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ElNahass Y, Mekky N, Abdelfattah NM, Abdelfattah R, Samra M, Fahmy OA, Fathy G, Elmetnawy W, Sabet S, Bassiouny H, Nader H, ElHaddad A, Mahmoud HK. HLA alleles, haplotypes frequencies, and their association with hematological disorders: a report from 1550 families whose patients underwent allogeneic bone marrow transplantation in Egypt. Immunogenetics 2024; 76:243-260. [PMID: 38904751 DOI: 10.1007/s00251-024-01343-x] [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: 04/17/2024] [Accepted: 06/15/2024] [Indexed: 06/22/2024]
Abstract
HLA alleles are representative of ethnicities and may play important roles in predisposition to hematological disorders. We analyzed DNA samples for HLA-A, -B, -C, -DRB1, and -DQB1 loci, from 1550 patients and 4450 potential related donors by PCR-SSO (Polymerase chain reaction sequence-specific oligonucleotides) and estimated allele frequencies in donors and patients from 1550 families who underwent bone marrow transplantation (BMT) in Egypt. We also studied the association between HLA allele frequencies and incidence of acute myeloid leukemia, acute lymphoblastic leukemia, and severe aplastic anemia. The most frequently observed HLA class I alleles were HLA- A*01:01 (16.9%), A*02:01 (16.1%), B*41:01 (8.7%), B*49:01 (7.3%), C*06:02 (25.1%), and C*07:01 (25.1%), and the most frequently observed class II alleles were HLA-DRB1*11:01 (11.8%), DRB1*03:01 (11.6%), DQB1*03:01 (27.5%), and DQB1*05:01 (18.9%). The most frequently observed haplotypes were A*33:01~B*14:02 ~ DRB1*01:02 (2.35%) and A*01:01~B*52:01~DRB1*15:01 (2.11%). HLA-DRB1*07:01 was associated with higher AML odds (OR, 1.26; 95% CI, 1.02-1.55; p = 0.030). Only HLA-B38 antigen showed a trend towards increased odds of ALL (OR, 1.52; 95% CI, 1.00-2.30; p = 0.049) HLA-A*02:01, -B*14:02, and -DRB1*15:01 were associated with higher odds of SAA (A*02:01: OR, 1.35; 95% CI, 1.07-1.70; p = 0.010; B*14:02: OR, 1.43; 95% CI, 1.06-1.93; p = 0.020; DRB1*15:01: OR, 1.32; 95% CI, 1.07-1.64; p = 0.011). This study provides estimates of HLA allele and haplotype frequencies and their association with hematological disorders in an Egyptian population.
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Affiliation(s)
- Yasser ElNahass
- National Cancer Institute, Cairo University, Cairo, Egypt
- Nasser Institute, Ministry of Health, Cairo, Egypt
| | | | | | - Raafat Abdelfattah
- National Cancer Institute, Cairo University, Cairo, Egypt
- Nasser Institute, Ministry of Health, Cairo, Egypt
| | - Mohamed Samra
- National Cancer Institute, Cairo University, Cairo, Egypt
- Nasser Institute, Ministry of Health, Cairo, Egypt
| | - Omar A Fahmy
- Faculty of Medicine, Cairo University, Cairo, Egypt
- Nasser Institute, Ministry of Health, Cairo, Egypt
| | - Gamal Fathy
- Nasser Institute, Ministry of Health, Cairo, Egypt
| | | | - Salwa Sabet
- Faculty of Science, Cairo University, Cairo, Egypt
| | | | | | - Alaa ElHaddad
- National Cancer Institute, Cairo University, Cairo, Egypt
- Nasser Institute, Ministry of Health, Cairo, Egypt
| | - H K Mahmoud
- National Cancer Institute, Cairo University, Cairo, Egypt
- Nasser Institute, Ministry of Health, Cairo, Egypt
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2
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Strehler Y, Lachmann N, Niemann M, Halleck F, Budde K, Pruß A. Positive Long-Term Outcome of Kidney Allocation via Acceptable Mismatch Program in Highly Sensitized Patients. Transfus Med Hemother 2024; 51:140-151. [PMID: 38867807 PMCID: PMC11166408 DOI: 10.1159/000536533] [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: 09/21/2023] [Accepted: 01/29/2024] [Indexed: 06/14/2024] Open
Abstract
Introduction Eurotransplant established the acceptable mismatch (AM) program to facilitate timely kidney transplantations of highly sensitized patients, but long-term granular clinical and immunological outcomes regarding overall graft survival and de novo DSA (dnDSA) formation are still intensively researched. The right choice of induction therapy in patients with differing immunological risk is not conclusively determined, as well as the impact of human leukocyte antigen (HLA) epitope matching on dnDSA formation. Methods This monocentric, retrospective study analyzed 94 patients transplanted within the AM program between 2000 and 2019 compared to case-control matched cohorts of non- (PRA 0-5%; PRA-0) and intermediately sensitized (PRA 6-84%; PRA-6/84) patients transplanted through Eurotransplant Kidney Allocation System. Results Estimated 10-year overall graft survival between the PRA-0 and AM cohorts was similar, whereas PRA-6/84 was significantly disadvantageous compared to PRA-0. Estimated 10-year incidence of antibody-mediated rejection rates was significantly lower in the PRA-0 group compared to AM and PRA-6/84 groups. Compared to the AM group, estimated incidence of de novo donor-specific antibody (dnDSA) was significantly lower in PRA-0 patients, with no differences between the AM and PRA-6/84 cohorts. The PRA-6/84 cohort was the only subgroup in which interleukin-2 receptor antagonist (IL2RA) induction was associated with longer overall graft survival, patient survival, and graft survival compared to depleting induction (ATG or OKT3). Broad HLA-A, -B, -DR mismatches (mmABDR) and HLA epitope mismatches determined by Eplets and PIRCHE-II were predictive for dnDSA formation in the total cohort, and the AM subgroup. Discussion The high efforts expended on AM patients are justified to allow timely organ transplantation with acceptable risk profile and non-inferior outcomes. IL2RA induction in intermediately sensitized patients is associated with superior overall graft survival, patient survival, and graft survival compared to ATG/OKT3 induction, without negative effects on rejection episodes or dnDSA formation. In silico epitope matching might further help reduce dnDSA formation, particularly in high-risk AM patients.
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Affiliation(s)
- Yara Strehler
- Institute of Transfusion Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Nils Lachmann
- Institute of Transfusion Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | | | - Fabian Halleck
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Klemens Budde
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Axel Pruß
- Institute of Transfusion Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
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3
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Lim WC, Marques Da Costa ME, Godefroy K, Jacquet E, Gragert L, Rondof W, Marchais A, Nhiri N, Dalfovo D, Viard M, Labaied N, Khan AM, Dessen P, Romanel A, Pasqualini C, Schleiermacher G, Carrington M, Zitvogel L, Scoazec JY, Geoerger B, Salmon J. Divergent HLA variations and heterogeneous expression but recurrent HLA loss-of- heterozygosity and common HLA-B and TAP transcriptional silencing across advanced pediatric solid cancers. Front Immunol 2024; 14:1265469. [PMID: 38318504 PMCID: PMC10839790 DOI: 10.3389/fimmu.2023.1265469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/06/2023] [Indexed: 02/07/2024] Open
Abstract
The human leukocyte antigen (HLA) system is a major factor controlling cancer immunosurveillance and response to immunotherapy, yet its status in pediatric cancers remains fragmentary. We determined high-confidence HLA genotypes in 576 children, adolescents and young adults with recurrent/refractory solid tumors from the MOSCATO-01 and MAPPYACTS trials, using normal and tumor whole exome and RNA sequencing data and benchmarked algorithms. There was no evidence for narrowed HLA allelic diversity but discordant homozygosity and allele frequencies across tumor types and subtypes, such as in embryonal and alveolar rhabdomyosarcoma, neuroblastoma MYCN and 11q subtypes, and high-grade glioma, and several alleles may represent protective or susceptibility factors to specific pediatric solid cancers. There was a paucity of somatic mutations in HLA and antigen processing and presentation (APP) genes in most tumors, except in cases with mismatch repair deficiency or genetic instability. The prevalence of loss-of-heterozygosity (LOH) ranged from 5.9 to 7.7% in HLA class I and 8.0 to 16.7% in HLA class II genes, but was widely increased in osteosarcoma and glioblastoma (~15-25%), and for DRB1-DQA1-DQB1 in Ewing sarcoma (~23-28%) and low-grade glioma (~33-50%). HLA class I and HLA-DR antigen expression was assessed in 194 tumors and 44 patient-derived xenografts (PDXs) by immunochemistry, and class I and APP transcript levels quantified in PDXs by RT-qPCR. We confirmed that HLA class I antigen expression is heterogeneous in advanced pediatric solid tumors, with class I loss commonly associated with the transcriptional downregulation of HLA-B and transporter associated with antigen processing (TAP) genes, whereas class II antigen expression is scarce on tumor cells and occurs on immune infiltrating cells. Patients with tumors expressing sufficient HLA class I and TAP levels such as some glioma, osteosarcoma, Ewing sarcoma and non-rhabdomyosarcoma soft-tissue sarcoma cases may more likely benefit from T cell-based approaches, whereas strategies to upregulate HLA expression, to expand the immunopeptidome, and to target TAP-independent epitopes or possibly LOH might provide novel therapeutic opportunities in others. The consequences of HLA class II expression by immune cells remain to be established. Immunogenetic profiling should be implemented in routine to inform immunotherapy trials for precision medicine of pediatric cancers.
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Affiliation(s)
- Wan Ching Lim
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
| | | | - Karine Godefroy
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Loren Gragert
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Windy Rondof
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Naima Nhiri
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Davide Dalfovo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Mathias Viard
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Nizar Labaied
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Asif M. Khan
- School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
| | - Philippe Dessen
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Alessandro Romanel
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Claudia Pasqualini
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Gudrun Schleiermacher
- INSERM U830, Recherche Translationnelle en Oncologie Pédiatrique (RTOP), and SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), PSL Research University, Institut Curie, Paris, France
| | - Mary Carrington
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, United States
| | - Laurence Zitvogel
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Jean-Yves Scoazec
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Birgit Geoerger
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Jerome Salmon
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
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4
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Truong L, Matern BM, El-Lagta N, Mobegi FM, Askar M, Ogret Y, Oguz FS, Kwok J, D'Orsogna L, Martinez P, Petersdorf E, Tilanus MGJ, De Santis D. Report from the extended HLA-DPA1 ~ promoter ~ HLA-DPB1 haplotype of the 18th international HLA and immunogenetics workshop. HLA 2023; 102:690-706. [PMID: 37452528 DOI: 10.1111/tan.15155] [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: 03/27/2023] [Revised: 06/04/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
The primary goal of the HLA-DPA1 ~ promoter ~ HLA-DPB1 haplotype component of the 18th IHIWS was to characterise the extended haplotypes within the HLA-DP region and survey the extent of genetic diversity in this region across human populations. In this report, we analysed single-nucleotide polymorphisms (SNPs) in 255 subjects from 6 different cohorts. The results from the HLA-DP haplotype component have validated findings from the initial pilot study. SNPs in this region were inherited in strong linkage, particularly HLA-DPA1, SNP-linked promoter haplotypes and motifs in exon 2 of HLA-DPB1. We reported 17 SNP-linked haplotypes in the promoter region. Together with HLA-DPA1 and HLA-DPB1 alleles, they formed 74 distinct extended HLA-DP haplotypes in 438 sequences. We also observed the presence of region-specific alleles and promoter haplotypes. Our approach involved phasing extended SNPs including promoter SNPs, HLA-DPA1 and HLA-DPB1 alleles, in a 22 kb region, GRCh38/hg38 (chr6:33,064,111-33,086,679), followed by clustering of these SNPs as one extended haplotype. This hierarchical clustering revealed four major clades, suggesting that haplotypes within each clade may have diverged from a common ancestral haplotype and undergone similar evolutionary processes. The correlation between HLA-DPA1 and the promoter region raises questions about the role of HLA-DPA1 antigen in the heterodimer. This finding requires validation on a larger sample size specifically designed for anthropological analysis. Nevertheless, the results from this study highlight the clinical potential of selecting better-matched donors for patients awaiting haematopoietic stem cell transplants from genetically overlapping groups that share common ancestral haplotypes.
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Affiliation(s)
- Linh Truong
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
- UWA Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Benedict M Matern
- Central Diagnostic Laboratory, University Medical Center Utrecht, Utrecht, Netherlands
| | - Naser El-Lagta
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Fredrick M Mobegi
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Medhat Askar
- QU Health Cluster & Department of Basic Sciences, College of Medicine, Qatar University, Doha, Qatar
| | - Yeliz Ogret
- Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Fatma S Oguz
- Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Janette Kwok
- Division of Transplantation and Immunogenetics, Queen Mary Hospital, Hong Kong, China
| | - Lloyd D'Orsogna
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
- UWA Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Patricia Martinez
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
- UWA Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Effie Petersdorf
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Marcel G J Tilanus
- School for Oncology and Reproduction, GROW, Maastricht University, Maastricht, Netherlands
| | - Dianne De Santis
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
- UWA Medical School, The University of Western Australia, Perth, Western Australia, Australia
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5
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Laboux T, Lenain R, Visentin J, Flahaut G, Chamley P, Provôt F, Top I, Kerleau C, Labalette M, Choukroun G, Couzi L, Blancho G, Hazzan M, Maanaoui M. Impact of Preformed Donor-Specific Anti-HLA-Cw and Anti-HLA-DP Antibodies on Acute Antibody-Mediated Rejection in Kidney Transplantation. Transpl Int 2023; 36:11416. [PMID: 38076227 PMCID: PMC10698113 DOI: 10.3389/ti.2023.11416] [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: 03/29/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023]
Abstract
Given the risk of rejection, the presence of preformed donor specific antibodies (DSA) contraindicates transplantation in most allocation systems. However, HLA-Cw and -DP DSA escape this censorship. We performed a multicentric observational study, in which the objective was to determinate risk factors of acute antibody-mediated rejection (aABMR) in recipients transplanted with preformed isolated Cw- or DP-DSA. Between 2010 and 2019, 183 patients were transplanted with a preformed isolated Cw- or DP-DSA (92 Cw-DSA; 91 DP-DSA). At 2 years, the incidence of aABMR was 12% in the Cw-DSA group, versus 28% in the DP-DSA group. Using multivariable Cox regression model, the presence of a preformed DP-DSA was associated with an increased risk of aABMR (HR = 2.32 [1.21-4.45 (p = 0.001)]) compared with Cw-DSA. We also observed a significant association between the DSA's MFI on the day of transplant and the risk of aABMR (HR = 1.09 [1.08-1.18], p = 0.032), whatever the DSA was. Interaction term analysis found an increased risk of aABMR in the DP-DSA group compared with Cw-DSA, but only for MFI below 3,000. These results may plead for taking these antibodies into account in the allocation algorithms, in the same way as other DSA.
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Affiliation(s)
- Timothée Laboux
- Department of Nephrology, Kidney Transplantation and Dialysis, CHU Lille, University of Lille, Lille, France
- INSERM U1167, RID-AGE, University of Lille, Lille, France
| | - Rémi Lenain
- Department of Nephrology, Kidney Transplantation and Dialysis, CHU Lille, University of Lille, Lille, France
- INSERM UMR 1246 – SPHERE, Nantes University, Tours University, Nantes, France
| | - Jonathan Visentin
- Department of Immunology and Immunogenetics, CHU Bordeaux, Bordeaux, France
- ImmunoConceEpT, CNRS UMR5164, Inserm ERL U1303, University of Bordeaux, Bordeaux, France
| | - Gauthier Flahaut
- Department of Nephrology, Internal Medicine, Dialysis and Transplantation, CHU Amiens, Jules Verne University of Picardie, Amiens, France
- EA7517, MP3CV Laboratory, Jules Verne University of Picardie, Amiens, France
| | - Paul Chamley
- Department of Nephrology, CH Roubaix, Roubaix, France
| | - François Provôt
- Department of Nephrology, Kidney Transplantation and Dialysis, CHU Lille, University of Lille, Lille, France
| | - Isabelle Top
- Department of Immunology-HLA, CHU Lille, University of Lille, Lille, France
| | - Clarisse Kerleau
- CHU Nantes, Service de Néphrologie-Immunologie Clinique, ITUN, Nantes, France
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Nantes, France
| | - Myriam Labalette
- Department of Immunology-HLA, CHU Lille, University of Lille, Lille, France
- INSERM UMR1286, INFINITE, University of Lille, Lille, France
| | - Gabriel Choukroun
- Department of Nephrology, Internal Medicine, Dialysis and Transplantation, CHU Amiens, Jules Verne University of Picardie, Amiens, France
- EA7517, MP3CV Laboratory, Jules Verne University of Picardie, Amiens, France
| | - Lionel Couzi
- ImmunoConceEpT, CNRS UMR5164, Inserm ERL U1303, University of Bordeaux, Bordeaux, France
- Department of Nephrology, Transplantation, Dialysis and Apheresis, CHU Bordeaux, Bordeaux, France
| | - Gilles Blancho
- CHU Nantes, Service de Néphrologie-Immunologie Clinique, ITUN, Nantes, France
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Nantes, France
| | - Marc Hazzan
- Department of Nephrology, Kidney Transplantation and Dialysis, CHU Lille, University of Lille, Lille, France
| | - Mehdi Maanaoui
- Department of Nephrology, Kidney Transplantation and Dialysis, CHU Lille, University of Lille, Lille, France
- INSERM U1190, EGID, Institut Pasteur Lille, CHU Lille, University of Lille, Lille, France
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6
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López del Moral C, Wu K, Naik M, Osmanodja B, Akifova A, Lachmann N, Stauch D, Hergovits S, Choi M, Bachmann F, Halleck F, Schrezenmeier E, Schmidt D, Budde K. The natural history of de novo donor-specific HLA antibodies after kidney transplantation. Front Med (Lausanne) 2022; 9:943502. [PMID: 36186822 PMCID: PMC9523126 DOI: 10.3389/fmed.2022.943502] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
Background De novo donor-specific HLA antibodies (dnDSA) are key factors in the diagnosis of antibody-mediated rejection (ABMR) and related to graft loss. Methods This retrospective study was designed to evaluate the natural course of dnDSA in graft function and kidney allograft survival and to assess the impact of mean fluorescence intensity (MFI) evolution as detected by annual Luminex® screening. All 400 kidney transplant recipients with 731 dnDSA against the last graft (01/03/2000-31/05/2021) were included. Results During 8.3 years of follow-up, ABMR occurred in 24.8% and graft loss in 33.3% of the cases, especially in patients with class I and II dnDSA, and those with multiple dnDSA. We observed frequent changes in MFI with 5-year allograft survivals post-dnDSA of 74.0% in patients with MFI reduction ≥ 50%, 62.4% with fluctuating MFI (MFI reduction ≥ 50% and doubling), and 52.7% with doubling MFI (log-rank p < 0.001). Interestingly, dnDSA in 168 (24.3%) cases became negative at some point during follow-up, and 38/400 (9.5%) patients became stable negative, which was associated with better graft survival. Multivariable analysis revealed the importance of MFI evolution and rejection, while class and number of dnDSA were not contributors in this model. Conclusion In summary, we provide an in-depth analysis of the natural course of dnDSA after kidney transplantation, first evidence for the impact of MFI evolution on graft outcomes, and describe a relevant number of patients with a stable disappearance of dnDSA, related to better allograft survival.
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Affiliation(s)
- Covadonga López del Moral
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Valdecilla Biomedical Research Institute (IDIVAL), Santander, Spain
- *Correspondence: Covadonga López del Moral,
| | - Kaiyin Wu
- Department of Pathology, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Marcel Naik
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Bilgin Osmanodja
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Aylin Akifova
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nils Lachmann
- Institute for Transfusion Medicine, HLA-Laboratory, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Diana Stauch
- Institute for Transfusion Medicine, HLA-Laboratory, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Sabine Hergovits
- Institute for Transfusion Medicine, HLA-Laboratory, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Mira Choi
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Friederike Bachmann
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Fabian Halleck
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Eva Schrezenmeier
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health Charité – Universitätsmedizin Berlin, BIH Academy, Berlin, Germany
| | - Danilo Schmidt
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Klemens Budde
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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7
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Hod‐Dvorai R, Schiller JJ, Riddick MC, Gallay B. Identification of a
DRB1*04:07
–
DRB4*01:03:01:02N
haplotype in a native
American
individual. HLA 2022; 100:500-504. [DOI: 10.1111/tan.14762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/26/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Reut Hod‐Dvorai
- Department of Pathology SUNY Upstate Medical University Syracuse New York USA
| | | | - Mary C. Riddick
- Department of Pathology SUNY Upstate Medical University Syracuse New York USA
| | - Brian Gallay
- Department of Medicine SUNY Upstate Medical University Syracuse New York USA
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8
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Dashti M, Al-Matrouk A, Channanath A, Hebbar P, Al-Mulla F, Thanaraj TA. Distribution of HLA-B Alleles and Haplotypes in Qatari: Recommendation for Establishing Pharmacogenomic Markers Screening for Drug Hypersensitivity. Front Pharmacol 2022; 13:891838. [PMID: 36003520 PMCID: PMC9393242 DOI: 10.3389/fphar.2022.891838] [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: 03/08/2022] [Accepted: 06/14/2022] [Indexed: 11/18/2022] Open
Abstract
Human leukocyte antigen (HLA) proteins are present at the cellular surface of antigen-presenting cells and play a crucial role in the adaptive immune response. Class I genes, specifically certain HLA-B alleles, are associated with adverse drug reactions (ADRs) and are used as pharmacogenetic markers. Although ADRs are a common causes of hospitalization and mortality, the data on the prevalence of HLA-B pharmacogenetics markers in Arab countries are scarce. In this study, we investigated the frequencies of major HLA-B pharmacogenomics markers in the Qatari population. Next-generation sequencing data from 1,098 Qatari individuals were employed for HLA-B typing using HLA-HD version 1.4.0 and IPD-IMGT/HLA database. In addition, HLA-B pharmacogenetics markers were obtained from the HLA Adverse Drug Reaction Database. In total, 469 major HLA-B pharmacogenetic markers were identified, with HLA-B*51:01 being the most frequent pharmacogenetic marker (26.67%) in the Qatari population. Moreover, HLA-B*51:01 is associated with phenytoin- and clindamycin-induced ADRs. The second most frequent pharmacogenetic marker was the HLA-B*58:01 allele (6.56%), which is associated with allopurinol-induced ADRs. The third most frequent pharmacogenetic marker was the HLA-B*44:03 allele, which is associated with phenytoin-induced ADRs. The establishment of a pharmacogenetics screening program in Qatar for cost effective interventions aimed at preventing drug-induced hypersensitivity can be aided by the highly prevalent HLA-B pharmacogenetic markers detected here.
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Affiliation(s)
- Mohammed Dashti
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Abdullah Al-Matrouk
- Narcotic and Psychotropic Department, Ministry of Interior, Farwaniya, Kuwait
| | - Arshad Channanath
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Prashantha Hebbar
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Fahd Al-Mulla
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
- *Correspondence: Fahd Al-Mulla, ; Thangavel Alphonse Thanaraj,
| | - Thangavel Alphonse Thanaraj
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
- *Correspondence: Fahd Al-Mulla, ; Thangavel Alphonse Thanaraj,
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9
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Yu N, Askar M, Wadsworth K, Gragert L, Fernández-Viña MA. Current HLA testing recommendations to support HCT. Hum Immunol 2022; 83:665-673. [DOI: 10.1016/j.humimm.2022.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 11/29/2022]
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10
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Que TN, Khanh NB, Khanh BQ, Van Son C, Van Anh NT, Anh TTT, Tung PD, Thang ND. Allele and Haplotype Frequencies of HLA-A, -B, -C, and -DRB1 Genes in 3,750 Cord Blood Units From a Kinh Vietnamese Population. Front Immunol 2022; 13:875283. [PMID: 35844516 PMCID: PMC9277059 DOI: 10.3389/fimmu.2022.875283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
The frequencies and diversities of human leukocyte antigen (HLA) alleles and haplotypes are representative of ethnicities. Matching HLA alleles is essential for many clinical applications, including blood transfusion, stem cell transplantation, and tissue/organ transplantation. To date, the information about the frequencies and distributions of HLA alleles and haplotypes among the Kinh Vietnamese population is limited because of the small sample size. In this study, more than 3,750 cord blood units from individuals belonging to the Kinh Vietnamese population were genotyped using PCR sequence-specific oligonucleotide (PCR-SSO) for HLA testing. The results of the study demonstrated that the most frequently occurring HLA-A, -B, -C, and -DRB1 alleles were A*11:01 (25%), A*24:02 (12.3%), A*02:01 (11.2); A*03:03 (8.95%), A*02:03 (7.81%), A*29:01 (7.03%); B*15:02 (15.1%), B*46:01 (10.7%), B*58:01 (7.65%), B*38:02 (7.29%); C*08:01 (17.2), C*07:02 (16.2%), C*01:02 (15.2), C*03:02 (8.3%), C*15:05 (6.13); DRB1*12:02 (31.0%), DRB1*09:01 (10.47%), DRB1*15:02 (7.54%); DRB1*07:01 (6.68%), DRB1*10:01 (6.63%), respectively, with the highest allele diversity level observed in locus B (93 alleles). The most frequent haplotypes of two-locus combinations of HLA-A–B, HLA-A–C, HLA-A–DRB1, HLA-B–C, HLA-B–DRB1, and HLA-C–DRB1 haplotypes were A*11:01–B*15:02 (7.63%), A*11:01–C*08:01 (7.98%), A*11:01–DRB1*12:02 (10.56%), B*15:02–C*08:01 (14.0%), B*15:02–DRB1*12:02 (10.47%), and C*08:01–DRB1*12:02 (11.38%), respectively. In addition, the most frequent haplotypes of three- and four-locus sets of HLA-A–B–C, HLA-A–B–DRB1, HLA-A–C–DRB1, HLA-B–C–DRB1, and HLA-A–B–C–DRB1 were A*11:01–B*15:02–C*08:01 (7.57%), A*11:01–B*15:02–DRB1*12:02 (5.39%), A*11:01–C*08:01–DRB1*12:02 (5.54%), B*15:02–C*08:01–DRB1*12:02 (10.21%), and A*11:01–B*15:02–C*08:01–DRB1*12:02 (5.45%), respectively. This study provides critical information on the frequencies and distributions of HLA alleles and haplotypes in the Kinh Vietnamese population, accounting for more than 85% of Vietnamese citizens. It paves the way to establish an umbilical cord blood bank for cord blood transplantation programs in Vietnam.
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Affiliation(s)
- Tran Ngoc Que
- Stem Cell Bank, National Institute of Hematology and Blood Transfusion, Pham Van Bach, Cau Giay, Hanoi, Vietnam
- Department of Hematology, Hanoi Medical University, 1 Ton That Tung, Dong Da, Hanoi, Vietnam
| | - Nguyen Ba Khanh
- Stem Cell Bank, National Institute of Hematology and Blood Transfusion, Pham Van Bach, Cau Giay, Hanoi, Vietnam
- Department of Hematology, Hanoi Medical University, 1 Ton That Tung, Dong Da, Hanoi, Vietnam
| | - Bach Quoc Khanh
- Stem Cell Bank, National Institute of Hematology and Blood Transfusion, Pham Van Bach, Cau Giay, Hanoi, Vietnam
- Department of Hematology, Hanoi Medical University, 1 Ton That Tung, Dong Da, Hanoi, Vietnam
| | - Chu Van Son
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University-Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Nguyen Thi Van Anh
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University-Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Tran Thi Thuy Anh
- Faculty of Biology, VNU University of Science, Vietnam National University-Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Pham Dinh Tung
- Department of Probability and Statistics, Faculty of Mathematics–Mechanics–Informatics, VNU University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Nguyen Dinh Thang
- Faculty of Biology, VNU University of Science, Vietnam National University-Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
- *Correspondence: Nguyen Dinh Thang,
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11
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Chentoufi AA, Uyar FA, Chentoufi HA, Alzahrani K, Paz M, Bahnassy A, Elyamany G, Elghazaly A. HLA Diversity in Saudi Population: High Frequency of Homozygous HLA Alleles and Haplotypes. Front Genet 2022; 13:898235. [PMID: 35754807 PMCID: PMC9218871 DOI: 10.3389/fgene.2022.898235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Human leukocyte antigens (HLA) diversity has a tremendous impact on shaping the transplantation practices, transfusion-associated graft versus host disease prevention strategies, and host-pathogen interactions. Here, we conducted a retrospective study of HLA class I and class II homozygosity at allelic and haplotype levels in unrelated individuals genotyped from 2012 to 2016 in a tertiary hospital in the capital of Saudi Arabia. Among 5,000 individuals, 2,773 individuals meet inclusion criteria and were retrospectively analyzed for HLA-A, -B, -C-DRB1, and -DQB1 homozygosity at allelic and haplotype levels. HLA molecular typing was performed using a commercial reverse sequence-specific oligonucleotide (rSSO) kit. We were able to identify 15 HLA-A, 20 HLA-B, 11 HLA-C, 13 HLA-DRB1, and five HLA-DQB1 homozygous alleles demonstrating a very low genetic diversity in the Saudi population. The highest homozygosity in HLA class I was found in locus C followed by A and B (20.3% > 16.1% > 15.5%; p < 0.001) where the most homozygote alleles were A*02 (9.2%), B*51 and B*50 (5.7% and 3.7%), and C*07, C*06, and C*15 (7.2%, 5.48%, and 3.3%) and in HLA class II, the highest homozygosity was found in locus DQB1 compared to DRB1 (31.71% > 19.2%; p < 0.001), with the most common homozygote alleles being DRB1*07 and DRB1*04 (5.33% and 4.2%) and DQB1*02, DQB1*06, and DQB1*03 (13.55%, 7.92%, and 7.64%). The frequency of finding an individual with one homozygote allele was (24.6%), two homozygote alleles (13.5%), three homozygote alleles (4.7%), four homozygote alleles (3.4%), and five alleles were (4.8%). The most frequent homozygote haplotypes are A*23∼C*06∼B*50∼DRB1*07∼DQB1*02 and A*02∼C*06∼B*50∼DRB1*07∼DQB1*02. This study shows low diversity of both class I and II alleles and haplotypes in the Saudi population, which would have a significant impact on shaping the transplantation practices, transfusion-associated graft versus host disease prevention strategies, and host-pathogen interactions.
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Affiliation(s)
- Aziz Alami Chentoufi
- King Fahad Medical City, Riyadh, Saudi Arabia.,Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - F Aytül Uyar
- Department of Physiology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | | | | | - Maria Paz
- King Fahad Medical City, Riyadh, Saudi Arabia
| | | | - Ghaleb Elyamany
- Department of Central Military Laboratory and Blood Bank, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Assem Elghazaly
- King Fahad Medical City, Riyadh, Saudi Arabia.,Department of Hematology/Oncology, King Saud Medical City, Riyadh, Saudi Arabia
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12
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Barton JC, Barton JC, Acton RT. HLA-A*03, the hemochromatosis ancestral haplotype, and phenotypes of referred hemochromatosis probands with HFE p.C282Y homozygosity. Hereditas 2022; 159:25. [PMID: 35659379 PMCID: PMC9169309 DOI: 10.1186/s41065-022-00237-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/11/2022] [Indexed: 11/10/2022] Open
Abstract
Background Human leukocyte antigen (HLA)-A*03, hemochromatosis ancestral haplotype marker, was associated with greater iron overload in hemochromatosis cohorts reported before discovery of the HFE gene. We sought to learn whether an A*03-linked locus influences phenotypes in referred HFE p.C282Y homozygotes. Methods We tabulated these phenotypes in probands with p.C282Y homozygosity: age, transferrin saturation (TS), serum ferritin (SF), conditions related to iron overload, fibrosis-four variables (FIB-4) index and aspartate aminotransferase-to-platelet ratio index (APRI) predictors of severe hepatic fibrosis, and iron removed to achieve depletion (QFe/age). We analyzed phenotypes of men and women separately across three A*03 subgroups. Results There were 104 men (57.8%) and 76 women (42.2%). Mean age (SD) was 49 ± 13 y. Mean TS was 79 ± 17%. Median SF (range) was 715 µg/L (28, 6103). Related conditions included: hemochromatosis arthropathy (21.7%); type 2 diabetes (18.9%); hypogonadotropic hypogonadism (5.8% of men); cardiomyopathy (0%); and cirrhosis (10.0%). Median QFe/age was 61 mg/y (0, 714). A*03 homozygosity, heterozygosity, and no A*03 occurred in 37 (20.6%), 104 (57.8%), and 39 probands (21.7%), respectively. In men, mean TS and median SF were significantly higher in A*03 homozygotes than heterozygotes but not A*03-negative probands. In men, median APRI was significantly lower in A*03 heterozygotes than homozygotes and A*03-negative probands. No other phenotypes, including QFe/age, differed significantly across A*03 subgroups in either men or women. Conclusions Our results suggest that an A*03-linked locus does not influence phenotypes in referred HFE p.C282Y homozygotes. It is unlikely that heritable factors that modify phenotypes of p.C282Y homozygotes are linked to the hemochromatosis ancestral haplotype.
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Affiliation(s)
- James C Barton
- Southern Iron Disorders Center, Birmingham, AL, USA. .,Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
| | | | - Ronald T Acton
- Southern Iron Disorders Center, Birmingham, AL, USA.,Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
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13
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Song C, Wang L, Li Q, Liao B, Qiao W, Li Q, Dong N, Li L. Generation of individualized immunocompatible endothelial cells from HLA-I-matched human pluripotent stem cells. Stem Cell Res Ther 2022; 13:48. [PMID: 35109922 PMCID: PMC8812039 DOI: 10.1186/s13287-022-02720-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/16/2022] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Endothelial cells (ECs) derived from human-induced pluripotent stem cell (iPSC) are a valuable cell resource for cardiovascular regeneration. To avoid time-consuming preparation from primary autologous cells, the allogeneic iPSC-ECs are being expected to become "off-the-shelf" cell products. However, allorejection caused by HLA mismatching is a major barrier for this strategy. Although the "hypoimmunogenic" iPSCs could be simply generated by inhibition of HLA-I expression via β-2 microglobulin knockout (B2M KO), the deletion of HLA-I expression will activate natural killer (NK) cells, which kill the HLA-I negative cells. To inhibit NK activation, we proposed to generate HLA-matched iPSCs based on patient's HLA genotyping by HLA exchanging approach to express the required HLA allele. METHODS To establish a prototype of HLA exchanging system, the expression of HLA-I molecules of iPSCs was inhibited by CRISPR/Cas9-mediated B2M KO, and then HLA-A*11:01 allele, as a model molecule, was introduced into B2M KO iPSCs by lentiviral gene transfer. HLA-I-modified iPSCs were tested for their pluripotency and ability to differentiate into ECs. The stimulation of iPSC-EC to allogeneic T and NK cells was detected by respective co-culture of PBMC-EC and NK-EC. Finally, the iPSC-ECs were used as the seeding cells to re-endothelialize the decellularized valves. RESULTS We generated the iPSCs only expressed one HLA-A allele (HLA-A *11:01) by B2M KO plus HLA gene transfer. These HLA-I-modified iPSCs maintained pluripotency and furthermore were successfully differentiated into functional ECs assessed by tube formation assay. Single HLA-A*11:01-matched iPSC-ECs significantly less induced the allogeneic response of CD8+ T cell and NK cells expressing matched HLA-A*11:01 and other HLA-A,-B and -C alleles. These cells were successfully used to re-endothelialize the decellularized valves. CONCLUSIONS In summary, a simple HLA-I exchanging system has been created by efficient HLA engineering of iPSCs to evade both of the alloresponse of CD8+ T cells and the activation of NK cells. This technology has been applied to generate iPSC-ECs for the engineering of cellular heart valves. Our strategy should be extremely useful if the "off-the-shelf" and "non-immunogenic" allogeneic iPSCs were created for the common HLA alleles.
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Affiliation(s)
- Chanchan Song
- Institute of Clinical Oncology, Research Center of Cancer Diagnosis and Therapy, and Department of Clinical Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Linlin Wang
- Guangzhou Future Homo Sapiens Institute of Biomedicine and Health (GFBH), Guangzhou, China.,Guangzhou Regenerative Medicine Research Center, Future Homo Sapiens Institute of Regenerative Medicine Co., Ltd (FHIR), Guangzhou, China
| | - Qingyang Li
- Institute of Clinical Oncology, Research Center of Cancer Diagnosis and Therapy, and Department of Clinical Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Baoyi Liao
- Institute of Clinical Oncology, Research Center of Cancer Diagnosis and Therapy, and Department of Clinical Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Weihua Qiao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiang Li
- Guangzhou Future Homo Sapiens Institute of Biomedicine and Health (GFBH), Guangzhou, China.,Guangzhou Regenerative Medicine Research Center, Future Homo Sapiens Institute of Regenerative Medicine Co., Ltd (FHIR), Guangzhou, China
| | - Nianguo Dong
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Liangping Li
- Institute of Clinical Oncology, Research Center of Cancer Diagnosis and Therapy, and Department of Clinical Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China.
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14
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Wang F, Dong L, Wang W, Chen N, Zhang W, He J, Zhu F. The polymorphism of HLA-A, -C, -B, -DRB3/4/5, -DRB1, -DQB1 loci in Zhejiang Han population, China using NGS technology. Int J Immunogenet 2021; 48:485-489. [PMID: 34553840 DOI: 10.1111/iji.12554] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 11/26/2022]
Abstract
The distributions of HLA allele and haplotype are various in the populations. Currently, the data for HLA alleles and haplotypes at three fields resolution level in Chinese Han population is rare. Here, the HLA alleles and haplotypes of the 1734 cord blood samples from Zhejiang Han population, China were reported at three fields resolution. All samples were randomly collected from the Zhejiang Cord Blood Bank, China. HLA-A, -B, -C, -DRB1, -DQB1, -DRB3/4/5 loci was genotyped using next generation sequencing method. The genotypes of the samples were assigned using the HLA TypeStream Visual Software version 1.2.0. The frequency of alleles, haplotype estimation and linkage disequilibrium analysis were performed with the Arlequin software 3.5.2.2. It was found that the top three frequent alleles of HLA-A, -B, -C, -DRB1, -DQB1, -DRB3/4/5 loci were A*11:01:01 (25.81%), A*24:02:01 (16.70%), A*02:01:01 (10.61%); B*40:01:02 (15.97%), B*46:01:01 (11.48%), B*58:01:01 (7.96%); C*07:02:01 (19.03%), C*01:02:01 (17.65%), C*03:04:01 (10.41%); DRB1*09:01:02G (17.96%), DRB1*12:02:01 (9.57%), DRB1*08:03:02 (9.54%); DQB1*03:01:01G (21.05%), DQB1*03:03:02 (19.15%), DQB1*06:01:01G (12.08%); DRB4*01:03:01 (25.72%), DRB3*02:02:01 (20.27%), DRB5*01:01:01 (10.96%), respectively. A total of 1528 distinct A∼C∼B∼DRB3/4/5∼DRB1∼DQB1 haplotypes were estimated, and the top three most common haplotypes were A*33:03:01∼C*03:02:02∼B*58:01:01∼DRB3*02:02:01∼DRB1*03:01:01∼ DQB1*02:01:01 (4.02%), A*30:01:01∼C*06:02:01∼B*13:02:01∼DRB4*01:03:01∼ DRB1*07:01:01 ∼DQB1*02:02:01 (3.11%) and A*02:07:01∼C*01:02:01∼B*46:01:01 ∼DRB4*01:03:01∼DRB1*09:01:02G∼DQB1*03:03:02 (3.05%). Some alleles of different HLA loci were shown strong linkage disequilibrium. In conclusion, the data of allele and haplotype of HLA-A, -B, -C, -DRB1, -DQB1 and -DRB3/4/5 loci at three fields resolution level were obtained in Zhejiang Han population, thus contributing to analyze the HLA ploymorphism in the populations.
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Affiliation(s)
- Fang Wang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang Province, China.,Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang Province, 310052, China
| | - Lina Dong
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang Province, China.,Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang Province, 310052, China
| | - Wei Wang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang Province, China.,Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang Province, 310052, China
| | - Nanying Chen
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang Province, China.,Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang Province, 310052, China
| | - Wei Zhang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang Province, China.,Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang Province, 310052, China
| | - Ji He
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang Province, China.,Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang Province, 310052, China
| | - Faming Zhu
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang Province, China.,Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang Province, 310052, China
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15
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Rostaminia S, Aghaei SS, Farahmand B, Nazari R, Ghaemi A. Computational Design and Analysis of a Multi-epitope Against Influenza A virus. Int J Pept Res Ther 2021; 27:2625-2638. [PMID: 34539293 PMCID: PMC8435298 DOI: 10.1007/s10989-021-10278-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2021] [Indexed: 12/28/2022]
Abstract
Influenza A viruses are among the most studied viruses, however no effective prevention against influenza infection has been developed. So, designing an effective vaccine against Influenza A virus is a critical issue in the field of medical biotechnology. For this reason, to combat this disease, we have designed a novel multi-epitope vaccine candidate based on the several conserved and potential linear B-cell and T-cell binding epitopes by using the in silico approach. This vaccine consists of an ER signal conserved sequence, the PADRE conserved epitope and two conserved epitopes of Influenza matrix protein 2. T-cell binding epitopes from Matrix protein 2 were predicted by in silico tools of epitope prediction. The selected epitopes were joined by flexible linkers and physicochemical properties, toxicity, and allergenecity were investigated. The designed vaccine was antigenic, immunogenic, and non-allergenic with suitable physicochemical properties and has higher solubility. The final multi-epitope construct was modeled, confirmed by different programs and the molecular interactions with immune receptors were considered. The molecular docking assay indicated the interactions with immune-stimulatory toll-like receptor 3 (TLR3) and major histocompatibility complex class I (MHCI). The HADDOCK and H DOCK servers were used to make docking analysis, respectively. The docking analysis indicated a strong and stable binding interaction between the vaccine construct with major histocompatibility complex (MHC) class I and toll-like receptor 3. Overall, the findings suggest that the current vaccine may be a promising vaccine to prevent Influenza infection.
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Affiliation(s)
- Samaneh Rostaminia
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran
| | | | - Behrokh Farahmand
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, 69, P.O.Box: 1316943551, Tehran, Iran
| | - Raziye Nazari
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran
| | - Amir Ghaemi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, 69, P.O.Box: 1316943551, Tehran, Iran
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16
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Challenges for the standardized reporting of NGS HLA genotyping: Surveying gaps between clinical and research laboratories. Hum Immunol 2021; 82:820-828. [PMID: 34479742 DOI: 10.1016/j.humimm.2021.08.011] [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: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 11/21/2022]
Abstract
Next generation sequencing (NGS) is being applied for HLA typing in research and clinical settings. NGS HLA typing has made it feasible to sequence exons, introns and untranslated regions simultaneously, with significantly reduced labor and reagent cost per sample, rapid turnaround time, and improved HLA genotype accuracy. NGS technologies bring challenges for cost-effective computation, data processing and exchange of NGS-based HLA data. To address these challenges, guidelines and specifications such as Genotype List (GL) String, Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING), and Histoimmunogenetics Markup Language (HML) were proposed to streamline and standardize reporting of HLA genotypes. As part of the 17th International HLA and Immunogenetics Workshop (IHIW), we implemented standards and systems for HLA genotype reporting that included GL String, MIRING and HML, and found that misunderstanding or misinterpretations of these standards led to inconsistencies in the reporting of NGS HLA genotyping results. This may be due in part to a historical lack of centralized data reporting standards in the histocompatibility and immunogenetics community. We have worked with software and database developers, clinicians and scientists to address these issues in a collaborative fashion as part of the Data Standard Hackathons (DaSH) for NGS. Here we report several categories of challenges to the consistent exchange of NGS HLA genotyping data we have observed. We hope to address these challenges in future DaSH for NGS efforts.
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17
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Fukunaga K, Chinuki Y, Hamada Y, Fukutomi Y, Sugiyama A, Kishikawa R, Fukunaga A, Oda Y, Ugajin T, Yokozeki H, Harada N, Suehiro M, Hide M, Nakagawa Y, Noguchi E, Nakamura M, Matsunaga K, Yagami A, Morita E, Mushiroda T. Genome-wide association study reveals an association between the HLA-DPB1 ∗02:01:02 allele and wheat-dependent exercise-induced anaphylaxis. Am J Hum Genet 2021; 108:1540-1548. [PMID: 34246321 PMCID: PMC8387458 DOI: 10.1016/j.ajhg.2021.06.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/15/2021] [Indexed: 12/27/2022] Open
Abstract
Wheat-dependent exercise-induced anaphylaxis (WDEIA) is a life-threatening food allergy triggered by wheat in combination with the second factor such as exercise. The identification of potential genetic risk factors for this allergy might help high-risk individuals before consuming wheat-containing food. We aimed to identify genetic variants associated with WDEIA. A genome-wide association study was conducted in a discovery set of 77 individuals with WDEIA and 924 control subjects via three genetic models. The associations were confirmed in a replication set of 91 affected individuals and 435 control individuals. Summary statistics from the combined set were analyzed by meta-analysis with a random-effect model. In the discovery set, a locus on chromosome 6, rs9277630, was associated with WDEIA in the dominant model (OR = 3.95 [95% CI, 2.31-6.73], p = 7.87 × 10-8). The HLA-DPB1∗02:01:02 allele displayed the most significant association with WDEIA (OR = 4.51 [95% CI, 2.66-7.63], p = 2.28 × 10-9), as determined via HLA imputation following targeted sequencing. The association of the allele with WDEIA was confirmed in replication samples (OR = 3.82 [95% CI, 2.33-6.26], p = 3.03 × 10-8). A meta-analysis performed in the combined set revealed that the HLA-DPB1∗02:01:02 allele was significantly associated with an increased risk of WDEIA (OR = 4.13 [95% CI, 2.89-5.93], p = 1.06 × 10-14). Individuals carrying the HLA-DPB1∗02:01:02 allele have a significantly increased risk of WDEIA. Further validation of these findings in independent multiethnic cohorts is needed.
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Affiliation(s)
- Koya Fukunaga
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yuko Chinuki
- Department of Dermatology, Shimane University Faculty of Medicine, Shimane 693-0021, Japan
| | - Yuto Hamada
- Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital, Kanagawa 252-0392, Japan
| | - Yuma Fukutomi
- Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital, Kanagawa 252-0392, Japan
| | - Akiko Sugiyama
- Department of Allergology, National Hospital Organization Fukuoka National Hospital, Fukuoka 810-0062, Japan
| | - Reiko Kishikawa
- Department of Allergology, National Hospital Organization Fukuoka National Hospital, Fukuoka 810-0062, Japan
| | - Atsushi Fukunaga
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Yoshiko Oda
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Tsukasa Ugajin
- Department of Dermatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hiroo Yokozeki
- Department of Dermatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Naoe Harada
- Department of Dermatology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Masataka Suehiro
- Department of Dermatology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Michihiro Hide
- Department of Dermatology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Yukinobu Nakagawa
- Department of Dermatology, Course of Integrated Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Emiko Noguchi
- Department of Medical Genetics, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Masashi Nakamura
- Department of Integrative Medical Science for Allergic Disease, Fujita Health University School of Medicine, Nagoya 454-8509, Japan; General Research and Development Institute, Hoyu, Nagakute 454-8509, Japan
| | - Kayoko Matsunaga
- Department of Integrative Medical Science for Allergic Disease, Fujita Health University School of Medicine, Nagoya 454-8509, Japan
| | - Akiko Yagami
- Department of Allergology, Fujita Health University School of Medicine, Nagoya 454-8509, Japan; Fujita Health University General Allergy Center in Bantane Hospital, Nagoya 454-8509, Japan
| | - Eishin Morita
- Department of Dermatology, Shimane University Faculty of Medicine, Shimane 693-0021, Japan.
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
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18
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Relevance of Polymorphic KIR and HLA Class I Genes in NK-Cell-Based Immunotherapies for Adult Leukemic Patients. Cancers (Basel) 2021; 13:cancers13153767. [PMID: 34359667 PMCID: PMC8345033 DOI: 10.3390/cancers13153767] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Immunotherapies are promising approaches to curing different acute leukemias. Natural killer (NK) cells are lymphocytes that are efficient in the elimination of leukemic cells. NK-cell-based immunotherapies are particularly attractive, but the landscape of the heterogeneity of NK cells must be deciphered. This review provides an overview of the polymorphic KIR and HLA class I genes that modulate the NK cell repertoire and how these markers can improve the outcomes of patients with acute leukemia. A better knowledge of these genetic markers that are linked to NK cell subsets that are efficient against hematological diseases will optimize hematopoietic stem-cell donor selection and NK immunotherapy design. Abstract Since the mid-1990s, the biology and functions of natural killer (NK) cells have been deeply investigated in healthy individuals and in people with diseases. These effector cells play a particularly crucial role after allogeneic hematopoietic stem-cell transplantation (HSCT) through their graft-versus-leukemia (GvL) effect, which is mainly mediated through polymorphic killer-cell immunoglobulin-like receptors (KIRs) and their cognates, HLA class I ligands. In this review, we present how KIRs and HLA class I ligands modulate the structural formation and the functional education of NK cells. In particular, we decipher the current knowledge about the extent of KIR and HLA class I gene polymorphisms, as well as their expression, interaction, and functional impact on the KIR+ NK cell repertoire in a physiological context and in a leukemic context. In addition, we present the impact of NK cell alloreactivity on the outcomes of HSCT in adult patients with acute leukemia, as well as a description of genetic models of KIRs and NK cell reconstitution, with a focus on emergent T-cell-repleted haplo-identical HSCT using cyclosphosphamide post-grafting (haplo-PTCy). Then, we document how the immunogenetics of KIR/HLA and the immunobiology of NK cells could improve the relapse incidence after haplo-PTCy. Ultimately, we review the emerging NK-cell-based immunotherapies for leukemic patients in addition to HSCT.
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19
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Nygård L, Laine AP, Kiviniemi M, Toppari J, Härkönen T, Knip M, Veijola R, Lempainen J, Ilonen J. Tri-SNP polymorphism in the intron of HLA-DRA1 affects type 1 diabetes susceptibility in the Finnish population. Hum Immunol 2021; 82:912-916. [PMID: 34311991 DOI: 10.1016/j.humimm.2021.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/22/2021] [Accepted: 07/15/2021] [Indexed: 10/20/2022]
Abstract
Genes in the HLA class II region include the most important inherited risk factors for type 1 diabetes (T1D) although also polymorphisms outside the HLA region modulate the predisposition to T1D. This study set out to confirm a recent observation in which a novel expression quantitative trait locus was formed by three single nucleotide polymorphisms (SNP) in the intron of HLA-DRA1 in DR3-DQ2 haplotypes. The SNPs significantly increased the risk for T1D in DR3-DQ2 homozygous individuals and we intended to further explore this association, in the Finnish population, by comparing two DR3-DQ2 positive genotypes. Cohorts with DR3-DQ2/DR3-DQ2 (N = 570) and DR3-DQ2/DR1-DQ5 (N = 1035) genotypes were studied using TaqMan analysis that typed for rs3135394, rs9268645 and rs3129877. The tri-SNP haplotype was significantly more common in cases than controls in the DR3-DQ2/DR3-DQ2 cohort (OR = 1.70 CI 95% = 1.15-2.51P = 0.007). However, no significant associations could be observed in the DR3-DQ2/DR1-DQ5 cohort.
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Affiliation(s)
- Lucas Nygård
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland; Faculty of Science and Engineering, Cell Biology, Åbo Akademi, Turku, Finland
| | - Antti-Pekka Laine
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Minna Kiviniemi
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Jorma Toppari
- Department of Pediatrics, University of Turku and Turku University Hospital, Turku, Finland; Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, and Centre for Population Health Research, University of Turku, Turku, Finland
| | - Taina Härkönen
- Children's Hospital, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland; Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Mikael Knip
- Children's Hospital, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland; Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland; Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland; Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Riitta Veijola
- Department of Paediatrics, PEDEGO Research Unit, Medical Research Center, University of Oulu, Oulu, Finland
| | - Johanna Lempainen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland.
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20
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Creary LE, Sacchi N, Mazzocco M, Morris GP, Montero-Martin G, Chong W, Brown CJ, Dinou A, Stavropoulos-Giokas C, Gorodezky C, Narayan S, Periathiruvadi S, Thomas R, De Santis D, Pepperall J, ElGhazali GE, Al Yafei Z, Askar M, Tyagi S, Kanga U, Marino SR, Planelles D, Chang CJ, Fernández-Viña MA. High-resolution HLA allele and haplotype frequencies in several unrelated populations determined by next generation sequencing: 17th International HLA and Immunogenetics Workshop joint report. Hum Immunol 2021; 82:505-522. [PMID: 34030896 PMCID: PMC8315142 DOI: 10.1016/j.humimm.2021.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
The primary goal of the unrelated population HLA diversity (UPHD) component of the 17th International HLA and Immunogenetics Workshop was to characterize HLA alleles at maximum allelic-resolution in worldwide populations and re-evaluate patterns of HLA diversity across populations. The UPHD project included HLA genotype and sequence data, generated by various next-generation sequencing methods, from 4,240 individuals collated from 12 different countries. Population data included well-defined large datasets from the USA and smaller samples from Europe, Australia, and Western Asia. Allele and haplotype frequencies varied across populations from distant geographical regions. HLA genetic diversity estimated at 2- and 4-field allelic resolution revealed that diversity at the majority of loci, particularly for European-descent populations, was lower at the 2-field resolution. Several common alleles with identical protein sequences differing only by intronic substitutions were found in distinct haplotypes, revealing a more detailed characterization of linkage between variants within the HLA region. The examination of coding and non-coding nucleotide variation revealed many examples in which almost complete biunivocal relations between common alleles at different loci were observed resulting in higher linkage disequilibrium. Our reference data of HLA profiles characterized at maximum resolution from many populations is useful for anthropological studies, unrelated donor searches, transplantation, and disease association studies.
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Affiliation(s)
- Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA.
| | - Nicoletta Sacchi
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Michela Mazzocco
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Gonzalo Montero-Martin
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA
| | - Winnie Chong
- Histocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK
| | - Colin J Brown
- Department of Histocompatibility and Immunogenetics, NHS Blood and Transplant, London, UK; Faculty of Life Sciences and Medicine, King's College London, University of London, England, UK
| | - Amalia Dinou
- Biomedical Research Foundation Academy of Athens, Hellenic Cord Blood Bank, Athens, Greece
| | | | - Clara Gorodezky
- Laboratory of Immunology and Immunogenetics, Fundación Comparte Vida, A.C. Mexico City, Mexico
| | | | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, USA
| | | | - Jennifer Pepperall
- Welsh Transplant and Immunogenetics Laboratory, Welsh Blood Service, Pontyclun, United Kingdom
| | - Gehad E ElGhazali
- Sheikh Khalifa Medical City-Union 71, Abu Dhabi and the Department of Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Zain Al Yafei
- Sheikh Khalifa Medical City-Union 71, Abu Dhabi and the Department of Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical center, Dallas, USA
| | - Shweta Tyagi
- Department of Transplant Immunology and Immunogenetics, 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
| | - Susana R Marino
- Department of Pathology, The University of Chicago Medicine, Chicago, IL, USA
| | - Dolores Planelles
- Histocompatibility, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain; Grupo Español de Trabajo en Histocompatibilidad e Inmunología del Trasplante (GETHIT), Spanish Society for Immunology, Madrid, Spain
| | | | - 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.
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21
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Creary LE, Gangavarapu S, Caillier SJ, Cavalcante P, Frangiamore R, Lie BA, Bengtsson M, Harbo HF, Brauner S, Hollenbach JA, Oksenberg JR, Bernasconi P, Maniaol AH, Hammarström L, Mantegazza R, Fernández-Viña MA. Next-Generation Sequencing Identifies Extended HLA Class I and II Haplotypes Associated With Early-Onset and Late-Onset Myasthenia Gravis in Italian, Norwegian, and Swedish Populations. Front Immunol 2021; 12:667336. [PMID: 34163474 PMCID: PMC8215161 DOI: 10.3389/fimmu.2021.667336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/27/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic susceptibility to myasthenia gravis (MG) associates with specific HLA alleles and haplotypes at the class I and II regions in various populations. Previous studies have only examined alleles at a limited number of HLA loci that defined only broad serotypes or alleles defined at the protein sequence level. Consequently, genetic variants in noncoding and untranslated HLA gene segments have not been fully explored but could also be important determinants for MG. To gain further insight into the role of HLA in MG, we applied next-generation sequencing to analyze sequence variation at eleven HLA genes in early-onset (EO) and late-onset (LO) non-thymomatous MG patients positive for the acetylcholine receptor (AChR) antibodies and ethnically matched controls from Italy, Norway, and Sweden. For all three populations, alleles and haplotype blocks present on the ancestral haplotype AH8.1 were associated with risk in AChR-EOMG patients. HLA-B*08:01:01:01 was the dominant risk allele in Italians (OR = 3.28, P = 1.83E-05), Norwegians (OR = 3.52, P = 4.41E-16), and in Swedes HLA-B*08:01 was the primary risk allele (OR = 4.24, P <2.2E-16). Protective alleles and haplotype blocks were identified on the HLA-DRB7, and HLA-DRB13.1 class II haplotypes in Italians and Norwegians, whereas in Swedes HLA-DRB7 exhibited the main protective effect. For AChR-LOMG patients, the HLA-DRB15.1 haplotype and associated alleles were significantly associated with susceptibility in all groups. The HLA-DR13-HLA-DR-HLA-DQ haplotype was associated with protection in all AChR-LOMG groups. This study has confirmed and extended previous findings that the immunogenetic predisposition profiles for EOMG and LOMG are distinct. In addition, the results are consistent with a role for non-coding HLA genetic variants in the pathogenesis of MG.
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Affiliation(s)
- Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States.,Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Sridevi Gangavarapu
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Stacy J Caillier
- Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Paola Cavalcante
- Neurology IV Unit Neuroimmunology and Neuromuscular Diseases, Fondazione I.R.C.C.S Istituto Neurologico Carlo Besta (INCB), Milan, Italy
| | - Rita Frangiamore
- Neurology IV Unit Neuroimmunology and Neuromuscular Diseases, Fondazione I.R.C.C.S Istituto Neurologico Carlo Besta (INCB), Milan, Italy
| | - Benedicte A Lie
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Mats Bengtsson
- Department of Immunology, Genetics and Pathology (IGP), Rudbeck Laboratory, Uppsala University and University Hospital, Uppsala, Sweden
| | - Hanne Flinstad Harbo
- Department of Neurology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Susanna Brauner
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Jill A Hollenbach
- Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Jorge R Oksenberg
- Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Pia Bernasconi
- Neurology IV Unit Neuroimmunology and Neuromuscular Diseases, Fondazione I.R.C.C.S Istituto Neurologico Carlo Besta (INCB), Milan, Italy
| | | | - Lennart Hammarström
- The Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Renato Mantegazza
- Neurology IV Unit Neuroimmunology and Neuromuscular Diseases, Fondazione I.R.C.C.S Istituto Neurologico Carlo Besta (INCB), Milan, Italy.,Department of Clinical Research and Innovation, Fondazione I.R.C.C.S Istituto Neurologico Carlo Besta (INCB), Milan, Italy
| | - Marcelo A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States.,Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, United States
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22
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Osoegawa K, Creary LE, Montero-Martín G, Mallempati KC, Gangavarapu S, Caillier SJ, Santaniello A, Isobe N, Hollenbach JA, Hauser SL, Oksenberg JR, Fernández-Viňa MA. High Resolution Haplotype Analyses of Classical HLA Genes in Families With Multiple Sclerosis Highlights the Role of HLA-DP Alleles in Disease Susceptibility. Front Immunol 2021; 12:644838. [PMID: 34211458 PMCID: PMC8240666 DOI: 10.3389/fimmu.2021.644838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
Multiple sclerosis (MS) susceptibility shows strong genetic associations with HLA alleles and haplotypes. We genotyped 11 HLA genes in 477 non-Hispanic European MS patients and their 954 unaffected parents using a validated next-generation sequencing (NGS) methodology. HLA haplotypes were assigned unequivocally by tracing HLA allele transmissions. We explored HLA haplotype/allele associations with MS using the genotypic transmission disequilibrium test (gTDT) and multiallelic TDT (mTDT). We also conducted a case-control (CC) study with all patients and 2029 healthy unrelated ethnically matched controls. We performed separate analyses of 54 extended multi-case families by reviewing transmission of haplotype blocks. The haplotype fragment including DRB5*01:01:01~DRB1*15:01:01:01 was significantly associated with predisposition (gTDT: p < 2.20e-16; mTDT: p =1.61e-07; CC: p < 2.22e-16) as reported previously. A second risk allele, DPB1*104:01 (gTDT: p = 3.69e-03; mTDT: p = 2.99e-03; CC: p = 1.00e-02), independent from the haplotype bearing DRB1*15:01 was newly identified. The allele DRB1*01:01:01 showed significant protection (gTDT: p = 8.68e-06; mTDT: p = 4.50e-03; CC: p = 1.96e-06). Two DQB1 alleles, DQB1*03:01 (gTDT: p = 2.86e-03; mTDT: p = 5.56e-02; CC: p = 4.08e-05) and DQB1*03:03 (gTDT: p = 1.17e-02; mTDT: p = 1.16e-02; CC: p = 1.21e-02), defined at two-field level also showed protective effects. The HLA class I block, A*02:01:01:01~C*03:04:01:01~B*40:01:02 (gTDT: p = 5.86e-03; mTDT: p = 3.65e-02; CC: p = 9.69e-03) and the alleles B*27:05 (gTDT: p = 6.28e-04; mTDT: p = 2.15e-03; CC: p = 1.47e-02) and B*38:01 (gTDT: p = 3.20e-03; mTDT: p = 6.14e-03; CC: p = 1.70e-02) showed moderately protective effects independently from each other and from the class II associated factors. By comparing statistical significance of 11 HLA loci and 19 haplotype segments with both untruncated and two-field allele names, we precisely mapped MS candidate alleles/haplotypes while eliminating false signals resulting from 'hitchhiking' alleles. We assessed genetic burden for the HLA allele/haplotype identified in this study. This family-based study including the highest-resolution of HLA alleles proved to be powerful and efficient for precise identification of HLA genotypes associated with both, susceptibility and protection to development of MS.
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Affiliation(s)
- Kazutoyo Osoegawa
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Lisa E. Creary
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Gonzalo Montero-Martín
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Kalyan C. Mallempati
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Sridevi Gangavarapu
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Stacy J. Caillier
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Adam Santaniello
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Noriko Isobe
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Stephen L. Hauser
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jorge R. Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Marcelo A. Fernández-Viňa
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
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23
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Yin Y, Butler C, Zhang Q. Challenges in the application of NGS in the clinical laboratory. Hum Immunol 2021; 82:812-819. [PMID: 33892986 DOI: 10.1016/j.humimm.2021.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/25/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS), also known as massively parallel sequencing, has revolutionized genomic research. The current advances in NGS technology make it possible to provide high resolution, high throughput HLA typing in clinical laboratories. The focus of this review is on the recent development and implementation of NGS in clinical laboratories. Here, we examine the critical role of NGS technologies in clinical immunology for HLA genotyping. Two major NGS platforms (Illumina and Ion Torrent) are characterized including NGS library preparation, data analysis, and validation. Challenges of NGS implementation in the clinical laboratory are also discussed, including sequencing error rate, bioinformatics, result interpretation, analytic sensitivity, as well as large data storage. This review aims to promote the broader applications of NGS technology in clinical laboratories and advocate for the novel applications of NGS to drive future research.
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Affiliation(s)
- Yuxin Yin
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA
| | - Carrie Butler
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA
| | - Qiuheng Zhang
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA.
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24
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Qi J, Zhang R, Cai C, Wang H, Zhou M, Shen W, Tang Y, Pan T, Wu D, Han Y. HLA-DQB1 mismatch increase risk of severe bleeding independently in recipients of allogeneic stem cell transplant. Ann Hematol 2021; 100:2351-2361. [PMID: 33846855 DOI: 10.1007/s00277-021-04520-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 04/07/2021] [Indexed: 12/19/2022]
Abstract
Severe bleeding is a major cause of death in acute leukemia (AL) patients with graft-versus-host disease (GVHD) after allogene hematopoietic stem-cell transplantation (allo-HSCT). However, the prognostic value and prediction of HSCT-associated severe bleeding in GVHD patients have not been reported in cohort studies. We did a retrospective analysis of 200 AL patients with GVHD after allo-HSCT from Feb 1, 2014, to Dec 1, 2015. Multivariate analysis showed that the severe bleeding class was associated with the risk of death (HR 2.26, 95% CI 1.31-3.92, p<0.001***). In order to predict severe bleeding and figure out the solution to bleeding events, we established a multiple logistic regression model. HLA-DQB1 unmatching, megakaryocyte reconsititution failure, and III or IV GVHD were the independent risk factors for severe bleeding. Among all the variations above, OR of HLA-DQB1 was the highest (OR: 16.02, 95% CI: 11.54-48.68). Adding HLA-DQB1 to other factors improved the reclassification for predicting severe bleeding (NRI=0.195, z=2.634, p=0.008**; IDI=0.289, z=3.249, p<0.001***). Lasso regression was used to select variants. A nomogram of the logistic model was generated and displayed. Calibration curve demonstrated excellent accuracy in estimating severe bleeding (C index of 0.935). HLA-DQB1 showed excellent efficacy of predicting severe bleeding in HSCT patients.
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Affiliation(s)
- Jiaqian Qi
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, No.188 Shizi Street, Suzhou, 215000, China
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
- National Clinical Research Center for Hematologic Diseases, Suzhou, China
| | - Rui Zhang
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, No.188 Shizi Street, Suzhou, 215000, China
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Chengsen Cai
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, No.188 Shizi Street, Suzhou, 215000, China
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
- National Clinical Research Center for Hematologic Diseases, Suzhou, China
| | - Hong Wang
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, No.188 Shizi Street, Suzhou, 215000, China
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
- National Clinical Research Center for Hematologic Diseases, Suzhou, China
| | - Meng Zhou
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, No.188 Shizi Street, Suzhou, 215000, China
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
- National Clinical Research Center for Hematologic Diseases, Suzhou, China
| | - Wenhong Shen
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, No.188 Shizi Street, Suzhou, 215000, China
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
- National Clinical Research Center for Hematologic Diseases, Suzhou, China
| | - Yaqiong Tang
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, No.188 Shizi Street, Suzhou, 215000, China
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
- National Clinical Research Center for Hematologic Diseases, Suzhou, China
| | - Tingting Pan
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, No.188 Shizi Street, Suzhou, 215000, China
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Depei Wu
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, No.188 Shizi Street, Suzhou, 215000, China.
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
- Institute of Blood and Marrow Transplantation, Suzhou, China.
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China.
- National Clinical Research Center for Hematologic Diseases, Suzhou, China.
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China.
| | - Yue Han
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, No.188 Shizi Street, Suzhou, 215000, China.
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
- Institute of Blood and Marrow Transplantation, Suzhou, China.
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China.
- National Clinical Research Center for Hematologic Diseases, Suzhou, China.
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China.
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25
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Matern BM, Mack SJ, Osoegawa K, Maiers M, Niemann M, Robinson J, Heidt S, Spierings E. Standard reference sequences for submission of HLA genotyping for the 18th International HLA and Immunogenetics Workshop. HLA 2021; 97:512-519. [PMID: 33719220 PMCID: PMC8251737 DOI: 10.1111/tan.14259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/10/2021] [Indexed: 12/25/2022]
Abstract
The International human leukocyte antigen (HLA) and Immunogenetics Workshops (IHIWs) have fostered international collaborations of researchers and experts in the fields of HLA, histocompatibility and immunology. These IHIW collaborations have comprised many projects focused on achieving a variety of specific goals. The international and collaborative nature of these projects necessitates the collection and analysis of complex data generated in multiple laboratories, often using multiple methods of acquisition. Collection and storage of these data in a consistent way adds value to IHIW projects, which can be extended to future work. DNA‐based genotyping data, especially HLA genotyping data, can be transmitted in the form of a Histoimmunogenetics Markup Language (HML) document. HML facilitates clear communication of a genotype and supporting metadata, such as, sequencing platform, laboratory assays, consensus sequence, and interpretation. Sequence information can be reported relative to known reference sequences, which add meaning and context to genotypes. Selecting the correct reference sequence for a given allele sequence is nuanced, and guidelines have emerged through collaborative community efforts such as Data Standards Hackathons. Here, we describe the guidelines established for the selection of reference sequences to be used in transmission of HLA (and MICA/MICB) genotyping data for the 18th IHIW.
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Affiliation(s)
- Benedict M Matern
- Center of Translational Immunology, UMC Utrecht, Utrecht, the Netherlands
| | - Steven J Mack
- Department of Pediatrics, University of California, Oakland, California, USA
| | - Kazutoyo Osoegawa
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, California, USA
| | - Martin Maiers
- Bioinformatics, National Marrow Donor Program/Be The Match, Minneapolis, Minnesota, USA.,Bioinformatics, Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA
| | | | - James Robinson
- Anthony Nolan Research Institute, Royal Free Campus, London, UK.,UCL Cancer Institute, University College London (UCL), London, UK
| | - Sebastiaan Heidt
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric Spierings
- Center of Translational Immunology, UMC Utrecht, Utrecht, the Netherlands
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26
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Fernández Souto D, Rosello J, Lazo L, Veloso F, Gamba C, Kuperman S, Roca V. HLA diversity in the Argentinian Umbilical Cord Blood Bank: frequencies according to donor's reported ancestry and geographical distribution. Sci Rep 2021; 11:4140. [PMID: 33602993 PMCID: PMC7892815 DOI: 10.1038/s41598-021-83282-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/01/2021] [Indexed: 11/09/2022] Open
Abstract
Umbilical cord blood (UCB) is a suitable source for hematopoietic stem cell transplantation. The study of HLA genes by next generation sequencing is commonly used in transplants. Donor/patient HLA matching is often higher within groups of common ancestry, however "Hispanic" is a broad category that fails to represent Argentina's complex genetic admixture. Our aim is to describe HLA diversity of banked UCB units collected across the country taking into consideration donor's reported ancestral origins as well as geographic distribution. Our results showed an evenly distribution of units mainly for 2 groups: of European and of Native American descent, each associated to a defined geographic location pattern (Central vs. North regions). We observed differences in allele frequency distributions for some alleles previously described in Amerindian populations: for Class I (A*68:17, A*02:11:01G, A*02:22:01G, B*39:05:01, B*35:21, B*40:04, B*15:04:01G, B*35:04:01, B*51:13:01) and Class II (DRB1*04:11:01, DRB1*04:07:01G/03, DRB1*08:02:01, DRB1*08:07, DRB1*09:01:02G, DRB1*14:02:01, DRB1*16:02:01G). Our database expands the current knowledge of HLA diversity in Argentinian population. Although further studies are necessary to fully comprehend HLA heterogeneity, this report should prove useful to increase the possibility of finding compatible donors for successful allogeneic transplant and to improve recruitment strategies for UCB donors across the country.
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Affiliation(s)
- Daniela Fernández Souto
- Cord Blood Bank, Hemotherapy Regional Center, Hospital de Pediatría Dr.Juan P. Garrahan, Combate de los Pozos 1881, (1245), Buenos Aires, Argentina
| | - Julieta Rosello
- Cord Blood Bank, Hemotherapy Regional Center, Hospital de Pediatría Dr.Juan P. Garrahan, Combate de los Pozos 1881, (1245), Buenos Aires, Argentina
| | - Laura Lazo
- Cord Blood Bank, Hemotherapy Regional Center, Hospital de Pediatría Dr.Juan P. Garrahan, Combate de los Pozos 1881, (1245), Buenos Aires, Argentina
| | - Florencia Veloso
- Cord Blood Bank, Hemotherapy Regional Center, Hospital de Pediatría Dr.Juan P. Garrahan, Combate de los Pozos 1881, (1245), Buenos Aires, Argentina
| | - Cecilia Gamba
- Cord Blood Bank, Hemotherapy Regional Center, Hospital de Pediatría Dr.Juan P. Garrahan, Combate de los Pozos 1881, (1245), Buenos Aires, Argentina
| | - Silvina Kuperman
- Cord Blood Bank, Hemotherapy Regional Center, Hospital de Pediatría Dr.Juan P. Garrahan, Combate de los Pozos 1881, (1245), Buenos Aires, Argentina
| | - Valeria Roca
- Cord Blood Bank, Hemotherapy Regional Center, Hospital de Pediatría Dr.Juan P. Garrahan, Combate de los Pozos 1881, (1245), Buenos Aires, Argentina.
- National Research Council, Buenos Aires, Argentina.
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27
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Tao S, He Y, Wang F, He J, Zhu F. Identification of the novel HLA-A*02:837 and -A*02:888 alleles by next-generation sequencing in two Chinese individuals. HLA 2020; 97:345-349. [PMID: 33219630 DOI: 10.1111/tan.14144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/27/2022]
Abstract
Compared with HLA-A*02:06:01:01, HLA-A*02:837 and HLA-A*02:888 show one single nucleotide substitution respectively.
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Affiliation(s)
- Sudan Tao
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China.,HLA Typing Laboratory, Key Laboratory of Blood Safety Research, Zhejiang Province, Hangzhou, China
| | - Yanmin He
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China.,HLA Typing Laboratory, Key Laboratory of Blood Safety Research, Zhejiang Province, Hangzhou, China
| | - Fang Wang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China.,HLA Typing Laboratory, Key Laboratory of Blood Safety Research, Zhejiang Province, Hangzhou, China
| | - Ji He
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China.,HLA Typing Laboratory, Key Laboratory of Blood Safety Research, Zhejiang Province, Hangzhou, China
| | - Faming Zhu
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China.,HLA Typing Laboratory, Key Laboratory of Blood Safety Research, Zhejiang Province, Hangzhou, China
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28
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Abstract
A major problem in the analysis of vaccine candidates is the lack of any agreed upon surrogates of efficacy, which means that for diseases that depend on a strong T cell response (HIV, TB especially) the only option is to perform an efficacy trial, involving thousands of subjects, enormous costs, and years before the results are known [1]. We also know that T cell responses are an important part of most pathogen responses, and so identifying key T cell response metrics in early vaccine trials would be generally useful. Given our ignorance of what the most important variables are, what would we like to measure and how can this be accomplished, especially given the explosion of new technologies that are available? What follows is a consideration of what should be measured, with the caveat that some of these will be more important than others.
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Affiliation(s)
- Mark M Davis
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, United States; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, United States; Immunology Program, Stanford University School of Medicine, Stanford, CA, United States; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States.
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29
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Maloney EM, Busque VA, Hui ST, Toh J, Fernandez-Vina M, Krams SM, Esquivel CO, Martinez OM. Genomic variations in EBNA3C of EBV associate with posttransplant lymphoproliferative disorder. JCI Insight 2020; 5:131644. [PMID: 32213705 DOI: 10.1172/jci.insight.131644] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 02/26/2020] [Indexed: 01/22/2023] Open
Abstract
Epstein-Barr Virus (EBV) is a ubiquitous virus linked to a variety of lymphoid and epithelial malignancies. In solid organ and hematopoietic stem cell transplant recipients, EBV is causally associated with posttransplant lymphoproliferative disorder (PTLD), a group of heterogeneous lymphoid diseases. EBV+ B cell lymphomas that develop in the context of PTLD are generally attributed to the immunosuppression required to promote graft survival, but little is known regarding the role of EBV genome diversity in the development of malignancy. We deep-sequenced the EBV genome from the peripheral blood of 18 solid organ transplant recipients, including 6 PTLD patients. Sequences from 6 EBV+ spontaneous lymphoblastoid B cell lines (SLCL) were similarly analyzed. The EBV genome from PTLD patients had a significantly greater number of variations than EBV from transplant recipients without PTLD. Importantly, there were 15 nonsynonymous variations, including 8 in the latent cycle gene EBNA3C that were associated with the development of PTLD. One of the nonsynonymous variations in EBNA3C is located within a previously defined T cell epitope. These findings suggest that variations in the EBV genome can contribute to the pathogenesis of PTLD.
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Affiliation(s)
| | - Vincent A Busque
- Division of Abdominal Transplantation, Department of Surgery, and
| | - Sin Ting Hui
- Division of Abdominal Transplantation, Department of Surgery, and
| | | | - Marcelo Fernandez-Vina
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Sheri M Krams
- Stanford Immunology.,Division of Abdominal Transplantation, Department of Surgery, and
| | | | - Olivia M Martinez
- Stanford Immunology.,Division of Abdominal Transplantation, Department of Surgery, and
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30
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Marsh SGE. Nomenclature for factors of the HLA system, update October, November and December 2019. HLA 2020; 95:232-264. [PMID: 32037735 DOI: 10.1111/tan.13815] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
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31
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Vayntrub TA, Mack SJ, Fernandez-Viña MA. Preface: 17th International HLA and Immunogenetics Workshop. Hum Immunol 2020; 81:52-58. [PMID: 32051104 DOI: 10.1016/j.humimm.2020.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tamara A Vayntrub
- Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
| | - Steven J Mack
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA.
| | - Marcelo A Fernandez-Viña
- Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University Medical Center, Stanford, CA, USA.
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32
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Marsh SGE. Nomenclature for factors of the HLA system, update October, November and December 2019. Int J Immunogenet 2020; 47:190-225. [PMID: 32030885 DOI: 10.1111/iji.12478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
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33
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Barsakis K, Babrzadeh F, Chi A, Mallempati K, Pickle W, Mindrinos M, Fernández-Viña MA. Complete nucleotide sequence characterization of DRB5 alleles reveals a homogeneous allele group that is distinct from other DRB genes. Hum Immunol 2019; 80:437-448. [PMID: 30954494 PMCID: PMC6622178 DOI: 10.1016/j.humimm.2019.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/23/2019] [Accepted: 04/01/2019] [Indexed: 01/28/2023]
Abstract
Next Generation Sequencing allows for testing and typing of entire genes of the HLA region. A better and comprehensive sequence assessment can be achieved by the inclusion of full gene sequences of all the common alleles at a given locus. The common alleles of DRB5 are under-characterized with the full exon-intron sequence of two alleles available. In the present study the DRB5 genes from 18 subjects alleles were cloned and sequenced; haplotype analysis showed that 17 of them had a single copy of DRB5 and one consanguineous subject was homozygous at all HLA loci. Methodological approaches including robust and efficient long-range PCR amplification, molecular cloning, nucleotide sequencing and de novo sequence assembly were combined to characterize DRB5 alleles. DRB5 sequences covering from 5'UTR to the end of intron 5 were obtained for DRB5*01:01, 01:02 and 02:02; partial coverage including a segment spanning exon 2 to exon 6 was obtained for DRB5*01:03, 01:08N and 02:03. Phylogenetic analysis of the generated sequences showed that the DRB5 alleles group together and have distinctive differences with other DRB loci. Novel intron variants of DRB5*01:01:01, 01:02 and 02:02 were identified. The newly characterized DRB5 intron variants of each DRB5 allele were found in subjects harboring distinct associations with alleles of DRB1, B and/or ethnicity. The new information provided by this study provides reference sequences for HLA typing methodologies. Extending sequence coverage may lead to identify the disease susceptibility factors of DRB5 containing haplotypes while the unexpected intron variations may shed light on understanding of the evolution of the DRB region.
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Affiliation(s)
- Konstantinos Barsakis
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Biology, University of Crete, Heraklion, Crete 71003, Greece
| | - Farbod Babrzadeh
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Anjo Chi
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Kalyan Mallempati
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - William Pickle
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Michael Mindrinos
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
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