1
|
Ben Bnina A, Yessine A, El Bahri Y, Chouchene S, Ben Lazrek N, Mimouna M, Mlika Z, Messoudi A, Zellama D, Sahtout W, Bouatay A. Contribution of HLA class I (A, B, C) and HLA class II (DRB1, DQA1, DQB1) alleles and haplotypes in exploring ethnic origin of central Tunisians. BMC Med Genomics 2024; 17:65. [PMID: 38424564 PMCID: PMC10903062 DOI: 10.1186/s12920-024-01821-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: 10/11/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Estimation of HLA (Human leukocyte Antigen) alleles' frequencies in populations is essential to explore their ethnic origin. Anthropologic studies of central Tunisian population were rarely reported. Then, in this work, we aimed to explore the origin of central Tunisian population using HLA alleles and haplotypes frequencies. METHODS HLA class I (A, B, C) and HLA class II (DRB1, DQA1, DQB1) loci genotyping of 272 healthy unrelated organ donors was performed by Polymerase Chain Reaction-Sequence Specific Oligonucleotide (PCR-SSO). We compared central Tunisians with other populations (Arabs, Berbers, Mediterraneans, Europeans, Africans, etc.) using alleles and haplotypes frequencies, genetic distances, Neighbour-Joining dendrogram and correspondence analysis. RESULTS Among the 19 HLA A alleles, the 26 HLA B alleles, the 13 HLA C alleles, the 15 HLA DRB1 alleles, the 6 HLA DQA1 alleles and the 5 HLA DQB1 alleles identified in the studied population, HLA A*02 (22.8%), HLA B*50 (13.1%), HLA C*06 (21.8%), HLA DRB1*07 (17.8%), HLA DQA1*01 (32.1%) and HLA DQB1*03 (31.6%) were the most frequent alleles. The extended haplotypes HLA A*02-B*50-C*06-DRB1*07-DQA1*02-DQB1*02 (1.97%) was the most frequent HLA six-loci haplotype. CONCLUSION Central Tunisians were very close to other Tunisian populations, to Iberians and North Africans. They were rather distant from sub-Saharan populations and eastern Mediterraneans especially Arabs although the strong cultural and religious impact of Arabs in this population.
Collapse
Affiliation(s)
- Amène Ben Bnina
- Hematology Laboratory, Sahloul University Hospital, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Amri Yessine
- Biochemistry Laboratory, Béchir Hamza Children's Hospital, Bab Saadoun Square, 1007, Tunis, Tunisia.
- Department of Educational Sciences, University of Jendouba, Higher Institute of Applied Studies in Humanity Le Kef, Kef, Tunisia.
| | - Yasmine El Bahri
- Hematology Laboratory, Sahloul University Hospital, Sousse, Tunisia
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
| | - Saoussen Chouchene
- Hematology Laboratory, Fatouma Bourguiba Teaching Hospital, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Nada Ben Lazrek
- Hematology Laboratory, Sahloul University Hospital, Sousse, Tunisia
| | - Mariem Mimouna
- Hematology Laboratory, Sahloul University Hospital, Sousse, Tunisia
| | - Zeineb Mlika
- Hematology Laboratory, Sahloul University Hospital, Sousse, Tunisia
| | - Aziza Messoudi
- Hematology Laboratory, Sahloul University Hospital, Sousse, Tunisia
| | - Dorsaf Zellama
- Nephrology Department, Sahloul University Hospital, Sousse, Tunisia
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
| | - Wissal Sahtout
- Nephrology Department, Sahloul University Hospital, Sousse, Tunisia
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
| | - Amina Bouatay
- Hematology Laboratory, Sahloul University Hospital, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| |
Collapse
|
2
|
Tshabalala M, Mellet J, Vather K, Nelson D, Mohamed F, Christoffels A, Pepper MS. High Resolution HLA ∼A, ∼B, ∼C, ∼DRB1, ∼DQA1, and ∼DQB1 Diversity in South African Populations. Front Genet 2022; 13:711944. [PMID: 35309124 PMCID: PMC8931603 DOI: 10.3389/fgene.2022.711944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/17/2022] [Indexed: 01/10/2023] Open
Abstract
Background: Lack of HLA data in southern African populations hampers disease association studies and our understanding of genetic diversity in these populations. We aimed to determine HLA diversity in South African populations using high resolution HLA ∼A, ∼B, ∼C, ∼DRB1, ∼DQA1 and ∼DQB1 data, from 3005 previously typed individuals. Methods: We determined allele and haplotype frequencies, deviations from Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD) and neutrality test. South African HLA class I data was additionally compared to other global populations using non-metrical multidimensional scaling (NMDS), genetic distances and principal component analysis (PCA). Results: All loci strongly (p < 0.0001) deviated from HWE, coupled with excessive heterozygosity in most loci. Two of the three most frequent alleles, HLA ∼DQA1*05:02 (0.2584) and HLA ∼C*17:01 (0.1488) were previously reported in South African populations at lower frequencies. NMDS showed genetic distinctness of South African populations. Phylogenetic analysis and PCA clustered our current dataset with previous South African studies. Additionally, South Africans seem to be related to other sub-Saharan populations using HLA class I allele frequencies. Discussion and Conclusion: Despite the retrospective nature of the study, data missingness, the imbalance of sample sizes for each locus and haplotype pairs, and induced methodological difficulties, this study provides a unique and large HLA dataset of South Africans, which might be a useful resource to support anthropological studies, disease association studies, population based vaccine development and donor recruitment programs. We additionally provide simulated high resolution HLA class I data to augment the mixed resolution typing results generated from this study.
Collapse
Affiliation(s)
- Mqondisi Tshabalala
- Department of Immunology, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juanita Mellet
- Department of Immunology, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Kuben Vather
- South African National Blood Service (SANBS), Roodepoort, South Africa
| | - Derrick Nelson
- South African National Blood Service (SANBS), Roodepoort, South Africa
| | - Fathima Mohamed
- South African National Blood Service (SANBS), Roodepoort, South Africa
| | - Alan Christoffels
- SAMRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Michael S. Pepper
- Department of Immunology, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- *Correspondence: Michael S. Pepper,
| |
Collapse
|
3
|
Kyobe S, Mwesigwa S, Kisitu GP, Farirai J, Katagirya E, Mirembe AN, Ketumile L, Wayengera M, Katabazi FA, Kigozi E, Wampande EM, Retshabile G, Mlotshwa BC, Williams L, Morapedi K, Kasvosve I, Kyosiimire-Lugemwa J, Nsangi B, Tsimako-Johnstone M, Brown CW, Joloba M, Anabwani G, Bhekumusa L, Mpoloka SW, Mardon G, Matshaba M, Kekitiinwa A, Hanchard NA. Exome Sequencing Reveals a Putative Role for HLA-C*03:02 in Control of HIV-1 in African Pediatric Populations. Front Genet 2021; 12:720213. [PMID: 34512729 PMCID: PMC8428176 DOI: 10.3389/fgene.2021.720213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/05/2021] [Indexed: 12/28/2022] Open
Abstract
Human leucocyte antigen (HLA) class I molecules present endogenously processed antigens to T-cells and have been linked to differences in HIV-1 disease progression. HLA allelotypes show considerable geographical and inter-individual variation, as does the rate of progression of HIV-1 disease, with long-term non-progression (LTNP) of disease having most evidence of an underlying genetic contribution. However, most genetic analyses of LTNP have occurred in adults of European ancestry, limiting the potential transferability of observed associations to diverse populations who carry the burden of disease. This is particularly true of HIV-1 infected children. Here, using exome sequencing (ES) to infer HLA allelotypes, we determine associations with HIV-1 LTNP in two diverse African pediatric populations. We performed a case-control association study of 394 LTNPs and 420 rapid progressors retrospectively identified from electronic medical records of pediatric HIV-1 populations in Uganda and Botswana. We utilized high-depth ES to perform high-resolution HLA allelotyping and assessed evidence of association between HLA class I alleles and LTNP. Sixteen HLA alleles and haplotypes had significantly different frequencies between Uganda and Botswana, with allelic differences being more prominent in HLA-A compared to HLA-B and C allelotypes. Three HLA allelotypes showed association with LTNP, including a novel association in HLA-C (HLA-B∗57:03, aOR 3.21, Pc = 0.0259; B∗58:01, aOR 1.89, Pc = 0.033; C∗03:02, aOR 4.74, Pc = 0.033). Together, these alleles convey an estimated population attributable risk (PAR) of non-progression of 16.5%. We also observed novel haplotype associations with HLA-B∗57:03-C∗07:01 (aOR 5.40, Pc = 0.025) and HLA-B∗58:01-C∗03:02 (aOR 4.88, Pc = 0.011) with a PAR of 9.8%, as well as a previously unreported independent additive effect and heterozygote advantage of HLA-C∗03:02 with B∗58:01 (aOR 4.15, Pc = 0.005) that appears to limit disease progression, despite weak LD (r 2 = 0.18) between these alleles. These associations remained irrespective of gender or country. In one of the largest studies of HIV in Africa, we find evidence of a protective effect of canonical HLA-B alleles and a novel HLA-C association that appears to augment existing HIV-1 control alleles in pediatric populations. Our findings outline the value of using multi-ethnic populations in genetic studies and offer a novel HIV-1 association of relevance to ongoing vaccine studies.
Collapse
Affiliation(s)
- Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Savannah Mwesigwa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Grace P. Kisitu
- Baylor College of Medicine Children’s Foundation, Kampala, Uganda
| | - John Farirai
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Lesego Ketumile
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fred Ashaba Katabazi
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edward M. Wampande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gaone Retshabile
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Busisiwe C. Mlotshwa
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Lesedi Williams
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Koketso Morapedi
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Ishmael Kasvosve
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | - Betty Nsangi
- Baylor College of Medicine Children’s Foundation, Kampala, Uganda
| | | | - Chester W. Brown
- University of Tennessee Health Science Center, Memphis, TN, United States
| | - Moses Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
| | - Lukhele Bhekumusa
- Eswatini - Baylor College of Medicine Children’s Foundation, Mbabane, Eswatini
| | - Sununguko W. Mpoloka
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Mogomotsi Matshaba
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
- Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Adeodata Kekitiinwa
- Baylor College of Medicine Children’s Foundation, Kampala, Uganda
- Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Neil A. Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| |
Collapse
|
4
|
Hernández-Doño S, Jakez-Ocampo J, Márquez-García JE, Ruiz D, Acuña-Alonzo V, Lima G, Llorente L, Tovar-Méndez VH, García-Silva R, Granados J, Zúñiga J, Vargas-Alarcón G. Heterogeneity of Genetic Admixture Determines SLE Susceptibility in Mexican. Front Genet 2021; 12:701373. [PMID: 34413879 PMCID: PMC8369992 DOI: 10.3389/fgene.2021.701373] [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: 04/27/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022] Open
Abstract
Systemic Lupus Erythematosus (SLE) is an autoimmune inflammatory disorder for which Major Histocompatibility Complex (MHC) genes are well identified as risk factors. SLE patients present different clinical phenotypes, which are partly explained by admixture patterns variation among Mexicans. Population genetic has insight into the high genetic variability of Mexicans, mainly described through HLA gene studies with anthropological and biomedical importance. A prospective, case-control study was performed. In this study, we recruited 146 SLE patients, and 234 healthy individuals were included as a control group; both groups were admixed Mexicans from Mexico City. The HLA typing methods were based on Next Generation Sequencing and Sequence-Based Typing (SBT). The data analysis was performed with population genetic programs and statistical packages. The admixture estimations based on HLA-B and -DRB1 revealed that SLE patients have a higher Southwestern European ancestry proportion (48 ± 8%) than healthy individuals (30 ± 7%). In contrast, Mexican Native American components are diminished in SLE patients (44 ± 1%) and augmented in Healthy individuals (63 ± 4%). HLA alleles and haplotypes' frequency analysis found variants previously described in SLE patients from Mexico City. Moreover, a conserved extended haplotype that confers risk to develop SLE was found, the HLA-A∗29:02∼C∗16:01∼B∗44:03∼DRB1∗07:01∼DQB1∗02:02, pC = 0.02, OR = 1.41. Consistent with the admixture estimations, the origin of all risk alleles and haplotypes found in this study are European, while the protection alleles are Mexican Native American. The analysis of genetic distances supported that the SLE patient group is closer to the Southwestern European parental populace and farthest from Mexican Native Americans than healthy individuals. Heterogeneity of genetic admixture determines SLE susceptibility and protection in Mexicans. HLA sequencing is helpful to determine susceptibility alleles and haplotypes restricted to some populations.
Collapse
Affiliation(s)
- Susana Hernández-Doño
- Immunogenetics Division, Department of Transplant, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Juan Jakez-Ocampo
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - José Eduardo Márquez-García
- Molecular Biology Core Facility, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Daniela Ruiz
- Department of Dermatology, Hospital General Dr. Manuel Gea González, Mexico City, Mexico
| | - Víctor Acuña-Alonzo
- Laboratory of Physiology, Biochemistry, and Genetics, Escuela Nacional de Antropología e Historia, Mexico City, Mexico
| | - Guadalupe Lima
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Luis Llorente
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Víctor Hugo Tovar-Méndez
- Department of Endocrinology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Rafael García-Silva
- Department of Internal Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Julio Granados
- Immunogenetics Division, Department of Transplant, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Joaquín Zúñiga
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico.,Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | | |
Collapse
|
5
|
A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection. PLoS Pathog 2020; 16:e1008171. [PMID: 32492061 PMCID: PMC7295245 DOI: 10.1371/journal.ppat.1008171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 06/15/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
In the absence of effective antiviral therapy, HIV-1 evolves in response to the within-host environment, of which the immune system is an important aspect. During the earliest stages of infection, this process of evolution is very rapid, driven by a small number of CTL escape mutations. As the infection progresses, immune escape variants evolve under reduced magnitudes of selection, while competition between an increasing number of polymorphic alleles (i.e., clonal interference) makes it difficult to quantify the magnitude of selection acting upon specific variant alleles. To tackle this complex problem, we developed a novel multi-locus inference method to evaluate the role of selection during the chronic stage of within-host infection. We applied this method to targeted sequence data from the p24 and gp41 regions of HIV-1 collected from 34 patients with long-term untreated HIV-1 infection. We identify a broad distribution of beneficial fitness effects during infection, with a small number of variants evolving under strong selection and very many variants evolving under weaker selection. The uniquely large number of infections analysed granted a previously unparalleled statistical power to identify loci at which selection could be inferred to act with statistical confidence. Our model makes no prior assumptions about the nature of alleles under selection, such that any synonymous or non-synonymous variant may be inferred to evolve under selection. However, the majority of variants inferred with confidence to be under selection were non-synonymous in nature, and in most cases were have previously been associated with either CTL escape in p24 or neutralising antibody escape in gp41. We also identified a putative new CTL escape site (residue 286 in gag), and a region of gp41 (including residues 644, 648, 655 in env) likely to be associated with immune escape. Sites inferred to be under selection in multiple hosts have high within-host and between-host diversity although not all sites with high between-host diversity were inferred to be under selection at the within-host level. Our identification of selection at sites associated with resistance to broadly neutralising antibodies (bNAbs) highlights the need to fully understand the role of selection in untreated individuals when designing bNAb based therapies.
Collapse
|
6
|
Adusei-Poku MA, Matsuoka S, Bonney EY, Abana CZ, Duker EO, Nii-Trebi NI, Ofori SB, Mizutani T, Ishizaka A, Shiino T, Kawana-Tachikawa A, Ishikawa K, Ampofo WK, Matano T. Human Leukocyte Antigen-Associated HIV-1 CRF02_AG gag and vif Polymorphisms in Ghana. Jpn J Infect Dis 2019; 72:374-380. [PMID: 31257246 DOI: 10.7883/yoken.jjid.2019.201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In human immunodeficiency virus type-1 (HIV-1) infections, cytotoxic T-lymphocyte (CTL) responses targeting human leukocyte antigen (HLA)-restricted viral epitopes exert strong suppressive pressure on viral replication and frequently select for mutations resulting in viral escape from CTL recognition. Numerous data on these HLA-associated mutations in HIV-1 subtypes B and C have been amassed with few reports described in other subtypes. In the present study, we investigated the HLA-associated mutations in HIV-1 subtype CRF02_AG prevailing in Ghana, Western Africa. We determined viral gag sequences in 246 out of 324 HIV-1-infected Ghanaians. Phylogeny analysis revealed that 200 (81.3%) individuals were infected with HIV-1 CRF02_AG. Full gag and vif sequences were obtained from 199 and 138, respectively, out of the 200 individuals infected with CRF02_AG and subjected to determination of HLA-associated mutations. The analysis found HLA-associated HIV-1 CRF02_AG non-synonymous polymorphisms at 19 sites; 13 in gag and six in vif, including those that were newly determined. Generation of this data is an important contribution to our understanding of HIV-1 CRF02_AG and host T cell interaction.
Collapse
Affiliation(s)
- Mildred A Adusei-Poku
- Joint Research Center for Human Retrovirus Infection, Kumamoto University.,AIDS Research Center, National Institute of Infectious Diseases
| | - Saori Matsuoka
- AIDS Research Center, National Institute of Infectious Diseases
| | - Evelyn Y Bonney
- Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana
| | - Christopher Z Abana
- Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana
| | - Ewurabena O Duker
- Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana
| | - Nicholas I Nii-Trebi
- School of Biomedical and Allied Health, College of Health Sciences, University of Ghana
| | | | | | - Aya Ishizaka
- Institute of Medical Science, University of Tokyo
| | | | - Ai Kawana-Tachikawa
- Joint Research Center for Human Retrovirus Infection, Kumamoto University.,AIDS Research Center, National Institute of Infectious Diseases.,Institute of Medical Science, University of Tokyo
| | - Koichi Ishikawa
- AIDS Research Center, National Institute of Infectious Diseases
| | - William K Ampofo
- Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana
| | - Tetsuro Matano
- Joint Research Center for Human Retrovirus Infection, Kumamoto University.,AIDS Research Center, National Institute of Infectious Diseases.,Institute of Medical Science, University of Tokyo
| |
Collapse
|
7
|
Human Leukocyte Antigen-A, B, C, DRB1, and DQB1 Allele and Haplotype Frequencies in a Subset of 237 Donors in the South African Bone Marrow Registry. J Immunol Res 2018; 2018:2031571. [PMID: 29850621 PMCID: PMC5937380 DOI: 10.1155/2018/2031571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/30/2018] [Accepted: 04/11/2018] [Indexed: 12/31/2022] Open
Abstract
Human leukocyte antigen- (HLA-) A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 allele and haplotype frequencies were studied in a subset of 237 volunteer bone marrow donors registered at the South African Bone Marrow Registry (SABMR). Hapl-o-Mat software was used to compute allele and haplotype frequencies from individuals typed at various resolutions, with some alleles in multiple allele code (MAC) format. Four hundred and thirty-eight HLA-A, 235 HLA-B, 234 HLA-DRB1, 41 HLA-DQB1, and 29 HLA-C alleles are reported. The most frequent alleles were A∗02:02g (0.096), B∗07:02g (0.082), C∗07:02g (0.180), DQB1∗06:02 (0.157), and DRB1∗15:01 (0.072). The most common haplotype was A∗03:01g~B∗07:02g~C∗07:02g~DQB1∗06:02~DRB1∗15:01 (0.067), which has also been reported in other populations. Deviations from Hardy-Weinberg equilibrium were observed in A, B, and DRB1 loci, with C~DQB1 being the only locus pair in linkage disequilibrium. This study describes allele and haplotype frequencies from a subset of donors registered at SABMR, the only active bone marrow donor registry in Africa. Although the sample size was small, our results form a key resource for future population studies, disease association studies, and donor recruitment strategies.
Collapse
|
8
|
Wroblewski EE, Guethlein LA, Norman PJ, Li Y, Shaw CM, Han AS, Ndjango JBN, Ahuka-Mundeke S, Georgiev AV, Peeters M, Hahn BH, Parham P. Bonobos Maintain Immune System Diversity with Three Functional Types of MHC-B. THE JOURNAL OF IMMUNOLOGY 2017; 198:3480-3493. [PMID: 28348269 PMCID: PMC5469624 DOI: 10.4049/jimmunol.1601955] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/01/2017] [Indexed: 11/19/2022]
Abstract
Fast-evolving MHC class I polymorphism serves to diversify NK cell and CD8 T cell responses in individuals, families, and populations. Because only chimpanzee and bonobo have strict orthologs of all HLA class I, their study gives unique perspectives on the human condition. We defined polymorphism of Papa-B, the bonobo ortholog of HLA-B, for six wild bonobo populations. Sequences for Papa-B exon 2 and 3 were determined from the genomic DNA in 255 fecal samples, minimally representing 110 individuals. Twenty-two Papa-B alleles were defined, each encoding a different Papa-B protein. No Papa-B is identical to any chimpanzee Patr-B, human HLA-B, or gorilla Gogo-B. Phylogenetic analysis identified a clade of MHC-B, defined by residues 45-74 of the α1 domain, which is broadly conserved among bonobo, chimpanzee, and gorilla. Bonobo populations have 3-14 Papa-B allotypes. Three Papa-B are in all populations, and they are each of a different functional type: allotypes having the Bw4 epitope recognized by killer cell Ig-like receptors of NK cells, allotypes having the C1 epitope also recognized by killer cell Ig-like receptors, and allotypes having neither epitope. For population Malebo, these three Papa-B are the only Papa-B allotypes. Although small in number, their sequence divergence is such that the nucleotide diversity (mean proportional distance) of Papa-B in Malebo is greater than in the other populations and is also greater than expected for random combinations of three Papa-B Overall, Papa-B has substantially less diversity than Patr-B in chimpanzee subspecies and HLA-B in indigenous human populations, consistent with bonobo having experienced narrower population bottlenecks.
Collapse
Affiliation(s)
- Emily E Wroblewski
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Christiana M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alex S Han
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Jean-Bosco N Ndjango
- Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, 2012 Kisangani, Democratic Republic of the Congo
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomédicales, 1197 Kinshasa, Democratic Republic of the Congo.,University of Kinshasa, 190 Kinshasa, Democratic Republic of the Congo.,Institut de Recherche pour le Développement, Université de Montpellier, 34394 Montpellier, France; and
| | - Alexander V Georgiev
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Martine Peeters
- Institut de Recherche pour le Développement, Université de Montpellier, 34394 Montpellier, France; and
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| |
Collapse
|
9
|
Venner CM, Nankya I, Kyeyune F, Demers K, Kwok C, Chen PL, Rwambuya S, Munjoma M, Chipato T, Byamugisha J, Van Der Pol B, Mugyenyi P, Salata RA, Morrison CS, Arts EJ. Infecting HIV-1 Subtype Predicts Disease Progression in Women of Sub-Saharan Africa. EBioMedicine 2016; 13:305-314. [PMID: 27751765 PMCID: PMC5264310 DOI: 10.1016/j.ebiom.2016.10.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/06/2016] [Accepted: 10/09/2016] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Long-term natural history cohorts of HIV-1 in the absence of treatment provide the best measure of virulence by different viral subtypes. METHODS Newly HIV infected Ugandan and Zimbabwean women (N=303) were recruited and monitored for clinical, social, behavioral, immunological and viral parameters for 3 to 9.5years. RESULTS Ugandan and Zimbabwean women infected with HIV-1 subtype C had 2.5-fold slower rates of CD4 T-cell declines and higher frequencies of long-term non-progression than those infected with subtype A or D (GEE model, P<0.001), a difference not associated with any other clinical parameters. Relative replicative fitness and entry efficiency of HIV-1 variants directly correlated with virulence in the patients, subtype D>A>C (P<0.001, ANOVA). DISCUSSION HIV-1 subtype C was less virulent than either A or D in humans; the latter being the most virulent. Longer periods of asymptomatic HIV-1 subtype C could explain the continued expansion and dominance of subtype C in the global epidemic.
Collapse
Affiliation(s)
- Colin M Venner
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Immaculate Nankya
- Joint Clinical Research Centre, Kampala, Uganda; Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | | | - Korey Demers
- Joint Clinical Research Centre, Kampala, Uganda; Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Cynthia Kwok
- Family Health International 360, Durham, NC, USA
| | | | - Sandra Rwambuya
- Joint Clinical Research Centre, Kampala, Uganda; Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Marshall Munjoma
- Department of Obstetrics and Gynaecology, University of Zimbabwe, Harare, Zimbabwe
| | - Tsungai Chipato
- Department of Obstetrics and Gynaecology, University of Zimbabwe, Harare, Zimbabwe
| | | | - Barbara Van Der Pol
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, USA
| | | | - Robert A Salata
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | | | - Eric J Arts
- Department of Microbiology and Immunology, Western University, London, ON, Canada; Joint Clinical Research Centre, Kampala, Uganda; Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA.
| |
Collapse
|
10
|
Buteme HK, Axelsson-Robertson R, Benson L, Joloba ML, Boom WH, Kallenius G, Maeurer M. Human leukocyte antigen class 1 genotype distribution and analysis in persons with active tuberculosis and household contacts from Central Uganda. BMC Infect Dis 2016; 16:504. [PMID: 27659198 PMCID: PMC5034515 DOI: 10.1186/s12879-016-1833-3] [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: 10/31/2015] [Accepted: 09/14/2016] [Indexed: 11/10/2022] Open
Abstract
Background To determine the distribution of Human leukocyte antigen (HLA) class I genotypes in a Ugandan population of persons with tuberculosis (TB) and establish the relationship between class I HLA types and Mycobacterium tuberculosis (MTB) disease. Methods Blood samples were drawn from HIV negative individuals with active TB and HIV negative household controls. DNA was extracted from blood samples and HLA typed by the polymerase chain reaction-sequence specific primer method. The allelic frequencies were determined by direct count. Results HLA-A*02, B*15, C*07, C*03, B*58, C*04, A*01, A*74, C*02 and A*30 were the dominant genotypes in this Ugandan cohort. There were differences in the distribution of HLA types between the individuals with active TB and the household controls with only HLA-A*03 allele showing a statistically significant difference (p = 0.017 crude; OR = 6.29 and p = 0.016; OR = 11.67 after adjustment for age). However, after applying the Benjamini and Hochberg adjustment for multiple comparisons the difference was no longer statistically significant (p = 0.374 and p = 0.176 respectively). Conclusions We identified a number of HLA class I alleles in a population from Central Uganda which will enable us to carry out a functional characterization of CD8+ T-cell mediated immune responses to MTB. Our results do not show a positive association between the HLA class I alleles and TB in this Ugandan population however the study sample was too small to draw any firm conclusions about the role of HLA class I alleles and TB development in Uganda. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1833-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Helen K Buteme
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P.O Box 7072, Kampala, Uganda. .,Department of Clinical Science and Education, Karolinska Institute, Södersjukhuset, SE-118 83, Stockholm, Sweden.
| | - Rebecca Axelsson-Robertson
- Department of Microbiology, Tumor and Cell Biology (MTC), Nobels vag 16, KI Solna Campus Karolinska Institute, Box 280, SE-171 77, Stockholm, Sweden
| | - Lina Benson
- Department of Clinical Science and Education, Karolinska Institute, Södersjukhuset, SE-118 83, Stockholm, Sweden
| | - Moses L Joloba
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P.O Box 7072, Kampala, Uganda
| | - W Henry Boom
- Tuberculosis Research Unit, Case Western Reserve University and University Hospitals' Case Medical Center, 10900 Euclid Avenue, BRB 1031, Cleveland, OH, 44106-4984, USA
| | - Gunilla Kallenius
- Department of Clinical Science and Education, Karolinska Institute, Södersjukhuset, SE-118 83, Stockholm, Sweden
| | - Markus Maeurer
- Department of Microbiology, Tumor and Cell Biology (MTC), Nobels vag 16, KI Solna Campus Karolinska Institute, Box 280, SE-171 77, Stockholm, Sweden
| |
Collapse
|
11
|
Flanagan KL, Wilson KL, Plebanski M. Polymorphism in liver-stage malaria vaccine candidate proteins: immune evasion and implications for vaccine design. Expert Rev Vaccines 2015; 15:389-99. [PMID: 26610026 DOI: 10.1586/14760584.2016.1125785] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The pre-erythrocytic stage of infection by malaria parasites represents a key target for vaccines that aim to eradicate malaria. Two important broad immune evasion strategies that can interfere with vaccine efficacy include the induction of dendritic cell (DC) dysfunction and regulatory T cells (Tregs) by blood-stage malaria parasites, leading to inefficient priming of T cells targeting liver-stage infections. The parasite also uses 'surgical strike' strategies, whereby polymorphism in pre-erythrocytic antigens can interfere with host immunity. Specifically, we review how even single amino acid changes in T cell epitopes can lead to loss of binding to major histocompatibility complex (MHC), lack of cross-reactivity, or antagonism and immune interference, where simultaneous or sequential stimulation with related variants of the same T cell epitope can cause T cell anergy or the conversion of effector to immunosuppressive T cell phenotypes.
Collapse
Affiliation(s)
- Katie L Flanagan
- a Vaccine and Infectious Diseases Laboratory, Department of Immunology , Monash University , Melbourne , VIC , Australia
| | - Kirsty L Wilson
- a Vaccine and Infectious Diseases Laboratory, Department of Immunology , Monash University , Melbourne , VIC , Australia
| | - Magdalena Plebanski
- a Vaccine and Infectious Diseases Laboratory, Department of Immunology , Monash University , Melbourne , VIC , Australia
| |
Collapse
|
12
|
Testi M, Battarra M, Lucarelli G, Isgro A, Morrone A, Akinyanju O, Wakama T, Nunes JM, Andreani M, Sanchez-Mazas A. HLA-A-B-C-DRB1-DQB1 phased haplotypes in 124 Nigerian families indicate extreme HLA diversity and low linkage disequilibrium in Central-West Africa. ACTA ACUST UNITED AC 2015; 86:285-92. [DOI: 10.1111/tan.12642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 06/18/2015] [Accepted: 07/20/2015] [Indexed: 12/01/2022]
Affiliation(s)
- M. Testi
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation; Policlinic of the University of Tor Vergata; Rome Italy
| | - M. Battarra
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation; Policlinic of the University of Tor Vergata; Rome Italy
| | - G. Lucarelli
- International Center for Transplantation in Thalassemia and Sickle Cell Anemia, IME Foundation; Policlinic of the University of Tor Vergata; Rome Italy
| | - A. Isgro
- International Center for Transplantation in Thalassemia and Sickle Cell Anemia, IME Foundation; Policlinic of the University of Tor Vergata; Rome Italy
| | - A. Morrone
- International Center for Transplantation in Thalassemia and Sickle Cell Anemia, IME Foundation; Policlinic of the University of Tor Vergata; Rome Italy
| | | | | | - J. M. Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution-Anthropology Unit; University of Geneva; Geneva Switzerland
| | - M. Andreani
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation; Policlinic of the University of Tor Vergata; Rome Italy
| | - A. Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution-Anthropology Unit; University of Geneva; Geneva Switzerland
| |
Collapse
|
13
|
Wroblewski EE, Norman PJ, Guethlein LA, Rudicell RS, Ramirez MA, Li Y, Hahn BH, Pusey AE, Parham P. Signature Patterns of MHC Diversity in Three Gombe Communities of Wild Chimpanzees Reflect Fitness in Reproduction and Immune Defense against SIVcpz. PLoS Biol 2015; 13:e1002144. [PMID: 26020813 PMCID: PMC4447270 DOI: 10.1371/journal.pbio.1002144] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 04/02/2015] [Indexed: 11/19/2022] Open
Abstract
Major histocompatibility complex (MHC) class I molecules determine immune responses to viral infections. These polymorphic cell-surface glycoproteins bind peptide antigens, forming ligands for cytotoxic T and natural killer cell receptors. Under pressure from rapidly evolving viruses, hominoid MHC class I molecules also evolve rapidly, becoming diverse and species-specific. Little is known of the impact of infectious disease epidemics on MHC class I variant distributions in human populations, a context in which the chimpanzee is the superior animal model. Population dynamics of the chimpanzees inhabiting Gombe National Park, Tanzania have been studied for over 50 years. This population is infected with SIVcpz, the precursor of human HIV-1. Because HLA-B is the most polymorphic human MHC class I molecule and correlates strongly with HIV-1 progression, we determined sequences for its ortholog, Patr-B, in 125 Gombe chimpanzees. Eleven Patr-B variants were defined, as were their frequencies in Gombe's three communities, changes in frequency with time, and effect of SIVcpz infection. The growing populations of the northern and central communities, where SIVcpz is less prevalent, have stable distributions comprising a majority of low-frequency Patr-B variants and a few high-frequency variants. Driving the latter to high frequency has been the fecundity of immigrants to the northern community, whereas in the central community, it has been the fecundity of socially dominant individuals. In the declining population of the southern community, where greater SIVcpz prevalence is associated with mortality and emigration, Patr-B variant distributions have been changing. Enriched in this community are Patr-B variants that engage with natural killer cell receptors. Elevated among SIVcpz-infected chimpanzees, the Patr-B*06:03 variant has striking structural and functional similarities to HLA-B*57, the human allotype most strongly associated with delayed HIV-1 progression. Like HLA-B*57, Patr-B*06:03 correlates with reduced viral load, as assessed by detection of SIVcpz RNA in feces.
Collapse
Affiliation(s)
- Emily E. Wroblewski
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (EEW); (PP)
| | - Paul J. Norman
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Lisbeth A. Guethlein
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Rebecca S. Rudicell
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
- Sanofi, Cambridge, Massachusetts, United States of America
| | - Miguel A. Ramirez
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Anne E. Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
| | - Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (EEW); (PP)
| |
Collapse
|
14
|
Okello E, Beaton A, Mondo CK, Kruszka P, Kiwanuka N, Odoi-Adome R, Freers J. Rheumatic heart disease in Uganda: the association between MHC class II HLA DR alleles and disease: a case control study. BMC Cardiovasc Disord 2014; 14:28. [PMID: 24581333 PMCID: PMC3943278 DOI: 10.1186/1471-2261-14-28] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 02/26/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rheumatic heart disease (RHD), the only long term consequence of acute rheumatic fever, remains a leading cause of morbidity and mortality among young adults in Uganda. An inherited susceptibility to acute rheumatic fever centers around the major histocompatibility class II human leucocyte antigens. However, there is paucity of data from sub-Saharan Africa. This study compares the frequency of HLA class II DR alleles between RHD cases and normal controls in Uganda. METHODS One hundred ninety-nine participants including 96 established RHD cases aged 5-60 years and 103 age and sex matched normal controls were recruited for participation. DNA was manually extracted from buffy coat samples and HLA analysis was performed. HLA-DR allelic frequency comparison between cases and controls were estimated using conditional logistic regression with 95% confidence intervals. P -values were corrected for multiple hypothesis testing. RESULTS 199 participants (103 female, 51.8%) completed the study. The mean (SD) age in years for cases and controls were 29.6 (10.2) and 29(18), respectively. After conditional logistic regression and multiple hypothesis testing, HLA-DR1was associated with a decreased risk of RHD (OR = 0.42, CI 0.21-085, P = 0.01, Corrected P value (PC) = 0.09,) while HLA-DR11 was associated with increased risk of RHD (OR = 3.31, CI 1.57-6.97, P = <0.001, Pc < 0.001). No other significant associations were found. CONCLUSION In this first study of HLA genetic susceptibility to RHD in Uganda, HLA- DR1 was more common in normal controls while HLA- DR11 was more common among RHD cases suggesting a disease susceptibility association. In future studies, high resolution HLA analysis and genome wide studies should be carried out to confirm this pattern.
Collapse
Affiliation(s)
- Emmy Okello
- Department of Medicine, Makerere University/Uganda Heart Institute, Ward 1C, Mulago Hospital Complex,, PO Box 7051, Kampala, Uganda.
| | | | | | | | | | | | | |
Collapse
|
15
|
Norman PJ, Hollenbach JA, Nemat-Gorgani N, Guethlein LA, Hilton HG, Pando MJ, Koram KA, Riley EM, Abi-Rached L, Parham P. Co-evolution of human leukocyte antigen (HLA) class I ligands with killer-cell immunoglobulin-like receptors (KIR) in a genetically diverse population of sub-Saharan Africans. PLoS Genet 2013; 9:e1003938. [PMID: 24204327 PMCID: PMC3814319 DOI: 10.1371/journal.pgen.1003938] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 09/16/2013] [Indexed: 02/06/2023] Open
Abstract
Interactions between HLA class I molecules and killer-cell immunoglobulin-like receptors (KIR) control natural killer cell (NK) functions in immunity and reproduction. Encoded by genes on different chromosomes, these polymorphic ligands and receptors correlate highly with disease resistance and susceptibility. Although studied at low-resolution in many populations, high-resolution analysis of combinatorial diversity of HLA class I and KIR is limited to Asian and Amerindian populations with low genetic diversity. At the other end of the spectrum is the West African population investigated here: we studied 235 individuals, including 104 mother-child pairs, from the Ga-Adangbe of Ghana. This population has a rich diversity of 175 KIR variants forming 208 KIR haplotypes, and 81 HLA-A, -B and -C variants forming 190 HLA class I haplotypes. Each individual we studied has a unique compound genotype of HLA class I and KIR, forming 1-14 functional ligand-receptor interactions. Maintaining this exceptionally high polymorphism is balancing selection. The centromeric region of the KIR locus, encoding HLA-C receptors, is highly diverse whereas the telomeric region encoding Bw4-specific KIR3DL1, lacks diversity in Africans. Present in the Ga-Adangbe are high frequencies of Bw4-bearing HLA-B*53:01 and Bw4-lacking HLA-B*35:01, which otherwise are identical. Balancing selection at key residues maintains numerous HLA-B allotypes having and lacking Bw4, and also those of stronger and weaker interaction with LILRB1, a KIR-related receptor. Correspondingly, there is a balance at key residues of KIR3DL1 that modulate its level of cell-surface expression. Thus, capacity to interact with NK cells synergizes with peptide binding diversity to drive HLA-B allele frequency distribution. These features of KIR and HLA are consistent with ongoing co-evolution and selection imposed by a pathogen endemic to West Africa. Because of the prevalence of malaria in the Ga-Adangbe and previous associations of cerebral malaria with HLA-B*53:01 and KIR, Plasmodium falciparum is a candidate pathogen.
Collapse
Affiliation(s)
- Paul J. Norman
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
| | - Jill A. Hollenbach
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Neda Nemat-Gorgani
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Lisbeth A. Guethlein
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Hugo G. Hilton
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Marcelo J. Pando
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Kwadwo A. Koram
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Eleanor M. Riley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Laurent Abi-Rached
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Centre National de la Recherche Scientifique, Laboratoire d'Analyse, Topologie, Probabilités - Unité Mixte de Recherche 7353, Equipe ATIP, Aix-Marseille Université, Marseille, France
| | - Peter Parham
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| |
Collapse
|
16
|
Zúñiga J, Yu N, Barquera R, Alosco S, Ohashi M, Lebedeva T, Acuña-Alonzo V, Yunis M, Granados-Montiel J, Cruz-Lagunas A, Vargas-Alarcón G, Rodríguez-Reyna TS, Fernandez-Viña M, Granados J, Yunis EJ. HLA class I and class II conserved extended haplotypes and their fragments or blocks in Mexicans: implications for the study of genetic diversity in admixed populations. PLoS One 2013; 8:e74442. [PMID: 24086347 PMCID: PMC3781075 DOI: 10.1371/journal.pone.0074442] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 07/31/2013] [Indexed: 01/03/2023] Open
Abstract
Major histocompatibility complex (MHC) genes are highly polymorphic and informative in disease association, transplantation, and population genetics studies with particular importance in the understanding of human population diversity and evolution. The aim of this study was to describe the HLA diversity in Mexican admixed individuals. We studied the polymorphism of MHC class I (HLA-A, -B, -C), and class II (HLA-DRB1, -DQB1) genes using high-resolution sequence based typing (SBT) method and we structured the blocks and conserved extended haplotypes (CEHs) in 234 non-related admixed Mexican individuals (468 haplotypes) by a maximum likelihood method. We found that HLA blocks and CEHs are primarily from Amerindian and Caucasian origin, with smaller participation of African and recent Asian ancestry, demonstrating a great diversity of HLA blocks and CEHs in Mexicans from the central area of Mexico. We also analyzed the degree of admixture in this group using short tandem repeats (STRs) and HLA-B that correlated with the frequency of most probable ancestral HLA-C/−B and -DRB1/−DQB1 blocks and CEHs. Our results contribute to the analysis of the diversity and ancestral contribution of HLA class I and HLA class II alleles and haplotypes of Mexican admixed individuals from Mexico City. This work will help as a reference to improve future studies in Mexicans regarding allotransplantation, immune responses and disease associations.
Collapse
Affiliation(s)
- Joaquín Zúñiga
- Department of Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Neng Yu
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, Mexico
| | - Sharon Alosco
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Marina Ohashi
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Tatiana Lebedeva
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Víctor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, Mexico
| | - María Yunis
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Julio Granados-Montiel
- Tissue Engineering, Cell Therapy and Regenerative Medicine Research Unit, Instituto Nacional de Rehabilitación, Mexico City, Mexico
| | - Alfredo Cruz-Lagunas
- Department of Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Gilberto Vargas-Alarcón
- Laboratory of Genomics, Instituto Nacional de Cardiología Ignacio Chavez, Mexico City, Mexico
| | - Tatiana S. Rodríguez-Reyna
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Marcelo Fernandez-Viña
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Julio Granados
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- * E-mail: (EJY); (JG)
| | - Edmond J. Yunis
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (EJY); (JG)
| |
Collapse
|
17
|
Human leukocyte antigen profiles of latin american populations: differential admixture and its potential impact on hematopoietic stem cell transplantation. BONE MARROW RESEARCH 2012; 2012:136087. [PMID: 23213535 PMCID: PMC3506882 DOI: 10.1155/2012/136087] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 10/12/2012] [Indexed: 12/29/2022]
Abstract
The outcome of hematopoietic stem cell transplantation (HSCT) is shaped by both clinical and genetic factors that determine its success. Genetic factors including human leukocyte antigen (HLA) and non-HLA genetic variants are believed to influence the risk of potentially fatal complications after the transplant. Moreover, ethnicity has been proposed as a factor modifying the risk of graft-versus-host disease. The populations of Latin America are a complex array of different admixture processes with varying degrees of ancestral population proportions that came in different migration waves. This complexity makes the study of genetic risks in this region complicated unless the extent of this variation is thoroughly characterized. In this study we compared the HLA-A and HLA-B allele group profiles for 31 Latin American populations and 61 ancestral populations from Iberia, Italy, Sub-Saharan Africa, and America. Results from population genetics comparisons show a wide variation in the HLA profiles from the Latin American populations that correlate with different admixture proportions. Populations in Latin America seem to be organized in at least three groups with (1) strong Amerindian admixture, (2) strong Caucasian component, and (3) a Caucasian-African gradient. These results imply that genetic risk assessment for HSCT in Latin America has to be adapted for different population subgroups rather than as a pan-Hispanic/Latino analysis.
Collapse
|
18
|
Deng Z, Gao X, Kirk G, Wolinsky S, Carrington M. Characterization of the HLA-C*07:01:01G allele group in European and African-American cohorts. Hum Immunol 2012; 73:715-9. [PMID: 22548719 PMCID: PMC3377779 DOI: 10.1016/j.humimm.2012.04.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 04/06/2012] [Accepted: 04/23/2012] [Indexed: 11/15/2022]
Abstract
The HLA-C*07:01:01G allele group consists of three nonsynonymous alleles, C*07:01:01, C*07:06 and C*07:18, plus C*07:01:02, which is synonymous to C*07:01:01. All of these alleles have identical exons 2, 3 and 4, but differ in exons 5 or 6. Therefore routine sequence-based typing (SBT) of exons 2 and 3 is unable to resolve these subtypes, resulting in ambiguous typing results in population and disease cohort studies. In the present study, we fully characterized C*07:01:01G subtypes in European and African Americans and examined their relative frequency distributions. In European Americans C*07:01:01G is predominantly represented by C*07:01:01 (94.4%), whereas C*07:01:02 (1.1%) and C*07:18 (4.5%) were detected relatively infrequently. In African Americans C*07:18 (42.4%) showed a high frequency similar to that of C*07:01:01 (44.7%) whereas C*07:06 was detected at a low frequency (4.7%). C*07:06 was found exclusively on B*44:03 carrying haplotypes in both ethnic groups, but C*07:18 showed multiple linkage relationships with HLA-B. These results demonstrate that C*07:01:01G as defined by routine SBT is a heterogeneous group of alleles, especially among individuals of African origin. If C*07:01:01G subtypes prove to bear divergent functional significance, it would be necessary to include these subtypes in routine HLA-C typing for clinical transplantation and disease association studies.
Collapse
Affiliation(s)
- Zhihui Deng
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong 518035, China
| | - Xiaojiang Gao
- Cancer & Inflammation Program, Laboratory of Experimental Immunology, SAIC Frederick, NCI Frederick, P.O. Box B, Bldg. 560, Rm. 21-89, Frederick, MD 21702 and Ragon Institute of MGH, MIT and Harvard, 149 13th Street, Boston, MA, 02114, USA
| | - Greg Kirk
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Steven Wolinsky
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, 645 N. Michigan Avenue, Suite 900, Chicago, IL, 60611, USA
| | - Mary Carrington
- Cancer & Inflammation Program, Laboratory of Experimental Immunology, SAIC Frederick, NCI Frederick, P.O. Box B, Bldg. 560, Rm. 21-89, Frederick, MD 21702 and Ragon Institute of MGH, MIT and Harvard, 149 13th Street, Boston, MA, 02114, USA
| |
Collapse
|
19
|
Martinez NE, Sato F, Kawai E, Omura S, Chervenak RP, Tsunoda I. Regulatory T cells and Th17 cells in viral infections: implications for multiple sclerosis and myocarditis. Future Virol 2012; 7:593-608. [PMID: 23024699 DOI: 10.2217/fvl.12.44] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In immune-mediated diseases, Treg and proinflammatory Th17 cells have been suggested to play either suppressor (beneficial) or effector (detrimental) roles, respectively. Tissue damage in viral infections can be caused by direct viral replication or immunopathology. Viral replication can be enhanced by anti-inflammatory responses and suppressed by proinflammatory responses. However, Tregs could suppress proinflammatory responses, reducing immunopathology, while Th17 cell-induced inflammation may enhance immunopathology. Here, the roles of Treg and Th17 cells depend on whether tissue damage is caused by direct virus replication or immunopathology, which differ depending on the virus, disease stage and host immune background. Although the precise mechanisms of tissue damage in multiple sclerosis and myocarditis are unclear, both viral replication and immune effector cells have been proposed to cause pathogenesis. Personalized medicine that alters the balance between Treg and Th17 cells may ameliorate viral pathology during infections.
Collapse
Affiliation(s)
- Nicholas E Martinez
- Department of Microbiology & Immunology, Center for Molecular & Tumor Virology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | | | | | | | | | | |
Collapse
|
20
|
Kurose K, Sugiyama E, Saito Y. Population differences in major functional polymorphisms of pharmacokinetics/pharmacodynamics-related genes in Eastern Asians and Europeans: implications in the clinical trials for novel drug development. Drug Metab Pharmacokinet 2011; 27:9-54. [PMID: 22123129 DOI: 10.2133/dmpk.dmpk-11-rv-111] [Citation(s) in RCA: 181] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Drug lag, recently discussed extensively in Japan, can be divided into two phases: clinical development time and application review time. The former factor is still an important problem that might be improved by promoting multi-regional clinical trials and considering the results from other similar populations with Japanese, such as Koreans and Chinese. In this review, we compare the allelic or genotype frequencies of 30 relatively common functional alleles mainly between Eastern Asians and Europeans as well as among 3 major populations in Eastern Asian countries, Japan, Korea, and China, in 12 pharmacokinetics (PK)/pharmacodynamics (PD)-related genes; CYP2C9 (*2 and *3), CYP2C19 (*2, *3 and *17), 13 CYP2D6 haplotypes including *4, *5 and *10, CYP3A5 (*3), UGT1A1 (*28 and *6), NAT2 (*5, *6 and *7), GSTM1 and GSTT1 null genotypes, SLCO1B1 521T>C, ABCG2 421C>A, and HLA-A*31:01 and HLA-B*58:01. In this review, differences in allele frequencies (AFs) or genotype frequencies (GFs) less than 0.1 (in the cases of highest AF (GF) ≥0.1) or less than 0.05 (in the cases of lowest AF (GF) <0.1) were regarded as similar. Between Eastern Asians and Europeans, AFs (or GFs) are regarded as being different for many alleles such as CYP2C9 (*2), CYP2C19 (*2, *3 and *17), CYP2D6 (*4 and *10), CYP3A5 (*3), UGT1A1 (*28 and *6), NAT2 (*5*7), GSTT1 null and ABCG2 421C>A. Among the 3 Eastern Asian populations, however, only AFs of CYP2C19*3, CYP2D6*10, HLA-A*31:01 and HLA-B*58:01 are regarded as dissimilar. For CYP2C19*3, the total functional impact on CYP2C19 could be small if the frequencies of the two null alleles CYP2C19*2 and *3 are combined. Regarding CYP2D6*10, frequency difference over 0.1 is observed only between Japanese and Chinese (0.147). Although environmental factors should be considered for PK/PD differences, we could propose that among Japan, Korea, and China, genetic differences are very small for the analyzed common PK-related gene polymorphisms. On the other hand, AFs of the two HLA alleles important for cutaneous adverse drug reactions are diverse even among Eastern Asians and thus should be taken into account.
Collapse
Affiliation(s)
- Kouichi Kurose
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | | | | |
Collapse
|
21
|
Human immunodeficiency virus type 1 infection is associated with increased NK cell polyfunctionality and higher levels of KIR3DL1+ NK cells in ugandans carrying the HLA-B Bw4 motif. J Virol 2011; 85:4802-11. [PMID: 21411516 DOI: 10.1128/jvi.00111-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Natural killer (NK) cells are important innate effector cells controlled by an array of activating and inhibitory receptors. Some alleles of the inhibitory killer-cell immunoglobulin-like receptor KIR3DL1 in combination with its HLA class I ligand Bw4 have been genetically associated with slower HIV-1 disease progression. Here, we observed that the presence of HLA-B Bw4 was associated with elevated frequencies of KIR3DL1(+) CD56(dim) NK cells in chronically HIV-1-infected individuals from the rural district of Kayunga, Uganda. In contrast, levels of KIR2DL1(+) CD56(dim) NK cells were decreased, and levels of KIR2DL3(+) CD56(dim) NK cells were unchanged in infected subjects carrying their respective HLA-C ligands. Furthermore, the size of the KIR3DL1(+) NK cell subset correlated directly with viral load, and this effect occurred only in HLA-B Bw4(+) patients, suggesting that these cells expand in response to viral replication but may have relatively poor antiviral capacity. In contrast, no association with viral load was present for KIR2DL1(+) and KIR2DL3(+) NK cells. Interestingly, chronic HIV-1 infection was associated with an increased polyfunctional response in the NK cell compartment, and, upon further investigation, KIR3DL1(+) CD56(dim) NK cells exhibited a significantly increased functional response in the patients carrying HLA-B Bw4. These results indicate that chronic HIV-1 infection is associated with increased NK cell polyfunctionality and elevated levels of KIR3DL1(+) NK cells in Ugandans carrying the HLA-B Bw4 motif.
Collapse
|
22
|
Guech-Ongey M, Verboom M, Pfeiffer RM, Schulz TF, Ndugwa CM, Owor AM, Bakaki PM, Bhatia K, Figueiredo C, Eiz-Vesper B, Blasczyk R, Mbulaiteye SM. HLA polymorphisms and detection of kaposi sarcoma-associated herpesvirus DNA in saliva and peripheral blood among children and their mothers in the uganda sickle cell anemia KSHV Study. Infect Agent Cancer 2010; 5:21. [PMID: 21087485 PMCID: PMC2995779 DOI: 10.1186/1750-9378-5-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 11/18/2010] [Indexed: 11/10/2022] Open
Abstract
Kaposi sarcoma-associated herpesvirus (KSHV, also called Human herpesvirus 8 or HHV8) is a γ-2 herpesvirus that causes Kaposi sarcoma. KSHV seroprevalence rates vary geographically with variable rates recorded in different sub Sahara African countries, suggesting that effects of genetic and/or environmental factors may influence the risk of infection. One study conducted in South Africa, where KSHV seroprevalence is relatively low, found that carriage of human leukocyte antigen (HLA) alleles HLA-A*6801, HLA-A*30, HLA-A*4301, and HLA-DRB1*04 was associated with increased shedding of KSHV DNA in saliva. Confirmation of those results would strengthen the hypothesis that genetic factors may influence KSHV distribution by modulating KSHV shedding in saliva. To explore these associations in another setting, we used high resolution HLA-A, B, and DRB1 typing on residual samples from the Uganda Sickle Cell Anemia KSHV study, conducted in a high KSHV seroprevalence region, to investigate associations between HLA and KSHV shedding in saliva or peripheral blood among 233 children and their mothers. HLA-A and HLA-DRB1 alleles were not associated with KSHV shedding in our study, but our study was small and was not adequately powered to exclude small associations. In exploratory analyses, we found marginal association of KSHV DNA shedding in saliva but not in peripheral blood among children carrying HLA- B*4415 and marginal association of KSHV DNA shedding in peripheral blood but not in saliva among children carrying HLA- B*0801 alleles. The contribution of individual HLA polymorphisms to KSHV shedding is important but it may vary in different populations. Larger population-based studies are needed to estimate the magnitude and direction of association of HLA with KSHV shedding and viral control.
Collapse
Affiliation(s)
- Mercy Guech-Ongey
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Bethesda, Maryland, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Human leukocyte antigen-A, -B, and -DRB1 allele and haplotype frequencies in the Mozambican population: a blood donor-based population study. Hum Immunol 2010; 71:1027-32. [PMID: 20600444 DOI: 10.1016/j.humimm.2010.06.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2010] [Revised: 06/15/2010] [Accepted: 06/22/2010] [Indexed: 11/23/2022]
Abstract
Human leukocyte antigen (HLA) has been used for several decades as genetic markers for analyzing diversity of gene pool origin, platelet transfusion, tissue transplantation, disease susceptibility or resistance, and forensic and anthropological studies. In the present study, the allele and haplotype frequencies of HLA-A, -B, and -DRB1 were studied in 250 unrelated Mozambican individuals (black African from south of Mozambique Basin) by using a low-medium resolution polymerase chain reaction-Luminex typing method. A total of 18 A, 25 B, and 13 DRB1 alleles were identified. The most frequent HLA-A, -B, and -DRB1 alleles were HLA-A*30 (23.9%), HLA-B*15 (15.6%), and HLA-DRB1*13 (19.8%), respectively. The most frequent two-locus haplotypes were HLA-A*30-B*42 (7.4%) and HLA-B*42-DRB1*03 (5.4%), and three-locus haplotypes were HLA-A*30-B*42-DRB1*03 (4.9%), and HLA-A*02-B*58-DRB1*11 (4.1%). Allele distribution and haplotype analysis demonstrated that Mozambican population shares HLA patterns with sub-Saharan populations.
Collapse
|
24
|
Koehler RN, Walsh AM, Sanders-Buell EE, Eller LA, Eller M, Currier JR, Bautista CT, Wabwire-Mangen F, Hoelscher M, Maboko L, Kim J, Michael NL, Robb ML, McCutchan FE, Kijak GH. High-throughput high-resolution class I HLA genotyping in East Africa. PLoS One 2010; 5:e10751. [PMID: 20505773 PMCID: PMC2873994 DOI: 10.1371/journal.pone.0010751] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 04/14/2010] [Indexed: 11/18/2022] Open
Abstract
HLA, the most genetically diverse loci in the human genome, play a crucial role in host-pathogen interaction by mediating innate and adaptive cellular immune responses. A vast number of infectious diseases affect East Africa, including HIV/AIDS, malaria, and tuberculosis, but the HLA genetic diversity in this region remains incompletely described. This is a major obstacle for the design and evaluation of preventive vaccines. Available HLA typing techniques, that provide the 4-digit level resolution needed to interpret immune responses, lack sufficient throughput for large immunoepidemiological studies. Here we present a novel HLA typing assay bridging the gap between high resolution and high throughput. The assay is based on real-time PCR using sequence-specific primers (SSP) and can genotype carriers of the 49 most common East African class I HLA-A, -B, and -C alleles, at the 4-digit level. Using a validation panel of 175 samples from Kampala, Uganda, previously defined by sequence-based typing, the new assay performed with 100% sensitivity and specificity. The assay was also implemented to define the HLA genetic complexity of a previously uncharacterized Tanzanian population, demonstrating its inclusion in the major East African genetic cluster. The availability of genotyping tools with this capacity will be extremely useful in the identification of correlates of immune protection and the evaluation of candidate vaccine efficacy.
Collapse
Affiliation(s)
- Rebecca N. Koehler
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Anne M. Walsh
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Eric E. Sanders-Buell
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Leigh Anne Eller
- Makerere University Walter Reed Research Project, Henry M. Jackson Foundation, Kampala, Uganda
| | - Michael Eller
- Makerere University Walter Reed Research Project, Henry M. Jackson Foundation, Kampala, Uganda
| | - Jeffrey R. Currier
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Christian T. Bautista
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | | | - Michael Hoelscher
- Department of Infectious Diseases and Tropical Medicine, University of Munich, Munich, Germany
- Mbeya Medical Research Program, Mbeya, Tanzania
| | | | - Jerome Kim
- United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Nelson L. Michael
- United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Merlin L. Robb
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Francine E. McCutchan
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Gustavo H. Kijak
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
- * E-mail:
| |
Collapse
|
25
|
Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Fernández-Viña M, Geraghty DE, Holdsworth R, Hurley CK, Lau M, Lee KW, Mach B, Maiers M, Mayr WR, Müller CR, Parham P, Petersdorf EW, Sasazuki T, Strominger JL, Svejgaard A, Terasaki PI, Tiercy JM, Trowsdale J. Nomenclature for factors of the HLA system, 2010. TISSUE ANTIGENS 2010. [PMID: 20356336 DOI: 10.1111/j.1399‐0039.2010.01466.x] [Citation(s) in RCA: 163] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
26
|
Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Fernández-Viña M, Geraghty DE, Holdsworth R, Hurley CK, Lau M, Lee KW, Mach B, Maiers M, Mayr WR, Müller CR, Parham P, Petersdorf EW, Sasazuki T, Strominger JL, Svejgaard A, Terasaki PI, Tiercy JM, Trowsdale J. Nomenclature for factors of the HLA system, 2010. TISSUE ANTIGENS 2010; 75:291-455. [PMID: 20356336 PMCID: PMC2848993 DOI: 10.1111/j.1399-0039.2010.01466.x] [Citation(s) in RCA: 3014] [Impact Index Per Article: 215.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
27
|
Koehler RN, Walsh AM, Moqueet N, Currier JR, Eller MA, Eller LA, Wabwire-Mangen F, Michael NL, Robb ML, McCutchan FE, Kijak GH. High-throughput genotyping of KIR2DL2/L3, KIR3DL1/S1, and their HLA class I ligands using real-time PCR. ACTA ACUST UNITED AC 2009; 74:73-80. [PMID: 19522772 DOI: 10.1111/j.1399-0039.2009.01265.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Killer immunoglobulin-like receptors (KIRs) expressed on natural killer cells are critical components of innate immunity. Interactions between KIRs and their human leukocyte antigen (HLA) ligands have been shown to influence autoimmune and infectious disease course in defined populations. However, the low throughput and high cost of current methods impede confirmation of the universality of these findings. To support large epidemiology surveys, we developed a high-throughput real-time polymerase chain reaction-based assay to identify carriers of KIR3DL1, KIR3DS1, KIR2DL2, and KIR2DL3 and their HLA ligands. The platform performed with 100% sensitivity and specificity in detection of carrier and non-carrier on reference samples. The application of this platform will further clarify the nature and impact of the KIR-HLA epistatic interaction on disease course in large global population-based studies.
Collapse
Affiliation(s)
- R N Koehler
- Division of Retrovirology, US Military HIV Research Program/Henry M. Jackson Foundation, Rockville, MD 20850, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Marsh SGE. Nomenclature for factors of the HLA system, February 2009 update. Int J Immunogenet 2009. [DOI: 10.1111/j.1744-313x.2009.00851.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
29
|
Affiliation(s)
- Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London NW32QG, UK.
| | | |
Collapse
|
30
|
Marsh SG. Nomenclature for factors of the HLA system, update February 2009. Hum Immunol 2009. [DOI: 10.1016/j.humimm.2009.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|