/j.humimm.2019.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/17/2019] [Accepted: 02/11/2019] [Indexed: 01/02/2023]
Abstract
The Major Histocompatibility Complex (MHC) harbors key genes of the immune response that are likely useful as biomarkers for infectious diseases. However, little is known about their microRNAs and what role they play in infections. The present study aimed to describe the miRNA genes in the MHC (MHC-miRNA), their variability and associations with infectious diseases. Additionally, MHC-miRNA host and target genes were also evaluated in associations with infectious diseases. Surveys in several databases and literature reviews identified 48 MHC-miRNA genes, with high SNP and CNV variability able to disrupt MHC-miRNA expression and putatively under selective pressure. Eight MHC-miRNAs were found inside or close regions of classical MHC rearrangements (RCCX and DRB genome organization). The proportion of MHC-miRNAs associated with infections (23%) was higher than the proportion found for the 1917 hsa-miRNA (4%). Additionally, 35 MHC-miRNAs (57%) have at least one of their target genes associated with infectious diseases, while all nine MHC-miRNA whose host genes were associated with infections have also their target genes associated with infections, being host and target genes of five MHC-miRNAs reported to be associated with the same diseases. This finding may reflect a concerted miRNA-mediated immune response mechanism triggered by infection.
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Affiliation(s)
- Sâmila Natiane Ferreira
- Human and Medical Genetics Laboratory, Federal University of Pará, Brazil; Programa de Pós-Graduação em Biologia de Agentes Infecciosos e Parasitários, Brazil
| | - Mauro de Meira Leite
- Human and Medical Genetics Laboratory, Federal University of Pará, Brazil; Programa de Pós-Graduação em Biologia de Agentes Infecciosos e Parasitários, Brazil
| | | | | | | | - Eduardo José Melo Dos Santos
- Human and Medical Genetics Laboratory, Federal University of Pará, Brazil; Programa de Pós-Graduação em Biologia de Agentes Infecciosos e Parasitários, Brazil.
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9
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de Winter II, Qurkhuli T, de Groot N, de Vos-Rouweler AJM, van Hooft P, Heitkönig IMA, Prins HHT, Bontrop RE, Doxiadis GGM. Determining Mhc-DRB profiles in wild populations of three congeneric true lemur species by noninvasive methods. Immunogenetics 2018; 71:97-107. [PMID: 30324236 PMCID: PMC6327083 DOI: 10.1007/s00251-018-1085-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/10/2018] [Indexed: 12/22/2022]
Abstract
The major histocompatibility complex (MHC) is a highly polymorphic and polygenic genomic region that plays a crucial role in immune-related diseases. Given the need for comparative studies on the variability of immunologically important genes among wild populations and species, we investigated the allelic variation of MHC class II DRB among three congeneric true lemur species: the red-fronted lemur (Eulemur rufifrons), red-bellied lemur (Eulemur rubriventer), and black lemur (Eulemur macaco). We noninvasively collected hair and faecal samples from these species across different regions in Madagascar. We assessed DRB exon 2 polymorphism with a newly developed primer set, amplifying nearly all non-synonymous codons of the antigen-binding sites. We defined 26 DRB alleles from 45 individuals (17 alleles from E. rufifrons (N = 18); 5 from E. rubriventer (N = 7); and 4 from E. macaco (N = 20). All detected alleles are novel and show high levels of nucleotide (26.8%) and non-synonymous codon polymorphism (39.4%). In these lemur species, we found neither evidence of a duplication of DRB genes nor a sharing of alleles among sympatric groups or allopatric populations of the same species. The non-sharing of alleles may be the result of a geographical separation over a long time span and/or different pathogen selection pressures. We found dN/dS rates > 1 in the functionally important antigen recognition sites, providing evidence for balancing selection. Especially for small and isolated populations, quantifying and monitoring DRB variation are recommended to establish successful conservation plans that mitigate the possible loss of immunogenetic diversity in lemurs.
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Affiliation(s)
- Iris I de Winter
- Resource Ecology Group, Wageningen University, Wageningen, The Netherlands. .,Department of Biology, Utrecht University, Utrecht, The Netherlands.
| | - Tamar Qurkhuli
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Nanine de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Annemiek J M de Vos-Rouweler
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Pim van Hooft
- Resource Ecology Group, Wageningen University, Wageningen, The Netherlands
| | | | - Herbert H T Prins
- Resource Ecology Group, Wageningen University, Wageningen, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.,Department of Theoretical Biology and Bioinformatics, University of Utrecht, Utrecht, The Netherlands
| | - Gaby G M Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
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10
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Limited MHC class II gene polymorphism in the West African chimpanzee is distributed maximally by haplotype diversity. Immunogenetics 2018; 71:13-23. [PMID: 30159708 DOI: 10.1007/s00251-018-1080-4] [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: 06/26/2018] [Accepted: 08/22/2018] [Indexed: 10/28/2022]
Abstract
Chimpanzees have been used for some time as an animal model in research on immune-related diseases in humans. The major histocompatibility complex (MHC) region of the chimpanzee has also been the subject of studies in which the attention was mainly on the class I genes. Although full-length sequence information is available on the DRB region genes, such detailed information is lacking for the other class II genes and, if present, is based mainly on exon 2 sequences. In the present study, full-length sequencing was performed on DQ, DP, and DRA genes in a cohort of 67 pedigreed animals, thereby allowing a thorough analysis of the MHC class II repertoire. The results demonstrate that the number of MHC class II lineages and alleles is relatively low, whereas haplotype diversity (combination of genes/alleles on a chromosome) seems to have been maximised by crossing-over processes.
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11
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Gouw JW, Jo J, Meulenbroek LAPM, Heijjer TS, Kremer E, Sandalova E, Knulst AC, Jeurink PV, Garssen J, Rijnierse A, Knippels LMJ. Identification of peptides with tolerogenic potential in a hydrolysed whey-based infant formula. Clin Exp Allergy 2018; 48:1345-1353. [PMID: 29974988 DOI: 10.1111/cea.13223] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/08/2018] [Accepted: 06/28/2018] [Indexed: 12/29/2022]
Abstract
BACKGROUND Failure to induce oral tolerance may result in food allergy. Hydrolysed cow's milk-based infant formulas are recommended in subjects with a high risk of developing allergic disease. Presentation of T cell epitopes is a prerequisite to generate regulatory T cells that could contribute to oral tolerance. OBJECTIVE To investigate whether a specific hydrolysed whey-based infant formula contains peptides that function as T cell epitopes to support the development of oral tolerance to whey. METHODS First, a novel liquid chromatography-mass spectrometry (LC-MS) method was developed to characterize β-lactoglobulin-derived peptides present in a specific infant formula with a focus on region AA#13-48 of β-lactoglobulin, which has previously been described to contain T cell epitopes with tolerogenic potential. Second, the formula was subjected to the ProImmune ProPresent® antigen presentation assay and MHC class II binding algorithm to identify relevant HLA-DRB1-restricted peptides. Third, identified peptides were tested on human cow's milk protein-specific T cell lines to determine T cell recognition. RESULTS Thirteen peptides of minimal 9AAs long that overlap with AA#13-48 of β-lactoglobulin were identified. Six of them were found across all batches analysed. It was further confirmed that these peptides were processed and presented by human dendritic cells. The identified HLA-DRB1-restricted peptides were correlated to AA#11-30 and AA#23-39 of β-lactoglobulin. Importantly, the proliferation assay showed that the synthetic peptides were recognized by cow's milk protein-specific T cell lines and induced T cell proliferation. CONCLUSION AND CLINICAL RELEVANCE This study demonstrates that the tested hydrolysed infant formula contains functional HLA-DRB1-restricted T cell epitopes, which can potentially support the development of oral tolerance to whey.
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Affiliation(s)
- Joost W Gouw
- Danone Nutricia Research, Utrecht, The Netherlands
| | - Juandy Jo
- Danone Nutricia Research, Singapore.,Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Laura A P M Meulenbroek
- Danone Nutricia Research, Utrecht, The Netherlands.,Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - T Sam Heijjer
- Danone Nutricia Research, Utrecht, The Netherlands.,Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Erica Kremer
- Danone Nutricia Research, Utrecht, The Netherlands
| | - Elena Sandalova
- Danone Nutricia Research, Singapore.,Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - André C Knulst
- Department of Dermatology and Allergology, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Prescilla V Jeurink
- Danone Nutricia Research, Utrecht, The Netherlands.,Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Johan Garssen
- Danone Nutricia Research, Utrecht, The Netherlands.,Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | | | - Léon M J Knippels
- Danone Nutricia Research, Utrecht, The Netherlands.,Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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12
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Sypek M, Kausman J, Holt S, Hughes P. HLA Epitope Matching in Kidney Transplantation: An Overview for the General Nephrologist. Am J Kidney Dis 2017; 71:720-731. [PMID: 29246419 DOI: 10.1053/j.ajkd.2017.09.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 09/20/2017] [Indexed: 11/11/2022]
Abstract
Rapid changes in tissue-typing technology, including the widespread availability of highly specific molecular typing methods and solid-phase assays for the detection of allele-specific anti-HLA antibodies, make it increasingly challenging to remain up to date with developments in organ matching. Terms such as epitopes and eplets abound in the transplantation literature, but often it can be difficult to see what they might mean for the patient awaiting transplantation. In this review, we provide the historical context for current practice in tissue typing and explore the potential role of HLA epitopes in kidney transplantation. Despite impressive gains in preventing and managing T-cell-mediated rejection and the associated improvements in graft survival, the challenge of the humoral alloresponse remains largely unmet and is the major cause of late graft loss. Describing HLA antigens as a series of antibody targets, or epitopes, rather than based on broad seroreactivity patterns or precise amino acid sequences may provide a more practical and clinically relevant system to help avoid antibody-mediated rejection, reduce sensitization, and select the most appropriate organs in the setting of pre-existing alloantibodies. We explain the systems proposed to define HLA epitopes, summarize the evidence to date for their role in transplantation, and explore the potential benefits of incorporating HLA epitopes into clinical practice as this field continues to evolve toward everyday practice.
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Affiliation(s)
- Matthew Sypek
- Department of Nephrology, Royal Melbourne Hospital, Melbourne, Australia; The University of Melbourne, Melbourne, Australia; Department of Nephrology, Royal Children's Hospital, Melbourne, Australia.
| | - Joshua Kausman
- Department of Nephrology, Royal Melbourne Hospital, Melbourne, Australia; The University of Melbourne, Melbourne, Australia; Department of Nephrology, Royal Children's Hospital, Melbourne, Australia
| | - Steve Holt
- Department of Nephrology, Royal Melbourne Hospital, Melbourne, Australia; The University of Melbourne, Melbourne, Australia
| | - Peter Hughes
- Department of Nephrology, Royal Melbourne Hospital, Melbourne, Australia; The University of Melbourne, Melbourne, Australia
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13
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Parker A, Kaufman J. What chickens might tell us about the MHC class II system. Curr Opin Immunol 2017; 46:23-29. [PMID: 28433952 DOI: 10.1016/j.coi.2017.03.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/24/2017] [Indexed: 11/15/2022]
Abstract
Almost all knowledge about the structure and function of MHC class II molecules outside of mammals comes from work with chickens. Most of the genes implicated in the class II system are present in chickens, so it is likely that the machinery of antigen processing and peptide-loading is similar to mammals. However, there is only one isotype (lineage) of classical class II genes, with one monomorphic DR-like BLA gene and two polymorphic BLB genes, located near one DMA and two DMB genes. The DMB2 and BLB2 genes are widely expressed at high levels, whereas the DMB1 and BLB1 genes are only expressed at highest levels in spleen and intestine, suggesting the possibility of two class II systems in chickens.
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Affiliation(s)
- Aimée Parker
- Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom
| | - Jim Kaufman
- University of Cambridge, Department of Pathology, Cambridge CB2 1QP, United Kingdom; University of Cambridge, Department of Veterinary Medicine, Cambridge CB3 0ES, United Kingdom.
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14
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de Groot N, Stanbury K, de Vos-Rouweler AJM, de Groot NG, Poirier N, Blancho G, de Luna C, Doxiadis GGM, Bontrop RE. A quick and robust MHC typing method for free-ranging and captive primate species. Immunogenetics 2017; 69:231-240. [PMID: 28084496 PMCID: PMC5350218 DOI: 10.1007/s00251-016-0968-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/27/2016] [Indexed: 12/21/2022]
Abstract
Gene products of the major histocompatibility complex (MHC) of human and non-human primates play a crucial role in adaptive immunity, and most of the relevant genes not only show a high degree of variability (polymorphism) but also copy number variation (CNV) is observed. Due to this diversity, MHC proteins influence the capability of individuals to cope with various pathogens. MHC and/or MHC-linked gene products such as odorant receptor genes are thought to influence mate choice and reproductive success. Therefore, MHC typing of wild and captive primate populations is considered to be useful in conservation biology, which is, however, often hampered by the need of invasive and time-consuming methods. All intact Mhc-DRB genes in primates appear to possess a complex and highly divergent microsatellite, DRB-STR. A panel of 154 pedigreed olive baboons (Papio anubis) was examined for their DRB content by DRB-STR analysis of genomic DNA. Using the same methodology on DNA of feces samples, DRB variability of a silvery gibbon population (Hylobates moloch) (N = 24), an endangered species, could successfully be studied. In both species, length determination of the DRB-STR resulted in the definition of unique genotyping patterns that appeared to be specific for a certain chromosome. Moreover, the different STR lengths were shown to segregate with the allelic variation of the respective gene. The results obtained expand data gained previously on DRB-STR typing in macaques, great apes, and humans and strengthen the conclusion that this protocol is applicable in molecular ecology, conservation biology, and colony management, especially of endangered primate species.
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Affiliation(s)
- N de Groot
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - K Stanbury
- Writtle College, Essex University, Lordship Road, Writtle, Chelmsford, Essex, CM1 3RR, UK
| | - A J M de Vos-Rouweler
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - N G de Groot
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - N Poirier
- Institut National de la Sante et de la Recherche Medicale (INSERM) UMR1064, Institut de Transplantation-Urologie-Nephrologie (ITUN), 30 Bd Jean Monnet, 44093, Nantes, France
| | - G Blancho
- Institut National de la Sante et de la Recherche Medicale (INSERM) UMR1064, Institut de Transplantation-Urologie-Nephrologie (ITUN), 30 Bd Jean Monnet, 44093, Nantes, France
| | - C de Luna
- Writtle College, Essex University, Lordship Road, Writtle, Chelmsford, Essex, CM1 3RR, UK
| | - G G M Doxiadis
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.
| | - R E Bontrop
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.,Department of Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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15
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Yakubu A, Salako AE, De Donato M, Peters SO, Takeet MI, Wheto M, Okpeku M, Imumorin IG. Association of SNP variants of MHC Class II DRB gene with thermo-physiological traits in tropical goats. Trop Anim Health Prod 2016; 49:323-336. [PMID: 27909914 DOI: 10.1007/s11250-016-1196-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/24/2016] [Indexed: 11/30/2022]
Abstract
Host defense in vertebrates depend on many secreted regulatory proteins such as major histocompatibility complex (MHC) class II which provide important regulatory and effector functions of T cells. Gene polymorphism in the second exon of Capra-DRB gene in three major Nigerian goat breeds [West African Dwarf (WAD), Red Sokoto (RS), and Sahel (SH)] was analyzed by restriction fragment length polymorphisms (RFLP). Four restriction enzymes, BsaHI, AluI, HaeIII, and SacII, were utilized. The association between the polymorphic sites and some heat tolerance traits were also investigated in a total of 70 WAD, 90 RS, and 50 SH goats. Fourteen different types of alleles identified in the Nigerian goats, four of which were found in the peptide coding region (A57G, Q89R, G104D, and T112I), indicate a high degree of polymorphism at the DRB locus in this species. An obvious excess (P < 0.01) of non-synonymous substitutions than synonymous (dN/dS) in this locus is a reflection of adaptive evolution and positive selection. The phylogenetic trees revealed largely species-wise clustering in DRB gene. BsaHI, AluI, HaeIII, and SacII genotype frequencies were in Hardy-Weinberg equilibrium (P > 0.05), except AluI in RS goats and HaeIII in WAD goats (P < 0.05). The expected heterozygosity (H), which is a measure of gene diversity in the goat populations, ranged from 0.16 to 0.50. Genotypes AA (BsaHI), GG, GC and CC (AluI) and GG, GA, AA (HaeIII) appeared better in terms of heat tolerance. The heat-tolerant ability of SH and RS goats to the hot and humid tropical environment of Nigeria seemed better than that of the WAD goats. Sex effect (P < 0.05) was mainly on pulse rate and heat stress index, while there were varying interaction effects on heat tolerance. Variation at the DRB locus may prove to be important in possible selection and breeding for genetic resistance to heat stress in the tropics.
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Affiliation(s)
- Abdulmojeed Yakubu
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA. .,Department of Animal Science, Nasarawa State University, Lafia, Nigeria. .,Department of Animal Science, University of Ibadan, Ibadan, Nigeria.
| | | | - Marcos De Donato
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,Laboratorio Genetica Molecular, IBB, Universidad de Oriente, Cumana, Venezuela
| | - Sunday O Peters
- Department of Animal Science, Berry College, Mt Berry, GA, 30249, USA
| | - Michael I Takeet
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,Department of Veterinary Microbiology and Parasitology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Mathew Wheto
- Department of Animal Breeding and Genetics, University of Agriculture, Abeokuta, Nigeria
| | - Moses Okpeku
- Department of Livestock Production, Niger Delta University, Amassoma, Nigeria.,State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Science (CAS), Kunming Institute of Zoology, Kunming, Yunnan Province, China
| | - Ikhide G Imumorin
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.
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16
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Grogan KE, McGinnis GJ, Sauther ML, Cuozzo FP, Drea CM. Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications. BMC Genomics 2016; 17:204. [PMID: 26957424 PMCID: PMC4782575 DOI: 10.1186/s12864-016-2503-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 02/18/2016] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Across species, diversity at the Major Histocompatibility Complex (MHC) is critical to disease resistance and population health; however, use of MHC diversity to quantify the genetic health of populations has been hampered by the extreme variation found in MHC genes. Next generation sequencing (NGS) technology generates sufficient data to genotype even the most diverse species, but workflows for distinguishing artifacts from alleles are still under development. We used NGS to evaluate the MHC diversity of over 300 captive and wild ring-tailed lemurs (Lemur catta: Primates: Mammalia). We modified a published workflow to address errors that arise from deep sequencing individuals and tested for evidence of selection at the most diverse MHC genes. RESULTS In addition to evaluating the accuracy of 454 Titanium and Ion Torrent PGM for genotyping large populations at hypervariable genes, we suggested modifications to improve current methods of allele calling. Using these modifications, we genotyped 302 out of 319 individuals, obtaining an average sequencing depth of over 1000 reads per amplicon. We identified 55 MHC-DRB alleles, 51 of which were previously undescribed, and provide the first sequences of five additional MHC genes: DOA, DOB, DPA, DQA, and DRA. The additional five MHC genes had one or two alleles each with little sequence variation; however, the 55 MHC-DRB alleles showed a high dN/dS ratio and trans-species polymorphism, indicating a history of positive selection. Because each individual possessed 1-7 MHC-DRB alleles, we suggest that ring-tailed lemurs have four, putatively functional, MHC-DRB copies. CONCLUSIONS In the future, accurate genotyping methods for NGS data will be critical to assessing genetic variation in non-model species. We recommend that future NGS studies increase the proportion of replicated samples, both within and across platforms, particularly for hypervariable genes like the MHC. Quantifying MHC diversity within non-model species is the first step to assessing the relationship of genetic diversity at functional loci to individual fitness and population viability. Owing to MHC-DRB diversity and copy number, ring-tailed lemurs may serve as an ideal model for estimating the interaction between genetic diversity, fitness, and environment, especially regarding endangered species.
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Affiliation(s)
- Kathleen E Grogan
- University Program in Ecology, Duke University, Durham, NC, USA.
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA.
- Emory University, Room 2006 O. Wayne Rollins Research Center, 1510 Clifton Rd NE, Atlanta, GA, 30322, USA.
| | | | - Michelle L Sauther
- Department of Anthropology, University of Colorado-Boulder, Boulder, CO, USA
| | - Frank P Cuozzo
- Department of Anthropology, University of North Dakota, Grand Forks, ND, USA
| | - Christine M Drea
- University Program in Ecology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Department of Biology, Duke University, Durham, USA
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17
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Abstract
The world of primate genomics is expanding rapidly in new and exciting ways owing to lowered costs and new technologies in molecular methods and bioinformatics. The primate order is composed of 78 genera and 478 species, including human. Taxonomic inferences are complex and likely a consequence of ongoing hybridization, introgression, and reticulate evolution among closely related taxa. Recently, we applied large-scale sequencing methods and extensive taxon sampling to generate a highly resolved phylogeny that affirms, reforms, and extends previous depictions of primate speciation. The next stage of research uses this phylogeny as a foundation for investigating genome content, structure, and evolution across primates. Ongoing and future applications of a robust primate phylogeny are discussed, highlighting advancements in adaptive evolution of genes and genomes, taxonomy and conservation management of endangered species, next-generation genomic technologies, and biomedicine.
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Affiliation(s)
- Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702; Current Affiliation: Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia 22630;
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