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Mallis P, Siorenta A, Stamathioudaki E, Vrani V, Paterakis G. Frequency distribution of HLA class I and II alleles in Greek population and their significance in orchestrating the National Donor Registry Program. Int J Immunogenet 2024; 51:164-172. [PMID: 38459565 DOI: 10.1111/iji.12663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/14/2024] [Accepted: 02/22/2024] [Indexed: 03/10/2024]
Abstract
Human leukocyte antigens (HLA) represent one of the most polymorphic systems in humans, responsible for the identification of foreign antigens and the presentation of immune responses. Therefore, HLA is considered to play a major role in human disorders, donor-recipient matching and transplantation outcomes. This study aimed to determine the HLA class I and II alleles and haplotypes in the Greek population. Moreover, a comparative analysis of HLA alleles and haplotype frequencies found in Greek and pooled European populations was also performed to acquire a better knowledge about the HLA alleles distribution. A total number of 1896 healthy individuals were typed for their HLA alleles in the National Tissue Typing Center of Greece. High-resolution HLA typing for the HLA-A, -B, -C and -DR, -DQ, -DP with the use of the next-generation sequencing analysis was performed, followed by data analysis for establishing the HLA allele and haplotype differences. The results of this study showed that the most frequent alleles for the HLA-A were the A*02:01:01 (27.1%), *24:02:01 (14.4%), *01:01:01 (9.3%), for the HLA-B were the B*51:01:01 (15.3%), *18:01:01 (9.7%), *35:01:01 (6.8%) and for the HLA-C were the C*04:01:01 (15.4%), *07:01:01 (13.1%), *12:03:01 (9.6%). For the HLA class II, the most frequent alleles for the HLA-DRB1 were the DRB1*11:04:01 (16.4%), *16:01:01 (11.3%), *11:01:01 (9.5%), for the HLA-DQB1 were the DQB1*03:01:01 (30.5%), *05:02:01 (15.1%), *05:01:01 (10.6%) and for the HLA-DPB1 were the DPB1*04:01:01 (34.8%), *02:01:01 (11.6%), *04:02:01 (7.3%). Additionally, the most frequent haplotypes were the A*02:01:01∼C*07:01:01-B*18:01:01∼DRB1*11:04:01 (2.3%), followed by the A*01:01:01∼C*07:01:01∼B*08:01:01∼DRB1*03:01:01 (2.2%), A*24:02:01∼C*04:01:01∼B*35:02:01∼DRB1*11:04:01 (1.4%) and A*02:01:01∼C*04:01:01∼B*35:01:01-DRB1*14:01:01 (1.2%). The results herein were comparable to those obtained from the pooled European populations. Moreover, these results can be used for the improvement of the donor-recipient matching procedure and to understand better the disease association in Greece.
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Affiliation(s)
- Panagiotis Mallis
- Immunology Department & National Tissue Typing Center, General Hospital of Athens "G. Gennimatas", Athens, Greece
| | - Alexandra Siorenta
- Immunology Department & National Tissue Typing Center, General Hospital of Athens "G. Gennimatas", Athens, Greece
| | - Erasmia Stamathioudaki
- Immunology Department & National Tissue Typing Center, General Hospital of Athens "G. Gennimatas", Athens, Greece
| | - Vasiliki Vrani
- Immunology Department & National Tissue Typing Center, General Hospital of Athens "G. Gennimatas", Athens, Greece
| | - George Paterakis
- Immunology Department & National Tissue Typing Center, General Hospital of Athens "G. Gennimatas", Athens, Greece
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2
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Hayeck TJ, Li Y, Mosbruger TL, Bradfield JP, Gleason AG, Damianos G, Shaw GTW, Duke JL, Conlin LK, Turner TN, Fernández-Viña MA, Sarmady M, Monos DS. The Impact of Patterns in Linkage Disequilibrium and Sequencing Quality on the Imprint of Balancing Selection. Genome Biol Evol 2024; 16:evae009. [PMID: 38302106 PMCID: PMC10853003 DOI: 10.1093/gbe/evae009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 02/03/2024] Open
Abstract
Regions under balancing selection are characterized by dense polymorphisms and multiple persistent haplotypes, along with other sequence complexities. Successful identification of these patterns depends on both the statistical approach and the quality of sequencing. To address this challenge, at first, a new statistical method called LD-ABF was developed, employing efficient Bayesian techniques to effectively test for balancing selection. LD-ABF demonstrated the most robust detection of selection in a variety of simulation scenarios, compared against a range of existing tests/tools (Tajima's D, HKA, Dng, BetaScan, and BalLerMix). Furthermore, the impact of the quality of sequencing on detection of balancing selection was explored, as well, using: (i) SNP genotyping and exome data, (ii) targeted high-resolution HLA genotyping (IHIW), and (iii) whole-genome long-read sequencing data (Pangenome). In the analysis of SNP genotyping and exome data, we identified known targets and 38 new selection signatures in genes not previously linked to balancing selection. To further investigate the impact of sequencing quality on detection of balancing selection, a detailed investigation of the MHC was performed with high-resolution HLA typing data. Higher quality sequencing revealed the HLA-DQ genes consistently demonstrated strong selection signatures otherwise not observed from the sparser SNP array and exome data. The HLA-DQ selection signature was also replicated in the Pangenome samples using considerably less samples but, with high-quality long-read sequence data. The improved statistical method, coupled with higher quality sequencing, leads to more consistent identification of selection and enhanced localization of variants under selection, particularly in complex regions.
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Affiliation(s)
- Tristan J Hayeck
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yang Li
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy L Mosbruger
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Adam G Gleason
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - George Damianos
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Grace Tzun-Wen Shaw
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jamie L Duke
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura K Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marcelo A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Mahdi Sarmady
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dimitri S Monos
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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3
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Israeli S, Maiers M, Louzoun Y. Graph-Based Imputation Methods and Their Applications to Single Donors and Families. Methods Mol Biol 2024; 2809:193-214. [PMID: 38907899 DOI: 10.1007/978-1-0716-3874-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
The outcome of Hematopoietic Stem Cell (HSCT) and organ transplant is strongly affected by the matching of the HLA alleles of the donor and the recipient. However, donors and sometimes recipients are often typed at low resolution, with some alleles either missing or ambiguous. Thus, imputation methods are required to detect the most probably high-resolution HLA haplotypes consistent with a typing. Such imputation algorithms require predefined haplotype frequencies. As such, the phasing of the typing is required for both imputation and frequency generation.We have developed a new approach to HLA haplotype and genotype imputation, where first all candidate phases of a typing are explicated, and then the ambiguity within each phase is solved. This ambiguity is solved through a graph structure of all partial haplotypes and the haplotypes consistent with them.This phasing approach was used to produce an imputation algorithm (GRIMM-Graph Imputation and Matching). GRIMM was then combined with the possibility of combining information from multiple races to produce MR-GRIMM (Multi-Race GRIMM). When family information is available, the phasing of each family member can be restricted by the others. We propose GRAMM (GRaph-bAsed faMily iMputation) to phase alleles in family pedigree HLA typing data and in mother-cord blood unit pairs. Finally, we combined MR-GRIMM with an expectation-maximization (EM) algorithm to estimate haplotype frequencies sharing information between races to produce MR-GRIMME (MR-GRIMM EM).We have shown that these algorithms naturally combine information between races and family members. The accuracy of each of these algorithms is significantly better than its current parallel methods. MR-GRIMM leads to high accuracy in matching predictions. GRAMM better imputes family members than either MR-GRIMM or any existing algorithm and has practically no phasing errors. MR-GRIMME obtains a higher likelihood than existing algorithms.MR-GRIMM, MR-GRIMME, and GRAMM are available as servers or through stand-alone versions in GITHUB and PyPi, as detailed in the appropriate sections.
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Affiliation(s)
- Sapir Israeli
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Martin Maiers
- Center for International Blood and Marrow Transplant Research (CIBMTR), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel.
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Israeli S, Gragert L, Madbouly A, Bashyal P, Schneider J, Maiers M, Louzoun Y. Combined imputation of HLA genotype and self-identified race leads to better donor-recipient matching. Hum Immunol 2023; 84:110721. [PMID: 37867095 PMCID: PMC10842039 DOI: 10.1016/j.humimm.2023.110721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 09/05/2023] [Accepted: 10/14/2023] [Indexed: 10/24/2023]
Abstract
Allogeneic Hematopoietic Cell Transplantation (HCT) is a curative therapy for hematologic disorders and often requires human leukocyte antigen (HLA)-matched donors. Donor registries have recruited donors utilizing evolving technologies of HLA genotyping methods. This necessitates in-silico ambiguity resolution and statistical imputation based on haplotype frequencies estimated from donor data stratified by self-identified race and ethnicity (SIRE). However, SIRE has limited genetic validity and presents a challenge for individuals with unknown or mixed SIRE. We present MR-GRIMM "Multi-Race Graph IMputation and Matching" that simultaneously imputes the race/ethnic category and HLA genotype using a SIRE based prior. Additionally, we propose a novel method to impute HLA typing inconsistent with current haplotype frequencies. The performance of MR-GRIMM was validated using a dataset of 170,000 donor-recipient pairs. MR-GRIMM has an average 20 % lower matching error (1-AUC) than single-race imputation. The recall metric (sensitivity) of the race/ethnic category imputation from HLA was measured by comparing the imputed donor race with the donor-provided SIRE. Accuracies of 0.74 and 0.55 were obtained for the prediction of 5 broad and 21 detailed US population groups respectively. The operational implementation of this algorithm in a registry search could help improve match predictions and access to HLA-matched donors.
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Affiliation(s)
- Sapir Israeli
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Loren Gragert
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Abeer Madbouly
- National Marrow Donor Program/Be The Match, Minneapolis, MN, United States; Center for International Blood and Marrow Transplant Research, Minneapolis, MN, United States
| | - Pradeep Bashyal
- National Marrow Donor Program/Be The Match, Minneapolis, MN, United States; Center for International Blood and Marrow Transplant Research, Minneapolis, MN, United States
| | - Joel Schneider
- National Marrow Donor Program/Be The Match, Minneapolis, MN, United States
| | - Martin Maiers
- National Marrow Donor Program/Be The Match, Minneapolis, MN, United States; Center for International Blood and Marrow Transplant Research, Minneapolis, MN, United States
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel.
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Levi R, Levi L, Louzoun Y. Bw4 ligand and direct T-cell receptor binding induced selection on HLA A and B alleles. Front Immunol 2023; 14:1236080. [PMID: 38077375 PMCID: PMC10703150 DOI: 10.3389/fimmu.2023.1236080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction The HLA region is the hallmark of balancing selection, argued to be driven by the pressure to present a wide variety of viral epitopes. As such selection on the peptide-binding positions has been proposed to drive HLA population genetics. MHC molecules also directly binds to the T-Cell Receptor and killer cell immunoglobulin-like receptors (KIR). Methods We here combine the HLA allele frequencies in over six-million Hematopoietic Stem Cells (HSC) donors with a novel machine-learning-based method to predict allele frequency. Results We show for the first time that allele frequency can be predicted from their sequences. This prediction yields a natural measure for selection. The strongest selection is affecting KIR binding regions, followed by the peptide-binding cleft. The selection from the direct interaction with the KIR and TCR is centered on positively charged residues (mainly Arginine), and some positions in the peptide-binding cleft are not associated with the allele frequency, especially Tyrosine residues. Discussion These results suggest that the balancing selection for peptide presentation is combined with a positive selection for KIR and TCR binding.
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Affiliation(s)
| | | | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
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Howard-McCombe J, Jamieson A, Carmagnini A, Russo IRM, Ghazali M, Campbell R, Driscoll C, Murphy WJ, Nowak C, O'Connor T, Tomsett L, Lyons LA, Muñoz-Fuentes V, Bruford MW, Kitchener AC, Larson G, Frantz L, Senn H, Lawson DJ, Beaumont MA. Genetic swamping of the critically endangered Scottish wildcat was recent and accelerated by disease. Curr Biol 2023; 33:4761-4769.e5. [PMID: 37935118 DOI: 10.1016/j.cub.2023.10.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/24/2023] [Accepted: 10/17/2023] [Indexed: 11/09/2023]
Abstract
The European wildcat population in Scotland is considered critically endangered as a result of hybridization with introduced domestic cats,1,2 though the time frame over which this gene flow has taken place is unknown. Here, using genome data from modern, museum, and ancient samples, we reconstructed the trajectory and dated the decline of the local wildcat population from viable to severely hybridized. We demonstrate that although domestic cats have been present in Britain for over 2,000 years,3 the onset of hybridization was only within the last 70 years. Our analyses reveal that the domestic ancestry present in modern wildcats is markedly over-represented in many parts of the genome, including the major histocompatibility complex (MHC). We hypothesize that introgression provides wildcats with protection against diseases harbored and introduced by domestic cats, and that this selection contributes to maladaptive genetic swamping through linkage drag. Using the case of the Scottish wildcat, we demonstrate the importance of local ancestry estimates to both understand the impacts of hybridization in wild populations and support conservation efforts to mitigate the consequences of anthropogenic and environmental change.
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Affiliation(s)
- Jo Howard-McCombe
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK; RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK.
| | - Alexandra Jamieson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK; Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilians University of Munich, Munich, Germany
| | - Alberto Carmagnini
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilians University of Munich, Munich, Germany; School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
| | | | - Muhammad Ghazali
- RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK
| | - Ruairidh Campbell
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney OX13 5QL, UK; NatureScot, Great Glen House, Leachkin Road, Inverness IV3 8NW, UK
| | | | - William J Murphy
- Texas A&M University, Veterinary Integrative Biosciences, College Station, TX 77843, USA
| | - Carsten Nowak
- Senckenberg Research Institute and Natural History Museum, Center for Wildlife Genetics, 63571 Weimar, Germany
| | - Terry O'Connor
- BioArCh, Department of Archaeology, University of York, York YO10 5NG, UK
| | - Louise Tomsett
- Mammal Section, Science Department, Natural History Museum, London SW7 5BD, UK
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh EH1 1JF, UK; School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilians University of Munich, Munich, Germany; School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Helen Senn
- RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK.
| | - Daniel J Lawson
- School of Mathematics, University of Bristol, Bristol BS8 1UG, UK.
| | - Mark A Beaumont
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK.
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Ansbacher-Feldman Z, Israeli S, Maiers M, Gragert L, De Santis D, Israeli M, Louzoun Y. GRAMM: A new method for analysis of HLA in families. HLA 2023; 102:477-488. [PMID: 37102220 DOI: 10.1111/tan.15075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 03/23/2023] [Accepted: 04/05/2023] [Indexed: 04/28/2023]
Abstract
Recently, haplo-identical transplantation with multiple HLA mismatches has become a viable option for stem cell transplants. Haplotype sharing detection requires the imputation of donor and recipient. We show that even in high-resolution typing when all alleles are known, there is a 15% error rate in haplotype phasing, and even more in low-resolution typings. Similarly, in related donors, the parents' haplotypes should be imputed to determine what haplotype each child inherited. We propose graph-based family imputation (GRAMM) to phase alleles in family pedigree HLA typing data, and in mother-cord blood unit pairs. We show that GRAMM has practically no phasing errors when pedigree data are available. We apply GRAMM to simulations with different typing resolutions as well as paired cord-mother typings, and show very high phasing accuracy, and improved allele imputation accuracy. We use GRAMM to detect recombination events and show that the rate of falsely detected recombination events (false-positive rate) in simulations is very low. We then apply recombination detection to typed families to estimate the recombination rate in Israeli and Australian population datasets. The estimated recombination rate has an upper bound of 10%-20% per family (1%-4% per individual).
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Affiliation(s)
| | - Sapir Israeli
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Martin Maiers
- Center for Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA
- National Marrow Donor Program/Be The Match, Minneapolis, Minnesota, USA
| | - Loren Gragert
- Center for Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA
- National Marrow Donor Program/Be The Match, Minneapolis, Minnesota, USA
- Department of Pathology and Laboratory Medicine, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Dianne De Santis
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Australia
| | - Moshe Israeli
- Tissue Typing Laboratory, Beilinson Hospital, Rabin Medical Center, Petach-Tikva, Israel
- Department of Digital Medical Technologies, Holon Institute of Technology, Holon, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
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Hartman K, Steiner G, Siegel M, Looney CM, Hickling TP, Bray-French K, Springer S, Marban-Doran C, Ducret A. Expanding the MAPPs Assay to Accommodate MHC-II Pan Receptors for Improved Predictability of Potential T Cell Epitopes. BIOLOGY 2023; 12:1265. [PMID: 37759665 PMCID: PMC10525474 DOI: 10.3390/biology12091265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
A critical step in the immunogenicity cascade is attributed to human leukocyte antigen (HLA) II presentation triggering T cell immune responses. The liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based major histocompatibility complex (MHC) II-associated peptide proteomics (MAPPs) assay is implemented during preclinical risk assessments to identify biotherapeutic-derived T cell epitopes. Although studies indicate that HLA-DP and HLA-DQ alleles are linked to immunogenicity, most MAPPs studies are restricted to using HLA-DR as the dominant HLA II genotype due to the lack of well-characterized immunoprecipitating antibodies. Here, we address this issue by testing various commercially available clones of MHC-II pan (CR3/43, WR18, and Tü39), HLA-DP (B7/21), and HLA-DQ (SPV-L3 and 1a3) antibodies in the MAPPs assay, and characterizing identified peptides according to binding specificity. Our results reveal that HLA II receptor-precipitating reagents with similar reported specificities differ based on clonality and that MHC-II pan antibodies do not entirely exhibit pan-specific tendencies. Since no individual antibody clone is able to recover the complete HLA II peptide repertoire, we recommend a mixed strategy of clones L243, WR18, and SPV-L3 in a single immunoprecipitation step for more robust compound-specific peptide detection. Ultimately, our optimized MAPPs strategy improves the predictability and additional identification of T cell epitopes in immunogenicity risk assessments.
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Affiliation(s)
- Katharina Hartman
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
| | - Guido Steiner
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
| | - Michel Siegel
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
| | - Cary M. Looney
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
| | - Timothy P. Hickling
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
| | - Katharine Bray-French
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
| | - Sebastian Springer
- School of Science, Department of Biochemistry and Cell Biology, Constructor University, Campus Ring 1, 28759 Bremen, Germany
| | - Céline Marban-Doran
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
| | - Axel Ducret
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
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9
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Biancolella M, Colona VL, Luzzatto L, Watt JL, Mattiuz G, Conticello SG, Kaminski N, Mehrian-Shai R, Ko AI, Gonsalves GS, Vasiliou V, Novelli G, Reichardt JKV. COVID-19 annual update: a narrative review. Hum Genomics 2023; 17:68. [PMID: 37488607 PMCID: PMC10367267 DOI: 10.1186/s40246-023-00515-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/16/2023] [Indexed: 07/26/2023] Open
Abstract
Three and a half years after the pandemic outbreak, now that WHO has formally declared that the emergency is over, COVID-19 is still a significant global issue. Here, we focus on recent developments in genetic and genomic research on COVID-19, and we give an outlook on state-of-the-art therapeutical approaches, as the pandemic is gradually transitioning to an endemic situation. The sequencing and characterization of rare alleles in different populations has made it possible to identify numerous genes that affect either susceptibility to COVID-19 or the severity of the disease. These findings provide a beginning to new avenues and pan-ethnic therapeutic approaches, as well as to potential genetic screening protocols. The causative virus, SARS-CoV-2, is still in the spotlight, but novel threatening virus could appear anywhere at any time. Therefore, continued vigilance and further research is warranted. We also note emphatically that to prevent future pandemics and other world-wide health crises, it is imperative to capitalize on what we have learnt from COVID-19: specifically, regarding its origins, the world's response, and insufficient preparedness. This requires unprecedented international collaboration and timely data sharing for the coordination of effective response and the rapid implementation of containment measures.
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Affiliation(s)
| | - Vito Luigi Colona
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy
| | - Lucio Luzzatto
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- University of Florence, 50121, Florence, Italy
| | - Jessica Lee Watt
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Smithfield, QLD, 4878, Australia
| | | | - Silvestro G Conticello
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Florence, Italy
- Institute of Clinical Physiology - National Council of Research (IFC-CNR), 56124, Pisa, Italy
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ruty Mehrian-Shai
- Pediatric Hemato-Oncology, Edmond and Lilly Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 2 Sheba Road, 52621, Ramat Gan, Israel
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
- Instituto Gonçalo MonizFundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - Gregg S Gonsalves
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, USA
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy.
- IRCCS Neuromed, 86077, Pozzilli, IS, Italy.
- Department of Pharmacology, School of Medicine, University of Nevada, 89557, Reno, NV, USA.
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, QLD, 4878, Australia
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10
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Jung K, Kim JG, Shin S, Roh EY, Hong YJ, Song EY. Allele and haplotype frequencies of 11 HLA loci in Koreans by next-generation sequencing. HLA 2023; 101:602-612. [PMID: 36719349 DOI: 10.1111/tan.14980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 12/24/2022] [Accepted: 01/27/2023] [Indexed: 02/01/2023]
Abstract
Data on HLA genotype distribution, including DQA1 and DPA1, in the Korean population are limited. We aimed to investigate the allele and haplotype frequencies of 11 HLA loci in 339 Korean subjects using next-generation sequencing (NGS)-based HLA typing. A total of 339 samples from unrelated healthy subjects were genotyped for HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQB1, -DQA1, -DPB1, and -DPA1 using two different NGS-based HLA typing kits (166 tested using the NGSgo-MX11-3 kit [GenDx, Netherlands] and 173 by the AllType NGS 11 Loci Amplification kit [One Lambda, USA]). PyPop software was used to estimate allele and haplotype frequencies and linkage disequilibrium between the loci. Additionally, a principal component analysis was performed to compare the allele distribution of Koreans with that of other populations. A total of 214 HLA alleles (97 class I and 117 class II alleles) were assigned. The most frequent alleles for each locus were A*24:02:01 (24.78%), B*15:01:01 (10.18%), C*01:02:01 (18.44%), DRB1*04:05:01 (9.59%), DRB3*02:02:01 (13.72%), DRB4*01:03:01 (25.81%), DRB5*01:01:01 (9.0%), DQA1*01:02:01 (16.96%), DQB1*03:01:01 (14.31%), DPA1*01:03:01 (44.4%), and DPB1*05:01:01 (35.1%), respectively. The most frequent haplotypes were A*33:03:01-C*03:02:02-B*58:01:01 for HLA class I (5.01%) and DRB1*04:05:01-DQA1*03:03:01-DQB1*04:01:01-DPA1*02:02:02-DPB1*05:01:01 for HLA class II (6.23%). The total allelic ambiguities by NGS were estimated to be minimal and considerably decreased compared with those by Sanger sequencing. The Japanese population had the most similar allele distribution to Koreans, followed by the Chinese population. Frequency data of 11 HLA loci in Koreans can provide essential data for population genetics and disease association studies.
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Affiliation(s)
- Kiwook Jung
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Jisoo G Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Yun Ji Hong
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Eun Young Song
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
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11
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Oliveira MLG, Castelli EC, Veiga‐Castelli LC, Pereira ALE, Marcorin L, Carratto TMT, Souza AS, Andrade HS, Simões AL, Donadi EA, Courtin D, Sabbagh A, Giuliatti S, Mendes‐Junior CT. Genetic diversity of the
LILRB1
and
LILRB2
coding regions in an admixed Brazilian population sample. HLA 2022; 100:325-348. [DOI: 10.1111/tan.14725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/02/2022] [Accepted: 06/24/2022] [Indexed: 11/27/2022]
Affiliation(s)
| | - Erick C. Castelli
- Pathology Department, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Luciana C. Veiga‐Castelli
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Alison Luis E. Pereira
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Letícia Marcorin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Thássia M. T. Carratto
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Andreia S. Souza
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Heloisa S. Andrade
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Aguinaldo L. Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Eduardo A. Donadi
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | | | | | - Silvana Giuliatti
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Celso Teixeira Mendes‐Junior
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
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12
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Redondo MJ, Gignoux CR, Dabelea D, Hagopian WA, Onengut-Gumuscu S, Oram RA, Rich SS. Type 1 diabetes in diverse ancestries and the use of genetic risk scores. Lancet Diabetes Endocrinol 2022; 10:597-608. [PMID: 35724677 PMCID: PMC10024251 DOI: 10.1016/s2213-8587(22)00159-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/16/2022] [Accepted: 05/06/2022] [Indexed: 02/06/2023]
Abstract
Over 75 genetic loci within and outside of the HLA region influence type 1 diabetes risk. Genetic risk scores (GRS), which facilitate the integration of complex genetic information, have been developed in type 1 diabetes and incorporated into models and algorithms for classification, prognosis, and prediction of disease and response to preventive and therapeutic interventions. However, the development and validation of GRS across different ancestries is still emerging, as is knowledge on type 1 diabetes genetics in populations of diverse genetic ancestries. In this Review, we provide a summary of the current evidence on the evolutionary genetic variation in type 1 diabetes and the racial and ethnic differences in type 1 diabetes epidemiology, clinical characteristics, and preclinical course. We also discuss the influence of genetics on type 1 diabetes with differences across ancestries and the development and validation of GRS in various populations.
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Affiliation(s)
- Maria J Redondo
- Division of Diabetes and Endocrinology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA.
| | - Christopher R Gignoux
- Department of Medicine and Colorado Center for Personalized Medicine, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA
| | - Dana Dabelea
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - William A Hagopian
- Division of Diabetes Programs, Pacific Northwest Research Institute, Seattle, WA, USA
| | - Suna Onengut-Gumuscu
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Richard A Oram
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, UK; The Academic Kidney Unit, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Stephen S Rich
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
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13
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Melka AB, Louzoun Y. High fraction of silent recombination in a finite-population two-locus neutral birth-death-mutation model. Phys Rev E 2022; 106:024409. [PMID: 36109958 DOI: 10.1103/physreve.106.024409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
A precise estimate of allele and haplotype polymorphism is of great interest in theoretical population genetics, but also has practical applications, such as bone marrow registries management. Allele polymorphism is driven mainly by point mutations, while haplotype polymorphism is also affected by recombination. Current estimates treat recombination as mutations in an infinite site model. We here show that even in the simple case of two loci in a haploid individual, for a finite population, most recombination events produce existing haplotypes, and as such are silent. Silent recombination considerably reduces the total number of haplotypes expected from the infinite site model for populations that are not much larger than one over the mutation rate. Moreover, in contrast with mutations, the number of haplotypes does not grow linearly with the population size. We hence propose a more accurate estimate of the total number of haplotypes that takes into account silent recombination. We study large-scale human leukocyte antigen (HLA) haplotype frequencies from human populations to show that the current estimated recombination rate in the HLA region is underestimated.
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Affiliation(s)
- A B Melka
- Department of Mathematics, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Y Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan 52900, Israel
- Gonda Brain Research Center, Bar-Ilan University, Ramat Gan 52900, Israel
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14
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Tshabalala M, Mellet J, Vather K, Nelson D, Mohamed F, Christoffels A, Pepper MS. High Resolution HLA ∼A, ∼B, ∼C, ∼DRB1, ∼DQA1, and ∼DQB1 Diversity in South African Populations. Front Genet 2022; 13:711944. [PMID: 35309124 PMCID: PMC8931603 DOI: 10.3389/fgene.2022.711944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/17/2022] [Indexed: 01/10/2023] Open
Abstract
Background: Lack of HLA data in southern African populations hampers disease association studies and our understanding of genetic diversity in these populations. We aimed to determine HLA diversity in South African populations using high resolution HLA ∼A, ∼B, ∼C, ∼DRB1, ∼DQA1 and ∼DQB1 data, from 3005 previously typed individuals. Methods: We determined allele and haplotype frequencies, deviations from Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD) and neutrality test. South African HLA class I data was additionally compared to other global populations using non-metrical multidimensional scaling (NMDS), genetic distances and principal component analysis (PCA). Results: All loci strongly (p < 0.0001) deviated from HWE, coupled with excessive heterozygosity in most loci. Two of the three most frequent alleles, HLA ∼DQA1*05:02 (0.2584) and HLA ∼C*17:01 (0.1488) were previously reported in South African populations at lower frequencies. NMDS showed genetic distinctness of South African populations. Phylogenetic analysis and PCA clustered our current dataset with previous South African studies. Additionally, South Africans seem to be related to other sub-Saharan populations using HLA class I allele frequencies. Discussion and Conclusion: Despite the retrospective nature of the study, data missingness, the imbalance of sample sizes for each locus and haplotype pairs, and induced methodological difficulties, this study provides a unique and large HLA dataset of South Africans, which might be a useful resource to support anthropological studies, disease association studies, population based vaccine development and donor recruitment programs. We additionally provide simulated high resolution HLA class I data to augment the mixed resolution typing results generated from this study.
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Affiliation(s)
- Mqondisi Tshabalala
- Department of Immunology, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juanita Mellet
- Department of Immunology, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Kuben Vather
- South African National Blood Service (SANBS), Roodepoort, South Africa
| | - Derrick Nelson
- South African National Blood Service (SANBS), Roodepoort, South Africa
| | - Fathima Mohamed
- South African National Blood Service (SANBS), Roodepoort, South Africa
| | - Alan Christoffels
- SAMRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Michael S. Pepper
- Department of Immunology, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- *Correspondence: Michael S. Pepper,
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15
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Kyobe S, Mwesigwa S, Kisitu GP, Farirai J, Katagirya E, Mirembe AN, Ketumile L, Wayengera M, Katabazi FA, Kigozi E, Wampande EM, Retshabile G, Mlotshwa BC, Williams L, Morapedi K, Kasvosve I, Kyosiimire-Lugemwa J, Nsangi B, Tsimako-Johnstone M, Brown CW, Joloba M, Anabwani G, Bhekumusa L, Mpoloka SW, Mardon G, Matshaba M, Kekitiinwa A, Hanchard NA. Exome Sequencing Reveals a Putative Role for HLA-C*03:02 in Control of HIV-1 in African Pediatric Populations. Front Genet 2021; 12:720213. [PMID: 34512729 PMCID: PMC8428176 DOI: 10.3389/fgene.2021.720213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/05/2021] [Indexed: 12/28/2022] Open
Abstract
Human leucocyte antigen (HLA) class I molecules present endogenously processed antigens to T-cells and have been linked to differences in HIV-1 disease progression. HLA allelotypes show considerable geographical and inter-individual variation, as does the rate of progression of HIV-1 disease, with long-term non-progression (LTNP) of disease having most evidence of an underlying genetic contribution. However, most genetic analyses of LTNP have occurred in adults of European ancestry, limiting the potential transferability of observed associations to diverse populations who carry the burden of disease. This is particularly true of HIV-1 infected children. Here, using exome sequencing (ES) to infer HLA allelotypes, we determine associations with HIV-1 LTNP in two diverse African pediatric populations. We performed a case-control association study of 394 LTNPs and 420 rapid progressors retrospectively identified from electronic medical records of pediatric HIV-1 populations in Uganda and Botswana. We utilized high-depth ES to perform high-resolution HLA allelotyping and assessed evidence of association between HLA class I alleles and LTNP. Sixteen HLA alleles and haplotypes had significantly different frequencies between Uganda and Botswana, with allelic differences being more prominent in HLA-A compared to HLA-B and C allelotypes. Three HLA allelotypes showed association with LTNP, including a novel association in HLA-C (HLA-B∗57:03, aOR 3.21, Pc = 0.0259; B∗58:01, aOR 1.89, Pc = 0.033; C∗03:02, aOR 4.74, Pc = 0.033). Together, these alleles convey an estimated population attributable risk (PAR) of non-progression of 16.5%. We also observed novel haplotype associations with HLA-B∗57:03-C∗07:01 (aOR 5.40, Pc = 0.025) and HLA-B∗58:01-C∗03:02 (aOR 4.88, Pc = 0.011) with a PAR of 9.8%, as well as a previously unreported independent additive effect and heterozygote advantage of HLA-C∗03:02 with B∗58:01 (aOR 4.15, Pc = 0.005) that appears to limit disease progression, despite weak LD (r 2 = 0.18) between these alleles. These associations remained irrespective of gender or country. In one of the largest studies of HIV in Africa, we find evidence of a protective effect of canonical HLA-B alleles and a novel HLA-C association that appears to augment existing HIV-1 control alleles in pediatric populations. Our findings outline the value of using multi-ethnic populations in genetic studies and offer a novel HIV-1 association of relevance to ongoing vaccine studies.
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Affiliation(s)
- Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Savannah Mwesigwa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Grace P. Kisitu
- Baylor College of Medicine Children’s Foundation, Kampala, Uganda
| | - John Farirai
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Lesego Ketumile
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fred Ashaba Katabazi
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edward M. Wampande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gaone Retshabile
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Busisiwe C. Mlotshwa
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Lesedi Williams
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Koketso Morapedi
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Ishmael Kasvosve
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | - Betty Nsangi
- Baylor College of Medicine Children’s Foundation, Kampala, Uganda
| | | | - Chester W. Brown
- University of Tennessee Health Science Center, Memphis, TN, United States
| | - Moses Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
| | - Lukhele Bhekumusa
- Eswatini - Baylor College of Medicine Children’s Foundation, Mbabane, Eswatini
| | - Sununguko W. Mpoloka
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Mogomotsi Matshaba
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
- Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Adeodata Kekitiinwa
- Baylor College of Medicine Children’s Foundation, Kampala, Uganda
- Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Neil A. Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
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16
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MHC Haplotyping of SARS-CoV-2 Patients: HLA Subtypes Are Not Associated with the Presence and Severity of COVID-19 in the Israeli Population. J Clin Immunol 2021; 41:1154-1161. [PMID: 34050837 PMCID: PMC8164405 DOI: 10.1007/s10875-021-01071-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023]
Abstract
HLA haplotypes were found to be associated with increased risk for viral infections or disease severity in various diseases, including SARS. Several genetic variants are associated with COVID-19 severity. Studies have proposed associations, based on a very small sample and a large number of tested HLA alleles, but no clear association between HLA and COVID-19 incidence or severity has been reported. We conducted a large-scale HLA analysis of Israeli individuals who tested positive for SARS-CoV-2 infection by PCR. Overall, 72,912 individuals with known HLA haplotypes were included in the study, of whom 6413 (8.8%) were found to have SARS-CoV-2 by PCR. A total of 20,937 subjects were of Ashkenazi origin (at least 2/4 grandparents). One hundred eighty-one patients (2.8% of the infected) were hospitalized due to the disease. None of the 66 most common HLA loci (within the five HLA subgroups: A, B, C, DQB1, DRB1) was found to be associated with SARS-CoV-2 infection or hospitalization in the general Israeli population. Similarly, no association was detected in the Ashkenazi Jewish subset. Moreover, no association was found between heterozygosity in any of the HLA loci and either infection or hospitalization. We conclude that HLA haplotypes are not a major risk/protecting factor among the Israeli population for SARS-CoV-2 infection or severity. Our results suggest that if any HLA association exists with the disease it is very weak, and of limited effect on the pandemic.
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17
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Baxter-Lowe LA. The changing landscape of HLA typing: Understanding how and when HLA typing data can be used with confidence from bench to bedside. Hum Immunol 2021; 82:466-477. [PMID: 34030895 DOI: 10.1016/j.humimm.2021.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022]
Abstract
Human leukocyte antigen (HLA) genes are extraordinary for their extreme diversity and widespread impact on human health and disease. More than 30,000 HLA alleles have been officially named and more alleles continue to be discovered at a rapid pace. HLA typing systems which have been developed to detect HLA diversity have advanced rapidly and are revolutionizing our understanding of HLA's clinical importance. However, continuous improvements in knowledge and technology have created challenges for clinicians and scientists. This review explains how differences in HLA typing systems can impact the HLA types that are assigned. The consequences of differences in laboratory testing methods and reference databases are described. The challenges of using HLA types that are not equivalent are illustrated. A fundamental understanding of the continual expansion of our understanding of HLA diversity and limitations in some of the typing data is essential for using typing data appropriately in clinical and research settings.
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Affiliation(s)
- Lee Ann Baxter-Lowe
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, USA; Department of Pathology, University of Southern California, USA.
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18
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Hyun YS, Jo HA, Lee YH, Kim SM, Baek IC, Sohn HJ, Cho HI, Kim TG. Comprehensive Analysis of CD4 + T Cell Responses to CMV pp65 Antigen Restricted by Single HLA-DR, -DQ, and -DP Allotype Within an Individual. Front Immunol 2021; 11:602014. [PMID: 33658991 PMCID: PMC7917246 DOI: 10.3389/fimmu.2020.602014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/15/2020] [Indexed: 01/18/2023] Open
Abstract
Within an individual, six different HLA class II heterodimers are expressed co-dominantly by two alleles of HLA-DR, -DQ, and -DP loci. However, it remained unclear which HLA allotypes were used in T cell responses to a given antigen. For the measurement of the CD4+ T cell responses restricted by a single HLA allotype, we established a panel of artificial antigen-presenting cells (aAPCs) expressing each single HLA allele of 20 HLA-DRB1, 16 HLA-DQ, and 13 HLA-DP alleles. CD4+ T cell responses to cytomegalovirus (CMV) pp65 restricted by single HLA class II allotype defined in 45 healthy donors. The average magnitude of CD4+ T cell responses by HLA-DR allotypes was higher than HLA-DQ and HLA-DP allotypes. CD4+ T cell responses by DRA*01:01/DRB1*04:06, DQA1*01:02/DQB1*06:02, DPA1*02:02/DPB1*05:01 were higher among the other alleles in each HLA-DR, -DQ, and -DP locus. Interestingly, the frequencies of HLA-DR alleles and the positivity of specific allotypes showed an inverse correlation. One allotype within individuals is dominantly used in CD4+ T cell response in 49% of donors, and two allotypes showed that in 7% of donors, and any positive response was detected in 44% of donors. Even if one individual had several dominant alleles, CD4+ T cell responses tended to be restricted by only one of them. Furthermore, CD8+ and CD4+ T cell responses by HLA class I and class II were correlated. Our results demonstrate that the CD4+ T cell preferentially use a few dominant HLA class II allotypes within individuals, similar to CD8+ T cell response to CMV pp65.
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Affiliation(s)
- You-Seok Hyun
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyeong-A Jo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Yong-Hun Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Sun-Mi Kim
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - In-Cheol Baek
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyun-Jung Sohn
- Translational and Clinical Division, ViGenCell Inc., Seoul, South Korea
| | - Hyun-Il Cho
- Translational and Clinical Division, ViGenCell Inc., Seoul, South Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
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19
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Shin S, Song EY, Kwon YW, Oh S, Park H, Kim NH, Roh EY. Usefulness of the Hematopoietic Stem Cell Donor Pool as a Source of HLA-Homozygous Induced Pluripotent Stem Cells for Haplobanking: Combined Analysis of the Cord Blood Inventory and Bone Marrow Donor Registry. Biol Blood Marrow Transplant 2020; 26:e202-e208. [PMID: 32439474 DOI: 10.1016/j.bbmt.2020.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/24/2020] [Accepted: 05/10/2020] [Indexed: 12/22/2022]
Abstract
Induced pluripotent stem cells (iPSCs) have opened up unprecedented opportunities for novel therapeutic options for precision medicine. Hematopoietic stem cell (HSC) donor pools with previously determined HLA types may be ideal sources for iPSC production. Based on the HLA distribution of cryopreserved cord blood units (CBUs) and registered bone marrow (BM) donors, we estimated how much of the Korean population could be covered by HLA-homozygous iPSCs. We analyzed a total of 143,866 Korean HSC donors (27,904 CBUs and 115,962 BM donors). Each donor sample was typed for the HLA-A, -B, and -DRB1 alleles at low to intermediate resolution by DNA-based molecular techniques: PCR sequence-specific oligonucleotide (PCR-SSOP), PCR with sequence-specific primers (PCR-SSP) and PCR with sequence-based typing (PCR-SBT). We also identified individuals possessing homozygous HLA haplotypes by direct counting. The matching probabilities for zero-mismatch transplantation were calculated for 143,866 Koreans and 50 million potential Korean patients. Among the HSC donor pool, 17 HLA-A alleles, 41 HLA-B alleles, and 13 HLA-DRB1 alleles, as well as 128 homozygous HLA-A-B-DRB1 haplotypes, were identified at serologic equivalents, and those haplotypes cumulatively matched 93.20% of the 143,866 Korean donors as zero HLA-mismatch iPSC sources. Among the combinations of 2,056 haplotypes with frequencies ≥ 0.001% in a population of 50 million, those 128 homozygous haplotypes can provide 93.65% coverage for potential Korean recipients. Haplobanking of a reasonable number of HLA-A, -B, and -DRB1 homozygous iPSC lines derived from CBUs and cells of registered BM donors may be an efficient option for allogenic iPSC therapy.
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Affiliation(s)
- Sue Shin
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea; Seoul Metropolitan Government Public Cord Blood Bank-ALLCORD, Seoul, Republic of Korea; Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eun Young Song
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoo-Wook Kwon
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sohee Oh
- Department of Biostatistics, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Hyunwoong Park
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea; Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Nam-Hee Kim
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea; Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea; Seoul Metropolitan Government Public Cord Blood Bank-ALLCORD, Seoul, Republic of Korea; Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
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20
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Melka A, Dori N, Louzoun Y. Invasion Rate Versus Diversity in Population Dynamics with Catastrophes. PHYSICAL REVIEW LETTERS 2020; 124:158301. [PMID: 32357052 DOI: 10.1103/physrevlett.124.158301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
A key question in the current diversity crisis is how diversity has been maintained throughout evolution and how to preserve it. Modern coexistence theories suggest that a high invasion rate of rare new types is directly related to diversity. We show that adding almost any mechanism of catastrophes to a stochastic birth, death, and mutation process with limited carrying capacity induces a novel phase transition characterized by a positive invasion rate but a low diversity. In this phase, new types emerge and grow rapidly, but the resulting growth of very large types decreases diversity. This model also resolves two major drawbacks of neutral evolution models: their failure to explain balancing selection without resorting to fitness differences and the unrealistic time required for the creation of the observed large types. We test this model on a classical case of genetic polymorphism: the HLA locus.
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Affiliation(s)
- A Melka
- Department of Mathematics, Bar-Ilan University, Ramat Gan 52900, Israel
| | - N Dori
- Gonda Brain Research Center, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Y Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan 52900, Israel
- Gonda Brain Research Center, Bar-Ilan University, Ramat Gan 52900, Israel
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21
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Huang C, Chen SP, Huang YH, Chen HY, Wang YF, Lee MH, Wang SJ. HLA class I alleles are associated with clinic-based migraine and increased risks of chronic migraine and medication overuse. Cephalalgia 2020; 40:493-502. [PMID: 31973566 DOI: 10.1177/0333102420902228] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE We aimed to evaluate associations of human leukocyte antigen variants with migraine or headache in hospital and population-based settings. METHODS The case-control study population, aged 30-70, included 605 clinic-based migraine patients in a medical center and 8449 population-based participants in Taiwan Biobank (TWB). Clinic-based cases were ascertained by neurologists. Participants in Taiwan Biobank were interviewed by a structured questionnaire including headache and migraine history; among them, 2394 had headache or migraine history while 6055 were free of headache and served as controls. All subjects were genotyped by Axiom Genome-Wide Single Nucleotide Polymorphism Arrays and imputed for eight classical human leukocyte antigen genes. Human leukocyte antigen frequencies were compared between clinic-based and self-reported patients and controls. We utilized likelihood ratio tests to examine human leukocyte antigen-disease associations and logistic regressions to estimate the effect of human leukocyte antigen alleles on migraine. RESULTS Human leukocyte antigen-B and C showed significant associations with clinic-based migraine (q-value < 0.05). Human leukocyte antigen-B*39:01, human leukocyte antigen-B*51:01, human leukocyte antigen-B*58:01 and human leukocyte antigen-C*03:02 were significantly associated with migraine, with age and sex-adjusted odds ratios (95% CIs) of 1.80 (1.28-2.53), 1.50 (1.15-1.97), 1.36 (1.14-1.62) and 1.36 (1.14-1.62), correspondingly. Clinic-based migraineurs carrying human leukocyte antigen-B*58:01 or human leukocyte antigen-C*03:02 had 1.63 (1.11-2.39) -fold likelihood to have chronic migraine with medication-overuse headache compared to episodic migraine. However, no human leukocyte antigen genes were associated with self-reported headache or migraine in the community. CONCLUSIONS Human leukocyte antigen class I genetic variants are positively associated with risk of clinic-based migraine but not self-reported migraine or headache and may contribute to migraine chronification and medication overuse.
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Affiliation(s)
- Claire Huang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei.,Faculty of Medicine, National Yang-Ming University School of Medicine, Taipei
| | - Shih-Pin Chen
- Institute of Clinical Medicine, National Yang-Ming University, Taipei.,Faculty of Medicine, National Yang-Ming University School of Medicine, Taipei.,Brain Research Center, National Yang-Ming University, Taipei.,Division of Translational Research, Department of Medical Research, Taipei Veterans General Hospital, Taipei.,Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei
| | - Yu-Han Huang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei
| | - Hsuan-Yu Chen
- Institute of Statistical Science, Academia Sinica, Taipei
| | - Yen-Feng Wang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei.,Faculty of Medicine, National Yang-Ming University School of Medicine, Taipei.,Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei
| | - Mei-Hsuan Lee
- Institute of Clinical Medicine, National Yang-Ming University, Taipei
| | - Shuu-Jiun Wang
- Faculty of Medicine, National Yang-Ming University School of Medicine, Taipei.,Brain Research Center, National Yang-Ming University, Taipei.,Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei
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22
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Reply to Hedrick and Klitz: High haplotype discovery rate in the HLA locus. Proc Natl Acad Sci U S A 2019; 116:23388-23389. [PMID: 31662470 PMCID: PMC6876207 DOI: 10.1073/pnas.1916124116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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23
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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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24
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Evolution of the human MHC: New haplotype frequency analysis is not informative. Proc Natl Acad Sci U S A 2019; 116:23386-23387. [PMID: 31662471 DOI: 10.1073/pnas.1911794116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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25
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Next-generation sequencing reveals new information about HLA allele and haplotype diversity in a large European American population. Hum Immunol 2019; 80:807-822. [PMID: 31345698 DOI: 10.1016/j.humimm.2019.07.275] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 06/21/2019] [Accepted: 07/06/2019] [Indexed: 12/11/2022]
Abstract
The human leukocyte antigen (HLA) genes are extremely polymorphic and are useful molecular markers to make inferences about human population history. However, the accuracy of the estimation of genetic diversity at HLA loci very much depends on the technology used to characterize HLA alleles; high-resolution genotyping of long-range HLA gene products improves the assessment of HLA population diversity as well as other population parameters compared to lower resolution typing methods. In this study we examined allelic and haplotype HLA diversity in a large healthy European American population sourced from the UCSF-DNA bank. A high-resolution next-generation sequencing method was applied to define non-ambiguous 3- and 4-field alleles at the HLA-A, HLA-C, HLA-B, HLA-DRB1, HLA-DRB3/4/5, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1 loci in samples provided by 2248 unrelated individuals. A number of population parameters were examined including balancing selection and various measurements of linkage disequilibrium were calculated. There were no detectable deviations from Hardy-Weinberg proportions at HLA-A, HLA-DRB1, HLA-DQA1 and HLA-DQB1. For the remaining loci moderate and significant deviations were detected at HLA-C, HLA-B, HLA-DRB3/4/5, HLA-DPA1 and HLA-DPB1 loci mostly from population substructures. Unique 4-field associations were observed among alleles at 2 loci and haplotypes extending large intervals that were not apparent in results obtained using testing methodologies with limited sequence coverage and phasing. The high diversity at HLA-DPA1 results from detection of intron variants of otherwise well conserved protein sequences. It may be speculated that divergence in exon sequences may be negatively selected. Our data provides a valuable reference source for future population studies that may allow for precise fine mapping of coding and non-coding sequences determining disease susceptibility and allo-immunogenicity.
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26
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Arrieta-Bolaños E, Madrigal-Sánchez JJ, Stein JE, Órlich-Pérez P, Moreira-Espinoza MJ, Paredes-Carias E, Vanegas-Padilla Y, Salazar-Sánchez L, Madrigal JA, Marsh SGE, Shaw BE. High-resolution HLA allele and haplotype frequencies in majority and minority populations of Costa Rica and Nicaragua: Differential admixture proportions in neighboring countries. HLA 2019; 91:514-529. [PMID: 29687625 DOI: 10.1111/tan.13280] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 04/13/2018] [Accepted: 04/18/2018] [Indexed: 02/03/2023]
Abstract
The HLA system shows the most extensive polymorphism in the human genome. Allelic and haplotypic frequencies of HLA genes vary dramatically across human populations. Due to a complex history of migration, populations in Latin America show a broad variety of admixture proportions, usually varying not only between countries, but also within countries. Knowledge of HLA allele and haplotype frequencies is essential for medical fields such as transplantation, but also serves as a means to assess genetic diversity and ancestry in human populations. Here, we have determined high-resolution HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies in a sample of 713 healthy subjects from three Mestizo populations, one population of African descent, and Amerindians of five different groups from Costa Rica and Nicaragua and compared their profiles to a large set of indigenous populations from Iberia, Sub-Saharan Africa, and the Americas. Our results show a great degree of allelic and haplotypic diversity within and across these populations, with most extended haplotypes being private. Mestizo populations show alleles and haplotypes of putative European, Amerindian, and Sub-Saharan African origin, albeit with differential proportions. Despite some degree of gene flow, Amerindians and Afro-descendants show great similarity to other Amerindian and West African populations, respectively. This is the first comprehensive study reporting high-resolution HLA diversity in Central America, and its results will shed light into the genetic history of this region while also supporting the development of medical programs for organ and stem cell transplantation.
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Affiliation(s)
- E Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital, Essen, Germany.,Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA), Universidad de Costa Rica, San José, Costa Rica
| | | | - J E Stein
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - P Órlich-Pérez
- Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA), Universidad de Costa Rica, San José, Costa Rica.,División de Banco de Células Madre, Laboratorio Clínico, Hospital San Juan de Dios, San José, Costa Rica
| | - M J Moreira-Espinoza
- Departamento de Ciencias Morfológicas, Universidad Nacional Autónoma de Nicaragua, León, Nicaragua
| | - E Paredes-Carias
- Departamento de Ciencias Morfológicas, Universidad Nacional Autónoma de Nicaragua, León, Nicaragua
| | - Y Vanegas-Padilla
- Departamento de Ciencias Morfológicas, Universidad Nacional Autónoma de Nicaragua, León, Nicaragua
| | - L Salazar-Sánchez
- Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica
| | - J A Madrigal
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,Cancer Institute, University College London, London, UK
| | - S G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,Cancer Institute, University College London, London, UK
| | - B E Shaw
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,Center for International Blood and Marrow Transplant Research, Department of Medicine, Medical College of Wisconsin, Milwaukee, USA
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27
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Multiplicative fitness, rapid haplotype discovery, and fitness decay explain evolution of human MHC. Proc Natl Acad Sci U S A 2019; 116:14098-14104. [PMID: 31227609 DOI: 10.1073/pnas.1714436116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The major histocompatibility complex (MHC) is a central component of the vertebrate immune system and hence evolves in the regime of a host-pathogen evolutionary race. The MHC is associated with quantitative traits which directly affect fitness and are subject to selection pressure. The evolution of haplotypes at the MHC HLA (HLA) locus is generally thought to be governed by selection for increased diversity that is manifested in overdominance and/or negative frequency-dependent selection (FDS). However, recently, a model combining purifying selection on haplotypes and balancing selection on alleles has been proposed. We compare the predictions of several population dynamics models of haplotype frequency evolution to the distributions derived from 6.59-million-donor HLA typings from the National Marrow Donor Program registry. We show that models that combine a multiplicative fitness function, extremely high haplotype discovery rates, and exponential fitness decay over time produce the best fit to the data for most of the analyzed populations. In contrast, overdominance is not supported, and population substructure does not explain the observed haplotype frequencies. Furthermore, there is no evidence of negative FDS. Thus, multiplicative fitness, rapid haplotype discovery, and rapid fitness decay appear to be the major factors shaping the HLA haplotype frequency distribution in the human population.
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28
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Kulski JK. Long Noncoding RNA HCP5, a Hybrid HLA Class I Endogenous Retroviral Gene: Structure, Expression, and Disease Associations. Cells 2019; 8:cells8050480. [PMID: 31137555 PMCID: PMC6562477 DOI: 10.3390/cells8050480] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 02/06/2023] Open
Abstract
The HCP5 RNA gene (NCBI ID: 10866) is located centromeric of the HLA-B gene and between the MICA and MICB genes within the major histocompatibility complex (MHC) class I region. It is a human species-specific gene that codes for a long noncoding RNA (lncRNA), composed mostly of an ancient ancestral endogenous antisense 3′ long terminal repeat (LTR, and part of the internal pol antisense sequence of endogenous retrovirus (ERV) type 16 linked to a human leukocyte antigen (HLA) class I promoter and leader sequence at the 5′-end. Since its discovery in 1993, many disease association and gene expression studies have shown that HCP5 is a regulatory lncRNA involved in adaptive and innate immune responses and associated with the promotion of some autoimmune diseases and cancers. The gene sequence acts as a genomic anchor point for binding transcription factors, enhancers, and chromatin remodeling enzymes in the regulation of transcription and chromatin folding. The HCP5 antisense retroviral transcript also interacts with regulatory microRNA and immune and cellular checkpoints in cancers suggesting its potential as a drug target for novel antitumor therapeutics.
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Affiliation(s)
- Jerzy K Kulski
- Faculty of Health and Medical Sciences, UWA Medical School, The University of Western Australia, Crawley, WA 6009, Australia.
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan.
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29
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MHC haplotype diversity in Icelandic horses determined by polymorphic microsatellites. Genes Immun 2019; 20:660-670. [PMID: 31068686 DOI: 10.1038/s41435-019-0075-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/07/2019] [Accepted: 03/18/2019] [Indexed: 01/31/2023]
Abstract
The Icelandic horse has been maintained as a closed population in its eponymous homeland for many generations, with no recorded introductions of new horses of any breed since the year 1000 CE. Here we determined the diversity of major histocompatibility complex (MHC) haplotypes in 156 Icelandic horses from two groups, based on a panel of 12 polymorphic intra-MHC microsatellites tested in families of various composition. We identified a total of 79 MHC haplotypes in these two groups, including one documented intra-MHC recombination event from a total of 147 observed meioses. None of these MHC haplotypes have been previously described in any other horse breed. Only one MHC homozygote was found in the entire population studied. These results indicate a very high level of MHC heterozygosity and haplotype diversity in the Icelandic horse. The environment in Iceland is remarkable for its lack of common agents of equine infectious disease, including equine herpesvirus type 1, influenza virus, and streptococcus equi. The driving forces for maintenance of MHC heterozygosity in Icelandic horses must thus be sought outside of these major horse pathogens. Based on our results, we propose that intra-MHC recombination may play a major role in the generation of novel haplotypes.
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30
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Shadabi E, Liang B, Plummer F, Luo M. Identification and Characterization of Positively Selected Mutations in Nef of Four HIV-1 Major Subtypes from Los Alamos National Laboratory. Curr HIV Res 2019; 16:130-142. [PMID: 29600767 DOI: 10.2174/1570162x16666180330140807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 03/07/2018] [Accepted: 03/20/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Human immunodeficiency virus-1 (HIV-1) mutates rapidly to escape host immune pressure. This results in the generation of positively selected mutations (PSM) throughout the viral genome. Escape mutations in Nef, one of the accessory proteins of HIV-1, which plays an important role in viral pathogenicity have previously been identified in several large cohort studies, but the evolution of PSMs overtime in various HIV-1 subtypes remains unknown. METHODS 161 clade A1, 3093 clade B, 647 clade C and 115 clade D HIV-1 nef sequences were obtained from the HIV Database of Los Alamos National Laboratory and aligned using MEGA 6.0. The sequences from each clade were grouped based on the year of collection. Quasi analysis was used to identify PSMs and the number and locations of PSMs were compared among different subtypes. RESULTS PSMs for all four subtypes were distributed across the sequence of Nef, and conserved residues F90, W113, PxxPxR (a.a 72-77) remain unaltered overtime. The frequency of PSMs was stable among subtype B sequences but increased overtime for other subtypes. Phylogenetic analysis shows that sequences containing PSMs tend to cluster together at both inter and intra- subtype levels. CONCLUSION Identification of PSMs and their changes overtime within various subtypes of HIV-1 is important in defining global viral evolutionary patterns that can provide insights for designing therapeutic strategies.
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Affiliation(s)
- Elnaz Shadabi
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Binhua Liang
- JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Frank Plummer
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ma Luo
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.,JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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31
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Gasparini SJ, Llonch S, Borsch O, Ader M. Transplantation of photoreceptors into the degenerative retina: Current state and future perspectives. Prog Retin Eye Res 2018; 69:1-37. [PMID: 30445193 DOI: 10.1016/j.preteyeres.2018.11.001] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/29/2018] [Accepted: 11/06/2018] [Indexed: 12/12/2022]
Abstract
The mammalian retina displays no intrinsic regenerative capacities, therefore retinal degenerative diseases such as age-related macular degeneration (AMD) or retinitis pigmentosa (RP) result in a permanent loss of the light-sensing photoreceptor cells. The degeneration of photoreceptors leads to vision impairment and, in later stages, complete blindness. Several therapeutic strategies have been developed to slow down or prevent further retinal degeneration, however a definitive cure i.e. replacement of the lost photoreceptors, has not yet been established. Cell-based treatment approaches, by means of photoreceptor transplantation, have been studied in pre-clinical animal models over the last three decades. The introduction of pluripotent stem cell-derived retinal organoids represents, in principle, an unlimited source for the generation of transplantable human photoreceptors. However, safety, immunological and reproducibility-related issues regarding the use of such cells still need to be solved. Moreover, the recent finding of cytoplasmic material transfer between donor and host photoreceptors demands reinterpretation of several former transplantation studies. At the same time, material transfer between healthy donor and dysfunctional patient photoreceptors also offers a potential alternative strategy for therapeutic intervention. In this review we discuss the history and current state of photoreceptor transplantation, the techniques used to assess rescue of visual function, the prerequisites for effective transplantation as well as the main roadblocks, including safety and immune response to the graft, that need to be overcome for successful clinical translation of photoreceptor transplantation approaches.
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Affiliation(s)
- Sylvia J Gasparini
- CRTD/Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 01307, Dresden, Germany
| | - Sílvia Llonch
- CRTD/Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 01307, Dresden, Germany
| | - Oliver Borsch
- CRTD/Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 01307, Dresden, Germany
| | - Marius Ader
- CRTD/Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 01307, Dresden, Germany.
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