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Simanovsky AL, Madbouly A, Halagan M, Maiers M, Louzoun Y. Single haplotype admixture models using large scale HLA genotype frequencies to reproduce human admixture. Immunogenetics 2019; 71:589-604. [PMID: 31741008 DOI: 10.1007/s00251-019-01144-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/19/2019] [Indexed: 12/20/2022]
Abstract
The human leukocyte antigen (HLA) is the most polymorphic region in humans. Anthropologists use HLA to trace populations' migration and evolution. However, recent admixture between populations can mask the ancestral haplotype frequency distribution. We present a statistical method based on high-resolution HLA haplotype frequencies to resolve population admixture using a non-negative matrix factorization formalism and validated using haplotype frequencies from 56 world populations. The result is a minimal set of source components (SCs) decoding roughly 90% of the total variance in the studied admixtures. These SCs agree with the geographical distribution, phylogenies, and recent admixture events of the studied groups. With the growing population of multi-ethnic individuals, or individuals that do not report race/ethnic information, the HLA matching process for stem-cell and solid organ transplants is becoming more challenging. The presented algorithm provides a framework that facilitates the breakdown of highly admixed populations into SCs, which can be used to better match the rapidly growing population of multi-ethnic individuals worldwide.
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Affiliation(s)
| | - Abeer Madbouly
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Michael Halagan
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Martin Maiers
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Yoram Louzoun
- Department of Mathematics and Gonda brain research institute, Bar-Ilan University, 52900, Ramat-Gan, Israel.
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52
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Chowell D, Krishna C, Pierini F, Makarov V, Rizvi NA, Kuo F, Morris LGT, Riaz N, Lenz TL, Chan TA. Evolutionary divergence of HLA class I genotype impacts efficacy of cancer immunotherapy. Nat Med 2019; 25:1715-1720. [PMID: 31700181 DOI: 10.1038/s41591-019-0639-4] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/03/2019] [Indexed: 12/22/2022]
Abstract
Functional diversity of the highly polymorphic human leukocyte antigen class I (HLA-I) genes underlies successful immunologic control of both infectious disease and cancer. The divergent allele advantage hypothesis dictates that an HLA-I genotype with two alleles with sequences that are more divergent enables presentation of more diverse immunopeptidomes1-3. However, the effect of sequence divergence between HLA-I alleles-a quantifiable measure of HLA-I evolution-on the efficacy of immune checkpoint inhibitor (ICI) treatment for cancer remains unknown. In the present study the germline HLA-I evolutionary divergence (HED) of patients with cancer treated with ICIs was determined by quantifying the physiochemical sequence divergence between HLA-I alleles of each patient's genotype. HED was a strong determinant of survival after treatment with ICIs. Even among patients fully heterozygous at HLA-I, patients with an HED in the upper quartile respond better to ICIs than patients with a low HED. Furthermore, HED strongly impacts the diversity of tumor, viral and self-immunopeptidomes and intratumoral T cell receptor clonality. Similar to tumor mutation burden, HED is a fundamental metric of diversity at the major histocompatibility complex-peptide complex, which dictates ICI efficacy. The data link divergent HLA allele advantage to immunotherapy efficacy and unveil how ICI response relies on the evolved efficiency of HLA-mediated immunity.
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Affiliation(s)
- Diego Chowell
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chirag Krishna
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Federica Pierini
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Naiyer A Rizvi
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Fengshen Kuo
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luc G T Morris
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell School of Medicine, New York, NY, USA.
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53
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Kwak Y, Seo AN, Lee HE, Lee HS. Tumor immune response and immunotherapy in gastric cancer. J Pathol Transl Med 2019; 54:20-33. [PMID: 31674166 PMCID: PMC6986974 DOI: 10.4132/jptm.2019.10.08] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/08/2019] [Indexed: 02/07/2023] Open
Abstract
Remarkable developments in immuno-oncology have changed the landscape of gastric cancer (GC) treatment. Because immunotherapy intervenes with tumor immune response rather than directly targeting tumor cells, it is important to develop a greater understanding of tumor immunity. This review paper summarizes the tumor immune reaction and immune escape mechanisms while focusing on the role of T cells and their co-inhibitory signals, such as the immune checkpoint molecules programmed death-1 and programmed deathligand 1 (PD-L1). This paper also describes past clinical trials of immunotherapy for patients with GC and details their clinical implications. Strong predictive markers are essential to improve response to immunotherapy. Microsatellite instability, Epstein-Barr virus, PD-L1 expression, and tumor mutational burden are now regarded as potent predictive markers for immunotherapy in patients with GC. Novel immunotherapy and combination therapy targeting new immune checkpoint molecules such as lymphocyte-activation gene 3, T cell immunoglobulin, and mucin domain containing-3, and indoleamine 2,3-dioxygenase have been suggested, and trials are ongoing to evaluate their safety and efficacy. Immunotherapy is an important treatment option for patients with GC and has great potential for improving patient outcome, and further research in immuno-oncology should be carried out.
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Affiliation(s)
- Yoonjin Kwak
- Department of Pathology, Seoul National University Hospital, Seoul, Korea.,Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - An Na Seo
- Department of Pathology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu, Korea
| | - Hee Eun Lee
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Hye Seung Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea.,Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
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54
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Integrate CRISPR/Cas9 for protein expression of HLA-B*38:68Q via precise gene editing. Sci Rep 2019; 9:8067. [PMID: 31147565 PMCID: PMC6542842 DOI: 10.1038/s41598-019-44336-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 05/14/2019] [Indexed: 11/16/2022] Open
Abstract
The determination of null- or low-expressed HLA alleles is clinically relevant in both hematopoietic stem cell transplantation and solid organ transplantation. We studied the expression level of a questionable (Q) HLA-B*38:68Q allele, which carries a 9-nucleotide (nt) deletion at codon 230–232 in exon 4 of HLA-B*38:01:01:01 using CRISPR/Cas9 gene editing technology. CRISPR/Cas9 gene editing of HLA-B*38:01:01:01 homozygous EBV B cell line resulted in one HLA-B*38:68Q/B*38:01:01:01 heterozygous and one HLA-B*38:68Q homozygous clone. Flow cytometric analysis of monoclonal anti-Bw4 antibody showed the protein expression of HLA-B*38:01:01:01 in homozygous cells was 2.2 fold higher than HLA-B*38:68Q/B*38:01:01:01 heterozygous cells, and the expression of HLA-B*38:68Q/B*38:01:01:01 heterozygous cells was over 2.0 fold higher than HLA-B*38:68Q homozygous cells. The HLA-B*38:68Q expression was further confirmed using anti-B38 polyclonal antibody. Similarly, the expression of the HLA-B*38:01:01:01 homozygous cells was 1.5 fold higher than that of HLA-B*38:68Q/B*38:01:01:01 heterozygous cells, and the HLA-B*38:68Q/B*38:01:01:01 heterozygous cells was over 1.6 fold higher than that of HLA-B*38:68Q homozygous cells. The treatment of HLA-B*38:68Q homozygous cells with IFN-γ significantly increased its expression. In conclusion, we demonstrate that HLA-B*38:68Q is a low-expressing HLA allele. The CRISPR/Cas9 technology is a useful tool to induce precise gene editing in HLA genes to enable the characterization of HLA gene variants on expression and function.
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55
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Keenan TE, Burke KP, Van Allen EM. Genomic correlates of response to immune checkpoint blockade. Nat Med 2019; 25:389-402. [PMID: 30842677 PMCID: PMC6599710 DOI: 10.1038/s41591-019-0382-x] [Citation(s) in RCA: 299] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 12/12/2022]
Abstract
Despite impressive durable responses, immune checkpoint inhibitors do not provide a long-term benefit to the majority of patients with cancer. Understanding genomic correlates of response and resistance to checkpoint blockade may enhance benefits for patients with cancer by elucidating biomarkers for patient stratification and resistance mechanisms for therapeutic targeting. Here we review emerging genomic markers of checkpoint blockade response, including those related to neoantigens, antigen presentation, DNA repair, and oncogenic pathways. Compelling evidence also points to a role for T cell functionality, checkpoint regulators, chromatin modifiers, and copy-number alterations in mediating selective response to immune checkpoint blockade. Ultimately, efforts to contextualize genomic correlates of response into the larger understanding of tumor immune biology will build a foundation for the development of novel biomarkers and therapies to overcome resistance to checkpoint blockade.
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Affiliation(s)
- Tanya E Keenan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kelly P Burke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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56
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Abstract
Checkpoint inhibitor-based immunotherapies that target cytotoxic T lymphocyte antigen 4 (CTLA4) or the programmed cell death 1 (PD1) pathway have achieved impressive success in the treatment of different cancer types. Yet, only a subset of patients derive clinical benefit. It is thus critical to understand the determinants driving response, resistance and adverse effects. In this Review, we discuss recent work demonstrating that immune checkpoint inhibitor efficacy is affected by a combination of factors involving tumour genomics, host germline genetics, PD1 ligand 1 (PDL1) levels and other features of the tumour microenvironment, as well as the gut microbiome. We focus on recently identified molecular and cellular determinants of response. A better understanding of how these variables cooperate to affect tumour-host interactions is needed to optimize the implementation of precision immunotherapy.
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Affiliation(s)
- Jonathan J Havel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diego Chowell
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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57
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Kennedy PR, Barthen C, Williamson DJ, Davis DM. HLA-B and HLA-C Differ in Their Nanoscale Organization at Cell Surfaces. Front Immunol 2019; 10:61. [PMID: 30761133 PMCID: PMC6362897 DOI: 10.3389/fimmu.2019.00061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/11/2019] [Indexed: 12/30/2022] Open
Abstract
The particular HLA class I variants an individual carries influences their resistance and susceptibility to a multitude of diseases. Expression level and variation in the peptide binding region correlates with, for example, a person's progression to AIDS after HIV infection. One factor which has not yet been addressed is whether or not different HLA class I proteins organize differently in the cell membrane on a nanoscale. Here, we examined the organization of three HLA-B allotypes (B*2705, B*5301, and B*5701) and two HLA-C allotypes (C*0602 and C*0702) in the membrane of 721.221 cells which otherwise lack expression of HLA-B or HLA-C. All these allotypes are ligands for the T cell receptor and leukocyte immunoglobulin-like receptors, but additionally, the HLA-B allotypes are ligands for the killer-cell immunoglobulin-like receptor family member KIR3DL1, HLA-C*0602 is a ligand for KIR2DL1, and HLA-C*0702 is a ligand for KIR2DL2/3. Using super-resolution microscopy, we found that both HLA-B and HLA-C formed more clusters and a greater proportion of HLA contributed to clusters, when expressed at lower levels. Thus, HLA class I organization is a covariate in genetic association studies of HLA class I expression level with disease progression. Surprisingly, we also found that HLA-C was more clustered than HLA-B when expression level was controlled. HLA-C consistently formed larger and more numerous clusters than HLA-B and a greater proportion of HLA-C contributed to clusters than for HLA-B. We also found that the organization of HLA class I proteins varied with cell type. T cells exhibited a particularly clustered organization of HLA class I while B cells expressed a more uniform distribution. In summary, HLA class I variants are organized differently in the cell surface membrane which may impact their functions.
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Affiliation(s)
- Philippa R Kennedy
- Faculty of Biology, Medicine and Health, Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, United Kingdom
| | - Charlotte Barthen
- Faculty of Biology, Medicine and Health, Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, United Kingdom.,Division of Cell and Molecular Biology, Imperial College London, London, United Kingdom
| | - David J Williamson
- Faculty of Biology, Medicine and Health, Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, United Kingdom
| | - Daniel M Davis
- Faculty of Biology, Medicine and Health, Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, United Kingdom
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58
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Ballingall KT, Dicks K, Kyriazopoulou P, Herrmann-Hoesing L. Allelic nomenclature for the duplicated MHC class II DQ genes in sheep. Immunogenetics 2018; 71:347-351. [PMID: 30415411 DOI: 10.1007/s00251-018-1096-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/06/2018] [Indexed: 10/27/2022]
Abstract
The principal MHC class II molecules involved in the presentation of peptides to the antigen specific receptors on CD4+ T cells genes in sheep are derived from DR and DQ genes. Allelic nomenclature systems for the DRB1 and its partner DRA loci are available for Ovid's; however, no official nomenclature is available for the DQ genes which creates ambiguity within the research community. Ovine MHC haplotypes include at least two pairs of DQA and DQB genes, termed DQA1, DQB1 and DQA2, DQB2 and both sets are polymorphic and both seem to be functional. In a number of haplotypes, the DQA1 locus appears to be absent (DQA1-null) and is replaced by a second locus termed DQA2-like. Here, we identify families of alleles based on sequence similarity and phylogenetic clustering which correspond to each of the DQA and DQB genes identified in previous genomic and transcript analyses of homozygous animals. Using such criteria to cluster sequences, we have named 82 full-length and partial cDNA transcripts derived from domestic sheep (Ovis aries) which correspond to alleles at the Ovar-DQA1, DQA2, DQA2-like, DQB1, DQB2 and DQB2-like genes and provide associated sequence resources available to the research community through the IPD-MHC Database. This sets the basis for naming and annotation of DQ genes within the ovine MHC and may be used as a template for DQ genes in other ruminant species which will ultimately support research in livestock infectious disease.
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Affiliation(s)
| | - Kara Dicks
- The University of Edinburgh, Edinburgh, UK
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59
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Aliseychik MP, Andreeva TV, Rogaev EI. Immunogenetic Factors of Neurodegenerative Diseases: The Role of HLA Class II. BIOCHEMISTRY (MOSCOW) 2018; 83:1104-1116. [DOI: 10.1134/s0006297918090122] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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60
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Cao Z, Wang L, Xiang Y, Liu X, Tu Z, Sun Y, Zhou Y. MHC class IIα polymorphism and its association with resistance/susceptibility to Vibrio harveyi in golden pompano (Trachinotus ovatus). FISH & SHELLFISH IMMUNOLOGY 2018; 80:302-310. [PMID: 29902561 DOI: 10.1016/j.fsi.2018.06.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/13/2018] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
The major histocompatibility complex (MHC) plays an important role in the vertebrate immune response to antigenic peptides, and it is essential for recognizing foreign pathogens in organisms. In this study, MHC class IIα (Trov-MHC IIα) from the golden pompano (Trachinotus ovatus) was first cloned and identified. The gene structure of Trov-MHC IIα was contained four exons and three introns. High levels of polymorphism were found in the exon 2 of Trov-MHC IIα. A total of 29 different MHC class IIα alleles with high polymorphism were identified from 80 individuals. The ratio of non-synonymous substitutions (dN) to synonymous substitutions (dS) was 3.157 (>1) in the peptide binding regions (PBRs) of Trov-MHC IIα, suggesting positive balancing selection. Six alleles were selected to analyze the association between alleles and resistance/susceptibility to Vibrio harveyi in golden pompano. The results showed that Trov-DAA*6401 and Trov-DAA*6702 alleles were associated with the resistance to V. harveyi in golden pompano, while alleles Trov-DAA*6304 and Trov-DAA*7301 were associated with the susceptibility to V. harveyi in golden pompano. This study confirmed the association between alleles of MHC class IIα and disease resistance, and also detected some alleles which might be correlated with high V. harveyi-resistance. These disease resistance-related MHC alleles could be used as potential genetic markers for molecular marker-assisted selective breeding in the golden pompano.
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Affiliation(s)
- Zhenjie Cao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, PR China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, PR China; Institute of Tropical Agriculture and Forestry, Hainan University, PR China
| | - Lu Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, PR China; Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, PR China
| | - Yajing Xiang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, PR China; Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, PR China
| | - Xiaocen Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, PR China; Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, PR China
| | - Zhigang Tu
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, Hainan, China
| | - Yun Sun
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, PR China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, PR China.
| | - Yongcan Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, PR China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, PR China.
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61
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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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62
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Ramarathinam SH, Croft NP, Illing PT, Faridi P, Purcell AW. Employing proteomics in the study of antigen presentation: an update. Expert Rev Proteomics 2018; 15:637-645. [PMID: 30080115 DOI: 10.1080/14789450.2018.1509000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Our immune system discriminates self from non-self by examining the peptide cargo of human leukocyte antigen (HLA) molecules displayed on the cell surface. Successful recognition of HLA-bound non-self peptides can induce T cell responses leading to, for example, the destruction of infected cells. Today, largely due to advances in technology, we have an unprecedented capability to identify the nature of these presented peptides and unravel the true complexity of antigen presentation. Areas covered: In addition to conventional linear peptides, HLA molecules also present post-translationally modified sequences comprising a wealth of chemical and structural modifications, including a novel class of noncontiguous spliced peptides. This review focuses on these emerging themes in antigen presentation and how mass spectrometry in particular has contributed to a new view of the antigenic landscape that is presented to the immune system. Expert Commentary: Advances in the sensitivity of mass spectrometers and use of hybrid fragmentation technologies will provide more information-rich spectra of HLA bound peptides leading to more definitive identification of T cell epitopes. Coupled with improvements in sample preparation and new informatics workflows, studies will access novel classes of peptide antigen and allow interrogation of rare and clinically relevant samples.
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Affiliation(s)
- Sri H Ramarathinam
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Nathan P Croft
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Patricia T Illing
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Pouya Faridi
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Anthony W Purcell
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
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63
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Voorter CEM, Matern B, Tran TH, Fink A, Vidan-Jeras B, Montanic S, Fischer G, Fae I, de Santis D, Whidborne R, Andreani M, Testi M, Groeneweg M, Tilanus MGJ. Full-length extension of HLA allele sequences by HLA allele-specific hemizygous Sanger sequencing (SSBT). Hum Immunol 2018; 79:763-772. [PMID: 30107213 DOI: 10.1016/j.humimm.2018.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 12/27/2022]
Abstract
The gold standard for typing at the allele level of the highly polymorphic Human Leucocyte Antigen (HLA) gene system is sequence based typing. Since sequencing strategies have mainly focused on identification of the peptide binding groove, full-length sequence information is lacking for >90% of the HLA alleles. One of the goals of the 17th IHIWS workshop is to establish full-length sequences for as many HLA alleles as possible. In our component "Extension of HLA sequences by full-length HLA allele-specific hemizygous Sanger sequencing" we have used full-length hemizygous Sanger Sequence Based Typing to achieve this goal. We selected samples of which full length sequences were not available in the IPD-IMGT/HLA database. In total we have generated the full-length sequences of 48 HLA-A, 45 -B and 31 -C alleles. For HLA-A extended alleles, 39/48 showed no intron differences compared to the first allele of the corresponding allele group, for HLA-B this was 26/45 and for HLA-C 20/31. Comparing the intron sequences to other alleles of the same allele group revealed that in 5/48 HLA-A, 16/45 HLA-B and 8/31 HLA-C alleles the intron sequence was identical to another allele of the same allele group. In the remaining 10 cases, the sequence either showed polymorphism at a conserved nucleotide or was the result of a gene conversion event. Elucidation of the full-length sequence gives insight in the polymorphic content of the alleles and facilitates the identification of its evolutionary origin.
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Affiliation(s)
- Christina E M Voorter
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands.
| | - Ben Matern
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Thuong Hien Tran
- Transplantation Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Annette Fink
- Transplantation Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Blanka Vidan-Jeras
- Tissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Sendi Montanic
- Tissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Gottfried Fischer
- Department for Blood Group Serology and Blood Transfusion Medicine, Medical University Vienna, Vienna, Austria
| | - Ingrid Fae
- Department for Blood Group Serology and Blood Transfusion Medicine, Medical University Vienna, Vienna, Austria
| | - Dianne de Santis
- Department of Clinical Immunology, PathWest, Royal Perth Hospital, Perth, Australia
| | - Rebecca Whidborne
- Department of Clinical Immunology, PathWest, Royal Perth Hospital, Perth, Australia
| | - Marco Andreani
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Manuela Testi
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - 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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Tucci S, Vohr SH, McCoy RC, Vernot B, Robinson MR, Barbieri C, Nelson BJ, Fu W, Purnomo GA, Sudoyo H, Eichler EE, Barbujani G, Visscher PM, Akey JM, Green RE. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science 2018; 361:511-516. [PMID: 30072539 PMCID: PMC6709593 DOI: 10.1126/science.aar8486] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 06/22/2018] [Indexed: 12/21/2022]
Abstract
Flores Island, Indonesia, was inhabited by the small-bodied hominin species Homo floresiensis, which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale single-nucleotide polymorphism data and whole-genome sequences from a contemporary human pygmy population living on Flores near the cave where H. floresiensis was found. The genomes of Flores pygmies reveal a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins. Modern individuals bear the signatures of recent positive selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related to diet, and polygenic selection acting on standing variation that contributed to their short-stature phenotype. Thus, multiple independent instances of hominin insular dwarfism occurred on Flores.
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Affiliation(s)
- Serena Tucci
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute, Princeton University, Princeton, NJ, USA
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Samuel H Vohr
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Rajiv C McCoy
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute, Princeton University, Princeton, NJ, USA
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthew R Robinson
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Génopode, Quatier Sorge, Lausanne, Switzerland
| | - Chiara Barbieri
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
| | - Brad J Nelson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Wenqing Fu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Gludhug A Purnomo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Guido Barbujani
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Joshua M Akey
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute, Princeton University, Princeton, NJ, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA.
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65
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Hoover B, Alcaide M, Jennings S, Sin SYW, Edwards SV, Nevitt GA. Ecology can inform genetics: Disassortative mating contributes to MHC polymorphism in Leach's storm-petrels (Oceanodroma leucorhoa). Mol Ecol 2018; 27:3371-3385. [PMID: 30010226 DOI: 10.1111/mec.14801] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/31/2018] [Accepted: 06/20/2018] [Indexed: 01/03/2023]
Abstract
Studies of MHC-based mate choice in wild populations often test hypotheses on species exhibiting female choice and male-male competition, which reflects the general prevalence of females as the choosy sex in natural systems. Here, we examined mutual mate-choice patterns in a small burrow-nesting seabird, the Leach's storm-petrel (Oceanodroma leucorhoa), using the major histocompatibility complex (MHC). The life history and ecology of this species are extreme: both partners work together to fledge a single chick during the breeding season, a task that requires regularly travelling hundreds of kilometres to and from foraging grounds over a 6- to 8-week provisioning period. Using a 5-year data set unprecedented for this species (n = 1078 adults and 925 chicks), we found a positive relationship between variation in the likelihood of female reproductive success and heterozygosity at Ocle-DAB2, a MHC class IIB locus. Contrary to previous reports rejecting disassortative mating as a mechanism for maintaining genetic polymorphism in this species, here we show that males make significant disassortative mate-choice decisions. Variability in female reproductive success suggests that the most common homozygous females (Ocle-DAB2*01/Ocle-DAB2*01) may be physiologically disadvantaged and, therefore, less preferred as lifelong partners for choosy males. The results from this study support the role of mate choice in maintaining high levels of MHC variability in a wild seabird species and highlight the need to incorporate a broader ecological framework and sufficient sample sizes into studies of MHC-based mating patterns in wild populations in general.
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Affiliation(s)
- Brian Hoover
- Graduate Group in Ecology, University of California, Davis, California
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California
| | - Miguel Alcaide
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Sarah Jennings
- Graduate Group in Ecology, University of California, Davis, California
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California
| | - Simon Yung Wa Sin
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Gabrielle A Nevitt
- Graduate Group in Ecology, University of California, Davis, California
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California
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66
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DeWitt WS, Yu KKQ, Wilburn DB, Sherwood A, Vignali M, Day CL, Scriba TJ, Robins HS, Swanson WJ, Emerson RO, Bradley PH, Seshadri C. A Diverse Lipid Antigen-Specific TCR Repertoire Is Clonally Expanded during Active Tuberculosis. THE JOURNAL OF IMMUNOLOGY 2018; 201:888-896. [PMID: 29914888 DOI: 10.4049/jimmunol.1800186] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/21/2018] [Indexed: 01/06/2023]
Abstract
Human T cells that recognize lipid Ags presented by highly conserved CD1 proteins often express semi-invariant TCRs, but the true diversity of lipid Ag-specific TCRs remains unknown. We use CD1b tetramers and high-throughput immunosequencing to analyze thousands of TCRs from ex vivo-sorted or in vitro-expanded T cells specific for the mycobacterial lipid Ag, glucose monomycolate. Our results reveal a surprisingly diverse repertoire resulting from editing of germline-encoded gene rearrangements analogous to MHC-restricted TCRs. We used a distance-based metric (TCRDist) to show how this diverse TCR repertoire builds upon previously reported conserved motifs by including subject-specific TCRs. In a South African cohort, we show that TCRDist can identify clonal expansion of diverse glucose monomycolate-specific TCRs and accurately distinguish patients with active tuberculosis from control subjects. These data suggest that similar mechanisms govern the selection and expansion of peptide and lipid Ag-specific T cells despite the nonpolymorphic nature of CD1.
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Affiliation(s)
- William S DeWitt
- Adaptive Biotechnologies, Seattle, WA 98102.,Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109.,Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Krystle K Q Yu
- Department of Medicine, University of Washington, Seattle, WA 98195
| | - Damien B Wilburn
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | | | | | - Cheryl L Day
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322.,Emory Vaccine Center, Atlanta, GA 30329
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.,Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - Harlan S Robins
- Adaptive Biotechnologies, Seattle, WA 98102.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Willie J Swanson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | | | - Philip H Bradley
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and.,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Chetan Seshadri
- Department of Medicine, University of Washington, Seattle, WA 98195;
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67
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Human Leukocyte Antigen-A, B, C, DRB1, and DQB1 Allele and Haplotype Frequencies in a Subset of 237 Donors in the South African Bone Marrow Registry. J Immunol Res 2018; 2018:2031571. [PMID: 29850621 PMCID: PMC5937380 DOI: 10.1155/2018/2031571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/30/2018] [Accepted: 04/11/2018] [Indexed: 12/31/2022] Open
Abstract
Human leukocyte antigen- (HLA-) A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 allele and haplotype frequencies were studied in a subset of 237 volunteer bone marrow donors registered at the South African Bone Marrow Registry (SABMR). Hapl-o-Mat software was used to compute allele and haplotype frequencies from individuals typed at various resolutions, with some alleles in multiple allele code (MAC) format. Four hundred and thirty-eight HLA-A, 235 HLA-B, 234 HLA-DRB1, 41 HLA-DQB1, and 29 HLA-C alleles are reported. The most frequent alleles were A∗02:02g (0.096), B∗07:02g (0.082), C∗07:02g (0.180), DQB1∗06:02 (0.157), and DRB1∗15:01 (0.072). The most common haplotype was A∗03:01g~B∗07:02g~C∗07:02g~DQB1∗06:02~DRB1∗15:01 (0.067), which has also been reported in other populations. Deviations from Hardy-Weinberg equilibrium were observed in A, B, and DRB1 loci, with C~DQB1 being the only locus pair in linkage disequilibrium. This study describes allele and haplotype frequencies from a subset of donors registered at SABMR, the only active bone marrow donor registry in Africa. Although the sample size was small, our results form a key resource for future population studies, disease association studies, and donor recruitment strategies.
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68
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Linnenbrink M, Teschke M, Montero I, Vallier M, Tautz D. Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice ( Mus musculus). Front Zool 2018; 15:15. [PMID: 29721030 PMCID: PMC5910556 DOI: 10.1186/s12983-018-0266-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022] Open
Abstract
Background The MHC class I and II loci mediate the adaptive immune response and belong to the most polymorphic loci in vertebrate genomes. In fact, the number of different alleles in a given species is often so large that it remains a challenge to provide an evolutionary model that can fully account for this. Results We provide here a general survey of MHC allele numbers in house mouse populations and two sub-species (M. m. domesticus and M. m. musculus) for H2 class I D and K, as well as class II A and E loci. Between 50 and 90% of the detected different sequences constitute new alleles, confirming that the discovery of new alleles is indeed far from complete. House mice live in separate demes with small effective population sizes, factors that were proposed to reduce, rather than enhance the possibility for the maintenance of many different alleles. To specifically investigate the occurrence of alleles within demes, we focused on the class II H2-Aa and H2-Eb exon 2 alleles in nine demes of M. m. domesticus from two different geographic regions. We find on the one hand a group of alleles that occur in different sampling regions and three quarters of these are also found in both sub-species. On the other hand, the larger group of different alleles (56%) occurs only in one of the regions and most of these (89%) only in single demes. We show that most of these region-specific alleles have apparently arisen through recombination and/or partial gene conversion from already existing alleles. Conclusions Demes can act as sources of alleles that outnumber the set of alleles that are shared across the species range. These findings support the reservoir model proposed for human MHC diversity, which states that large pools of rare MHC allele variants are continuously generated by neutral mutational mechanisms. Given that these can become important in the defense against newly emerging pathogens, the reservoir model complements the selection based models for MHC diversity and explains why the exceptional diversity exists. Electronic supplementary material The online version of this article (10.1186/s12983-018-0266-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miriam Linnenbrink
- 3Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306 Plön, Germany
| | - Meike Teschke
- 1Present address: Deutsche Forschungsgemeinschaft, 53170 Bonn, Germany.,3Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306 Plön, Germany
| | - Inka Montero
- 2Present address: Medical Faculty, Eberhard Karls Universität Tübingen, Tübingen, Germany.,3Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306 Plön, Germany
| | - Marie Vallier
- 3Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306 Plön, Germany
| | - Diethard Tautz
- 3Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306 Plön, Germany
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69
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Chowell D, Morris LGT, Grigg CM, Weber JK, Samstein RM, Makarov V, Kuo F, Kendall SM, Requena D, Riaz N, Greenbaum B, Carroll J, Garon E, Hyman DM, Zehir A, Solit D, Berger M, Zhou R, Rizvi NA, Chan TA. Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy. Science 2018; 359:582-587. [PMID: 29217585 PMCID: PMC6057471 DOI: 10.1126/science.aao4572] [Citation(s) in RCA: 730] [Impact Index Per Article: 121.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/29/2017] [Indexed: 12/15/2022]
Abstract
CD8+ T cell-dependent killing of cancer cells requires efficient presentation of tumor antigens by human leukocyte antigen class I (HLA-I) molecules. However, the extent to which patient-specific HLA-I genotype influences response to anti-programmed cell death protein 1 or anti-cytotoxic T lymphocyte-associated protein 4 is currently unknown. We determined the HLA-I genotype of 1535 advanced cancer patients treated with immune checkpoint blockade (ICB). Maximal heterozygosity at HLA-I loci ("A," "B," and "C") improved overall survival after ICB compared with patients who were homozygous for at least one HLA locus. In two independent melanoma cohorts, patients with the HLA-B44 supertype had extended survival, whereas the HLA-B62 supertype (including HLA-B*15:01) or somatic loss of heterozygosity at HLA-I was associated with poor outcome. Molecular dynamics simulations of HLA-B*15:01 revealed different elements that may impair CD8+ T cell recognition of neoantigens. Our results have important implications for predicting response to ICB and for the design of neoantigen-based therapeutic vaccines.
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Affiliation(s)
- Diego Chowell
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Luc G T Morris
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Claud M Grigg
- NewYork-Presbyterian/Columbia University Medical Center, 177 Fort Washington Avenue, New York, NY 10032, USA
| | - Jeffrey K Weber
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Robert M Samstein
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Fengshen Kuo
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sviatoslav M Kendall
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David Requena
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Nadeem Riaz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Benjamin Greenbaum
- Tisch Cancer Institute, Departments of Medicine, Oncological Sciences, and Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James Carroll
- David Geffen School of Medicine, University of California, Los Angeles, 2825 Santa Monica Boulevard, Suite 200, Santa Monica, CA 90404, USA
| | - Edward Garon
- David Geffen School of Medicine, University of California, Los Angeles, 2825 Santa Monica Boulevard, Suite 200, Santa Monica, CA 90404, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell School of Medicine, New York, NY 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ruhong Zhou
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Naiyer A Rizvi
- NewYork-Presbyterian/Columbia University Medical Center, 177 Fort Washington Avenue, New York, NY 10032, USA.
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell School of Medicine, New York, NY 10065, USA
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70
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Dendrou CA, Petersen J, Rossjohn J, Fugger L. HLA variation and disease. Nat Rev Immunol 2018; 18:325-339. [PMID: 29292391 DOI: 10.1038/nri.2017.143] [Citation(s) in RCA: 416] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fifty years since the first description of an association between HLA and human disease, HLA molecules have proven to be central to physiology, protective immunity and deleterious, disease-causing autoimmune reactivity. Technological advances have enabled pivotal progress in the determination of the molecular mechanisms that underpin the association between HLA genetics and functional outcome. Here, we review our current understanding of HLA molecules as the fundamental platform for immune surveillance and responsiveness in health and disease. We evaluate the scope for personalized antigen-specific disease prevention, whereby harnessing HLA-ligand interactions for clinical benefit is becoming a realistic prospect.
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Affiliation(s)
- Calliope A Dendrou
- Nuffield Department of Medicine, The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jan Petersen
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.,Infection and Immunity Programme and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.,Infection and Immunity Programme and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.,Division of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Lars Fugger
- Danish National Research Foundation Centre PERSIMUNE, Rigshospitalet, University of Copenhagen, Copenhagen DK-2100, Denmark.,Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK
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71
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Meyer D, C Aguiar VR, Bitarello BD, C Brandt DY, Nunes K. A genomic perspective on HLA evolution. Immunogenetics 2018; 70:5-27. [PMID: 28687858 PMCID: PMC5748415 DOI: 10.1007/s00251-017-1017-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 06/16/2017] [Indexed: 12/20/2022]
Abstract
Several decades of research have convincingly shown that classical human leukocyte antigen (HLA) loci bear signatures of natural selection. Despite this conclusion, many questions remain regarding the type of selective regime acting on these loci, the time frame at which selection acts, and the functional connections between genetic variability and natural selection. In this review, we argue that genomic datasets, in particular those generated by next-generation sequencing (NGS) at the population scale, are transforming our understanding of HLA evolution. We show that genomewide data can be used to perform robust and powerful tests for selection, capable of identifying both positive and balancing selection at HLA genes. Importantly, these tests have shown that natural selection can be identified at both recent and ancient timescales. We discuss how findings from genomewide association studies impact the evolutionary study of HLA genes, and how genomic data can be used to survey adaptive change involving interaction at multiple loci. We discuss the methodological developments which are necessary to correctly interpret genomic analyses involving the HLA region. These developments include adapting the NGS analysis framework so as to deal with the highly polymorphic HLA data, as well as developing tools and theory to search for signatures of selection, quantify differentiation, and measure admixture within the HLA region. Finally, we show that high throughput analysis of molecular phenotypes for HLA genes-namely transcription levels-is now a feasible approach and can add another dimension to the study of genetic variation.
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Affiliation(s)
- Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil.
| | - Vitor R C Aguiar
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Bárbara D Bitarello
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Débora Y C Brandt
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
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72
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Shi B, Thomas AJ, Benninghoff AD, Sessions BR, Meng Q, Parasar P, Rutigliano HM, White KL, Davies CJ. Genetic and epigenetic regulation of major histocompatibility complex class I gene expression in bovine trophoblast cells. Am J Reprod Immunol 2017; 79. [PMID: 29131441 PMCID: PMC5728445 DOI: 10.1111/aji.12779] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 10/10/2017] [Indexed: 11/28/2022] Open
Abstract
Problem The regulatory mechanisms governing differential expression of classical major histocompatibility complex (MHC) class I (MHC‐Ia) and non‐classical MHC class I (MHC‐Ib) genes are poorly understood. Method of study Quantitative reverse transcription‐ polymerase chain reaction (PCR) was used to compare the abundance of MHC‐I transcripts and related transcription factors in peripheral blood mononuclear cells (PBMC) and placental trophoblast cells (PTC). Methylation of MHC‐I CpG islands was detected by bisulfite treatment and next‐generation sequencing. Demethylation of PBMC and PTC with 5′‐aza‐deoxycytidine was used to assess the role of methylation in gene regulation. Results MHC‐I expression was higher in PBMC than PTC and was correlated with expression of IRF1, class II MHC transactivator (CIITA), and STAT1. The MHC‐Ia genes and BoLA‐NC1 were devoid of CpG methylation in PBMC and PTC. In contrast, CpG sites in the gene body of BoLA‐NC2, ‐NC3, and ‐NC4 were highly methylated in PBMC but largely unmethylated in normal PTC and moderately methylated in somatic cell nuclear transfer PTC. In PBMC, demethylation resulted in upregulation of MHC‐Ib by 2.8‐ to 6‐fold, whereas MHC‐Ia transcripts were elevated less than 2‐fold. Conclusion DNA methylation regulates bovine MHC‐Ib expression and is likely responsible for the different relative levels of MHC‐Ib to MHC‐Ia transcripts in PBMC and PTC.
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Affiliation(s)
- Bi Shi
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA
| | - Aaron J Thomas
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA
| | - Abby D Benninghoff
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,School of Veterinary Medicine, Utah State University, Logan, UT, USA
| | - Benjamin R Sessions
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA
| | - Qinggang Meng
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA
| | - Parveen Parasar
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA
| | - Heloisa M Rutigliano
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,School of Veterinary Medicine, Utah State University, Logan, UT, USA
| | - Kenneth L White
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA.,School of Veterinary Medicine, Utah State University, Logan, UT, USA
| | - Christopher J Davies
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA.,School of Veterinary Medicine, Utah State University, Logan, UT, USA
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73
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Abstract
In comparison to humans and chimpanzees, gorillas show low diversity at MHC class I genes (Gogo), as reflected by an overall reduced level of allelic variation as well as the absence of a functionally important sequence motif that interacts with killer cell immunoglobulin-like receptors (KIR). Here, we use recently generated large-scale genomic sequence data for a reassessment of allelic diversity at Gogo-C, the gorilla orthologue of HLA-C. Through the combination of long-range amplifications and long-read sequencing technology, we obtained, among the 35 gorillas reanalyzed, three novel full-length genomic sequences including a coding region sequence that has not been previously described. The newly identified Gogo-C*03:01 allele has a divergent recombinant structure that sets it apart from other Gogo-C alleles. Domain-by-domain phylogenetic analysis shows that Gogo-C*03:01 has segments in common with Gogo-B*07, the additional B-like gene that is present on some gorilla MHC haplotypes. Identified in ~ 50% of the gorillas analyzed, the Gogo-C*03:01 allele exclusively encodes the C1 epitope among Gogo-C allotypes, indicating its important function in controlling natural killer cell (NK cell) responses via KIR. We further explored the hypothesis whether gorillas experienced a selective sweep which may have resulted in a general reduction of the gorilla MHC class I repertoire. Our results provide little support for a selective sweep but rather suggest that the overall low Gogo class I diversity can be best explained by drastic demographic changes gorillas experienced in the ancient and recent past.
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74
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Ballingall KT, Lantier I, Todd H, Lantier F, Rocchi M. Structural and functional diversity arising from intra- and inter-haplotype combinations of duplicated DQA and B loci within the ovine MHC. Immunogenetics 2017; 70:257-269. [PMID: 28889256 DOI: 10.1007/s00251-017-1029-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/03/2017] [Indexed: 11/27/2022]
Abstract
In sheep, the A and B loci encoding the α and β chains of the classical class II MHC molecules are DRA and DRB and DQA and DQB. Previous analyses described the duplication of the DQA and DQB genes. The majority of haplotypes include DQA1 and DQA2 loci, however, in a number of haplotypes, DQA1 appears absent and these haplotypes have been described as DQA1 null. In these haplotypes, the DQA2 locus is found in combination with a second locus which appeared more closely related to DQA2 than DQA1, hence the description of this locus as DQA2-like. Here we combine our previous analysis of the DQA transcripts with an analysis of the associated DQB transcripts in ten haplotypes from MHC homozygous animals. This allows the potential for surface expression of different haplotype combinations of DQA and B genes and the functional significance of DQA2-like and its predicted DQB partner to be determined. Atypical DQB transcripts (DQB2-like) were identified in haplotypes classified as DQA1-null and conserved DQB2-like orthologues were identified in other Bovidae indicating trans-species conservation of the allelic lineage. Functional combinations detected by co-transfection of DQ1, DQ2 and DQ2-like genes demonstrates the potential for a wide range of DQ molecules derived from both intra- and inter-haplotype as well as inter-locus combinations. We provide evidence that DQA2-like and B2-like genes form an evolutionary conserved pair which generates structurally distinct class II molecules that are likely to present a distinct range of peptides to CD4+ T cells.
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Affiliation(s)
- Keith T Ballingall
- Moredun Research Institute, Pentland Science Park, Bush Loan, Penicuik, EH26 OPZ, Midlothian, UK.
| | - Isabelle Lantier
- INRA-Centre Val de Loire, UMR 1282, Infectiologie et Santé Publique, 37380, Nouzilly, France
| | - Helen Todd
- Moredun Research Institute, Pentland Science Park, Bush Loan, Penicuik, EH26 OPZ, Midlothian, UK
| | - Frederic Lantier
- INRA-Centre Val de Loire, UMR 1282, Infectiologie et Santé Publique, 37380, Nouzilly, France
| | - Mara Rocchi
- Moredun Research Institute, Pentland Science Park, Bush Loan, Penicuik, EH26 OPZ, Midlothian, UK
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75
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Mouafo LCM, Dambaya B, Ngoufack NN, Nkenfou CN. Host Molecular Factors and Viral Genotypes in the Mother-to-Child HIV-1 Transmission in Sub-Saharan Africa. J Public Health Afr 2017; 8:594. [PMID: 28748061 PMCID: PMC5510234 DOI: 10.4081/jphia.2017.594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 05/02/2017] [Indexed: 12/22/2022] Open
Abstract
Maternal viral load and immune status, timing and route of delivery, viral subtype, and host genetics are known to influence the transmission, acquisition and disease progression of human immunodeficiency virus-1 (HIV-1) infection. This review summarizes the findings from published works on host molecular factors and virus genotypes affecting mother to child transmission (MTCT) in Africa and identifies the gaps that need to be addressed in future research. Articles in PubMed, Google and AIDSearch and relevant conference abstracts publications were searched. Accessible articles on host factors and viral genetics impacting the MTCT of HIV, done on African populations till 2015 were downloaded. Forty-six articles were found and accessed; 70% described host genes impacting the transmission. The most studied gene was the CCR5 promoter, followed by the CCR2-64I found to reduce MTCT; then SDF1-3’A shown to have no effect on MTCT and others like the DC-SIGNR, CD4, CCL3 and IP-10. The HLA class I was most studied and was generally linked to the protective effect on MTCT. Breast milk constituents were associated to protection against MTCT. However, existing studies in Sub Saharan Africa were done just in few countries and some done without control groups. Contradictory results obtained may be due to different genetic background, type of controls, different socio-cultural and economic environment and population size. More studies are thus needed to better understand the mechanism of transmission or prevention.
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Affiliation(s)
- Linda Chapdeleine M Mouafo
- Department of Biochemistry, University of Dschang, Yaoundé, Cameroon.,Systems Biology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Béatrice Dambaya
- Systems Biology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon.,Department of Animal Sciences, University of Yaounde 1, Cameroon
| | - Nicole N Ngoufack
- Systems Biology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon.,Department of Biochemistry, University of Yaounde 1, Cameroon
| | - Céline N Nkenfou
- Systems Biology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon.,Higher Teachers' Training College, University of Yaounde 1, Cameroon
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76
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Grosberg RK, Levitan DR, Cameron BB. EVOLUTIONARY GENETICS OF ALLORECOGNITION IN THE COLONIAL HYDROID HYDRACTINIA SYMBIOLONGICARPUS. Evolution 2017; 50:2221-2240. [PMID: 28565652 DOI: 10.1111/j.1558-5646.1996.tb03612.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/1995] [Accepted: 05/14/1996] [Indexed: 12/01/2022]
Abstract
Many sedentary, clonal marine invertebrates compete intensively with conspecifics for habitable space. Allorecognition systems mediate the nature and outcome of these intraspecific competitive interactions, such that the initiation of agonistic behavior and the potential for intergenotypic fusion depend strongly on the relatedness of the contestants. The dependence of these behaviors on relatedness, along with the extraordinary precision with which self can be discriminated from nonself, suggest that allorecognition systems are highly polymorphic genetically. However, allotypic specificity of this sort could be produced by any number of genetic scenarios, ranging from relatively few loci with abundant allelic variation to numerous loci with relatively few alleles per locus. At this point, virtually nothing is known of the formal genetics of allorecognition in marine invertebrates; consequently, the evolutionary dynamics of such systems remain poorly understood. In this paper, we characterize the formal genetics of allorecognition in the marine hydrozoan Hydractinia symbiolongicarpus. Hydractinia symbiolongicarpus colonizes gastropod shells occupied by hermit crabs. When two or more individuals grow into contact, one of three outcomes ensues: fusion (compatibility), transitory fusion (a temporary state of compatibility), and rejection (incompatibility, often accompanied by the production of agonistic structures termed hyperplastic stolons). Observed patterns of compatibility between unrelated, half-sib pairs, and full-sib pairs show that unrelated and half-sib pairs under laboratory culture have a very low probability of being fusible, whereas full sibs have a roughly 30% rate of fusion in experimental pairings. The genetic simulations indicate that roughly five loci, with 5-7 alleles per locus, confer specificity in this species. In ecological terms, the reproductive ecology of H. symbiolongicarpus should promote the cosettlement of kin, some of which should be full sibs, and some half sibs. Thus, there is potential for kin selection to play a major role in the evolution of the H. symbiolongicarpus allorecognition system. In genetic terms, this system conforms to theoretical predictions for a recognition system selected to distinguish among classes of kin, in addition to self from nonself.
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Affiliation(s)
- Richard K Grosberg
- Center for Population Biology, University of California, Davis, California, 95616
| | - Don R Levitan
- Department of Biological Sciences, Florida State University, Tallahassee, Florida, 32306-2043
| | - Brenda B Cameron
- Center for Population Biology, University of California, Davis, California, 95616
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77
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Hedrick PW, Parker KM. MHC VARIATION IN THE ENDANGERED GILA TOPMINNOW. Evolution 2017; 52:194-199. [PMID: 28568136 DOI: 10.1111/j.1558-5646.1998.tb05152.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/1997] [Accepted: 11/13/1997] [Indexed: 11/30/2022]
Abstract
Sequence variation at a major histocompatibility complex (MHC) gene, assumed to be involved in parasite and pathogen resistance, was examined in the endangered Gila topminnow (Poeciliopis o. occidentalis), from the four watersheds where they remain in the United States. This is the first estimate of variation in MHC genes in natural populations of an endangered species. The population that has experienced the most bottlenecks historically was monomorphic for MHC variation. Another population, which earlier had been found to be the only population polymorphic for allozymes, had five MHC alleles, four different from those found in the other populations. Overall, nine different alleles were found. The four populations were highly divergent at MHC with four of the six population pairs not sharing any alleles. However, the magnitude of differentiation between populations on the amino-acid level varied fivefold for the populations that shared no alleles. Using single-stranded conformational polymorphism (SSCP), these alleles segregated consistently with Mendelian expectations in families. Because of the high genetic differentiation between these populations for a potentially adaptive gene, we recommend that the four watersheds be examined further for separate conservation and management.
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Affiliation(s)
- Philip W Hedrick
- Department of Biology, Arizona State University, Tempe, Arizona, 85287-1501
| | - Karen M Parker
- Department of Biology, Arizona State University, Tempe, Arizona, 85287-1501
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78
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Cohen CS, Saito Y, Weissman IL. EVOLUTION OF ALLORECOGNITION IN BOTRYLLID ASCIDIANS INFERRED FROM A MOLECULAR PHYLOGENY. Evolution 2017; 52:746-756. [PMID: 28565254 DOI: 10.1111/j.1558-5646.1998.tb03699.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/1997] [Accepted: 03/06/1998] [Indexed: 11/26/2022]
Abstract
Despite the functional and phyletic ubiquity of highly polymorphic genetic recognition systems, the evolution and maintenance of these remarkable loci remain an empirical and theoretical puzzle. Many clonal invertebrates use polymorphic genetic recognition systems to discriminate kin from unrelated individuals during behavioral interactions that mediate competition for space. Space competition may have been a selective force promoting the evolution of highly polymorphic recognition systems, or preexisting polymorphic loci may have been coopted for the purpose of mediating space competition. Ascidian species in the family Botryllidae have an allorecognition system in which fusion or rejection between neighboring colonies is controlled by allele-sharing at a single, highly polymorphic locus. The behavioral sequence involved in allorecognition varies in a species-specific fashion with some species requiring extensive intercolony tissue integration prior to the allorecognition response, while other species contact opposing colonies at only a few points on the outer surface before resolving space conflicts. Due to an apparent species-specific continuum of behavioral variation in the degree of intercolony tissue integration required for allorecognition, this system lends itself to a phylogenetic analysis of the evolution of an allorecognition system. We constructed a molecular phylogeny of the botryllids based on 18S rDNA sequence and mapped allorecognition behavioral variation onto the phylogeny. Our phylogeny shows the basal allorecognition condition for the group is the most internal form of the recognition reaction. More derived species show progressively more external allorecognition responses, and in some cases loss of some features of internal function. We suggest that external allorecognition appears to be a secondary function of a polymorphic discriminatory system that was already in place due to other selective pressures such as gamete, pathogen, or developmental cell lineage recognition.
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Affiliation(s)
- C Sarah Cohen
- Department of Developmental Biology and Hopkins Marine Station, Stanford University, Stanford, California, 94305
| | - Yasunori Saito
- Shimoda Marine Research Station, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415, Japan
| | - Irving L Weissman
- Department of Developmental Biology and Hopkins Marine Station, Stanford University, Stanford, California, 94305
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79
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André A, Millien V, Galan M, Ribas A, Michaux JR. Effects of parasite and historic driven selection on the diversity and structure of a MHC-II gene in a small mammal species (Peromyscus leucopus) undergoing range expansion. Evol Ecol 2017. [DOI: 10.1007/s10682-017-9898-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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80
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Gorilla MHC class I gene and sequence variation in a comparative context. Immunogenetics 2017; 69:303-323. [PMID: 28332079 PMCID: PMC5400801 DOI: 10.1007/s00251-017-0974-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/04/2017] [Indexed: 12/13/2022]
Abstract
Comparisons of MHC gene content and diversity among closely related species can provide insights into the evolutionary mechanisms shaping immune system variation. After chimpanzees and bonobos, gorillas are humans’ closest living relatives; but in contrast, relatively little is known about the structure and variation of gorilla MHC class I genes (Gogo). Here, we combined long-range amplifications and long-read sequencing technology to analyze full-length MHC class I genes in 35 gorillas. We obtained 50 full-length genomic sequences corresponding to 15 Gogo-A alleles, 4 Gogo-Oko alleles, 21 Gogo-B alleles, and 10 Gogo-C alleles including 19 novel coding region sequences. We identified two previously undetected MHC class I genes related to Gogo-A and Gogo-B, respectively, thereby illustrating the potential of this approach for efficient and highly accurate MHC genotyping. Consistent with their phylogenetic position within the hominid family, individual gorilla MHC haplotypes share characteristics with humans and chimpanzees as well as orangutans suggesting a complex history of the MHC class I genes in humans and the great apes. However, the overall MHC class I diversity appears to be low further supporting the hypothesis that gorillas might have experienced a reduction of their MHC repertoire.
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81
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Arnaiz-Villena A, Muñiz E, del Palacio-Gruber J, Campos C, Alonso-Rubio J, Gomez-Casado E, Lopez-Pacheco F, Martin-Villa M, Silvera C. Ancestry of Amerindians and its Impact in Anthropology, Transplantation, HLA Pharmacogenomics and Epidemiology by HLA Study in Wiwa Colombian Population. ACTA ACUST UNITED AC 2016. [DOI: 10.2174/1874220301603010269] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:HLA autosomic genes are unique because they conform the most polymorphic human system. Importance of this system is recognized in Medicine for Transplantation, Epidemiology (HLA and disease linkage), Pharmacogenomics (HLA linked to drug side effects) and for defining the origin of populations in both male and female lineages.Objectives:Studying HLA profile of a isolated Amerindian group from North Colombia (Wiwa) in order to draw conclusions about its Preventive Medicine, the genetic relationship with Worldwide populations and America peopling, since this last issue is hotly debated.Methodology:A total of 14,660 HLA chromosomes were included. Peripheral blood was obtained from volunteer blood donors belonging to Wiwa (also named Arsario) ethnic group. HLA-A, -B, -C, -DRB1 and -DQB1 genes were analyzed by standard methods. Wiwa Amerindians relationships with others were calculated by using Arlequin, Dispan and Vista software computer packages.Results:Extended HLA, -A, -B, -C, -DRB1 and -DQB1 haplotypes have been studied for the first time in this population. Classical Amerindian haplotypes have been found and also new Wiwa (Arsario) Amerindian haplotypes. New haplotypes are A*68:01 - B*15:01 - C*03:03 - DRB1*14:02 - DQB1*03:02, A*11:01 - B*07:02 - C*07:02 - DRB1*15:03 - DQB1*06:02 and A*68:01 - B*15:01 - C*03:04 - DRB1*14:02 - DQB1*03:01.Conclusion:They have been reached after exhaustive comparisons of Wiwa with other Amerindians and Worldwide populations by using genetic distances, Neighbor Joining trees, correspondence analysis and specific group of alleles which are common and frequent in both Amerindians and Pacific Islanders. They are: 1) The Americas First Inhabitants have been probably come through Bering Strait and also through Pacific (from Austronesia and Asia) and Atlantic (from Europe) routes. A bidirectional gene flow is not discarded. 2) Genetic HLA Amerindian profile is separated from that of other Worldwide populations. 3) Amerindians geographical proximity groups’ relatedness is not concordant with HLA genetic relatedness, neither with language. This may be explained by a substantial population decrease that occurred after Europeans invaded America in 1492 and carried new pathogens and epidemics. 4) Our results are also useful for Wiwa and other Amerindians future preventive medicine (HLA linked diseases), HLA pharmacogenomics and transplantation regional programs.
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82
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Neehus AL, Wistuba J, Ladas N, Eiz-Vesper B, Schlatt S, Müller T. Gene conversion of the major histocompatibility complex class I Caja-G in common marmosets (Callithrix jacchus). Immunology 2016; 149:343-352. [PMID: 27450742 PMCID: PMC5046058 DOI: 10.1111/imm.12652] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 06/30/2016] [Accepted: 07/13/2016] [Indexed: 01/13/2023] Open
Abstract
Currently, the amount of sequenced and classified MHC class I genes of the common marmoset is limited, in spite of the wide use of this species as an animal model for biomedical research. In this study, 480 clones of MHC class I G locus (Caja‐G) cDNA sequences were obtained from 21 common marmosets. Up to 10 different alleles were detected in each common marmoset, leading to the assumption that the Caja‐G loci duplicated in the marmoset genome. In the investigated population, four alleles occurred more often, giving evidence for higher immunological advantage of these alleles. In contrast to the human non‐classical MHC class I genes, Caja‐G shows high rates of polymorphism at the relevant peptide‐binding sites, despite its phylogenetic relationship to the non‐classical HLA‐G. Our results provide information for better understanding of the immunological properties of the common marmoset and confirm the theory of a gene conversion of the Caja‐G due to its detected plasticity and the absence of any known HLA‐A equivalent.
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Affiliation(s)
- Anna-Lena Neehus
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | - Joachim Wistuba
- Institute of Reproductive and Regenerative Biology, Centre of Reproductive Medicine and Andrology, University Münster, Münster, Germany
| | - Nektarios Ladas
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | - Britta Eiz-Vesper
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | - Stefan Schlatt
- Institute of Reproductive and Regenerative Biology, Centre of Reproductive Medicine and Andrology, University Münster, Münster, Germany
| | - Thomas Müller
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany. .,Synlab Medical Care Centre Weiden Ltd, Weiden, Germany.
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83
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sNebula, a network-based algorithm to predict binding between human leukocyte antigens and peptides. Sci Rep 2016; 6:32115. [PMID: 27558848 PMCID: PMC4997263 DOI: 10.1038/srep32115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/02/2016] [Indexed: 12/19/2022] Open
Abstract
Understanding the binding between human leukocyte antigens (HLAs) and peptides is important to understand the functioning of the immune system. Since it is time-consuming and costly to measure the binding between large numbers of HLAs and peptides, computational methods including machine learning models and network approaches have been developed to predict HLA-peptide binding. However, there are several limitations for the existing methods. We developed a network-based algorithm called sNebula to address these limitations. We curated qualitative Class I HLA-peptide binding data and demonstrated the prediction performance of sNebula on this dataset using leave-one-out cross-validation and five-fold cross-validations. This algorithm can predict not only peptides of different lengths and different types of HLAs, but also the peptides or HLAs that have no existing binding data. We believe sNebula is an effective method to predict HLA-peptide binding and thus improve our understanding of the immune system.
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84
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Serão NVL, Kemp RA, Mote BE, Willson P, Harding JCS, Bishop SC, Plastow GS, Dekkers JCM. Genetic and genomic basis of antibody response to porcine reproductive and respiratory syndrome (PRRS) in gilts and sows. Genet Sel Evol 2016; 48:51. [PMID: 27417876 PMCID: PMC4944421 DOI: 10.1186/s12711-016-0230-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/06/2016] [Indexed: 12/19/2022] Open
Abstract
Background Our recent research showed that antibody response to porcine reproductive and respiratory syndrome (PRRS), measured as sample-to-positive (S/P) ratio, is highly heritable and has a high genetic correlation with reproductive performance during a PRRS outbreak. Two major quantitative trait loci (QTL) on Sus scrofa chromosome 7 (SSC7; QTLMHC and QTL130) accounted for ~40 % of the genetic variance for S/P. Objectives of this study were to estimate genetic parameters for PRRS S/P in gilts during acclimation, identify regions associated with S/P, and evaluate the accuracy of genomic prediction of S/P across populations with different prevalences of PRRS and using different single nucleotide polymorphism (SNP) sets. Methods Phenotypes and high-density SNP genotypes of female pigs from two datasets were used. The outbreak dataset included 607 animals from one multiplier herd, whereas the gilt acclimation (GA) dataset included data on 2364 replacement gilts from seven breeding companies placed on health-challenged farms. Genomic prediction was evaluated using GA for training and validation, and using GA for training and outbreak for validation. Predictions were based on SNPs across the genome (SNPAll), SNPs in one (SNPMHC and SNP130) or both (SNPSSC7) QTL, or SNPs outside the QTL (SNPRest). Results Heritability of S/P in the GA dataset increased with the proportion of PRRS-positive animals in the herd (from 0.28 to 0.47). Genomic prediction accuracies ranged from low to moderate. Average accuracies were highest when using only the 269 SNPs in both QTL regions (SNPSSC7, with accuracies of 0.39 and 0.31 for outbreak and GA validation datasets, respectively. Average accuracies for SNPALL, SNPMHC, SNP130, and SNPRest were, respectively, 0.26, 0.39, 0.21, and 0.05 for the outbreak, and 0.28, 0.25, 0.22, and 0.12, for the GA validation datasets. Conclusions Moderate genomic prediction accuracies can be obtained for PRRS antibody response using SNPs located within two major QTL on SSC7, while the rest of the genome showed limited predictive ability. Results were obtained using data from multiple genetic sources and farms, which further strengthens these findings. Further research is needed to validate the use of S/P ratio as an indicator trait for reproductive performance during PRRS outbreaks. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0230-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nick V L Serão
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.,Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Benny E Mote
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Philip Willson
- Canadian Centre for Health and Safety in Agriculture, University of Saskatchewan, Saskatoon, SK, S7N 2Z4, Canada
| | - John C S Harding
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - Stephen C Bishop
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Graham S Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
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85
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Liu J, Sun Y, Xu T. Identification of 48 full-length MHC-DAB functional alleles in miiuy croaker and evidence for positive selection. FISH & SHELLFISH IMMUNOLOGY 2016; 54:544-550. [PMID: 27164216 DOI: 10.1016/j.fsi.2016.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 05/05/2016] [Accepted: 05/05/2016] [Indexed: 06/05/2023]
Abstract
Major histocompatibility complex (MHC) molecules play a vital role in the immune response and are a highly polymorphic gene superfamily in vertebrates. As the molecular marker associated with polymorphism and disease susceptibility/resistance, the polymorphism of MHC genes has been investigated in many tetrapods and teleosts. Most studies were focused on the polymorphism of the second exon, which encodes the peptide-binding region (PBR) in the α1- or β1-domain, but few studies have examined the full-length coding region. To comprehensive investigate the polymorphism of MHC gene, we identified 48 full-length miiuy croaker (Miichthys miiuy) MHC class IIB (Mimi-DAB) functional alleles from 26 miiuy croaker individuals. All of the alleles encode 34 amino acid sequences, and a high level of polymorphism was detected in Mimi-DAB alleles. The rate of non-synonymous substitutions (dN) occurred at a significantly higher frequency than that of synonymous substitutions (dS) in the PBR, and this result suggests that balancing selection maintains polymorphisms at the Mimi-DAB locus. Phylogenetic analysis based on the full-length and exon 2 sequences of Mimi-DAB alleles both showed that the Mimi-DAB alleles were clustered into two major groups. A total of 19 positive selected sites were identified on the Mimi-DAB alleles after testing for positive selection, and 14 sites were predicted to be associated with antigen-binding sites, which suggests that most of selected sites are significant for disease resistance. The polymorphism of Mimi-DAB alleles provides an important resource for analyzing the association between the polymorphism of MHC gene and disease susceptibility/resistance, and for researching the molecular selective breeding of miiuy croaker with enhanced disease resistance.
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Affiliation(s)
- Jiang Liu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Yueyan Sun
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China.
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86
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de Groot NG, Blokhuis JH, Otting N, Doxiadis GGM, Bontrop RE. Co-evolution of the MHC class I and KIR gene families in rhesus macaques: ancestry and plasticity. Immunol Rev 2016; 267:228-45. [PMID: 26284481 PMCID: PMC4544828 DOI: 10.1111/imr.12313] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Researchers dealing with the human leukocyte antigen (HLA) class I and killer immunoglobulin receptor (KIR) multi‐gene families in humans are often wary of the complex and seemingly different situation that is encountered regarding these gene families in Old World monkeys. For the sake of comparison, the well‐defined and thoroughly studied situation in humans has been taken as a reference. In macaques, both the major histocompatibility complex class I and KIR gene families are plastic entities that have experienced various rounds of expansion, contraction, and subsequent recombination processes. As a consequence, haplotypes in macaques display substantial diversity with regard to gene copy number variation. Additionally, for both multi‐gene families, differential levels of polymorphism (allelic variation), and expression are observed as well. A comparative genetic approach has allowed us to answer questions related to ancestry, to shed light on unique adaptations of the species’ immune system, and to provide insights into the genetic events and selective pressures that have shaped the range of these gene families.
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Affiliation(s)
- Natasja G de Groot
- Department of Comparative Genetics & Refinement, BPRC, Rijswijk, The Netherlands
| | - Jeroen H Blokhuis
- Department of Comparative Genetics & Refinement, BPRC, Rijswijk, The Netherlands
| | - Nel Otting
- Department of Comparative Genetics & Refinement, BPRC, Rijswijk, The Netherlands
| | - Gaby G M Doxiadis
- Department of Comparative Genetics & Refinement, BPRC, Rijswijk, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics & Refinement, BPRC, Rijswijk, The Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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87
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Zeng QQ, He K, Sun DD, Ma MY, Ge YF, Fang SG, Wan QH. Balancing selection and recombination as evolutionary forces caused population genetic variations in golden pheasant MHC class I genes. BMC Evol Biol 2016; 16:42. [PMID: 26892934 PMCID: PMC4758006 DOI: 10.1186/s12862-016-0609-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 02/02/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) genes are vital partners in the acquired immune processes of vertebrates. MHC diversity may be directly associated with population resistance to infectious pathogens. Here, we screened for polymorphisms in exons 2 and 3 of the IA1 and IA2 genes in 12 golden pheasant populations across the Chinese mainland to characterize their genetic variation levels, to understand the effects of historical positive selection and recombination in shaping class I diversity, and to investigate the genetic structure of wild golden pheasant populations. RESULTS Among 339 individual pheasants, we identified 14 IA1 alleles in exon 2 (IA1-E2), 11 IA1-E3 alleles, 27 IA2-E2 alleles, and 28 IA2-E3 alleles. The non-synonymous substitution rate was significantly greater than the synonymous substitution rate at sequences in the IA2 gene encoding putative peptide-binding sites but not in the IA1 gene; we also found more positively selected sites in IA2 than in IA1. Frequent recombination events resulted in at least 9 recombinant IA2 alleles, in accordance with the intermingling pattern of the phylogenetic tree. Although some IA alleles are widely shared among studied populations, large variation occurs in the number of IA alleles across these populations. Allele frequency analysis across 2 IA loci showed low levels of genetic differentiation among populations on small geographic scales; however, significant genetic differentiation was observed between pheasants from the northern and southern regions of the Yangtze River. Both STRUCTURE analysis and F-statistic (F ST ) value comparison classified those populations into 2 major groups: the northern region of the Yangtze River (NYR) and the southern region of the Yangtze River (SYR). CONCLUSIONS More extensive polymorphisms in IA2 than IA1 indicate that IA2 has undergone much stronger positive-selection pressure during evolution. Moreover, the recombination events detected between the genes and the intermingled phylogenetic pattern indicate that interlocus recombination accounts for much of the allelic variation in IA2. Analysis of the population differentiation implied that homogenous balancing selection plays an important part in maintaining an even distribution of MHC variations. The natural barrier of the Yangtze River and heterogeneous balancing selection might help shape the NYR-SYR genetic structure in golden pheasants.
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Affiliation(s)
- Qian-Qian Zeng
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Ke He
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang, 311300, China.
| | - Dan-Dan Sun
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Mei-Ying Ma
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Yun-Fa Ge
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Sheng-Guo Fang
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Qiu-Hong Wan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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88
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Xu T, Liu J, Sun Y, Zhu Z, Liu T. Characterization of 40 full-length MHC class IIA functional alleles in miiuy croaker: Polymorphism and positive selection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 55:138-143. [PMID: 26598111 DOI: 10.1016/j.dci.2015.10.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 10/21/2015] [Accepted: 10/22/2015] [Indexed: 06/05/2023]
Abstract
The major histocompatibility complex is a highly polymorphic gene superfamily in vertebrates that plays an important role in adaptive immune response. In the present study, we identified 40 full-length miiuy croaker MHC class IIA (Mimi-DAA) functional alleles from 26 miiuy croaker individuals and found that the alleles encode 30 amino acid sequences. A high level of polymorphism in Mimi-DAA was detected in miiuy croaker. The rate of non-synonymous substitutions (d(N)) occurred at a significantly higher frequency than that of synonymous substitutions (d(S)) in the peptide-binding region (PBR) and non-PBR. This result suggests that balancing selection maintains polymorphisms at the Mimi-DAA locus. Phylogenetic analysis based on the full-length sequences showed that the Mimi-DAA alleles clustered into three groups. However, the phylogenetic tree constructed using the exon 2 sequences indicated that the Mimi-DAA alleles clustered into two groups. A total of 22 positively selected sites were identified on the Mimi-DAA alleles after testing for positive selection, and five sites were predicted to be associated with the binding of peptide antigen, suggesting that a few selected residues may play a significant role in immune function.
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Affiliation(s)
- Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Jiang Liu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Yueyan Sun
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Zhihuang Zhu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Tianxing Liu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
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89
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Coppari E, Santini S, Bizzarri AR, Cannistraro S. Kinetics and binding geometries of the complex between β2-microglobulin and its antibody: An AFM and SPR study. Biophys Chem 2016; 211:19-27. [PMID: 26803406 DOI: 10.1016/j.bpc.2016.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 12/30/2015] [Accepted: 01/12/2016] [Indexed: 11/18/2022]
Abstract
β2-Microglobulin (B2M) is a human protein involved in the regulation of immune response and represents a useful biomarker for several diseases. Recently, anti-B2M monoclonal antibodies have been introduced as innovative therapeutic agents. A deeper understanding of the molecular interaction between the two partners could be of utmost relevance for both designing array-based analytical devices and improving current immunotherapies. A visualization at the nanoscale performed by Atomic Force Microscopy revealed that binding of B2M to the antibody occurred according to two preferred interaction geometries. Additionally, Atomic Force Spectroscopy and Surface Plasmon Resonance provided us with detailed information on the binding kinetics and the energy landscape of the complex, both at the single molecule level and in bulk conditions. Combination of these complementary techniques contributed to highlight subtle differences in the kinetics behaviour characterizing the complexes. Collectively, the results may deserve significant interest for designing, development and optimization of novel generations of nanobiosensor platforms.
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Affiliation(s)
- Emilia Coppari
- Biophysics and Nanoscience Centre, Dipartimento DEB, Università della Tuscia, Viterbo, Italy
| | - Simona Santini
- Biophysics and Nanoscience Centre, Dipartimento DEB, Università della Tuscia, Viterbo, Italy
| | - Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, Dipartimento DEB, Università della Tuscia, Viterbo, Italy.
| | - Salvatore Cannistraro
- Biophysics and Nanoscience Centre, Dipartimento DEB, Università della Tuscia, Viterbo, Italy
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90
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Dai CS, Chu CC, Chen SF, Sun CY, Lin M, Lee CC. Association between human leucocyte antigen subtypes and risk of end stage renal disease in Taiwanese: a retrospective study. BMC Nephrol 2015; 16:177. [PMID: 26518904 PMCID: PMC4627610 DOI: 10.1186/s12882-015-0165-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 10/14/2015] [Indexed: 02/06/2023] Open
Abstract
Background End stage renal disease (ESRD) is prevalent in Taiwan. Human leukocyte antigens (HLA) have been found to be associated with the pathogenesis of autoimmune diseases, allergies and inflammatory bowel diseases, and there are emerging evidences of correlations between HLA genotypes and renal diseases such as diabetic nephropathy, IgA nephropathy, and glomerulonephritis. The aim of this study is to investigate detailed HLA subtypes in a case-control study of Taiwanese individuals. Methods The polymorphisms of HLA class I and II antigens in ESRD patients and a healthy control group were retrospectively analyzed. The information of 141 ESRD patients was obtained from the medical record of the Keelung branch of Chang Gung Memorial Hospital and was compared to the HLA type of a control group comprized of 190 healthy unrelated Taiwanese from one of our previous studies. In order to standardize the HLA designation of prior low-resolution typings with the more advanced DNA based typings, all HLA-A, −B and -DR were analyzed using a low resolution serologic equivalent. Results The current work suggests that HLA-DR3 (odds ratio = 1.91, 95 % CI = 1.098–3.324, P = 0.024, Pc = 0.312) and HLA-DR11 (odds ratio = 2.06, 95 % CI = 1.133–3.761, P = 0.021, Pc = 0.273) may represent susceptibility risk factors for the development of ESRD in Taiwanese individuals. On the other hand, HLA-DR8 (odds ratio = 0.47, 95 % CI = 0.236–0.920, p = 0.027. Pc = 0.351) may be a protective factor. HLA-A and -B antigens did not show any contribution of progression to ESRD. However, we note that the significance of all these findings is lost when the results are corrected for multiple comparisons according to Bonferroni. Further investigation with a larger group of patients and control is needed to resolve this issue. Conclusions HLA typing might be a useful clinical method for screening patients with high risk of progression to ESRD.
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Affiliation(s)
- Ciou-Sia Dai
- Department of Internal Medicine, Division of Nephrology, Chang Gung Memorial Hospital, Keelung, Taiwan.
| | - Chen-Chung Chu
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan. .,Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan.
| | - Shin-Fan Chen
- Department of Internal Medicine, Division of Nephrology, Chang Gung Memorial Hospital, Keelung, Taiwan.
| | - Chiao-Yin Sun
- Department of Internal Medicine, Division of Nephrology, Chang Gung Memorial Hospital, Keelung, Taiwan.
| | - Marie Lin
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan.
| | - Chin-Chan Lee
- Department of Internal Medicine, Division of Nephrology, Chang Gung Memorial Hospital, Keelung, Taiwan. .,Department of Nephrology, Chang Gung Memorial Hospital, Keelung, Taiwan.
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91
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Lei J, Osen W, Gardyan A, Hotz-Wagenblatt A, Wei G, Gissmann L, Eichmüller S, Löchelt M. Replication-Competent Foamy Virus Vaccine Vectors as Novel Epitope Scaffolds for Immunotherapy. PLoS One 2015; 10:e0138458. [PMID: 26397953 PMCID: PMC4580568 DOI: 10.1371/journal.pone.0138458] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/31/2015] [Indexed: 12/19/2022] Open
Abstract
The use of whole viruses as antigen scaffolds is a recent development in vaccination that improves immunogenicity without the need for additional adjuvants. Previous studies highlighted the potential of foamy viruses (FVs) in prophylactic vaccination and gene therapy. Replication-competent FVs can trigger immune signaling and integrate into the host genome, resulting in persistent antigen expression and a robust immune response. Here, we explored feline foamy virus (FFV) proteins as scaffolds for therapeutic B and T cell epitope delivery in vitro. Infection- and cancer-related B and T cell epitopes were grafted into FFV Gag, Env, or Bet by residue replacement, either at sites of high local sequence homology between the epitope and the host protein or in regions known to tolerate sequence alterations. Modified proviruses were evaluated in vitro for protein steady state levels, particle release, and virus titer in permissive cells. Modification of Gag and Env was mostly detrimental to their function. As anticipated, modification of Bet had no impact on virion release and affected virus titers of only some recombinants. Further evaluation of Bet as an epitope carrier was performed using T cell epitopes from the model antigen chicken ovalbumin (OVA), human tyrosinase-related protein 2 (TRP-2), and oncoprotein E7 of human papillomavirus type 16 (HPV16E7). Transfection of murine cells with constructs encoding Bet-epitope chimeric proteins led to efficient MHC-I-restricted epitope presentation as confirmed by interferon-gamma enzyme-linked immunospot assays using epitope-specific cytotoxic T lymphocyte (CTL) lines. FFV infection-mediated transduction of cells with epitope-carrying Bet also induced T-cell responses, albeit with reduced efficacy, in a process independent from the presence of free peptides. We show that primate FV Bet is also a promising T cell epitope carrier for clinical translation. The data demonstrate the utility of replication-competent and -attenuated FVs as antigen carriers in immunotherapy.
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Affiliation(s)
- Janet Lei
- Division of Molecular Diagnostics of Oncogenic Infections, Research Program Infection and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfram Osen
- Division of Translational Immunology, Research Program Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Adriane Gardyan
- Division of Translational Immunology, Research Program Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Bioinformatics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Guochao Wei
- Division of Molecular Diagnostics of Oncogenic Infections, Research Program Infection and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lutz Gissmann
- Division of Molecular Diagnostics of Oncogenic Infections, Research Program Infection and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Eichmüller
- Division of Translational Immunology, Research Program Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Löchelt
- Division of Molecular Diagnostics of Oncogenic Infections, Research Program Infection and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
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92
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Zhang W, He Y, Wang W, Han Z, He J, Chen N, Dong L, Tao S, He J, Zhu F, Lv H. HLA-A locus allelic dropout in Sanger sequence-based typing due to the single nucleotide polymorphism of exon 1. Int J Immunogenet 2015; 42:457-60. [DOI: 10.1111/iji.12234] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/20/2015] [Accepted: 07/24/2015] [Indexed: 11/26/2022]
Affiliation(s)
- W. Zhang
- Blood Center of Zhejiang Province; Hangzhou Zhejiang China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou Zhejiang China
| | - Y. He
- Blood Center of Zhejiang Province; Hangzhou Zhejiang China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou Zhejiang China
| | - W. Wang
- Blood Center of Zhejiang Province; Hangzhou Zhejiang China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou Zhejiang China
| | - Z. Han
- Blood Center of Zhejiang Province; Hangzhou Zhejiang China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou Zhejiang China
| | - J. He
- Blood Center of Zhejiang Province; Hangzhou Zhejiang China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou Zhejiang China
| | - N. Chen
- Blood Center of Zhejiang Province; Hangzhou Zhejiang China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou Zhejiang China
| | - L. Dong
- Blood Center of Zhejiang Province; Hangzhou Zhejiang China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou Zhejiang China
| | - S. Tao
- Blood Center of Zhejiang Province; Hangzhou Zhejiang China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou Zhejiang China
| | - J. He
- Blood Center of Zhejiang Province; Hangzhou Zhejiang China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou Zhejiang China
| | - F. Zhu
- Blood Center of Zhejiang Province; Hangzhou Zhejiang China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou Zhejiang China
| | - H. Lv
- Blood Center of Zhejiang Province; Hangzhou Zhejiang China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou Zhejiang China
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93
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Hans JB, Haubner A, Arandjelovic M, Bergl RA, Fünfstück T, Gray M, Morgan DB, Robbins MM, Sanz C, Vigilant L. Characterization of MHC class II B polymorphism in multiple populations of wild gorillas using non-invasive samples and next-generation sequencing. Am J Primatol 2015; 77:1193-206. [PMID: 26283172 DOI: 10.1002/ajp.22458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 07/08/2015] [Accepted: 08/03/2015] [Indexed: 01/03/2023]
Abstract
Genes encoded by the major histocompatibility complex (MHC) are crucial for the recognition and presentation of antigens to the immune system. In contrast to their closest relatives, chimpanzees and humans, much less is known about variation in gorillas at these loci. This study explored the exon 2 variation of -DPB1, -DQB1, and -DRB genes in 46 gorillas from four populations while simultaneously evaluating the feasibility of using fecal samples for high-throughput MHC genotyping. By applying strict similarity- and frequency-based analysis, we found, despite our modest sample size, a total of 18 alleles that have not been described previously, thereby illustrating the potential for efficient and highly accurate MHC genotyping from non-invasive DNA samples. We emphasize the importance of controlling for multiple potential sources of error when applying this massively parallel short-read sequencing technology to PCR products generated from low concentration DNA extracts. We observed pronounced differences in MHC variation between species, subspecies and populations that are consistent with both the ancient and recent demographic histories experienced by gorillas.
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Affiliation(s)
- Jörg B Hans
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anne Haubner
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Richard A Bergl
- North Carolina Zoological Park, Asheboro, North Carolina, USA
| | | | - Maryke Gray
- International Gorilla Conservation Program, Kigali, Rwanda
| | | | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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94
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Human Leukocyte Antigen Diversity: A Southern African Perspective. J Immunol Res 2015; 2015:746151. [PMID: 26347896 PMCID: PMC4549606 DOI: 10.1155/2015/746151] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/26/2015] [Indexed: 12/30/2022] Open
Abstract
Despite the increasingly well-documented evidence of high genetic, ethnic, and linguistic diversity amongst African populations, there is limited data on human leukocyte antigen (HLA) diversity in these populations. HLA is part of the host defense mechanism mediated through antigen presentation to effector cells of the immune system. With the high disease burden in southern Africa, HLA diversity data is increasingly important in the design of population-specific vaccines and the improvement of transplantation therapeutic interventions. This review highlights the paucity of HLA diversity data amongst southern African populations and defines a need for information of this kind. This information will support disease association studies, provide guidance in vaccine design, and improve transplantation outcomes.
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95
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Choi Y, Hua C, Sentman CL, Ackerman ME, Bailey-Kellogg C. Antibody humanization by structure-based computational protein design. MAbs 2015; 7:1045-57. [PMID: 26252731 PMCID: PMC5045135 DOI: 10.1080/19420862.2015.1076600] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 07/06/2015] [Accepted: 07/20/2015] [Indexed: 12/15/2022] Open
Abstract
Antibodies derived from non-human sources must be modified for therapeutic use so as to mitigate undesirable immune responses. While complementarity-determining region (CDR) grafting-based humanization techniques have been successfully applied in many cases, it remains challenging to maintain the desired stability and antigen binding affinity upon grafting. We developed an alternative humanization approach called CoDAH ("Computationally-Driven Antibody Humanization") in which computational protein design methods directly select sets of amino acids to incorporate from human germline sequences to increase humanness while maintaining structural stability. Retrospective studies show that CoDAH is able to identify variants deemed beneficial according to both humanness and structural stability criteria, even for targets lacking crystal structures. Prospective application to TZ47, a murine anti-human B7H6 antibody, demonstrates the approach. Four diverse humanized variants were designed, and all possible unique VH/VL combinations were produced as full-length IgG1 antibodies. Soluble and cell surface expressed antigen binding assays showed that 75% (6 of 8) of the computationally designed VH/VL variants were successfully expressed and competed with the murine TZ47 for binding to B7H6 antigen. Furthermore, 4 of the 6 bound with an estimated KD within an order of magnitude of the original TZ47 antibody. In contrast, a traditional CDR-grafted variant could not be expressed. These results suggest that the computational protein design approach described here can be used to efficiently generate functional humanized antibodies and provide humanized templates for further affinity maturation.
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Affiliation(s)
- Yoonjoo Choi
- Department of Computer Science; Dartmouth College; Hanover, NH USA
| | - Casey Hua
- Thayer School of Engineering; Dartmouth College; Hanover, NH USA
- Department of Microbiology and Immunology; Geisel School of Medicine; Dartmouth College; Lebanon, NH USA
| | - Charles L Sentman
- Department of Microbiology and Immunology; Geisel School of Medicine; Dartmouth College; Lebanon, NH USA
| | - Margaret E Ackerman
- Thayer School of Engineering; Dartmouth College; Hanover, NH USA
- Department of Microbiology and Immunology; Geisel School of Medicine; Dartmouth College; Lebanon, NH USA
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96
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Lyons AC, Hoostal MJ, Bouzat JL. Characterization of major histocompatibility complex class I loci of the lark sparrow (Chondestes grammacus) and insights into avian MHC evolution. Genetica 2015; 143:521-34. [PMID: 26071093 DOI: 10.1007/s10709-015-9850-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 06/06/2015] [Indexed: 11/29/2022]
Abstract
The major histocompatibilty complex (MHC) has become increasingly important in the study of the immunocapabilities of non-model vertebrates due to its direct involvement in the immune response. The characterization of MHC class I loci in the lark sparrow (Chondestes grammacus) revealed multiple MHC class I loci with elevated genetic diversity at exon 3, evidence of differential selection between the peptide binding region (PBR) and non-PBR, and the presence of multiple pseudogenes with limited divergence. The minimum number of functional MHC class I loci was estimated at four. Sequence analysis revealed d N /d S ratios significantly less than one at non-PBR sites, indicative of negative selection, whereas PBR sites associated with antigen recognition showed ratios greater than 1 but non-significant. GenBank surveys and phylogenetic analyses of previously reported avian MHC class I sequences revealed variable signatures of evolutionary processes acting upon this gene family, including gene duplication and potential concerted evolution. An increase in the number of class I loci across species coincided with an increase in pseudogene prevalence, revealing the importance of gene duplication in the expansion of multigene families and the creation of pseudogenes.
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Affiliation(s)
- Amanda C Lyons
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
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97
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Westbrook CJ, Karl JA, Wiseman RW, Mate S, Koroleva G, Garcia K, Sanchez-Lockhart M, O'Connor DH, Palacios G. No assembly required: Full-length MHC class I allele discovery by PacBio circular consensus sequencing. Hum Immunol 2015; 76:891-6. [PMID: 26028281 DOI: 10.1016/j.humimm.2015.03.022] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/18/2015] [Indexed: 11/17/2022]
Abstract
Single-molecule real-time (SMRT) sequencing technology with the Pacific Biosciences (PacBio) RS II platform offers the potential to obtain full-length coding regions (∼1100-bp) from MHC class I cDNAs. Despite the relatively high error rate associated with SMRT technology, high quality sequences can be obtained by circular consensus sequencing (CCS) due to the random nature of the error profile. In the present study we first validated the ability of SMRT-CCS to accurately identify class I transcripts in Mauritian-origin cynomolgus macaques (Macaca fascicularis) that have been characterized previously by cloning and Sanger-based sequencing as well as pyrosequencing approaches. We then applied this SMRT-CCS method to characterize 60 novel full-length class I transcript sequences expressed by a cohort of cynomolgus macaques from China. The SMRT-CCS method described here provides a straightforward protocol for characterization of unfragmented single-molecule cDNA transcripts that will potentially revolutionize MHC class I allele discovery in nonhuman primates and other species.
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Affiliation(s)
- Catherine J Westbrook
- U.S. Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD 21702, United States
| | - Julie A Karl
- Wisconsin National Primate Research Center, 555 Science Drive, University of Wisconsin-Madison, Madison, WI 53711, United States
| | - Roger W Wiseman
- Wisconsin National Primate Research Center, 555 Science Drive, University of Wisconsin-Madison, Madison, WI 53711, United States
| | - Suzanne Mate
- U.S. Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD 21702, United States
| | - Galina Koroleva
- U.S. Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD 21702, United States
| | - Karla Garcia
- U.S. Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD 21702, United States
| | - Mariano Sanchez-Lockhart
- U.S. Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD 21702, United States.
| | - David H O'Connor
- Wisconsin National Primate Research Center, 555 Science Drive, University of Wisconsin-Madison, Madison, WI 53711, United States; Department of Pathology and Laboratory Medicine, 1685 Highland Ave., University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Gustavo Palacios
- U.S. Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD 21702, United States
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98
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Mayor NP, Robinson J, McWhinnie AJM, Ranade S, Eng K, Midwinter W, Bultitude WP, Chin CS, Bowman B, Marks P, Braund H, Madrigal JA, Latham K, Marsh SGE. HLA Typing for the Next Generation. PLoS One 2015; 10:e0127153. [PMID: 26018555 PMCID: PMC4446346 DOI: 10.1371/journal.pone.0127153] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/12/2015] [Indexed: 11/30/2022] Open
Abstract
Allele-level resolution data at primary HLA typing is the ideal for most histocompatibility testing laboratories. Many high-throughput molecular HLA typing approaches are unable to determine the phase of observed DNA sequence polymorphisms, leading to ambiguous results. The use of higher resolution methods is often restricted due to cost and time limitations. Here we report on the feasibility of using Pacific Biosciences’ Single Molecule Real-Time (SMRT) DNA sequencing technology for high-resolution and high-throughput HLA typing. Seven DNA samples were typed for HLA-A, -B and -C. The results showed that SMRT DNA sequencing technology was able to generate sequences that spanned entire HLA Class I genes that allowed for accurate allele calling. Eight novel genomic HLA class I sequences were identified, four were novel alleles, three were confirmed as genomic sequence extensions and one corrected an existing genomic reference sequence. This method has the potential to revolutionize the field of HLA typing. The clinical impact of achieving this level of resolution HLA typing data is likely to considerable, particularly in applications such as organ and blood stem cell transplantation where matching donors and recipients for their HLA is of utmost importance.
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Affiliation(s)
- Neema P. Mayor
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
- UCL Cancer Institute, Royal Free Campus, London, United Kingdom
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
- UCL Cancer Institute, Royal Free Campus, London, United Kingdom
| | | | - Swati Ranade
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Kevin Eng
- Pacific Biosciences, Menlo Park, California, United States of America
| | - William Midwinter
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
| | - Will P. Bultitude
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
| | - Chen-Shan Chin
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Brett Bowman
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Patrick Marks
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Henny Braund
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
| | - J. Alejandro Madrigal
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
- UCL Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Katy Latham
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
| | - Steven G. E. Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
- UCL Cancer Institute, Royal Free Campus, London, United Kingdom
- * E-mail:
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99
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Tian W, Zhu FM, Wang WY, Cai JH, Zhang W, Li LX, Liu KL, Jin HK, Wang F. Sequence-based typing of HLA-A gene in 930 patients with nasopharyngeal carcinoma in Hunan province, southern China. ACTA ACUST UNITED AC 2015; 86:15-20. [PMID: 25940993 DOI: 10.1111/tan.12576] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 03/12/2015] [Accepted: 04/12/2015] [Indexed: 11/30/2022]
Abstract
In this study, we typed 930 cases of nasopharyngeal carcinoma (NPC) and 1134 normal controls recruited from Hunan province, southern China for human leukocyte antigen-A (HLA-A) locus by sequencing exons 2-4. Very significant associations between HLA-A*02:07, HLA-A*11:01 and NPC were established [25.7% vs 16.18%; odds ratio, OR (95% confidence interval, CI) = 1.79 (1.54-2.09), P < 0.0001 and 21.1% vs 30.42%, OR (95% CI) = 0.61 (0.53-0.70), P<0.0001, respectively]. Further analysis of the molecular basis underlying these associations suggests that cysteine (C) at codon 99 of α2-helix of HLA-A protein is probably deleterious and confers risk to NPC. Convincing evidence was uncovered for negative association of a rare allele in southern Chinese populations, HLA-A*31:01, with NPC [0.22% vs 2.12%, OR (95% CI) = 0.1 (0.04-0.28), P < 0.0001]. rs1059449-A, which encodes arginine (R) at codon 56 of α1-helix of HLA-A protein, was postulated to be crucial for such a pattern of negative association with NPC. A subset of NPC cases (N = 632) and normal controls (N=712) were tested for anti-virus capsid antigen (anti-VCA) immunoglobulin A (IgA), very significant difference in seropositivity for anti-VCA IgA was observed between the two groups [67.56% vs 6.46%, OR (95% CI) = 30.16 (21.42-42.46), P < 0.0001]. However, seropositivity for anti-VCA IgA did not correlate with HLA-A allelic typing in both groups.
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Affiliation(s)
- W Tian
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, China.,Laboratory of Cellular and Molecular Biology, College of Basic Medical Sciences, Central South University, Changsha, China
| | - F-M Zhu
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China.,Key Laboratory of Blood Safety Research, Ministry of Health, Hangzhou, China
| | - W-Y Wang
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, China
| | - J-H Cai
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, China
| | - W Zhang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China.,Key Laboratory of Blood Safety Research, Ministry of Health, Hangzhou, China
| | - L-X Li
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, China.,Laboratory of Cellular and Molecular Biology, College of Basic Medical Sciences, Central South University, Changsha, China
| | - K-L Liu
- Department of Nuclear Medicine, Hunan Cancer Hospital, The Affiliated Cancer Hospital of XiangYa School of Medicine of Central South University, Changsha, China
| | - H-K Jin
- Department of Radiotherapy, Hunan Cancer Hospital, The Affiliated Cancer Hospital of XiangYa School of Medicine of Central South University, Changsha, China
| | - F Wang
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, China
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100
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Gerritsen K, Voorter C, Joannes M, Senden-Gijsbers B, Agis F, Wieten L, Tilanus M. RNA and protein expression of HLA-A∗23:19Q. Hum Immunol 2015; 76:286-91. [DOI: 10.1016/j.humimm.2015.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/03/2015] [Indexed: 11/28/2022]
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