1
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Wang G, Warrington NM, Evans DM. Partitioning genetic effects on birthweight at classical human leukocyte antigen loci into maternal and fetal components, using structural equation modelling. Int J Epidemiol 2024; 53:dyad142. [PMID: 37831898 PMCID: PMC10859143 DOI: 10.1093/ije/dyad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Single nucleotide polymorphisms in the human leukocyte antigen (HLA) region in both maternal and fetal genomes have been robustly associated with birthweight (BW) in previous genetic association studies. However, no study to date has partitioned the association between BW and classical HLA alleles into maternal and fetal components. METHODS We used structural equation modelling (SEM) to estimate the maternal and fetal effects of classical HLA alleles on BW. Our SEM leverages the data structure of the UK Biobank (UKB), which includes ∼270 000 participants' own BW and/or the BW of their firstborn child. RESULTS We show via simulation that our model yields asymptotically unbiased estimates of the maternal and fetal allelic effects on BW and appropriate type I error rates, in contrast to simple regression models. Asymptotic power calculations show that we have sufficient power to detect moderate-sized maternal or fetal allelic effects of common HLA alleles on BW in the UKB. Applying our SEM to imputed classical HLA alleles and own and offspring BW from the UKB replicated the previously reported association at the HLA-C locus and revealed strong evidence for maternal (HLA-A*03:01, B*35:01, B*39:06, P <0.001) and fetal allelic effects (HLA-B*39:06, P <0.001) of non-HLA-C alleles on BW. CONCLUSIONS Our model yields asymptotically unbiased estimates, appropriate type I error rates and appreciable power to estimate maternal and fetal effects on BW. These novel allelic associations between BW and classical HLA alleles provide insight into the immunogenetics of fetal growth in utero.
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Affiliation(s)
- Geng Wang
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Nicole M Warrington
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - David M Evans
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
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2
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Zhou Y, Song L, Li H. Full resolution HLA and KIR genes annotation for human genome assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576452. [PMID: 38328160 PMCID: PMC10849470 DOI: 10.1101/2024.01.20.576452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The HLA (Human Leukocyte Antigen) genes and the KIR (Killer cell Immunoglobulin-like Receptor) genes are critical to immune responses and are associated with many immune-related diseases. Located in highly polymorphic regions, they are hard to be studied with traditional short-read alignment-based methods. Although modern long-read assemblers can often assemble these genes, using existing tools to annotate HLA and KIR genes in these assemblies remains a non-trivial task. Here, we describe Immuannot, a new computation tool to annotate the gene structures of HLA and KIR genes and to type the allele of each gene. Applying Immuannot to 56 regional and 212 whole-genome assemblies from previous studies, we annotated 9,931 HLA and KIR genes and found that almost half of these genes, 4,068, had novel sequences compared to the current Immuno Polymorphism Database (IPD). These novel gene sequences were represented by 2,664 distinct alleles, some of which contained non-synonymous variations resulting in 92 novel protein sequences. We demonstrated the complex haplotype structures at the two loci and reported the linkage between HLA/KIR haplotypes and gene alleles. We anticipate that Immuannot will speed up the discovery of new HLA/KIR alleles and enable the association of HLA/KIR haplotype structures with clinical outcomes in the future.
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Affiliation(s)
- Ying Zhou
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Li Song
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, 03755, USA
| | - Heng Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
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3
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Huang G, Tang X, Zheng P. DeepHLAPred: a deep learning-based method for non-classical HLA binder prediction. BMC Genomics 2023; 24:706. [PMID: 37993812 PMCID: PMC10666343 DOI: 10.1186/s12864-023-09796-2] [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: 06/20/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023] Open
Abstract
Human leukocyte antigen (HLA) is closely involved in regulating the human immune system. Despite great advance in detecting classical HLA Class I binders, there are few methods or toolkits for recognizing non-classical HLA Class I binders. To fill in this gap, we have developed a deep learning-based tool called DeepHLAPred. The DeepHLAPred used electron-ion interaction pseudo potential, integer numerical mapping and accumulated amino acid frequency as initial representation of non-classical HLA binder sequence. The deep learning module was used to further refine high-level representations. The deep learning module comprised two parallel convolutional neural networks, each followed by maximum pooling layer, dropout layer, and bi-directional long short-term memory network. The experimental results showed that the DeepHLAPred reached the state-of-the-art performanceson the cross-validation test and the independent test. The extensive test demonstrated the rationality of the DeepHLAPred. We further analyzed sequence pattern of non-classical HLA class I binders by information entropy. The information entropy of non-classical HLA binder sequence implied sequence pattern to a certain extent. In addition, we have developed a user-friendly webserver for convenient use, which is available at http://www.biolscience.cn/DeepHLApred/ . The tool and the analysis is helpful to detect non-classical HLA Class I binder. The source code and data is available at https://github.com/tangxingyu0/DeepHLApred .
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Affiliation(s)
- Guohua Huang
- School of Information Technology and Administration, Hunan University of Finance and Economics, Changsha, Hunan, 410215, China.
- College of Information Science and Engineering, Shaoyang University, Shaoyang, Hunan, 422000, China.
| | - Xingyu Tang
- College of Information Science and Engineering, Shaoyang University, Shaoyang, Hunan, 422000, China
| | - Peijie Zheng
- College of Information Science and Engineering, Shaoyang University, Shaoyang, Hunan, 422000, China
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4
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Irham LM, Adikusuma W, Lolita L, Puspitaningrum AN, Afief AR, Sarasmita MA, Dania H, Khairi S, Djalilah GN, Purwanto BD, Chong R. Investigation of susceptibility genes for chickenpox disease across multiple continents. Biochem Biophys Rep 2023; 33:101419. [PMID: 36620086 PMCID: PMC9816662 DOI: 10.1016/j.bbrep.2022.101419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/01/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023] Open
Abstract
Chickenpox (varicella) is caused by infection with the varicella-zoster virus (VZV), a neurotropic alpha herpes virus with a double-stranded DNA genome. Chickenpox can cause life-threatening complications, including subsequent bacterial infections, central nervous system symptoms, and even death without any risk factors. Few studies have been reported to investigate genetic susceptibility implicated in chickenpox. Herein, our study identified global genetic variants that potentially contributed to chickenpox susceptibility by utilizing the established bioinformatic-based approach. We integrated several databases, such as genome-wide association studies (GWAS) catalog, GTEx portal, HaploReg version 4.1, and Ensembl databases analyses to investigate susceptibility genes associated with chickenpox. Notably, increased expression of HLA-S, HCG4P5, and ABHD16A genes underlie enhanced chickenpox susceptibility in the European, American, and African populations. As compared to the Asian population, Europeans, Americans, and Africans have higher allele frequencies of the extant variants rs9266089, rs10947050, and rs79501286 from the susceptibility genes. Our study suggested that these susceptibility genes and associated genetic variants might play a critical role in chickenpox progression based on host genetics with clinical implications.
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Affiliation(s)
| | - Wirawan Adikusuma
- Department of Pharmacy, University of Muhammadiyah Mataram, Mataram, Indonesia
| | - Lolita Lolita
- Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta, Indonesia
| | | | | | - Made Ary Sarasmita
- Pharmacy Study Program, Faculty of Science and Mathematics, Udayana University, Bali, Indonesia
| | - Haafizah Dania
- Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta, Indonesia
| | - Sabiah Khairi
- School of Nursing, College of Nursing, Taipei Medical University, Taipei, 11031, Taiwan
| | | | - Barkah Djaka Purwanto
- Faculty of Medicine, University of Ahmad Dahlan, Yogyakarta, 55191, Indonesia
- PKU Muhammadiyah Bantul Hospital, Bantul, Yogyakarta, 55711, Indonesia
| | - Rockie Chong
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
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5
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HLA-A2 Promotes the Therapeutic Effect of Umbilical Cord Blood-Derived Mesenchymal Stem Cells in Hyperoxic Lung Injury. Bioengineering (Basel) 2022; 9:bioengineering9040177. [PMID: 35447737 PMCID: PMC9029550 DOI: 10.3390/bioengineering9040177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 12/03/2022] Open
Abstract
Mesenchymal stem cells (MSCs) are one of the most extensively studied stem cell types owing to their capacity for differentiation into multiple lineages as well as their ability to secrete regenerative factors and modulate immune functions. However, issues remain regarding their further application for cell therapy. Here, to demonstrate the superiority of the improvement of MSCs, we divided umbilical cord blood-derived MSCs (UCB-MSCs) from 15 donors into two groups based on efficacy and revealed donor-dependent variations in the anti-inflammatory effect of MSCs on macrophages as well as their immunoregulatory effect on T cells. Through surface marker analyses (242 antibodies), we found that HLA-A2 was positively related to the anti-inflammatory and immunoregulatory function of MSCs. Additionally, HLA-A2 mRNA silencing in MSCs attenuated their therapeutic effects in vitro; namely, the suppression of LPS-stimulated macrophages and phytohemagglutinin-stimulated T cells. Moreover, HLA-A2 silencing in MSCs significantly decreased their therapeutic effects in a rat model of hyperoxic lung damage. The present study provides novel insights into the quality control of donor-derived MSCs for the treatment of inflammatory conditions and diseases.
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6
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SimiC enables the inference of complex gene regulatory dynamics across cell phenotypes. Commun Biol 2022; 5:351. [PMID: 35414121 PMCID: PMC9005655 DOI: 10.1038/s42003-022-03319-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 03/24/2022] [Indexed: 11/08/2022] Open
Abstract
Single-cell RNA-Sequencing has the potential to provide deep biological insights by revealing complex regulatory interactions across diverse cell phenotypes at single-cell resolution. However, current single-cell gene regulatory network inference methods produce a single regulatory network per input dataset, limiting their capability to uncover complex regulatory relationships across related cell phenotypes. We present SimiC, a single-cell gene regulatory inference framework that overcomes this limitation by jointly inferring distinct, but related, gene regulatory dynamics per phenotype. We show that SimiC uncovers key regulatory dynamics missed by previously proposed methods across a range of systems, both model and non-model alike. In particular, SimiC was able to uncover CAR T cell dynamics after tumor recognition and key regulatory patterns on a regenerating liver, and was able to implicate glial cells in the generation of distinct behavioral states in honeybees. SimiC hence establishes a new approach to quantitating regulatory architectures between distinct cellular phenotypes, with far-reaching implications for systems biology.
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7
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Spencer Mangum D, Caywood E. A clinician’s guide to HLA matching in allogeneic hematopoietic stem cell transplant. Hum Immunol 2022; 83:687-694. [DOI: 10.1016/j.humimm.2022.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/14/2022] [Accepted: 03/02/2022] [Indexed: 12/26/2022]
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8
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Gautam S, Kumar U, Mishra R, Dada R. HLA-G 3'UTR polymorphisms & response to a yoga-based lifestyle intervention in rheumatoid arthritis: A randomized controlled trial. Indian J Med Res 2022; 155:253-263. [PMID: 35946202 PMCID: PMC9629524 DOI: 10.4103/ijmr.ijmr_3196_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background & objectives Human leucocyte antigen (HLA)-G plays a vital role in immunomodulation in rheumatoid arthritis (RA). The mounting evidence suggests a link between HLA-G gene polymorphisms, disease susceptibility and methotrexate treatment response. Various environmental factors influence the onset and progression of RA and its treatment outcomes. The aim is to identify the treatment response of HLA-G 3' untranslated region polymorphisms to yoga-based lifestyle intervention (YBLI). Methods In this eight-week single-blinded randomized controlled trial (CTRI/2017/05/008589), patients with RA (n=140) were randomized into two groups namely, yoga group or non-yoga group. Baseline genomic DNA was isolated using salting-out method. PCR-based methods were used for genotyping. The levels of soluble (s) HLA-G and disease activity were assessed by ELISA and disease activity score-28-erythrocyte sedimentation rate (DAS28-ESR), respectively, at baseline (day 0) and after eight weeks of intervention. Results Low-producing sHLA-G genotypes, i.e. +3142GG and 14 bp ins/ins, showed a significant increase in sHLA-G levels after YBLI. The association analysis between HLA-G polymorphisms and treatment for RA showed no considerable differential treatment remission in either of the groups (P>0.05). The percentages of improvement were higher in the yoga group as compared to the non-yoga group in both the HLA-G +3142G>C and 14 bp ins/del polymorphisms irrespective of their respective genotypes. No significant association was found between sHLA-G levels and disease activity with respect to genotypes. Interpretation & conclusions Yoga intervention results in improvement and reduced severity of RA in patients irrespective of the HLA-G 14 bp ins/del or +3142G>C polymorphisms. YBLI may be used as an adjunct therapy in RA independent of the genotypes.
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Affiliation(s)
- Surabhi Gautam
- Department of Anatomy, Laboratory for Molecular Reproduction & Genetics, New Delhi, India
| | - Uma Kumar
- Department of Rheumatology, All India Institute of Medical Sciences, New Delhi, India
| | - Richa Mishra
- Department of Anatomy, Laboratory for Molecular Reproduction & Genetics, New Delhi, India
| | - Rima Dada
- Department of Anatomy, Laboratory for Molecular Reproduction & Genetics, New Delhi, India
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9
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Castelli EC, de Almeida BS, Muniz YCN, Silva NSB, Passos MRS, Souza AS, Page AE, Dyble M, Smith D, Aguileta G, Bertranpetit J, Migliano AB, Duarte YAO, Scliar MO, Wang J, Passos-Bueno MR, Naslavsky MS, Zatz M, Mendes-Junior CT, Donadi EA. HLA-G genetic diversity and evolutive aspects in worldwide populations. Sci Rep 2021; 11:23070. [PMID: 34845256 PMCID: PMC8629979 DOI: 10.1038/s41598-021-02106-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/01/2021] [Indexed: 12/15/2022] Open
Abstract
HLA-G is a promiscuous immune checkpoint molecule. The HLA-G gene presents substantial nucleotide variability in its regulatory regions. However, it encodes a limited number of proteins compared to classical HLA class I genes. We characterized the HLA-G genetic variability in 4640 individuals from 88 different population samples across the globe by using a state-of-the-art method to characterize polymorphisms and haplotypes from high-coverage next-generation sequencing data. We also provide insights regarding the HLA-G genetic diversity and a resource for future studies evaluating HLA-G polymorphisms in different populations and association studies. Despite the great haplotype variability, we demonstrated that: (1) most of the HLA-G polymorphisms are in introns and regulatory sequences, and these are the sites with evidence of balancing selection, (2) linkage disequilibrium is high throughout the gene, extending up to HLA-A, (3) there are few proteins frequently observed in worldwide populations, with lack of variation in residues associated with major HLA-G biological properties (dimer formation, interaction with leukocyte receptors). These observations corroborate the role of HLA-G as an immune checkpoint molecule rather than as an antigen-presenting molecule. Understanding HLA-G variability across populations is relevant for disease association and functional studies.
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Affiliation(s)
- Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo, Brazil.
- Department of Pathology, School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo, CEP: 18618970, Brazil.
| | - Bibiana S de Almeida
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, CEP: 14049-900, Brazil
- Laboratório Multiusuário de Estudos em Biologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Brazil
| | - Yara C N Muniz
- Departamento de Biologia Celular, Embriologia e Genética, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Brazil
| | - Nayane S B Silva
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo, Brazil
| | - Marília R S Passos
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo, Brazil
| | - Andreia S Souza
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo, Brazil
| | - Abigail E Page
- Department of Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Mark Dyble
- Departament of Anthropology, University College London (UCL), London, UK
| | - Daniel Smith
- Bristol Medical School (PHS), University of Bristol, Bristol, UK
| | - Gabriela Aguileta
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jaume Bertranpetit
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Andrea B Migliano
- Departament of Anthropology, Unversity of Zurich, Zurich, Switzerland
| | - Yeda A O Duarte
- Escola de Enfermagem e Faculdade de Saúde Pública, Universidade de São Paulo (USP), São Paulo, State of São Paulo, Brazil
| | - Marília O Scliar
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
| | - Jaqueline Wang
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
| | - Michel S Naslavsky
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, State of São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
| | - Celso Teixeira Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto, SP, Brazil
| | - Eduardo A Donadi
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, CEP: 14049-900, Brazil.
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10
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Jacovas VC, Michita RT, Bisso-Machado R, Reales G, Tarazona-Santos EM, Sandoval JR, Salazar-Granara A, Chies JAB, Bortolini MC. HLA-G 3'UTR haplotype frequencies in highland and lowland South Native American populations. Hum Immunol 2021; 83:27-38. [PMID: 34563386 DOI: 10.1016/j.humimm.2021.09.002] [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: 03/18/2021] [Revised: 08/09/2021] [Accepted: 09/01/2021] [Indexed: 11/30/2022]
Abstract
Human Leukocyte Antigen (HLA)-G participates in several biological processes, including reproduction, vascular remodeling, immune tolerance, and hypoxia response. HLA-G is a potential candidate gene for high altitude adaptation since its expression is modulated in both micro and macro environment under hypoxia and constant cellular stress. Besides the promoter region, the HLA-G 3'untranslated region (UTR) influences HLA-G expression patterns through several post-transcriptional mechanisms. Currently, the 3'UTR genetic diversity in terms of altitude adaptation of Native American populations is still unexplored, particularly at high altitude ecoregions. Here, we evaluated 288 Native Americans from 9 communities located in the Andes [highland (HL); ≥2,500 m (range = 2,838-4,433 m)] and 8 populations located in lowland (LL) regions [<2,500 m (range = 80-431 m); Amazonian tropical forest, Brazilian central plateau, and Chaco] of South America. In total, nine polymorphic sites and ten haplotypes were observed. The most frequent haplotypes (UTR-1, UTR-2, and UTR-3) accounted for ∼ 77% of haplotypes found in LL, while in the HL, the same haplotypes reach ∼ 93%. Also, a remarkable high frequency of putative ancestral UTR-5 haplotype was observed in LL (21.5%), while in HL UTR-2 reaches up to 47%. Further, UTR-2 frequency positively correlates with altitude-related variables, while a negative correlation for UTR-5 was observed. From an evolutionary perspective, we observed a tendency towards balancing selection in HL and LL populations thus suggesting that haplotypes of ancient and more derived alleles may have been co-opted for relatively recent adaptations such as those experienced by modern humans in the highland and lowland of South America. We also discuss how long-term balancing selection can be a reservoir of genetic variants that can be positively selected. Finally, our study provides some pieces of evidence that HLA-G 3'UTR haplotypes may have contributed to high altitude adaptation in the Andes.
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Affiliation(s)
- Vanessa Cristina Jacovas
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Rafael Tomoya Michita
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil; Human Molecular Genetics Laboratory, Universidade Luterana do Brasil (ULBRA), Canoas, Rio Grande do Sul, Brazil
| | - Rafael Bisso-Machado
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Guillermo Reales
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Eduardo M Tarazona-Santos
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Minas Gerais, Brazil
| | - José Raul Sandoval
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Minas Gerais, Brazil
| | | | - José Artur Bogo Chies
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
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11
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Neuchel C, Fürst D, Tsamadou C, Schrezenmeier H, Mytilineos J. Extended loci histocompatibility matching in HSCT-Going beyond classical HLA. Int J Immunogenet 2021; 48:299-316. [PMID: 34109752 DOI: 10.1111/iji.12545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/26/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022]
Abstract
Unrelated haematopoietic stem cell transplantation (HSCT) has evolved from an experimental protocol to a potentially curative first-line treatment in a variety of haematologic malignancies. The continuous refinement of treatment protocols and supportive care paired with ongoing achievements in the technological field of histocompatibility testing enabled this transformation. Without a doubt, HLA matching is still the foremost criterion for donor selection in unrelated HSCT. However, HSCT-related treatment complications still occur frequently, often resulting in patients suffering severely or even dying as a consequence of such complications. Current literature indicates that other immune system modulating factors may play a role in the setting of HSCT. In this review, we discuss the current clinical evidence of a possible influence of nonclassical HLA antigens HLA-E, HLA-F, and HLA-G as well as the HLA-like molecules MICA and MICB, in HSCT.
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Affiliation(s)
- Christine Neuchel
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg-Hessen, and University Hospital Ulm, Ulm, Germany
- Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Daniel Fürst
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg-Hessen, and University Hospital Ulm, Ulm, Germany
- Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Chrysanthi Tsamadou
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg-Hessen, and University Hospital Ulm, Ulm, Germany
- Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Hubert Schrezenmeier
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg-Hessen, and University Hospital Ulm, Ulm, Germany
- Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Joannis Mytilineos
- ZKRD - Zentrales Knochenmarkspender-Register für Deutschland, German National Bone Marrow Donor Registry, Ulm, Germany
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12
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Ajith A, Mulloy LL, Musa MA, Bravo-Egana V, Horuzsko DD, Gani I, Horuzsko A. Humanized Mouse Model as a Novel Approach in the Assessment of Human Allogeneic Responses in Organ Transplantation. Front Immunol 2021; 12:687715. [PMID: 34177940 PMCID: PMC8226140 DOI: 10.3389/fimmu.2021.687715] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/28/2021] [Indexed: 02/02/2023] Open
Abstract
The outcome of organ transplantation is largely dictated by selection of a well-matched donor, which results in less chance of graft rejection. An allogeneic immune response is the main immunological barrier for successful organ transplantation. Donor and recipient human leukocyte antigen (HLA) mismatching diminishes outcomes after solid organ transplantation. The current evaluation of HLA incompatibility does not provide information on the immunogenicity of individual HLA mismatches and impact of non-HLA-related alloantigens, especially in vivo. Here we demonstrate a new method for analysis of alloimmune responsiveness between donor and recipient in vivo by introducing a humanized mouse model. Using molecular, cellular, and genomic analyses, we demonstrated that a recipient's personalized humanized mouse provided the most sensitive assessment of allogeneic responsiveness to potential donors. In our study, HLA typing provided a better recipient-donor match for one donor among two related donors. In contrast, assessment of an allogeneic response by mixed lymphocyte reaction (MLR) was indistinguishable between these donors. We determined that, in the recipient's humanized mouse model, the donor selected by HLA typing induced the strongest allogeneic response with markedly increased allograft rejection markers, including activated cytotoxic Granzyme B-expressing CD8+ T cells. Moreover, the same donor induced stronger upregulation of genes involved in the allograft rejection pathway as determined by transcriptome analysis of isolated human CD45+cells. Thus, the humanized mouse model determined the lowest degree of recipient-donor alloimmune response, allowing for better selection of donor and minimized immunological risk of allograft rejection in organ transplantation. In addition, this approach could be used to evaluate the level of alloresponse in allogeneic cell-based therapies that include cell products derived from pluripotent embryonic stem cells or adult stem cells, both undifferentiated and differentiated, all of which will produce allogeneic immune responses.
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Affiliation(s)
- Ashwin Ajith
- Georgia Cancer Center, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Laura L. Mulloy
- Nephrology Division, Department of Medicine, Augusta University, Augusta, GA, United States
| | - Md. Abu Musa
- Georgia Cancer Center, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Valia Bravo-Egana
- Histocompatibility and Immunology Laboratory, Department of Surgery, Medical College of Georgia, Augusta University Medical Center, Augusta, GA, United States
| | - Daniel David Horuzsko
- Program of Osteopathic Medicine, Philadelphia College of Osteopathic Medicine South Georgia, Moultrie, GA, United States
| | - Imran Gani
- Nephrology Division, Department of Medicine, Augusta University, Augusta, GA, United States
| | - Anatolij Horuzsko
- Georgia Cancer Center, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
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Abdul-Hussein SS, Ali EN, Zaki NH, Ad’hiah AH. Genetic polymorphism of HLA-G gene (G*01:03, G*01:04, and G*01:05N) in Iraqi patients with inflammatory bowel disease (ulcerative colitis and Crohn’s disease). EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00158-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Abstract
Background
Human leukocyte antigen-G (HLA-G) has been proposed to influence susceptibility to inflammatory bowel disease (IBD). Therefore, the genetic association between HLA-G alleles and two clinical phenotypes of IBD (ulcerative colitis [UC] and Crohn’s disease [CD]) was evaluated in Iraqi patients. A case-control study was performed on 50 UC and 50 CD patients and 100 healthy controls (HC). Three HLA-G alleles (G*01:03, G*01:04, and G*01:05N) were determined using sequence-specific polymerase chain reaction assay followed by product digestion with restriction endonucleases (Hinf-I, BseR-I, and PpuM-I, respectively).
Results
The G*01:03 allele was not detected in IBD patients (UC and CD) or HC, while G*01:04 and G*01:05N alleles showed polymorphic frequencies. The allele G*01:04 was significantly associated with susceptibility to UC (odds ratio [OR] = 2.55; 95% confidence interval [CI] = 1.27–5.13; corrected probability [pc] = 0.018) and CD (OR = 4.45; 95% CI = 2.11–9.41; pc < 0.001). The allele G*01:05N was also associated with increased risk of UC (OR = 4.17; 95% CI = 1.32–13.21; pc = 0.032) and CD (OR = 4.75; 95% CI = 1.53–14.78; pc = 0.014). These associations were more pronounced in IBD (UC + CD), and a significantly increased risk for IBD was found with the alleles G*01:04 (OR = 3.32; 95% CI = 1.86–5.95; pc < 0.001) and G*01:05N (OR = 4.46; 95% CI = 1.59–12.47; pc = 0.008). A stratification of IBD patients according to some demographic and clinical characteristics revealed that frequencies of both alleles showed no significant differences between the subgroups of patients in each stratum. Soluble HLA-G was not influenced by HLA-G alleles in patients or HC. UC was an exception, and the presence of G*01:04 allele was associated with a significantly higher mean of soluble HLA-G compared to patients without the allele (189.6 ± 24.0 vs. 168.6 ± 27.2 ng/mL; p = 0.033).
Conclusion
This study indicated that HLA-G*01:04 and HLA-G*01:05N alleles may influence susceptibility to UC and CD in Iraqi patients.
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Persson G, Picard C, Marin G, Isgaard C, Stæhr CS, Molinari N, Chiaroni J, Lebech M, Hviid TVF, Di Cristofaro J. Maternal HLA Ib Polymorphisms in Pregnancy Allo-Immunization. Front Immunol 2021; 12:657217. [PMID: 33859649 PMCID: PMC8042285 DOI: 10.3389/fimmu.2021.657217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/15/2021] [Indexed: 11/16/2022] Open
Abstract
During pregnancy the formation of alloreactive anti-human leukocyte antigen (HLA) antibodies are a major cause of acute rejection in organ transplantation and of adverse effects in blood transfusion. The purpose of the study was to identify maternal HLA class Ib genetic factors associated with anti-HLA allo-immunization in pregnancy and the degree of tolerance estimated by IgG4 expression. In total, 86 primiparous women with singleton pregnancies were included in the study. Maternal blood samples and umbilical cord samples were collected at delivery. Clinical data were obtained. Maternal blood serum was screened for HLA class I and II antibodies, identification of Donor Specific Antibody (DSA), activation of complement measured by C1q and IgG4 concentrations. Mothers were genotyped for HLA class Ib (HLA-E, -F and -G). Anti-HLA class I and II antibodies were identified in 24% of the women. The maternal HLA-E*01:06 allele was significantly associated with a higher fraction of anti-HLA I immunization (20.0% vs. 4.8%, p = 0.048). The maternal HLA-G 3’-untranslated region UTR4-HLA-G*01:01:01:05 haplotype and the HLA-F*01:03:01 allele were significantly associated with a low anti-HLA I C1q activation (16.7% vs. 57.1%, p = 0.028; 16.7% vs. 50.0%, p = 0.046; respectively). Both HLA‑G and HLA-F*01:03:01 showed significantly higher levels of IgG4 compared with the other haplotypes. The results support an association of certain HLA class Ib alleles with allo-immunization during pregnancy. Further studies are needed to elucidate the roles of HLA-E*01:06, HLA-F*01:03 and HLA‑G UTR4 in reducing the risk for allo-immunization.
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Affiliation(s)
- Gry Persson
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, The ReproHealth Research Consortium ZUH, Zealand University Hospital, Roskilde, Denmark
| | - Christophe Picard
- Aix Marseille Univ, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France.,Immunogenetics Laboratory, Etablissement français du Sang PACA Corse, Marseille, France
| | - Gregory Marin
- Unité de Recherche Clinique, Biostatistique et Epidémiologie, Département de l'Information Médicale (DIM) Hôpital La Colombière, Montpellier, France
| | - Cecilie Isgaard
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, The ReproHealth Research Consortium ZUH, Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christina Seefeldt Stæhr
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, The ReproHealth Research Consortium ZUH, Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nicolas Molinari
- Unité de Recherche Clinique, Biostatistique et Epidémiologie, Département de l'Information Médicale (DIM) Hôpital La Colombière, Montpellier, France
| | - Jacques Chiaroni
- Aix Marseille Univ, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France
| | - Morten Lebech
- Department of Obstetrics and Gynecology, Zealand University Hospital, Roskilde, Denmark
| | - Thomas Vauvert F Hviid
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, The ReproHealth Research Consortium ZUH, Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Julie Di Cristofaro
- Aix Marseille Univ, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France
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15
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Closa L, Vidal F, Herrero MJ, Caro JL. High-throughput genotyping of HLA-G, HLA-F, MICA, and MICB and analysis of frequency distributions in healthy blood donors from Catalonia. HLA 2021; 97:420-427. [PMID: 33599111 DOI: 10.1111/tan.14221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/19/2022]
Abstract
Similarly to HLA class I molecules, certain non-classical HLA class I genes and MHC class I polypeptide-related sequences A and B (MICA and MICB) act as ligands for KIR and NKG2D natural killer receptors. Although these genes are less polymorphic than HLA class I, few studies have analyzed their association with diseases. Information on allele frequencies in healthy donors is needed to map their distribution worldwide. This study is the first to analyze high-resolution HLA-G, HLA-F, MICA, and MICB allele frequencies using a novel high-throughput next generation-sequencing method. We analyzed DNA samples from 96 unrelated blood donors resident in Catalonia, Spain, and registered in the Barcelona Blood and Tissue Bank. Using the first two fields of the HLA nomenclature, we detected six HLA-G and two HLA-F alleles. The most frequent alleles were HLA-G*01:01 (77.08%) and HLA-F*01:01(84.90%). When the four fields were analyzed, we detected 16 and 10 alleles, respectively. Nineteen alleles were detected for MICA and 10 for MICB. The most frequent alleles in these cases were MICA*008:01 (16.15%) and MICB*005:02 (46.84%). All frequencies were in Hardy Weinberg equilibrium except MICA. We also estimated maximum-likelihood haplotype frequencies and calculated corresponding linkage disequilibrium (LD) values and found that few allele pairs were in disequilibrium. Strong LD between MICA and HLA-B (using data from a previous study) was observed. Our findings will be useful for guiding further research evaluating the functional role of these genes in different diseases and populations.
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Affiliation(s)
- Laia Closa
- Histocompatibility and Immunogenetics Laboratory, Blood and Tissue Bank, Barcelona, Spain.,Transfusional Medicine Group, Vall d'Hebron Research Institute-Autonomous University of Barcelona (VHIR-UAB), Barcelona, Spain
| | - Francisco Vidal
- Transfusional Medicine Group, Vall d'Hebron Research Institute-Autonomous University of Barcelona (VHIR-UAB), Barcelona, Spain.,Congenital Coagulopathy Laboratory, Blood and Tissue Bank, Barcelona, Spain.,CIBER of Cardiovascular Diseases, Barcelona, Spain
| | - Maria J Herrero
- Histocompatibility and Immunogenetics Laboratory, Blood and Tissue Bank, Barcelona, Spain
| | - Jose L Caro
- Department of Immunology, Hospital Clínic, Barcelona, Spain
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16
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Vicente LDM, Castelli EC, Veronese Rodrigues MDL, Deghaide NHS, Mendes-Junior CT, Furtado JM, Donadi EA. Variability at the 3' untranslated region of the HLA-G gene: a study on patients with AIDS and cytomegalovirus retinochoroiditis. Sci Rep 2020; 10:18646. [PMID: 33122781 PMCID: PMC7596709 DOI: 10.1038/s41598-020-75639-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 10/07/2020] [Indexed: 11/10/2022] Open
Abstract
Cytomegalovirus retinochoroiditis (CMV-R) is the primary cause of blindness among AIDS patients. Since HLA-G is associated with the modulation of the immune response, we hypothesized that variability at the 3′ untraslated region (3′UTR) of the gene could be implicated on the predisposition to CMV-R. We evaluated whether HLA-G 3′UTR influences CMV-R development in Brazilian AIDS patients. Peripheral blood DNA was obtained from two groups of patients: (1) AIDS exhibiting CMV-R (n = 40) and (2) AIDS without CMV-R (n = 147). HLA-G 3′UTR typing was performed using sequencing analysis. Allele, genotype and haplotype frequencies were evaluated using Fisher’s exact test accompanied by the calculation of the odds ratio and its 95% confidence interval (95% CI). The etiologic (EF) and preventive fractions were also estimated. Compared to AIDS patients without CMV-R, AIDS patients with CMV-R showed increased frequencies of the: (1) + 3001T allele, (2) the + 3001C/T genotype and (3) the UTR-17 (InsTTCCGTGACG) haplotype (EFs = 0.02–0.04). The UTR-3 (DelTCCGCGACG) haplotype was associated with protection against CMV-R development. Although the risk for developing CMR-V at the population level was relatively low (EF), the identification of HLA-G 3′UTR variation sites may help to further evaluate the role of post-transcriptional factors that may contribute to the existent immunosuppresion caused by HIV per se.
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Affiliation(s)
- Luciana de Morais Vicente
- Ophthalmology Division, Departament of Ophthalmology, Otorhinolaryngology and Head and Neck Surgery, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900, Ribeirão Preto, SP, 14049-900, Brazil
| | - Erick C Castelli
- Pathology Department, School of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Maria de Lourdes Veronese Rodrigues
- Ophthalmology Division, Departament of Ophthalmology, Otorhinolaryngology and Head and Neck Surgery, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900, Ribeirão Preto, SP, 14049-900, Brazil.
| | - Neifi Hassan Saloum Deghaide
- Ophthalmology Division, Departament of Ophthalmology, Otorhinolaryngology and Head and Neck Surgery, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900, Ribeirão Preto, SP, 14049-900, Brazil
| | - Celso Teixeira Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - João M Furtado
- Ophthalmology Division, Departament of Ophthalmology, Otorhinolaryngology and Head and Neck Surgery, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900, Ribeirão Preto, SP, 14049-900, Brazil
| | - Eduardo Antonio Donadi
- Clinical Immunology Division, Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
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17
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Variations in killer-cell immunoglobulin-like receptor and human leukocyte antigen genes and immunity to malaria. Cell Mol Immunol 2020; 17:799-806. [PMID: 32541835 PMCID: PMC7294524 DOI: 10.1038/s41423-020-0482-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/19/2020] [Indexed: 12/29/2022] Open
Abstract
Malaria is one of the deadliest infectious diseases in the world. Immune responses to Plasmodium falciparum malaria vary among individuals and between populations. Human genetic variation in immune system genes is likely to play a role in this heterogeneity. Natural killer (NK) cells produce inflammatory cytokines in response to malaria infection, kill intraerythrocytic Plasmodium falciparum parasites by cytolysis, and participate in the initiation and development of adaptive immune responses to plasmodial infection. These functions are modulated by interactions between killer-cell immunoglobulin-like receptors (KIRs) and human leukocyte antigens (HLAs). Therefore, variations in KIR and HLA genes can have a direct impact on NK cell functions. Understanding the role of KIRs and HLAs in immunity to malaria can help to better characterize antimalarial immune responses. In this review, we summarize the different KIRs and HLAs associated with immunity to malaria thus far.
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18
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Analysis of a large single institution cohort of related donors fails to detect a relation between SDF1/CXCR4 or VCAM/VLA4 genetic polymorphisms and the level of hematopoietic progenitor cell mobilization in response to G-CSF. PLoS One 2020; 15:e0228878. [PMID: 32134938 PMCID: PMC7058310 DOI: 10.1371/journal.pone.0228878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/24/2020] [Indexed: 02/07/2023] Open
Abstract
We studied a cohort of 367 healthy related donors who volunteered to donate their hematopoietic stem cells for allogeneic transplantation. All donors were homogeneously cared for at a single institution, and received rhG-CSF as a mobilization treatment prior to undergoing apheresis. Peripheral blood CD34+ cell counts were used as the main surrogate marker for rhG-CSF induced mobilization. We searched whether inter-individual variations in known genetic polymorphisms located in genes whose products are functionally important for mobilization, could affect the extent of CD34+ mobilization, either individually or in combination. We found little or no influence of individual SNPs or haplotypes for the SDF1, CXCR4, VCAM and VLA4 genes, whether using CD34+ cell counts as a continuous or a categorical variable. Simple clinical characteristics describing donors such as body mass index, age and possibly sex are more potent predictors of stem cell mobilization. The size of our cohort remains relatively small for genetic analyses, however compares favorably with cohorts analyzed in previously published reports suggesting associations of genetic traits to response to rhG-CSF; notwithstanding this limitation, our data do not support the use of genetic analyses when the choice exists of several potential donors for a given patient.
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19
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A new set of reagents and related software used for NGS based classical and non-classical HLA typing showing evidence for a greater HLA haplotype diversity. Hum Immunol 2020; 81:202-205. [PMID: 32122686 DOI: 10.1016/j.humimm.2020.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 02/01/2020] [Accepted: 02/12/2020] [Indexed: 01/28/2023]
Abstract
To evaluate the HLA typing performance of a new Long-Range PCR NGS set of reagents and its dedicated software, a panel of 41 reference homozygous cell lines from the International Histocompatibility Working Group (IHWG) and a panel of 376 volunteer bone marrow donors were analyzed for classical and non-classical HLA class I and class II genes. All results, except HLA-DPB1, were obtained without any ambiguities at the 3rd field level. Based on the high resolution performance of the reagents, a number of new alleles have been described not only for classical but also for non-classical HLA class I genes, leading to a more accurate haplotype definition. Linkage disequilibrium between HLA-A and HLA-G genes has been defined at 4th field level of resolution. Moreover, for the first time, HLA-DQA2 and DQB2 polymorphisms and their linkage disequilibrium with DQB1 were described.
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Jordier F, Gras D, De Grandis M, D'Journo XB, Thomas PA, Chanez P, Picard C, Chiaroni J, Paganini J, Di Cristofaro J. HLA-H: Transcriptional Activity and HLA-E Mobilization. Front Immunol 2020; 10:2986. [PMID: 32010122 PMCID: PMC6978722 DOI: 10.3389/fimmu.2019.02986] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/05/2019] [Indexed: 01/25/2023] Open
Abstract
Little attention is paid to pseudogenes from the highly polymorphic HLA genetic region. The pseudogene HLA-H is defined as a non-functional gene because it is deleted at different frequencies in humans and because it encodes a potentially non-functional truncated protein. However, different studies have shown HLA-H transcriptional activity. We formerly identified 13 novel HLA-H alleles, including the H*02:07 allele, which reaches 19.6% in East Asian populations and encodes a full-length HLA protein. The aims of this study were to explore the expression and possible function of the HLA-H molecule. HLA-H may act as a transmembrane molecule and/or indirectly via its signal peptide by mobilizing HLA-E to the cell surface. We analyzed HLA-H RNA expression in Peripheral Blood Mononuclear Cells (PBMC), Human Bronchial Epithelial Cells (HBEC), and available RNA sequencing data from lymphoblastoid cell lines, and we looked to see whether HLA-E was mobilized at the cell surface by the HLA-H signal peptide. Our data confirmed that HLA-H is transcribed at similar levels to HLA-G. We characterized a hemizygous effect in HLA-H expression, and expression differed according to HLA-H alleles; most interestingly, the HLA-H*02:07 allele had the highest level of mRNA expression. We showed that HLA-H signal peptide incubation mobilized HLA-E molecules at the cell surface of T-Lymphocytes, monocytes, B-Lymphocytes, and primary epithelial cells. Our results suggest that HLA-H may be functional but raises many biological issues that need to be addressed.
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Affiliation(s)
- François Jordier
- Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins”, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Delphine Gras
- Aix-Marseille University, INSERM, INRA, C2VN, Marseille, France
| | - Maria De Grandis
- Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins”, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Xavier-Benoît D'Journo
- Department of Thoracic Surgery, North Hospital, Aix-Marseille University & Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Pascal-Alexandre Thomas
- Department of Thoracic Surgery, North Hospital, Aix-Marseille University & Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Pascal Chanez
- Aix-Marseille University, INSERM, INRA, C2VN, Marseille, France
- Clinique des Bronches, Allergie et Sommeil, North Hospital, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Christophe Picard
- Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins”, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Jacques Chiaroni
- Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins”, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | | | - Julie Di Cristofaro
- Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins”, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
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21
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Veiga-Castelli L, de Oliveira ML, Pereira A, Debortoli G, Marcorin L, Fracasso N, Silva G, Souza A, Massaro J, Simões AL, Sabbagh A, Cardili R, Donadi E, Castelli E, Mendes-Junior C. HLA-G Polymorphisms Are Associated with Non-segmental Vitiligo among Brazilians. Biomolecules 2019; 9:biom9090463. [PMID: 31505868 PMCID: PMC6769860 DOI: 10.3390/biom9090463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 12/31/2022] Open
Abstract
(1) Background: Vitiligo is characterized by white patches on the skin caused by loss of melanocyte activity or the absence of these cells. The available treatments minimize the symptoms by retarding the process of skin depigmentation or re-pigmenting the affected regions. New studies are required for a better comprehension of the mechanisms that trigger the disease and for the development of more efficient treatments. Studies have suggested an autoimmune feature for vitiligo, based on the occurrence of other autoimmune diseases in vitiligo patients and their relatives, and on the involvement of genes related to the immune response. (2) Methods: We evaluated, by massive parallel sequencing, polymorphisms of the HLA-G gene in vitiligo patients and control samples, to verify if variants of this gene could influence the susceptibility to vitiligo. (3) Results: We detected an association with non-segmental vitiligo regarding the haplotype Distal-010101a/G*01:01:01:01/UTR-1, adjusting for population stratification by using ancestry-informative markers (AIMs). (4) Conclusions: It remains unclear whether the HLA-G variants associated with vitiligo were detected because of the high linkage disequilibrium (LD) with HLA-A*02, or if the HLA-A variants previously reported as associated with vitiligo were detected because of the high LD with HLA-G*01:01:01:01/UTR-1, or if both genes jointly contribute to vitiligo susceptibility.
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Affiliation(s)
- Luciana Veiga-Castelli
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (M.L.d.O.); (A.P.); (G.D.); (L.M.); (N.F.); (A.L.S.)
- Correspondence: ; Tel.: +55-16-3315-0417; Fax: +55-16-3315-4838
| | - Maria Luiza de Oliveira
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (M.L.d.O.); (A.P.); (G.D.); (L.M.); (N.F.); (A.L.S.)
| | - Alison Pereira
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (M.L.d.O.); (A.P.); (G.D.); (L.M.); (N.F.); (A.L.S.)
| | - Guilherme Debortoli
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (M.L.d.O.); (A.P.); (G.D.); (L.M.); (N.F.); (A.L.S.)
| | - Letícia Marcorin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (M.L.d.O.); (A.P.); (G.D.); (L.M.); (N.F.); (A.L.S.)
| | - Nádia Fracasso
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (M.L.d.O.); (A.P.); (G.D.); (L.M.); (N.F.); (A.L.S.)
| | - Guilherme Silva
- 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 14040-901, Brazil; (G.S.); (C.M.-J.)
| | - Andreia Souza
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (UNIPEX), School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo 18618-687, Brazil; (A.S.); (E.C.)
| | - Juliana Massaro
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (J.M.); (R.C.); (E.D.)
| | - Aguinaldo Luiz Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (M.L.d.O.); (A.P.); (G.D.); (L.M.); (N.F.); (A.L.S.)
| | - Audrey Sabbagh
- UMR 216 MERIT IRD, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France;
| | - Renata Cardili
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (J.M.); (R.C.); (E.D.)
| | - Eduardo Donadi
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (J.M.); (R.C.); (E.D.)
| | - Erick Castelli
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (UNIPEX), School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo 18618-687, Brazil; (A.S.); (E.C.)
| | - Celso 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 14040-901, Brazil; (G.S.); (C.M.-J.)
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Gautam S, Kumar U, Kumar M, Kanga U, Dada R. Association of HLA-G 3’UTR Polymorphisms with Soluble HLA-G Levels and Disease Activity in Patients with Rheumatoid Arthritis: A Case-Control Study. Immunol Invest 2019; 49:88-105. [DOI: 10.1080/08820139.2019.1657146] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Surabhi Gautam
- Laboratory for Molecular Reproduction and Genetics, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kumar
- Department of Rheumatology, All India Institute of Medical Sciences, New Delhi, India
| | - Manoj Kumar
- Laboratory for Molecular Reproduction and Genetics, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kanga
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Rima Dada
- Laboratory for Molecular Reproduction and Genetics, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
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23
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HLAIb worldwide genetic diversity: New HLA-H alleles and haplotype structure description. Mol Immunol 2019; 112:40-50. [PMID: 31078115 DOI: 10.1016/j.molimm.2019.04.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/09/2019] [Accepted: 04/23/2019] [Indexed: 01/01/2023]
Abstract
The classical HLA class I genes (HLA Ia) were extensively studied because of their implication in clinical fields and anthropology. Less is known about worldwide genetic diversity and linkage disequilibrium for non-classical HLA class I genes (HLA Ib) and HLA pseudogenes. Notably, HLA-H, which is deleted in a fraction of the population, remains scarcely explored. The aims of this study were 1/ to get further insight into HLA-H genetic diversity and into how this variability potentially affects its expression and 2/ to define HLA Ib worldwide allelic diversity and linkage. Exome sequence data from the 1000 Genomes Project were used to define second field HLA-A, -E, -F, -G and -H typing using PolyPheMe software. Allelic and two-loci haplotype frequencies were estimated using Gene[Rate] software both at worldwide and continental levels. Eleven novel HLA-H alleles identified in exome data were validated by NGS performed on 25 genomic DNA samples from the same cohort. Phylogenetic analysis and frequency distribution of HLA-H alleles revealed three clades, each predominantly represented in Admixed American, European and East Asian populations, African populations and South Asian populations. Among these eleven novel alleles, two potentially encode complete transmembrane HLA proteins. We confirm the high LD between HLA-H and -A, and between HLA-H and -G, and show the three genes have distinct worldwide allelic distribution. Conversely, HLA-E and HLA-F both showed little LD, displayed restricted allelic diversity and practically no difference in their distribution across the planet. Our work thus reveals an unexpectedly high HLA-H genetic diversity, with alleles highly represented in Asia possibly encoding a functional HLA protein. Functional implication of these results remains to be explored, both in physiological and pathological contexts.
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Maternal HLA-G*01:01:01:04 protects from anti-HLA-class II immunization in pregnant women. Hum Immunol 2018; 80:120-125. [PMID: 30414459 DOI: 10.1016/j.humimm.2018.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/15/2018] [Accepted: 11/05/2018] [Indexed: 12/11/2022]
Abstract
Factors determining anti-HLA immunization are poorly understood, although anti-HLA immunization following pregnancy is well described. The HLA-G molecule has been extensively described for its implication in immunological tolerance, especially during pregnancy. Transplant studies show an association between HLA-G haplotypes and alloimmunization. Our aim was to investigate the association of HLA-G haplotypes with anti-HLA class I and II immunization in a cohort of women having experienced one or more pregnancies and with no transfusion history. Maternal blood samples (n=270) collected at delivery and formerly screened for anti-HLA antibodies, HLA-A and HLA-B antigens, were screened by NGS for HLA-G gene polymorphism. Univariate analysis further confirmed that the number of pregnancies was significantly associated with anti-HLA class I immunization, whereas no other variable remained significant after Bonferroni correction. Our results showed however that anti-HLA class II immunization was associated with the number of children whereas the HLA-G*01:01:01:04 allele was protective against this immunization.
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Hacking J, Bertozzi T, Moussalli A, Bradford T, Gardner M. Characterisation of major histocompatibility complex class I transcripts in an Australian dragon lizard. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 84:164-171. [PMID: 29454831 DOI: 10.1016/j.dci.2018.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/10/2018] [Accepted: 02/10/2018] [Indexed: 06/08/2023]
Abstract
Characterisation of squamate major histocompatibility complex (MHC) genes has lagged behind other taxonomic groups. MHC genes encode cell-surface glycoproteins that present self- and pathogen-derived peptides to T cells and play a critical role in pathogen recognition. Here we characterise MHC class I transcripts for an agamid lizard (Ctenophorus decresii) and investigate the evolution of MHC class I in Iguanian lizards. An iterative assembly strategy was used to identify six full-length C. decresii MHC class I transcripts, which were validated as likely to encode classical class I MHC molecules. Evidence for exon shuffling recombination was uncovered for C. decresii transcripts and Bayesian phylogenetic analysis of Iguanian MHC class I sequences revealed a pattern expected under a birth-and-death mode of evolution. This work provides a stepping stone towards further research on the agamid MHC class I region.
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Affiliation(s)
- Jessica Hacking
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia.
| | - Terry Bertozzi
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, 5000, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Adnan Moussalli
- Sciences Department, Museum Victoria, Carlton Gardens, VIC, 3053, Australia.
| | - Tessa Bradford
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia; Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, 5000, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Michael Gardner
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia; Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, 5000, Australia.
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26
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Matey-Hernandez ML, Brunak S, Izarzugaza JMG. Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios. BMC Bioinformatics 2018; 19:239. [PMID: 29940840 PMCID: PMC6019707 DOI: 10.1186/s12859-018-2239-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/12/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transplantation. The cost and technical limitations of current laboratory techniques, together with advances in next-generation sequencing (NGS) methodologies, have increased the need for precise computational typing methods. RESULTS We tested two widespread HLA typing methods using high quality full genome sequencing data from 150 individuals in 50 family trios from the Genome Denmark project. First, we computed descendant accuracies assessing the agreement in the inheritance of alleles from parents to offspring. Second, we compared the locus-specific homozygosity rates as well as the allele frequencies; and we compared those to the observed values in related populations. We provide guidelines for testing the accuracy of HLA typing methods by comparing family information, which is independent of the availability of curated alleles. CONCLUSIONS Although current computational methods for HLA typing generally provide satisfactory results, our benchmark - using data with ultra-high sequencing depth - demonstrates the incompleteness of current reference databases, and highlights the importance of providing genomic databases addressing current sequencing standards, a problem yet to be resolved before benefiting fully from personalised medicine approaches HLA phenotyping is essential.
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Affiliation(s)
- Maria Luisa Matey-Hernandez
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, DK-2800 Lyngby, Denmark
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, DK-2800 Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jose M. G. Izarzugaza
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, DK-2800 Lyngby, Denmark
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27
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Abstract
Next-Generation Sequencing (NGS) enables the rapid generation of billions of short nucleic acid sequence fragments (i.e., "sequencing reads"). Especially, the adoption of gene expression profiling using whole transcriptome sequencing (i.e., "RNA-Seq") has been rapid. Here, we describe an in silico method, seq2HLA, that takes standard RNA-Seq reads as input and determines a sample's (classical and non-classical) HLA class I and class II types as well as HLA expression. We demonstrate the application of seq2HLA using publicly available RNA-Seq data from the Burkitt's lymphoma cell line DAUDI and the choriocarcinoma cell line JEG-3.
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