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Arumugam T, Adimulam T, Gokul A, Ramsuran V. Variation within the non-coding genome influences genetic and epigenetic regulation of the human leukocyte antigen genes. Front Immunol 2024; 15:1422834. [PMID: 39355248 PMCID: PMC11442197 DOI: 10.3389/fimmu.2024.1422834] [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: 04/24/2024] [Accepted: 08/26/2024] [Indexed: 10/03/2024] Open
Abstract
Variation within the non-coding genome may influence the regulation and expression of important genes involved in immune control such as the human leukocyte antigen (HLA) system. Class I and Class II HLA molecules are essential for peptide presentation which is required for T lymphocyte activation. Single nucleotide polymorphisms within non-coding regions of HLA Class I and Class II genes may influence the expression of these genes by affecting the binding of transcription factors and chromatin modeling molecules. Furthermore, an interplay between genetic and epigenetic factors may also influence HLA expression. Epigenetic factors such as DNA methylation and non-coding RNA, regulate gene expression without changing the DNA sequence. However, genetic variation may promote or allow genes to escape regulation by epigenetic factors, resulting in altered expression. The HLA system is central to most diseases, therefore, understanding the role of genetics and epigenetics on HLA regulation will tremendously impact healthcare. The knowledge gained from these studies may lead to novel and cost-effective diagnostic approaches and therapeutic interventions. This review discusses the role of non-coding variants on HLA regulation. Furthermore, we discuss the interplay between genetic and epigenetic factors on the regulation of HLA by evaluating literature based on polymorphisms within DNA methylation and miRNA regulatory sites within class I and Class II HLA genes. We also provide insight into the importance of the HLA non-coding genome on disease, discuss ethnic-specific differences across the HLA region and provide guidelines for future HLA studies.
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Affiliation(s)
- Thilona Arumugam
- School of Laboratory Medicine, Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Theolan Adimulam
- School of Laboratory Medicine, Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Anmol Gokul
- School of Laboratory Medicine, Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine, Medical Science, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
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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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Ndou L, Chambuso R, Valley-Omar Z, Rebello G, Algar U, Goldberg P, Boutall A, Ramesar R. Human Leukocyte Antigen-Allelic Variations May Influence the Age at Cancer Diagnosis in Lynch Syndrome. J Pers Med 2024; 14:575. [PMID: 38929796 PMCID: PMC11204704 DOI: 10.3390/jpm14060575] [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: 05/10/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Lynch syndrome (LS) is an inherited cancer predisposition disorder associated with an elevated risk of developing various solid cancers, but mostly colorectal cancer (CRC). Despite having the same germline pathogenic variant (PV) in one of the mis-match repair genes or the EPCAM gene, Lynch syndrome variant heterozygotes (LSVH) exhibit a remarkable phenotypic variability in the risk of developing cancer. The role of human leukocyte antigen (HLA) in modifying cancer development risk prompted our hypothesis into whether HLA variations act as potential genetic modifiers influencing the age at cancer diagnosis in LSVH. To investigate this, we studied a unique cohort of 426 LSVH carrying the same germline PV in the hMLH1 gene (MLH1:c.1528C > T) in South Africa. We intuitively selected 100 LSVH with the greatest diversity in age at cancer diagnosis (N = 80) and the oldest cancer unaffected LSVH (N = 20) for a high-throughput HLA genotyping of 11 HLA class I and class II loci using the shotgun next-generation sequencing (NGS) technique on the Illumina MiSeq platform. Statistical analyses employed Kaplan-Meier survival analyses with log-rank tests, and Cox proportional hazards using binned HLA data to minimize type I error. Significant associations were observed between young age at cancer diagnosis and HLA-DPB1*04:02 (mean age: 37 y (25-50); hazard ratio (HR) = 3.37; corrected p-value (q) = 0.043) as well as HLA-DPB1 binned alleles (including HLA-DPB1*09:01, HLA-DPB1*10:01, HLA-DPB1*106:01, HLA-DPB1*18:01, HLA-DPB1*20:01, HLA-DPB1*26:01, HLA-DPB1*28:01, HLA-DPB1*296:01, and HLA-DPB1*55:01) (mean age: 37 y (17-63); HR = 2.30, q = 0.045). The involvement of HLA-DPB1 alleles in the age at cancer diagnosis may highlight the potential role of HLA class II in the immune response against cancer development in LSVH. When validated in a larger cohort, these high-risk HLA-DPB1 alleles could be factored into cancer risk prediction models for personalized cancer screening in LSVH.
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Affiliation(s)
- Lutricia Ndou
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, The University of Cape Town, Affiliated Hospitals, Cape Town 7704, South Africa
| | - Ramadhani Chambuso
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, The University of Cape Town, Affiliated Hospitals, Cape Town 7704, South Africa
| | - Ziyaad Valley-Omar
- Medical Virology, National Health Laboratory Service, Groote Schuur Hospital, The University of Cape Town, Cape Town 7925, South Africa
| | - George Rebello
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, The University of Cape Town, Affiliated Hospitals, Cape Town 7704, South Africa
| | - Ursula Algar
- The Colorectal Unit of the Department of Surgery, Groote Schuur Hospital, The University of Cape Town, Cape Town 7925, South Africa
| | - Paul Goldberg
- The Colorectal Unit of the Department of Surgery, Groote Schuur Hospital, The University of Cape Town, Cape Town 7925, South Africa
| | - Adam Boutall
- The Colorectal Unit of the Department of Surgery, Groote Schuur Hospital, The University of Cape Town, Cape Town 7925, South Africa
| | - Raj Ramesar
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, The University of Cape Town, Affiliated Hospitals, Cape Town 7704, South Africa
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Agarwal D, Liu C, Bhoj V, Kearns J, Bharani T, Choe I, Vivek K, O'Connor DH, Wiseman RW, Duquesnoy RJ, Naji A, Kamoun M. Adaptation of HLA testing to characterize the cynomolgus macaque MHC polymorphisms and alloantibody signatures. HLA 2024; 103:e15239. [PMID: 37784210 DOI: 10.1111/tan.15239] [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: 03/20/2023] [Revised: 08/12/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023]
Abstract
Nonhuman primates are the closest animal models to humans with respect to genetics and physiology. Consequently, a critical component of immunogenetics research relies on drawing inferences from the cynomolgus macaque to inform human trials. Despite the conserved organization of the Major Histocompatibility Complex (MHC) between cynomolgus macaques and humans, MHC genotyping of cynomolgus macaques is challenging due to high rates of copy number variants, duplications, and rearrangements, particularly at the MHC class I loci. Furthermore, the limited availability of commercial reagents specific to cynomolgus macaques that can be used to characterize anti-MHC class I and class II antibody (Ab) specificities in cynomolgus macaques presents a major bottleneck in translational research. Here we successfully characterized cynomolgus macaque Mafa class I and class II serologic specificities in 86 animals originating from various geographical regions using the complement dependent cytotoxicity (CDC) assay with human HLA class I and class II monoclonal antibody (mAb) typing trays. Further, we successfully induced and characterized anti-Mafa class I and class II alloantibody specificity using HLA single antigen bead assays. We also subsequently tracked the alloAb burden in the animals during treatment with anti-B lymphocyte stimulator (BLyS) treatment. Altogether, these methods can be easily used in translational research to serotype MHC class I and class II specificity in macaques, characterize their alloAb specificity, and evaluate the efficacy of novel therapeutic modalities in depleting circulating alloAbs in these animals.
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Affiliation(s)
- Divyansh Agarwal
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Chengyang Liu
- Division of Transplantation, Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Vijay Bhoj
- Center for Cellular Immunotherapies and the Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jane Kearns
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Tina Bharani
- Thomas Jefferson University Hospitals, Sidney Kimmel Medical College, Philadelphia, Pennsylvania, USA
| | - Insuk Choe
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kumar Vivek
- Department of Anesthesiology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Roger W Wiseman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - René J Duquesnoy
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Ali Naji
- Division of Transplantation, Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Malek Kamoun
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Perspectives on establishing a public cord blood inventory in South Africa. Cytotherapy 2021; 23:548-557. [PMID: 33836979 DOI: 10.1016/j.jcyt.2021.02.116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 02/04/2023]
Abstract
The South African population is highly diverse, both ethnically and genetically. This diversity is particularly true for the African ancestry and various mixed ancestry population groups. These groups are under-represented in national and international bone marrow and peripheral blood donor registries, making it challenging to identify HLA-matched and mismatched unrelated donors when patients from these groups require allogeneic hematopoietic stem and progenitor cell transplantation. In most high-income countries, banked cord blood (CB) units provide an attractive source of hematopoietic progenitor cells for genetically diverse populations. SA does not have a public CB inventory, leaving many patients without access to this important treatment modality. Haploidentical transplantation provides an alternative. In recent years, the use of post-transplant cyclophosphamide has significantly reduced the incidence of graft-versus-host disease after haploidentical transplantation and has improved transplantation outcomes. However, it is difficult to identify suitable haploidentical donors in SA because of family disruption and a high prevalence of HIV. Here the authors provide a brief historical overview of the ethnic and genetic diversity of the country and region. The authors provide a southern African perspective on HLA diversity, consider the allogeneic hematopoietic stem and progenitor cell transplantation landscape and explore the need to establish a public CB bank (CBB) in SA. The health policy and regulatory frameworks that will impact on a CBB in the country SA are also explored. Finally, the authors discuss several matters we believe require attention when considering the establishment of a sustainable public CBB in the South African context.
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