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Hurrell T, Naidoo J, Ntlhafu T, Scholefield J. An African perspective on genetically diverse human induced pluripotent stem cell lines. Nat Commun 2024; 15:8581. [PMID: 39362853 PMCID: PMC11450012 DOI: 10.1038/s41467-024-52781-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 09/16/2024] [Indexed: 10/05/2024] Open
Affiliation(s)
- Tracey Hurrell
- Bioengineering and Integrated Genomics Group, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Jerolen Naidoo
- Bioengineering and Integrated Genomics Group, Council for Scientific and Industrial Research, Pretoria, South Africa
- Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | - Tiro Ntlhafu
- Bioengineering and Integrated Genomics Group, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Janine Scholefield
- Bioengineering and Integrated Genomics Group, Council for Scientific and Industrial Research, Pretoria, South Africa.
- Department of Human Biology, University of Cape Town, Cape Town, South Africa.
- Division of Human Genetics, University of the Witwatersrand, Johannesburg, South Africa.
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2
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Lee JW, Chen EY, Hu T, Perret R, Chaffee ME, Martinov T, Mureli S, McCurdy CL, Jones LA, Gafken PR, Chanana P, Su Y, Chapuis AG, Bradley P, Schmitt TM, Greenberg PD. Overcoming immune evasion from post-translational modification of a mutant KRAS epitope to achieve TCR-engineered T cell-mediated antitumor activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.612965. [PMID: 39345486 PMCID: PMC11429761 DOI: 10.1101/2024.09.18.612965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
T cell receptor (TCR)-T cell immunotherapy, in which T cells are engineered to express a TCR specific for a tumor epitope, is a form of adoptive cell therapy (ACT) that has demonstrated promise against various tumor types. Mutants of oncoprotein KRAS, particularly at glycine-12 (G12), are frequent drivers of tumorigenicity, but also attractive targets for TCR-T cell therapy. However, MHC class I-restricted TCRs specifically targeting G12-mutant KRAS epitopes in the context of tumors expressing HLA-A2, the most common human HLA-A allele, have remained elusive despite evidence that an epitope encompassing the mutation can bind HLA-A2 and induce T cell responses. We report that post-translational modifications of the protein on this epitope may allow tumor cells to evade immunologic pressure from TCR-T cells. A lysine side chain-methylated KRAS G12V peptide, rather than unmodified epitope, may be presented in HLA-A2 by tumor cells and impact recognition by TCRs. Using a novel computationally guided approach to design TCRs, we developed by mutagenesis TCRs that recognize this methylated peptide, enhancing tumor recognition and destruction. Additionally, we identified TCRs with similar functional activity in normal repertoires from rare primary T cells by stimulation with modified peptide, clonal expansion, and selection. Mechanistically, a gene knockout screen to identify mechanism(s) by which tumor cells methylate or demethylate this epitope unveiled SPT6 as a demethylating protein that could be targeted to improve effectiveness of these TCRs. These findings highlight the role of post-translational modifications in immune evasion and suggest that identifying and targeting such modifications should facilitate development of more effective TCR-T cell therapies.
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3
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Escribá R, Beksac M, Bennaceur-Griscelli A, Glover JC, Koskela S, Latsoudis H, Querol S, Alvarez-Palomo B. Submission to Stem Cells Reviews and Reports. Stem Cell Rev Rep 2024:10.1007/s12015-024-10783-7. [PMID: 39276260 DOI: 10.1007/s12015-024-10783-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2024] [Indexed: 09/16/2024]
Abstract
The use of allogeneic induced pluripotent stem cell (iPSC)-derived cell therapies for regenerative medicine offers an affordable and realistic alternative to producing individual iPSC lines for each patient in need. Human Leukocyte Antigens (HLA)-homozygous iPSCs matched in hemi-similarity could provide cell therapies with reduced immune rejection covering a wide range of the population with a few iPSC lines. Several banks of HLA-homozygous iPSCs (haplobanks) have been established worldwide or are underway, to provide clinical grade starting material for cell therapies covering the most frequent HLA haplotypes for certain populations. Harmonizing quality standards among haplobanks and creating a global registry could minimize the collective effort and provide a much wider access to HLA-compatible cell therapies for patients with less frequent haplotypes. In this review we present all the current haplobank initiatives and their potential benefits for the global population.
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Affiliation(s)
- Rubén Escribá
- Cell Therapy Service, Banc de Sang I Teixits, 106 Passeig de Taulat, 08005, Barcelona, Spain
| | - Meral Beksac
- Ankara Liv Hospital Istinye University and Cord Blood Bank, Ankara University, Ankara, Turkey
| | - Annelise Bennaceur-Griscelli
- CiTHERA, Center of iPS Cell Therapy, Infrastructure INGESTEM University Paris Saclay Inserm U1310, 28 Rue Henri Desbruères, 91100, Corbeil-Essonnes, France
| | - Joel C Glover
- Norwegian Center for Stem Cell Research and Norwegian Core Facility for Human Pluripotent Stem Cells, Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Satu Koskela
- Finnish Red Cross Blood Service Biobank, Härkälenkki 13, 01730, Vantaa, Finland
| | - Helen Latsoudis
- Information Systems Laboratory, Institute of Computer Sciences, Foundation for Research and Technology Hellas, 70013, Heraklion, Crete, Greece
- Haemopoiesis Research Laboratory, School of Medicine, University of Crete, 71003, Heraklion, Crete, Greece
| | - Sergi Querol
- Cell Therapy Service, Banc de Sang I Teixits, 106 Passeig de Taulat, 08005, Barcelona, Spain
| | - Belén Alvarez-Palomo
- Cell Therapy Service, Banc de Sang I Teixits, 106 Passeig de Taulat, 08005, Barcelona, Spain.
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4
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Banjoko AW, Ng'uni T, Naidoo N, Ramsuran V, Hyrien O, Ndhlovu ZM. High Resolution Class I HLA -A, -B, and - C Diversity in Eastern and Southern African Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.611164. [PMID: 39282263 PMCID: PMC11398358 DOI: 10.1101/2024.09.04.611164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
Africa remains significantly underrepresented in high-resolution Human Leukocyte Antigen (HLA) data, despite being one of the most genetically diverse regions in the world. This critical gap in genetic information poses a substantial barrier to HLA-based research on the continent. In this study, Class I HLA data from Eastern and Southern African populations were analysed to assess genetic diversity across the region. We examined allele and haplotype frequency distributions, deviations from Hardy-Weinberg Equilibrium (HWE), linkage disequilibrium (LD), and conducted neutrality tests of homozygosity across various populations. Additionally, the African HLA data were compared to those of Caucasian and African American populations using the Jaccard index and multidimensional scaling (MDS) methods. The study revealed that South African populations exhibited 50.4% more genetic diversity within the Class I HLA region compared to other African populations. Zambia showed an estimated 36.5% genetic diversity, with Kenya, Rwanda and Uganda showing 35.7%, 34.2%, and 31.1%, respectively. Furthermore, an analysis of in-country diversity among different tribes indicated an average Class I HLA diversity of 25.7% in Kenya, 17% in Rwanda, 2.8% in South Africa, 13.6% in Uganda, and 6.5% in Zambia. The study also highlighted the genetic distinctness of Caucasian and African American populations compared to African populations. Notably, the differential frequencies of disease-promoting and disease-preventing HLA alleles across these populations emphasize the urgent need to generate high-quality HLA data for all regions of Africa and its major ethnic groups. Such efforts will be crucial in enhancing healthcare outcomes across the continent.
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Affiliation(s)
- Alabi W Banjoko
- Africa Health Research Institute (AHRI), Nelson R. Mandela School of Medicine, Durban, South Africa
- Department of Statistics, University of Ilorin, Kwara state, Nigeria
| | - Tiza Ng'uni
- Africa Health Research Institute (AHRI), Nelson R. Mandela School of Medicine, Durban, South Africa
| | - Nitalia Naidoo
- Africa Health Research Institute (AHRI), Nelson R. Mandela School of Medicine, Durban, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Olivier Hyrien
- Fred Hutchinson Cancer Center, Vaccine and Infectious Disease Division, Vaccine and Immunology Statistical Centre, Seattle, USA
| | - Zaza M Ndhlovu
- Africa Health Research Institute (AHRI), Nelson R. Mandela School of Medicine, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, United States
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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5
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Mirza A, Ali Qadri MM, Zeshan B, Hafiz K, Abbas S, Ahmad N, Iqbal M. HLA class-I polymorphisms among the Punjabi population of Pakistan: A comparative analysis with country's other ethnic groups. Hum Immunol 2024; 85:111083. [PMID: 39111186 DOI: 10.1016/j.humimm.2024.111083] [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: 09/23/2023] [Revised: 07/20/2024] [Accepted: 07/31/2024] [Indexed: 09/15/2024]
Abstract
The Punjabi population, constituting over 45 % of the country's total population, holds the highest prevalence in Pakistan. To understand their HLA genetics, we genotyped 389 Punjabi subjects for major Class-I loci using the PCR-SSO Luminex® method. Our study identified a total of 162 alleles, including 41 different HLA-A, 72 HLA-B, and 49 HLA-C alleles. The most common alleles included A*11:01 (14.6 %), A*01:01 (11.8 %), A*24:02 (11.3 %); B*40:06 (13.3 %), B*08:01 (10.9 %), B*51:01 (8.7 %); C*15:02 (15.5 %), C*07:02 (15.3 %), and C*04:01 (10.8 %). However, only locus B showed a significant deviation from HWE. The dominant Class I haplotype was A*24:02-B*40:06-C*15:02, followed by A*11:01-B*40:06-C*15:02, while significant LD was observed between all pairs of HLA loci. A distinct genetic makeup was observed in the Pakistani Punjabis as compared to Indian Punjabis, emphasizing the impact of the Indo-Pak partition and religious choices for marriage. In comparison to country's other ethnic groups, the Pakistani population exhibited 76 different alleles at a low field-resolution, with the Punjabi population having highest polymorphism. Phylogenetic analysis revealed that the Punjabi population is most closely related to the Sindhi population, while both populations sharing ancient connections with the Burusho population. These findings have significant implications for transplantation procedures, personalized medicine, disease susceptibility, and evolutionary studies.
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Affiliation(s)
- Aliza Mirza
- School of Medical Lab Technology, Minhaj University Lahore, Main Campus, 45770 Lahore, Pakistan
| | - Mian Mubeen Ali Qadri
- School of Medical Lab Technology, Minhaj University Lahore, Main Campus, 45770 Lahore, Pakistan.
| | - Basit Zeshan
- Faculty of Sustainable Agriculture, University Malaysia Sabah (Sandakan Campus), 9000 Sabah, Malaysia.
| | - Kashif Hafiz
- School of Medical Lab Technology, Minhaj University Lahore, Main Campus, 45770 Lahore, Pakistan
| | - Saba Abbas
- School of Medical Lab Technology, Minhaj University Lahore, Main Campus, 45770 Lahore, Pakistan
| | - Nabeel Ahmad
- Pakistan Kidney and Liver Institute (PKLI) and Research Center, One PKLI Avenue, Opposite DHA Phase 6, 54792 Lahore, Pakistan
| | - Maryam Iqbal
- School of Medical Lab Technology, Riphah International University, Gulberg III Campus, 25 Raza Saeed Rd, 54660 Lahore, Pakistan
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6
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Konno H, Miyamae J, Kataoka H, Akai M, Miida H, Tsuchiya Y. Dog leukocyte antigen genotyping across class I and class II genes in beagle dogs as laboratory animals. Immunogenetics 2024; 76:261-270. [PMID: 38922357 DOI: 10.1007/s00251-024-01344-w] [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: 03/06/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024]
Abstract
Dog leukocyte antigen (DLA) polymorphisms have been found to be associated with inter-individual variations in the risk, susceptibility, and severity of immune-related phenomena. While DLA class II genes have been extensively studied, less research has been performed on the polymorphisms of DLA class I genes, especially in beagle dogs commonly used as laboratory animals for safety evaluations in drug development. We genotyped four DLA class I genes and four DLA class II genes by locus-specific Sanger sequencing using 93 laboratory beagle dogs derived from two different strains: TOYO and Marshall. The results showed that, for DLA class I genes, 11, 4, 1, and 2 alleles, including a novel allele, were detected in DLA-88, DLA-12/88L, DLA-64, and DLA-79, while, for DLA class II genes, 1, 10, 6, and 7 alleles were detected in DLA-DRA, DLA-DRB1, DLA-DQA1, and DLA-DQB1, respectively. It was estimated that there were 14 DLA haplotypes, six of which had a frequency of ≥ 5%. Furthermore, when comparing the DLA diversity between TOYO and Marshall strains, the most common alleles and haplotypes differed between them. This is the first study to genotype all DLA loci and determine DLA haplotypes including all DLA class I and class II genes in dogs. Integrating information on the DLA diversity of laboratory beagle dogs should reinforce their benefit as an animal model for understanding various diseases associated with a specific DLA type.
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Affiliation(s)
- Hiroya Konno
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-16-13 Kita-Kasai, Edogawa-ku, Tokyo, 134-8630, Japan.
| | - Jiro Miyamae
- Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoino-oka, Imabari, Japan
| | - Hiroko Kataoka
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-16-13 Kita-Kasai, Edogawa-ku, Tokyo, 134-8630, Japan
| | - Makoto Akai
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-16-13 Kita-Kasai, Edogawa-ku, Tokyo, 134-8630, Japan
| | - Hiroaki Miida
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-16-13 Kita-Kasai, Edogawa-ku, Tokyo, 134-8630, Japan
| | - Yoshimi Tsuchiya
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-16-13 Kita-Kasai, Edogawa-ku, Tokyo, 134-8630, Japan
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7
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Kim SH, Españo E, Padasas BT, Son JH, Oh J, Webby RJ, Lee YR, Park CS, Kim JK. Influenza Virus-Derived CD8 T Cell Epitopes: Implications for the Development of Universal Influenza Vaccines. Immune Netw 2024; 24:e19. [PMID: 38974213 PMCID: PMC11224667 DOI: 10.4110/in.2024.24.e19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 07/09/2024] Open
Abstract
The influenza virus poses a global health burden. Currently, an annual vaccine is used to reduce influenza virus-associated morbidity and mortality. Most influenza vaccines have been developed to elicit neutralizing Abs against influenza virus. These Abs primarily target immunodominant epitopes derived from hemagglutinin (HA) or neuraminidase (NA) of the influenza virus incorporated in vaccines. However, HA and NA are highly variable proteins that are prone to antigenic changes, which can reduce vaccine efficacy. Therefore, it is essential to develop universal vaccines that target immunodominant epitopes derived from conserved regions of the influenza virus, enabling cross-protection among different virus variants. The internal proteins of the influenza virus serve as ideal targets for universal vaccines. These internal proteins are presented by MHC class I molecules on Ag-presenting cells, such as dendritic cells, and recognized by CD8 T cells, which elicit CD8 T cell responses, reducing the likelihood of disease and influenza viral spread by inducing virus-infected cell apoptosis. In this review, we highlight the importance of CD8 T cell-mediated immunity against influenza viruses and that of viral epitopes for developing CD8 T cell-based influenza vaccines.
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Affiliation(s)
- Sang-Hyun Kim
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
- Department of Pharmaceutics, College of Pharmacy, Chungbuk National University, Cheongju 28644, Korea
| | - Erica Españo
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
| | | | - Ju-Ho Son
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
| | - Jihee Oh
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38195, USA
| | - Young-Ran Lee
- Bio-Convergence R&D Division, Korea Institute of Ceramic Engineering and Technology, Cheongju 28160, Korea
| | - Chan-Su Park
- Department of Pharmaceutics, College of Pharmacy, Chungbuk National University, Cheongju 28644, Korea
| | - Jeong-Ki Kim
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
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8
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Sanchez-Mazas A, Nunes JM. The most frequent HLA alleles around the world: A fundamental synopsis. Best Pract Res Clin Haematol 2024; 37:101559. [PMID: 39098805 DOI: 10.1016/j.beha.2024.101559] [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: 04/23/2024] [Revised: 06/10/2024] [Accepted: 06/27/2024] [Indexed: 08/06/2024]
Abstract
A comprehensive knowledge of human leukocyte antigen (HLA) molecular variation worldwide is essential in human population genetics research and disease association studies and is also indispensable for clinical applications such as allogeneic hematopoietic cell transplantation, where ensuring HLA compatibility between donors and recipients is paramount. Enormous progress has been made in this field thanks to several decades of HLA population studies allowing the development of helpful databases and bioinformatics tools. However, it is still difficult to appraise the global HLA population diversity in a synthetic way. We thus introduce here a novel approach, based on approximately 2000 data sets, to assess this complexity by providing a fundamental synopsis of the most frequent HLA alleles observed in different regions of the world. This new knowledge will be useful not only as a fundamental reference for basic research, but also as an efficient guide for clinicians working in the field of transplantation.
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Affiliation(s)
- Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History (AGP), Department of Genetics and Evolution & Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, 30 Quai Ernest-Ansermet, 1205, Geneva, Switzerland.
| | - José Manuel Nunes
- Laboratory of Anthropology, Genetics and Peopling History (AGP), Department of Genetics and Evolution & Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, 30 Quai Ernest-Ansermet, 1205, Geneva, Switzerland.
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9
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Roush SM, Coelho J, Xu AM, Puranam K, Mponda M, Kasonkanji E, Mulenga M, Tomoka T, Galeotti J, Brownlee A, Ghadially H, Chagomerana M, Damania B, Painschab M, Merchant A, Gopal S, Fedoriw Y. HIV infection and ART exposure affect tumor TCR repertoire of diffuse large B cell lymphoma. JCI Insight 2024; 9:e180771. [PMID: 38781015 PMCID: PMC11383373 DOI: 10.1172/jci.insight.180771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024] Open
Abstract
The most common subtype of lymphoma globally, diffuse large B cell lymphoma (DLBCL), is a leading cause of cancer death in people with HIV. The restructuring of the T cell compartment because of HIV infection and antiretroviral therapy (ART) may have implications for modern treatment selection, but current understanding of these dynamic interactions is limited. Here, we investigated the T cell response to DLBCL by sequencing the T cell receptor (TCR) repertoire in a cohort of HIV-negative (HIV-), HIV+/ART-experienced, and HIV+/ART-naive patients with DLBCL. HIV+/ART-naive tumor TCR repertoires were more clonal and more distinct from each other than HIV- and HIV+/ART-experienced ones. Further, increased overlap between tumor and blood TCR repertoires was associated with improved survival and HIV/ART status. Our study describes TCR repertoire characteristics for the first time to our knowledge in an African DLBCL cohort and demonstrates contributions of HIV infection and ART exposure to the DLBCL TCR repertoire.
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Affiliation(s)
- Sophia M Roush
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jenny Coelho
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alexander M Xu
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Kaushik Puranam
- University of North Carolina Project Malawi, Lilongwe, Malawi
| | - Marriam Mponda
- University of North Carolina Project Malawi, Lilongwe, Malawi
- University of Malawi College of Medicine, Lilongwe, Malawi
| | - Edwards Kasonkanji
- University of North Carolina Project Malawi, Lilongwe, Malawi
- University of Malawi College of Medicine, Lilongwe, Malawi
| | - Maurice Mulenga
- University of North Carolina Project Malawi, Lilongwe, Malawi
- University of Malawi College of Medicine, Lilongwe, Malawi
| | - Tamiwe Tomoka
- University of North Carolina Project Malawi, Lilongwe, Malawi
- University of Malawi College of Medicine, Lilongwe, Malawi
| | - Jonathan Galeotti
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Amy Brownlee
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Hormas Ghadially
- Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Lilongwe, Malawi
| | - Maganizo Chagomerana
- University of North Carolina Project Malawi, Lilongwe, Malawi
- University of Malawi College of Medicine, Lilongwe, Malawi
| | - Blossom Damania
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology and
| | - Matthew Painschab
- University of North Carolina Project Malawi, Lilongwe, Malawi
- University of Malawi College of Medicine, Lilongwe, Malawi
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
- Division of Hematology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Akil Merchant
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Division of Hematology and Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Satish Gopal
- National Cancer Institute Center for Global Health, Rockville, Maryland, USA
| | - Yuri Fedoriw
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
- University of North Carolina Project Malawi, Lilongwe, Malawi
- University of Malawi College of Medicine, Lilongwe, Malawi
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
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10
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Machraoui S, Errafii K, Oujamaa I, Belghali MY, Hakmaoui A, Lamjadli S, Eddehbi FE, Brahim I, Haida Y, Admou B. Frequency of the Main Human Leukocyte Antigen A, B, DR, and DQ Loci Known to Be Associated with the Clearance or Persistence of Hepatitis C Virus Infection in a Healthy Population from the Southern Region of Morocco: A Preliminary Study. Diseases 2024; 12:106. [PMID: 38785761 PMCID: PMC11120154 DOI: 10.3390/diseases12050106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 05/25/2024] Open
Abstract
Hepatitis C Virus (HCV) infection represents a significant global health challenge, with its natural course largely influenced by the host's immune response. Human Leukocyte Antigen (HLA) molecules, particularly HLA class I and II, play a crucial role in the adaptive immune response against HCV. The polymorphism of HLA molecules contributes to the variability in immune response, affecting the outcomes of HCV infection. This study aims to investigate the frequency of HLA A, B, DR, and DQ alleles known to be associated with HCV clearance or persistence in a healthy Moroccan population. Conducted at the University Hospital Center Mohammed VI, Marrakech, this study spanned from 2015 to 2022 and included 703 healthy Moroccan individuals. HLA class I and II typing was performed using complement-dependent cytotoxicity and polymerase chain reaction-based methodologies. The results revealed the distinct patterns of HLA-A, B, DRB1, and DQB1 alleles in the Moroccan population. Notably, alleles linked to favorable HCV outcomes, such as HLA-DQB1*0301, DQB1*0501, and DRB1*1101, were more prevalent. Conversely, alleles associated with increased HCV susceptibility and persistence, such as HLA-DQB1*02 and DRB1*03, were also prominent. Gender-specific variations in allele frequencies were observed, providing insights into genetic influences on HCV infection outcomes. The findings align with global trends in HLA allele associations with HCV infection outcomes. The study emphasizes the role of host genetics in HCV infection, highlighting the need for further research in the Moroccan community, including HCV-infected individuals. The prevalence of certain HLA alleles, both protective and susceptibility-linked, underscores the potential for a national HLA data bank in Morocco.
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Affiliation(s)
- Safa Machraoui
- Laboratory of Immunology and HLA, Center of Clinical Research, Mohammed VI University Hospital, Marrakech 40080, Morocco; (I.O.); (A.H.); (S.L.); (F.E.E.); (I.B.); (Y.H.); (B.A.)
- Biosciences Research Laboratory, Faculty of Medicine and Pharmacy, Cadi Ayyad University, Marrakech 40080, Morocco
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Ben Guerir 43151, Morocco;
| | - Khaoula Errafii
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Ben Guerir 43151, Morocco;
| | - Ider Oujamaa
- Laboratory of Immunology and HLA, Center of Clinical Research, Mohammed VI University Hospital, Marrakech 40080, Morocco; (I.O.); (A.H.); (S.L.); (F.E.E.); (I.B.); (Y.H.); (B.A.)
| | - Moulay Yassine Belghali
- Department of Biology, Faculty of Sciences Dhar El Mahraz, Sidi Mohammed Ben Abdellah University, Fez 30003, Morocco;
| | - Abdelmalek Hakmaoui
- Laboratory of Immunology and HLA, Center of Clinical Research, Mohammed VI University Hospital, Marrakech 40080, Morocco; (I.O.); (A.H.); (S.L.); (F.E.E.); (I.B.); (Y.H.); (B.A.)
| | - Saad Lamjadli
- Laboratory of Immunology and HLA, Center of Clinical Research, Mohammed VI University Hospital, Marrakech 40080, Morocco; (I.O.); (A.H.); (S.L.); (F.E.E.); (I.B.); (Y.H.); (B.A.)
| | - Fatima Ezzohra Eddehbi
- Laboratory of Immunology and HLA, Center of Clinical Research, Mohammed VI University Hospital, Marrakech 40080, Morocco; (I.O.); (A.H.); (S.L.); (F.E.E.); (I.B.); (Y.H.); (B.A.)
| | - Ikram Brahim
- Laboratory of Immunology and HLA, Center of Clinical Research, Mohammed VI University Hospital, Marrakech 40080, Morocco; (I.O.); (A.H.); (S.L.); (F.E.E.); (I.B.); (Y.H.); (B.A.)
| | - Yasmine Haida
- Laboratory of Immunology and HLA, Center of Clinical Research, Mohammed VI University Hospital, Marrakech 40080, Morocco; (I.O.); (A.H.); (S.L.); (F.E.E.); (I.B.); (Y.H.); (B.A.)
| | - Brahim Admou
- Laboratory of Immunology and HLA, Center of Clinical Research, Mohammed VI University Hospital, Marrakech 40080, Morocco; (I.O.); (A.H.); (S.L.); (F.E.E.); (I.B.); (Y.H.); (B.A.)
- Biosciences Research Laboratory, Faculty of Medicine and Pharmacy, Cadi Ayyad University, Marrakech 40080, Morocco
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11
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Yu SC, Lin ME. Kikuchi disease in acute leukaemia: a distinct clinical syndrome with HLA association. Histopathology 2024; 84:1003-1012. [PMID: 38275182 DOI: 10.1111/his.15145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/23/2023] [Accepted: 01/06/2024] [Indexed: 01/27/2024]
Abstract
AIMS To report the clinicopathological features of Kikuchi disease in patients with acute leukaemia, emphasising similarities among cases. METHODS AND RESULTS In a cohort of 454 Kikuchi disease patients, we identified three cases of concurrent acute leukaemia. These patients shared similar clinical traits, with Kikuchi disease emerging approximately a month after induction chemotherapy onset, featuring neck-region lymphadenopathy. Notably, two patients were middle-aged, deviating from the typical age distribution of Kikuchi disease. Histologically, these cases aligned with typical Kikuchi disease. Negative immunohistochemical stains (CD34, CD117, ERG, TdT) indicated the absence of extramedullary leukaemic infiltration. Herpes simplex virus immunohistochemical staining was also negative. Significantly, a human leucocyte antigen (HLA) association was observed in these three cases. HLA-B*15:01, C*04:01, and DRB1*04:06 were more prevalent in these patients compared to the general population (compared with three independent control cohorts: Taiwanese Han Chinese (n = 504), Tzu Chi Taiwanese bone marrow donors (n = 364) and Hong Kong Chinese (n = 5266)). CONCLUSIONS Our study underscores the unique link between Kikuchi disease and acute leukaemia, characterised by specific features and HLA associations. This underlines Kikuchi disease as a possible differential diagnosis in pertinent clinical scenarios. Furthermore, this syndrome offers insights into postchemotherapy immunology in acute leukaemia, enhancing comprehension.
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Affiliation(s)
- Shan-Chi Yu
- Department of Pathology and Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming-En Lin
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
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12
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Slieker RC, Warmerdam DO, Vermeer MH, van Doorn R, Heemskerk MHM, Scheeren FA. Reassessing human MHC-I genetic diversity in T cell studies. Sci Rep 2024; 14:7966. [PMID: 38575727 PMCID: PMC10995142 DOI: 10.1038/s41598-024-58777-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/03/2024] [Indexed: 04/06/2024] Open
Abstract
The Major Histocompatibility Complex class I (MHC-I) system plays a vital role in immune responses by presenting antigens to T cells. Allele specific technologies, including recombinant MHC-I technologies, have been extensively used in T cell analyses for COVID-19 patients and are currently used in the development of immunotherapies for cancer. However, the immense diversity of MHC-I alleles presents challenges. The genetic diversity serves as the foundation of personalized medicine, yet it also poses a potential risk of exacerbating healthcare disparities based on MHC-I alleles. To assess potential biases, we analysed (pre)clinical publications focusing on COVID-19 studies and T cell receptor (TCR)-based clinical trials. Our findings reveal an underrepresentation of MHC-I alleles associated with Asian, Australian, and African descent. Ensuring diverse representation is vital for advancing personalized medicine and global healthcare equity, transcending genetic diversity. Addressing this disparity is essential to unlock the full potential of T cells for enhancing diagnosis and treatment across all individuals.
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Affiliation(s)
- Roderick C Slieker
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniël O Warmerdam
- Centre for Future Affordable & Sustainable Therapy Development (FAST), The Hague, The Netherlands
| | - Maarten H Vermeer
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Dermatology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ferenc A Scheeren
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands.
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13
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Yin R, Melton S, Huseby ES, Kardar M, Chakraborty AK. How persistent infection overcomes peripheral tolerance mechanisms to cause T cell-mediated autoimmune disease. Proc Natl Acad Sci U S A 2024; 121:e2318599121. [PMID: 38446856 PMCID: PMC10945823 DOI: 10.1073/pnas.2318599121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024] Open
Abstract
T cells help orchestrate immune responses to pathogens, and their aberrant regulation can trigger autoimmunity. Recent studies highlight that a threshold number of T cells (a quorum) must be activated in a tissue to mount a functional immune response. These collective effects allow the T cell repertoire to respond to pathogens while suppressing autoimmunity due to circulating autoreactive T cells. Our computational studies show that increasing numbers of pathogenic peptides targeted by T cells during persistent or severe viral infections increase the probability of activating T cells that are weakly reactive to self-antigens (molecular mimicry). These T cells are easily re-activated by the self-antigens and contribute to exceeding the quorum threshold required to mount autoimmune responses. Rare peptides that activate many T cells are sampled more readily during severe/persistent infections than in acute infections, which amplifies these effects. Experiments in mice to test predictions from these mechanistic insights are suggested.
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Affiliation(s)
- Rose Yin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Samuel Melton
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Eric S. Huseby
- Basic Pathology, Department of Pathology, University of Massachusetts Medical School, Worcester, MA01655
| | - Mehran Kardar
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Arup K. Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
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14
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Marzouka NAD, Alnaqbi H, Al-Aamri A, Tay G, Alsafar H. Investigating the genetic makeup of the major histocompatibility complex (MHC) in the United Arab Emirates population through next-generation sequencing. Sci Rep 2024; 14:3392. [PMID: 38337023 PMCID: PMC10858242 DOI: 10.1038/s41598-024-53986-1] [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: 11/26/2023] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
The Human leukocyte antigen (HLA) molecules are central to immune response and have associations with the phenotypes of various diseases and induced drug toxicity. Further, the role of HLA molecules in presenting antigens significantly affects the transplantation outcome. The objective of this study was to examine the extent of the diversity of HLA alleles in the population of the United Arab Emirates (UAE) using Next-Generation Sequencing methodologies and encompassing a larger cohort of individuals. A cohort of 570 unrelated healthy citizens of the UAE volunteered to provide samples for Whole Genome Sequencing and Whole Exome Sequencing. The definition of the HLA alleles was achieved through the application of the bioinformatics tools, HLA-LA and xHLA. Subsequently, the findings from this study were compared with other local and international datasets. A broad range of HLA alleles in the UAE population, of which some were previously unreported, was identified. A comparison with other populations confirmed the current population's unique intertwined genetic heritage while highlighting similarities with populations from the Middle East region. Some disease-associated HLA alleles were detected at a frequency of > 5%, such as HLA-B*51:01, HLA-DRB1*03:01, HLA-DRB1*15:01, and HLA-DQB1*02:01. The increase in allele homozygosity, especially for HLA class I genes, was identified in samples with a higher level of genome-wide homozygosity. This highlights a possible effect of consanguinity on the HLA homozygosity. The HLA allele distribution in the UAE population showcases a unique profile, underscoring the need for tailored databases for traditional activities such as unrelated transplant matching and for newer initiatives in precision medicine based on specific populations. This research is part of a concerted effort to improve the knowledge base, particularly in the fields of transplant medicine and investigating disease associations as well as in understanding human migration patterns within the Arabian Peninsula and surrounding regions.
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Affiliation(s)
- Nour Al Dain Marzouka
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Halima Alnaqbi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Amira Al-Aamri
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan Tay
- Division of Psychiatry, Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
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15
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Rollin FG, Abaza S. The Careful Use of Racial Categories in Genetic Studies of Liver Injury. Am J Gastroenterol 2024; 119:391-392. [PMID: 38305249 DOI: 10.14309/ajg.0000000000002513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Affiliation(s)
- Francois G Rollin
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Suhaib Abaza
- Department of Emergency Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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16
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Elston DM. Letter from the Editor: Ensuring appropriate diversity in clinical trials. J Am Acad Dermatol 2024:S0190-9622(23)03397-2. [PMID: 38185253 DOI: 10.1016/j.jaad.2023.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Affiliation(s)
- Dirk M Elston
- Department of Dermatology and Dermatologic Surgery Medical University of South California, Charleston, South Carolina.
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17
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Shiina T, Kulski JK. HLA Genetics for the Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:237-258. [PMID: 38467984 DOI: 10.1007/978-981-99-9781-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Highly polymorphic human leukocyte antigen (HLA) molecules (alleles) expressed by different classical HLA class I and class II genes have crucial roles in the regulation of innate and adaptive immune responses, transplant rejection and in the pathogenesis of numerous infectious and autoimmune diseases. To date, over 35,000 HLA alleles have been published from the IPD-IMGT/HLA database, and specific HLA alleles and HLA haplotypes have been reported to be associated with more than 100 different diseases and phenotypes. Next generation sequencing (NGS) technology developed in recent years has provided breakthroughs in various HLA genomic/gene studies and transplant medicine. In this chapter, we review the current information on the HLA genomic structure and polymorphisms, as well as the genetic context in which numerous disease associations have been identified in this region.
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Affiliation(s)
| | - Jerzy K Kulski
- Tokai University School of Medicine, Isehara, Japan
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
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18
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Espada E, Ligeiro D, Trindade H, Lacerda JF. HLA frequency distribution of the Portuguese bone marrow donor registry. Front Immunol 2023; 14:1286001. [PMID: 38149254 PMCID: PMC10749969 DOI: 10.3389/fimmu.2023.1286001] [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: 08/30/2023] [Accepted: 11/22/2023] [Indexed: 12/28/2023] Open
Abstract
Introduction The Portuguese donor Registry of CEDACE was the fifth largest per capita bone marrow donor Registry of the WMDA as of 2019 and has yet to be thoroughly analyzed. We aimed to characterize its various aspects, including demographics and HLA allele and haplotype frequencies, to evaluate the genetic matching propensity score and ultimately further develop it. Methods We described and compared characteristics of the donor population with census data and used an Expectation-Maximization algorithm and analyses of molecular variance to assess haplotype frequencies and establish phylogenetic distances between regions and districts within the country. Results We identified 396545 donors, corresponding to 3.85% of the Portuguese population; the median donor age was 39 years, with 60.4% of female donors. Most donors were Portuguese nationals, although 40 other nationalities were present, with a significant proportion of donors from Brazil and Portuguese-speaking African Countries; almost all donors self-reported as Western, with the second largest group reporting African ancestry. There was an asymmetric contribution of donors from different districts and regions, with most coming from coastal districts and few from the southern districts and autonomous regions; foreign and self-declared non-Western donors were mainly located in the Metropolitan Area of Lisbon and the South. Although most donors were typed in three loci (HLA-A, HLA-B and HLA-DRB1), only 44% were also typed in HLA-C, 1.28% in HLA-DQB1 and only 0.77% in all five loci and in high-resolution. There were varying allele and haplotype frequencies across districts and regions, with the most common three loci, low-resolution haplotypes, being HLA-A*01~B*08~DRB1*03, A*29~B*44~DRB1*07 and HLA-A*02~B*44~DRB1*04; some haplotypes were more prevalent in the South, others in the North and a few in the autonomous regions; African and foreign donors presented relevant differences in haplotype frequency distributions, including rare haplotypes of potential interest. We also report on four loci, low-resolution frequency distributions. Using AMOVA, we compared genetic distances between districts and regions, which recapitulated the country's geography. Discussion Our analysis showed potential paths to optimization of the Registry, including increasing the male donor pool and focusing on underrepresented districts and particular populations of interest, such as donors from Portuguese-speaking African countries.
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Affiliation(s)
- Eduardo Espada
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Serviço de Hematologia e Transplantação de Medula, Hospital de Santa Maria, Centro Hospitalar Universitário de Lisboa Norte, EPE, Lisbon, Portugal
| | - Dário Ligeiro
- Centro de Sangue e Transplantação de Lisboa, Instituto Português do Sangue e da Transplantação, IP, Lisbon, Portugal
- Immunosurgery Unit, Centro Clínico Champalimaud, Lisbon, Portugal
| | - Hélder Trindade
- Centro de Sangue e Transplantação de Lisboa, Instituto Português do Sangue e da Transplantação, IP, Lisbon, Portugal
| | - João F. Lacerda
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Serviço de Hematologia e Transplantação de Medula, Hospital de Santa Maria, Centro Hospitalar Universitário de Lisboa Norte, EPE, Lisbon, Portugal
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19
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Al-Mendalawi MD. A call to establish HLA registry in Iraq. J Taibah Univ Med Sci 2023; 18:1507-1508. [PMID: 37693818 PMCID: PMC10482738 DOI: 10.1016/j.jtumed.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 07/22/2023] [Indexed: 09/12/2023] Open
Affiliation(s)
- Mahmood D. Al-Mendalawi
- Pediatrics and Child Health, Consultant Paediatrician, Department of Paediatrics, Al-Kindy College of Medicine, University of Baghdad, Baghdad, Iraq
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20
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Mrazek F. Population genetics and external proficiency testing for HLA disease associations. Front Genet 2023; 14:1268705. [PMID: 37937194 PMCID: PMC10626483 DOI: 10.3389/fgene.2023.1268705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/12/2023] [Indexed: 11/09/2023] Open
Abstract
Numerous associations of HLA variants with susceptibility to diseases, namely, those with an immunopathological component, have been described to date. The strongest HLA associations were incorporated into the standard algorithms for the diagnostics. Disease-associated HLA variants are routinely detected by various techniques including DNA-based assays. For the identification of HLA markers or their combinations with the highest diagnostic value and those with frequent clinical indications (e.g., HLA-B*27, -B*57:01, -DQ2/-DQ8, -DQB1*06:02), diagnostic tests that focus on a single or limited number of specific HLA antigens/alleles, have already been developed; the use of complete typing for particular HLA loci is a relevant alternative. Importantly, external proficiency testing (EPT) became an integral part of good laboratory practice for HLA disease associations in accredited laboratories and not only supports correct "technical" identification of the associated HLA variants, but also adequate interpretation of the results to the clinicians. In the present article selected aspects of EPT for HLA disease associations related to population genetics are reviewed and discussed with the emphasis on the optimal level of HLA typing resolution, population-based differences in disease associated HLA alleles within the allelic group, distribution and linkage disequilibrium of HLA alleles in particular populations and interpretation of the presence of less common HLA variants/haplotypes. In conclusion, the laboratories that perform and interpret the tests to the clinicians, producers of the certified diagnostics and EPT providers should consider, among others, the genetic characteristics of the populations in order to optimise the diagnostic value of the tests for disease-associated HLA variants.
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Affiliation(s)
- Frantisek Mrazek
- HLA laboratory, Department of Immunology, University Hospital, Olomouc, Czechia
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