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Prevalence of HLA-B*57:01 allele in HIV-positive and HIV-negative population of eastern India: An epidemiological study. CLINICAL EPIDEMIOLOGY AND GLOBAL HEALTH 2022. [DOI: 10.1016/j.cegh.2022.101181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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2
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Naemi FMA, Al‐adwani S, Al‐khatabi H, Al‐nazawi A. Association between the HLA genotype and the severity of COVID-19 infection among South Asians. J Med Virol 2021; 93:4430-4437. [PMID: 33830530 PMCID: PMC8251353 DOI: 10.1002/jmv.27003] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/04/2021] [Accepted: 04/06/2021] [Indexed: 12/21/2022]
Abstract
Regional variations are found in the incidence and severity of the COVID-19 infection. Human leukocyte antigen (HLA) polymorphism is one of the genetic factors that might have an impact on the outcome of the disease. This study explored the association between the HLA genotype and the severity of COVID-19 among patients from South Asia. Blood samples from 95 Asians (Bangladeshis, Indians, and Pakistanis) with COVID-19 were collected. The patients were divided according to the severity of their infection: mild (N = 64), severe (N = 31), and fatal (N = 20). DNA was extracted from all samples, and HLA genotyping was performed for both class I (A, B, and C) and class II (DRB1, DQA1, and DQB1) using the PCR-rSSO (polymerase chain reaction-reverse sequence-specific oligonucleotide) molecular method. The frequency of HLA-B*51 was significantly higher among patients in the fatal group than among those in the mild infection group (15% vs. 4.7%, p = 0.027). Additionally, the frequency of HLA-B*35 was significantly higher in the mild infection group than in the fatal group (21.1% vs. 7.5%, p = 0.050 [a borderline p-value]). In terms of HLA class II, DRB1*13 was significantly observed in the fatal group than in the mild infection group (17.5% vs. 11.3%, p = 0.049). However, the p-value for all alleles became insignificant after a statistical correction for the p-values (pc = 0.216, pc = 0.4, and pc = 0.49, respectively). Compared with all published data, this study highlights that the association between the HLA system and the COVID-19 outcome might be ethnic-dependent. Genetic variation between populations must be examined on a wider scale to assess infection prognosis and vaccine effectiveness.
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Affiliation(s)
- Fatmah M. A. Naemi
- Laboratory of Histocompatibility and Immunogenetics, King Fahd General HospitalMinistry of HealthJeddahKingdom of Saudi Arabia
| | - Shurooq Al‐adwani
- Laboratory of Histocompatibility and Immunogenetics, King Fahd General HospitalMinistry of HealthJeddahKingdom of Saudi Arabia
| | - Heba Al‐khatabi
- Center of Excellence in Genomic Medicine Research, King Fahd Medical Research CenterKing Abdul‐Aziz UniversityJeddahKingdom of Saudi Arabia
| | - Ashwaq Al‐nazawi
- Public Health VBDMinistry of HealthJeddahKingdom of Saudi Arabia
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3
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Rathinam SR, Tugal-Tutkun I, Agarwal M, Rajesh V, Egriparmak M, Patnaik G. Immunological tests and their interpretation in uveitis. Indian J Ophthalmol 2021; 68:1737-1748. [PMID: 32823389 PMCID: PMC7690523 DOI: 10.4103/ijo.ijo_570_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Uveitis is a complex disorder including both infectious and non-infectious etiologies. Clinical diagnosis is a challenge because many diseases share common clinical signs. Laboratory support is crucial for confirming the clinical diagnosis. Laboratory diagnosis includes direct tests and indirect tests. For example smear, culture, and molecular diagnostics demonstrate the pathogens, hence they are direct tests. Immunologic tests employ an antigen to detect presence of antibodies to a pathogen, or an antibody to detect the presence of an antigen, of the pathogen in the specimens. The immunological tests used in laboratories are made by producing artificial antibodies that exactly “match” the pathogen in question. When these antibodies come into contact with a sample they bind to the matching pathogen if found in the sample. Hence they are grouped under indirect evidence. There are several investigations in uveitis to reach the confirmed diagnosis including microbiological, immunological, imaging and molecular diagnostic testing. In this section we will discuss immunological investigations of infectious and non-infectious uveitis.
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Affiliation(s)
- S R Rathinam
- Uveitis Service, Aravind Eye Hospital, Madurai, Tamil Nadu, India
| | | | - Mamta Agarwal
- Uveitis Service, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | | | - Merih Egriparmak
- Department of Ophthalmology, Istanbul University, Istanbul, Turkey
| | - Gazal Patnaik
- Uveitis Service, Sankara Nethralaya, Chennai, Tamil Nadu, India
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4
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Analysis of HLA-B allele polymorphism in North Indian population: Experience at tertiary care centre. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2020.100996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Seshasubramanian V, SathishKannan AD, Naganathan C, Narayan S, Periathiruvadi S. Molecular analysis of HLA Class I and Class II genes in five different South Indian linguistic groups. HLA 2021; 97:399-419. [PMID: 33583139 DOI: 10.1111/tan.14219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 01/16/2021] [Accepted: 02/08/2021] [Indexed: 11/30/2022]
Abstract
South Indians are a heterogeneous population who speak different languages and differ in their life style and physical appearance. Major population movements, social structure and caste endogamy have influenced the genetic structure of Indian populations. The human leukocyte antigen (HLA) system of populations is highly informative because of the high level of polymorphisms. Knowledge of allele and haplotype frequencies of the HLA system is important in the search for unrelated bone marrow donors. We investigated the distribution of HLA A, B, C, DRB1 and DQB1 loci in five linguistic groups from South India. HLA-A*01:01:01~B*57:01:01:01~C*06:02:01~DRB1*07:01:01~DQB1*03:03:02 was the common haplotype with highest frequency in all the five populations studied. A few relevant haplotypes were identified as most common haplotypes in each linguistic group. Comparison of HLA-A, -B and -DRB1 allele distribution in these five linguistic groups with the other Asian population showed that the South Indian populations were closely related to Sri Lankan populations. A large South Indian donor registry might serve as good source of donors for patients from Sri Lanka and vice versa.
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Affiliation(s)
| | | | | | - Saranya Narayan
- JEENOMICS (NGS HLA laboratory), Jeevan Stem Cell Foundation, Chennai, India
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6
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Shanbhag SS, Koduri MA, Kannabiran C, Donthineni PR, Singh V, Basu S. Genetic Markers for Stevens-Johnson Syndrome/Toxic Epidermal Necrolysis in the Asian Indian Population: Implications on Prevention. Front Genet 2021; 11:607532. [PMID: 33510770 PMCID: PMC7837290 DOI: 10.3389/fgene.2020.607532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
This review attempts to collate all the studies performed in India or comprising a population originating from India and to find out if there is an association between the HLA (human leucocyte antigen) type of individual and development of Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) subsequent to medication use. The authors performed a PubMed search of all articles published in English from 2009 to 2019 for articles that studied HLA type in patients who developed SJS/TEN after intake of a specific drug in the Asian Indian population or in individuals of Asian Indian origin. The selection criteria were satisfied by a total of 11 studies that reported HLA associations with specific drugs, which induced SJS/TEN, mainly anti-epileptic drugs, and cold medicine/non-steroidal anti-inflammatory drugs. These studies involved a small number of patients, and hence, there is limited evidence to conclude if these associations can be extrapolated to a larger population of the same ethnicity. Similar multi-center studies need to be conducted with a larger sample size to confirm these associations. This would have implications in policy making and for understanding the potential of using genetic markers as a screening tool before prescribing a drug to a patient, which might make them susceptible to developing a potentially life-threatening disease such as SJS/TEN. This is possibly the only mode of primary prevention for this potentially fatal severe cutaneous adverse drug reaction.
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Affiliation(s)
| | - Madhuri A Koduri
- Brien Holden Eye Research Centre (BHERC), L.V. Prasad Eye Institute, Hyderabad, India.,Manipal Academy of Higher Education, Manipal, India
| | - Chitra Kannabiran
- Brien Holden Eye Research Centre (BHERC), L.V. Prasad Eye Institute, Hyderabad, India.,Kallam Anji Reddy Molecular Genetics Laboratory, L.V. Prasad Eye Institute, Hyderabad, India
| | | | - Vivek Singh
- Brien Holden Eye Research Centre (BHERC), L.V. Prasad Eye Institute, Hyderabad, India.,Center for Ocular Regeneration (CORE), L.V. Prasad Eye Institute, Hyderabad, India
| | - Sayan Basu
- The Cornea Institute, L.V. Prasad Eye Institute, Hyderabad, India.,Brien Holden Eye Research Centre (BHERC), L.V. Prasad Eye Institute, Hyderabad, India.,Center for Ocular Regeneration (CORE), L.V. Prasad Eye Institute, Hyderabad, India
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7
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Saxena P, Mishra S. Study of the Binding Pattern of HLA Class I Alleles of Indian Frequency and cTAP Binding Peptide for Chikungunya Vaccine Development. Int J Pept Res Ther 2020; 26:2437-2448. [PMID: 32421074 PMCID: PMC7223317 DOI: 10.1007/s10989-020-10038-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2020] [Indexed: 11/24/2022]
Abstract
Chikungunya is a mosquito-borne disease, caused by the member of the Togaviridae family belongs to the genus alphavirus, making it a major threat in all developing countries as well as some developed countries. The mosquito acts as a vector for the disease and carries the CHIK-Virus. To date there is no direct treatment available and that demands the development of more effective vaccines. In this study author employed Immune Epitope Database and Analysis Resource, a machine learning-based algorithm principally working on the Artificial Neural Network (ANN) algorithm, also known as (IEDB-ANN) for the prediction and analysis of Epitopes. A total of 173 epitopes were identified on the basis of IC50 values, among them 40 epitopes were found, sharing part with the linear B-cell epitopes and exposed to the cTAP1protein, and out of 40, 6 epitopes were noticed to show interactions with the cTAP with their binding energy ranging from - 3.61 to - 1.22 kcal/mol. The six epitopes identified were exposed to the HLA class I alleles and from this all revealed interaction with the HLA alleles and minimum binding energy that ranges from - 4.12 to - 5.88 kcal/mol. Besides, two T cell epitopes i.e. 145KVFTGVYPE153 and 395STVPVAPPR403 were found most promiscuous candidates. These promiscuous epitopes-HLA complexes were further analyzed by the molecular dynamics simulation to check the stability of the complex. Results obtained from this study suggest that the identified epitopes i.e. and 395 STVPVAPPR 403 , are likely to be capable of passing through the lumen of ER to bind withthe HLA class I allele and provide new insights and potential application in the designing and development of peptide-based vaccine candidate for the treatment of chikungunya.
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Affiliation(s)
- Prashant Saxena
- Department of Biotechnology, K. S. Vira College of Engineering & Management, Bijnor, UP(W) 246701 India
- School of Biotechnology, IFTM University, Delhi Road (NH 24), Moradabad, UP(W) 244102 India
| | - Sanjay Mishra
- School of Biotechnology, IFTM University, Delhi Road (NH 24), Moradabad, UP(W) 244102 India
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8
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Saxena A, Sharma G, Tyagi S, Mourya M, Coshic P, Tiwari PK, Mehra NK, Kanga U. HLA-A*02 repertoires in three defined population groups from North and Central India: Punjabi Khatries, Kashmiri Brahmins and Sahariya Tribe. HLA 2018; 93:16-23. [PMID: 30516033 DOI: 10.1111/tan.13447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 11/26/2018] [Accepted: 11/29/2018] [Indexed: 01/30/2023]
Abstract
The allelic family of HLA-A*02 with a repertoire of approximately 1022 alleles represents the predominant and most heterogeneous group at the HLA-A locus. This remarkable diversity signifies its evolutionary relevance. Its population-specific diversity is attributed to environmental factors and pathogen pressure and can be harnessed in biology and medicine, particularly in disease association and for HLA-based vaccination approaches. We therefore investigated the HLA-A*02 repertoire in two North Indian caste populations, viz Punjabi Khatries (PK, N = 250), Kashmiri Brahmins (KB, N = 160) and a Central Indian tribe Sahariya (ST, N = 100) using Luminex-based high-resolution rSSO method. When required, results were confirmed with high-resolution PCR-SSP and/or next-generation sequencing (NGS). In the three populations evaluated, HLA-A*02 was observed with an overall high phenotypic/allelic frequency, however, A*02 repertoire differed among them. A total of six alleles were observed (A*02:01, *02:03, *02:05, *02:06, *02:07 and *02:11) in the caste groups, compared with four (except *02:05 and *02:07) in the tribals. Our striking observation was the high occurrence of A*02:11 at the repertoire level (80.6% in ST, 39% in PK, 31.8% in KB). Globally, this allele is rare, observed with low frequencies in limited ethnic groups. The primordial A*02:01 allele, representative A*02 allele in most ethnicities was observed as the second predominant allele (PK = 27.3%, KB = 31.8% and ST = 11.9%). Extremely high occurrence of A*02:11 in ST may be representation of ancient Austro-Asiatic genetic pool. In caste populations, the observed A*02 repertoire may be a consequence of natural selection and/or admixture from different populations.
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Affiliation(s)
- Abhishweta Saxena
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Gaurav Sharma
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Shweta Tyagi
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Manish Mourya
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Poonam Coshic
- Department of Transfusion Medicine (Blood Bank), All India Institute of Medical Sciences, New Delhi, India
| | - Pramod K Tiwari
- Centre for Genomics Molecular and Human Genetics, School of studies in Zoology, Jiwaji University, Gwalior, India
| | - Narinder K Mehra
- Dr C.G Pandit National Chair and Former Dean (Research), All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kanga
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
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9
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Broad Recognition of Circulating HIV-1 by HIV-1-Specific Cytotoxic T-Lymphocytes with Strong Ability to Suppress HIV-1 Replication. J Virol 2018; 93:JVI.01480-18. [PMID: 30333175 DOI: 10.1128/jvi.01480-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/10/2018] [Indexed: 11/20/2022] Open
Abstract
HIV-1-specific cytotoxic T-lymphocytes (CTLs) with strong abilities to suppress HIV-1 replication and recognize most circulating HIV-1 strains are candidates for effector T cells for cure treatment and prophylactic AIDS vaccine. Previous studies demonstrated that the existence of CTLs specific for 11 epitopes was significantly associated with good clinical outcomes in Japan, although CTLs specific for one of these epitopes select for escape mutations. However, it remains unknown whether the CTLs specific for the remaining 10 epitopes suppress HIV-1 replication in vitro and recognize circulating HIV-1. Here, we investigated the abilities of these CTLs to suppress HIV-1 replication and to recognize variants in circulating HIV-1. CTL clones specific for 10 epitopes had strong abilities to suppress HIV-1 replication in vitro The ex vivo and in vitro analyses of T-cell responses to variant epitope peptides showed that the T cells specific for 10 epitopes recognized mutant peptides which are detected in 84.1% to 98.8% of the circulating HIV-1 strains found in HIV-1-infected Japanese individuals. In addition, the T cells specific for 5 epitopes well recognized target cells infected with 7 mutant viruses that had been detected in >5% of tested individuals. Taken together, these results suggest that CTLs specific for the 10 epitopes effectively suppress HIV-1 replication and broadly recognize the circulating HIV-1 strains in the HIV-1-infected individuals. This study suggests the use of these T cells in clinical trials.IMPORTANCE In recent T-cell AIDS vaccine trials, the vaccines did not prevent HIV-1 infection, although HIV-1-specific T cells were induced in the vaccinated individuals, suggesting that the T cells have a weak ability to suppress HIV-1 replication and fail to recognize circulating HIV-1. We previously demonstrated that the T-cell responses to 10 epitopes were significantly associated with good clinical outcome. However, there is no direct evidence that these T cells have strong abilities to suppress HIV-1 replication and recognize circulating HIV-1. Here, we demonstrated that the T cells specific for the 10 epitopes had strong abilities to suppress HIV-1 replication in vitro Moreover, the T cells cross-recognized most of the circulating HIV-1 in HIV-1-infected individuals. This study suggests the use of T cells specific for these 10 epitopes in clinical trials of T-cell vaccines as a cure treatment.
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10
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Singh MK, Jamal F, Dubey AK, Shivam P, Kumari S, Pushpanjali, Bordoloi C, Narayan S, Das VNR, Pandey K, Das P, Singh SK. Visceral leishmaniasis: A novel nuclear envelope protein 'nucleoporins-93 (NUP-93)' from Leishmania donovani prompts macrophage signaling for T-cell activation towards host protective immune response. Cytokine 2018; 113:200-215. [PMID: 30001865 DOI: 10.1016/j.cyto.2018.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 02/06/2023]
Abstract
The shift of macrophage and T-cell repertoires towards proinflammatory cytokine signalling ensures the generation of host-protective machinery that is otherwise compromised in cases of the intracellular Leishmania parasite. Different groups have attempted to restore host protective immunity. These vaccine candidates showed good responses and protective effects in murine models, but they generally failed during human trials. In the present study, we evaluated the effect of 97 kDa recombinant nucleoporin-93 of Leishmania donovani (rLd-NUP93) on mononuclear cells in healthy and treated visceral leishmaniasis (VL) patients and on THP-1 cell lines. rLd-NUP93 stimulation increased the expression of the early lymphocyte activation marker CD69 on CD4+ and CD8+ T cells. The expression of the host protective pro-inflammatory cytokines IFN-γ, IL-12 and TNF-α was increased, with a corresponding down-regulation of IL-10 and TGF-β upon rLd-NUP93 stimulation. This immune polarization resulted in the up-regulation of NF-κB p50 with scant expression of SMAD-4. Augmenting lymphocyte proliferation upon priming with rLd-NUP93 ensured its potential for activation and generation of strong T-cell mediated immune responses. This stimulation extended the leishmanicidal activity of macrophages by releasing high amounts of reactive oxygen species (ROS). Further, the leishmanicidal activity of macrophages was intensified by the elevated production of nitric oxide (NO). The fact that this antigen was earlier reported in circulating immune complexes of VL patients highlights its antigenic importance. In addition, in silico analysis suggested the presence of MHC class I and II-restricted epitopes that proficiently trigger CD8+ and CD4+ T-cells, respectively. This study reported that rLd-NUP93 was an effective immunoprophylactic agent that can be explored in future vaccine design.
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Affiliation(s)
- Manish K Singh
- Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Fauzia Jamal
- Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Amit K Dubey
- Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India; National Institute of Pharmaceutical Education and Research, Hajipur 844102, India
| | - Pushkar Shivam
- Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Sarita Kumari
- Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Pushpanjali
- Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Chayanika Bordoloi
- National Institute of Pharmaceutical Education and Research, Hajipur 844102, India
| | - S Narayan
- Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - V N R Das
- Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - K Pandey
- Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - P Das
- Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Shubhankar K Singh
- Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India.
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11
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Murakoshi H, Zou C, Kuse N, Akahoshi T, Chikata T, Gatanaga H, Oka S, Hanke T, Takiguchi M. CD8 + T cells specific for conserved, cross-reactive Gag epitopes with strong ability to suppress HIV-1 replication. Retrovirology 2018; 15:46. [PMID: 29970102 PMCID: PMC6029025 DOI: 10.1186/s12977-018-0429-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/25/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Development of AIDS vaccines for effective prevention of circulating HIV-1 is required, but no trial has demonstrated definitive effects on the prevention. Several recent T-cell vaccine trials showed no protection against HIV-1 acquisition although the vaccines induced HIV-1-specific T-cell responses, suggesting that the vaccine-induced T cells have insufficient capacities to suppress HIV-1 replication and/or cross-recognize circulating HIV-1. Therefore, it is necessary to develop T-cell vaccines that elicit T cells recognizing shared protective epitopes with strong ability to suppress HIV-1. We recently designed T-cell mosaic vaccine immunogens tHIVconsvX composed of 6 conserved Gag and Pol regions and demonstrated that the T-cell responses to peptides derived from the vaccine immunogens were significantly associated with lower plasma viral load (pVL) and higher CD4+ T-cell count (CD4 count) in HIV-1-infected, treatment-naive Japanese individuals. However, it remains unknown T cells of which specificities have the ability to suppress HIV-1 replication. In the present study, we sought to identify more T cells specific for protective Gag epitopes in the vaccine immunogens, and analyze their abilities to suppress HIV-1 replication and recognize epitope variants in circulating HIV-1. RESULTS We determined 17 optimal Gag epitopes and their HLA restriction, and found that T-cell responses to 9 were associated significantly with lower pVL and/or higher CD4 count. T-cells recognizing 5 of these Gag peptides remained associated with good clinical outcome in 221 HIV-1-infected individuals even when comparing responders and non-responders with the same restricting HLA alleles. Although it was known previously that T cells specific for 3 of these protective epitopes had strong abilities to suppress HIV-1 replication in vivo, here we demonstrated equivalent abilities for the 2 novel epitopes. Furthermore, T cells against all 5 Gag epitopes cross-recognized variants in majority of circulating HIV-1. CONCLUSIONS We demonstrated that T cells specific for 5 Gag conserved epitopes in the tHIVconsvX have ability to suppress replication of circulating HIV-1 in HIV-1-infected individuals. Therefore, the tHIVconsvX vaccines have the right specificity to contribute to prevention of HIV-1 infection and eradication of latently infected cells following HIV-1 reactivation.
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Affiliation(s)
- Hayato Murakoshi
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Chengcheng Zou
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Nozomi Kuse
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Tomohiro Akahoshi
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Takayuki Chikata
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan.,AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan.,AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Tomáš Hanke
- International Research Center of Medical Sciences, Kumamoto University, Kumamoto, Japan.,The Jenner Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan.
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12
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Ramanujam B, Ihtisham K, Kaur G, Srivastava S, Mehra NK, Khanna N, Singh M, Tripathi M. Spectrum of Cutaneous Adverse Reactions to Levetiracetam and Human Leukocyte Antigen Typing in North-Indian Patients. J Epilepsy Res 2016; 6:87-92. [PMID: 28101480 PMCID: PMC5206105 DOI: 10.14581/jer.16016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/05/2016] [Indexed: 12/17/2022] Open
Abstract
Background and Purpose Aromatic antiepileptic drugs are frequently implicated for cutaneous adverse drug reactions (cADRs); there are case-reports of even severe reactions like drug reaction eosinophilia and systemic symptoms (DRESS) and Stevens Johnson syndrome (SJS)-toxic epidermal necrolysis with Levetiracetam (LEV). Certain human leukocyte antigen (HLA)-alleles have strong association with cADRs due to specific drugs - HLA-B*15:02 and HLA-A*31:01 in Carbamazepine (CBZ)-related SJS in Han-Chinese and European populations, respectively. Here, the spectrum of cADRs to LEV was studied, and HLA-typing in patients with cADRs due to LEV and some who were LEV-tolerant was performed, in an attempt to find an association between HLA and such reactions. Methods 589 patients taking LEV were screened for skin reactions, and eight patients with LEV-related cADRs and 25 LEV-tolerant controls were recruited - all 33 of North Indian ethnicity, their HLA-A, B, DRB1 genotyping done. Statistical analysis was done to compare carrier-rates and allele-frequencies of HLA-alleles between cases and controls (and healthy population, where necessary) for alleles occurring more than two times in either group. Results Out of 589 patients on LEV screened, there were 8 cases of cADR: 5 with maculopapular exanthema (MPE), 2 of SJS, and 1 with DRESS. Although HLA-A*33:01 was seen to occur more in MPE cases as compared to tolerant controls, the difference was not statistically significant (odds ratio [OR] 6.00, 95% confidence interval [CI] 0.30–116.6; p = 0.31). HLA A*11:01 and 24:02 were found to occur more in LEV-tolerant controls than in cases (OR 0.23 [95% CI 0.02–2.36, p = 0.33] and 1.00 [95% CI 0.09–11.02, p = 1.00] respectively). Conclusions Cutaneous reactions to LEV are very unusual, and their association with HLA in North-Indian population was not statistically significant.
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Affiliation(s)
- Bhargavi Ramanujam
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Kavish Ihtisham
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Gurvinder Kaur
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Shivani Srivastava
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Narinder Kumar Mehra
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Neena Khanna
- Department of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, India
| | - Mahip Singh
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Manjari Tripathi
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
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Singh R, Garg N, Shukla G, Capalash N, Sharma P. Immunoprotective Efficacy of Acinetobacter baumannii Outer Membrane Protein, FilF, Predicted In silico as a Potential Vaccine Candidate. Front Microbiol 2016; 7:158. [PMID: 26904021 PMCID: PMC4751259 DOI: 10.3389/fmicb.2016.00158] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/29/2016] [Indexed: 11/22/2022] Open
Abstract
Acinetobacter baumannii is emerging as a serious nosocomial pathogen with multidrug resistance that has made it difficult to cure and development of efficacious treatment against this pathogen is direly needed. This has led to investigate vaccine approach to prevent and treat A. baumannii infections. In this work, an outer membrane putative pilus assembly protein, FilF, was predicted as vaccine candidate by in silico analysis of A. baumannii proteome and was found to be conserved among the A. baumannii strains. It was cloned and expressed in E. coli BL21(DE3) and purified by Ni-NTA chromatography. Immunization with FilF generated high antibody titer (>64,000) and provided 50% protection against a standardized lethal dose (108 CFU) of A. baumannii in murine pneumonia model. FilF immunization reduced the bacterial load in lungs by 2 and 4 log cycles, 12 and 24 h post infection as compared to adjuvant control; reduced the levels of pro-inflammatory cytokines TNF-α, IL-6, IL-33, IFN-γ, and IL-1β significantly and histology of lung tissue supported the data by showing considerably reduced damage and infiltration of neutrophils in lungs. These results demonstrate the in vivo validation of immunoprotective efficacy of a protein predicted as a vaccine candidate by in silico proteomic analysis and open the possibilities for exploration of a large array of uncharacterized proteins.
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Affiliation(s)
- Ravinder Singh
- Department of Microbiology, Panjab University Chandigarh, India
| | - Nisha Garg
- Department of Microbiology, Panjab University Chandigarh, India
| | - Geeta Shukla
- Department of Microbiology, Panjab University Chandigarh, India
| | - Neena Capalash
- Department of Biotechnology, Panjab University Chandigarh, India
| | - Prince Sharma
- Department of Microbiology, Panjab University Chandigarh, India
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Recombinant NAD-dependent SIR-2 protein of Leishmania donovani: immunobiochemical characterization as a potential vaccine against visceral leishmaniasis. PLoS Negl Trop Dis 2015; 9:e0003557. [PMID: 25745863 PMCID: PMC4351947 DOI: 10.1371/journal.pntd.0003557] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 01/21/2015] [Indexed: 12/02/2022] Open
Abstract
Background The development of a vaccine conferring long-lasting immunity remains a challenge against visceral leishmaniasis (VL). Immunoproteomic characterization of Leishmania donovani proteins led to the identification of a novel protein NAD+-dependent Silent Information regulatory-2 (SIR2 family or sirtuin) protein (LdSir2RP) as one of the potent immunostimulatory proteins. Proteins of the SIR2 family are characterized by a conserved catalytic domain that exerts unique NAD-dependent deacetylase activity. In the present study, an immunobiochemical characterization of LdSir2RP and further evaluation of its immunogenicity and prophylactic potential was done to assess for its possible involvement as a vaccine candidate against leishmaniasis. Methodology/Principal Findings LdSir2RP was successfully cloned, expressed and purified. The gene was present as a monomeric protein of ~45 kDa and further established by the crosslinking experiment. rLdSir2RP shown cytosolic localization in L. donovani and demonstrating NAD+-dependent deacetylase activity. Bioinformatic analysis also confirmed that LdSir2RP protein has NAD binding domain. The rLdSir2RP was further assessed for its cellular response by lymphoproliferative assay and cytokine ELISA in cured Leishmania patients and hamsters (Mesocricetus auratus) in comparison to soluble Leishmania antigen and it was observed to stimulate the production of IFN-γ, IL-12 and TNF-α significantly but not the IL-4 and IL-10. The naïve hamsters when vaccinated with rLdSir2RP alongwith BCG resisted the L. donovani challenge to the tune of ~75% and generated strong IL-12 and IFN-γ mediated Th1 type immune response thereof. The efficacy was further supported by remarkable increase in IgG2 antibody level which is indicative of Th1 type of protective response. Further, with a possible implication in vaccine design against VL, identification of potential T-cell epitopes of rLdSir2RP was done using computational approach. Conclusion/Significance The immunobiochemical characterization strongly suggest the potential of rLdSir2RP as vaccine candidate against VL and supports the concept of its being effective T-cell stimulatory antigen. Visceral Leishmaniasis (VL) is the most fatal form of leishmaniasis disease in Indian subcontinent. Through proteomic approaches, NAD-dependent Silent information regulator-2 was identified as one of the potent immunostimulatory proteins. Herein, it was first reported the cloning, expression, purification and immunobiochemical characterization of a NAD+-dependent protein from Leishmania donovani. The gene encodes a monomeric protein (LdSir2RP) of approximately 45 kDa and showed NAD+-dependent deacetylase activity. LdSir2RP was immunodetected in whole cell lysate of L. donovani and further it immunolocalized in cytoplasm of the Leishmania parasite. Recombinant protein rLdSir2RP shown immunogenicity in PBMCs of cured Leishmania patients and hamsters (Mesocricetus auratus). rLdSir2RP stimulated the production of IFN-γ, IL-12 and TNF-α but not IL-4 and IL-10. This was further supported by remarkable increase in IgG2 antibody level. It was further demonstrated that rLdSir2RP was able to provide considerable protection to hamsters against L. donovani challenge. These results supported by the increased iNOS mRNA transcript and the specific Th1-type cytokines—IFN-γ, IL-12 and TNF-α and down-regulation of IL-4, IL-10 and TGF-β. Hence, it is inferred that rLdSir2RP confer significant protection against experimental VL and considered as potential vaccine targets against visceral leishmaniasis.
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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.
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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)
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16
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Riccio ME, Nunes JM, Rahal M, Kervaire B, Tiercy JM, Sanchez-Mazas A. The Austroasiatic Munda population from India and Its enigmatic origin: a HLA diversity study. Hum Biol 2011; 83:405-35. [PMID: 21740156 DOI: 10.3378/027.083.0306] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The Austroasiatic linguistic family disputes its origin between two geographically distant regions of Asia, India, and Southeast Asia, respectively. As genetic studies based on classical and gender-specific genetic markers provided contradictory results to this debate thus far, we investigated the HLA diversity (HLA-A, -B, and -DRB1 loci) of an Austroasiatic Munda population from Northeast India and its relationships with other populations from India and Southeast Asia. Because molecular methods currently used to test HLA markers often provide ambiguous results due to the high complexity of this polymorphism, we applied two different techniques (reverse PCR-SSO typing on microbeads arrays based on Luminex technology, and PCR-SSP typing) to type the samples. After validating the resulting frequency distributions through the original statistical method described in our companion article ( Nunes et al. 2011 ), we compared the HLA genetic profile of the sampled Munda to those of other Asiatic populations, among which Dravidian and Indo-European-speakers from India and populations from East and Southeast Asia speaking languages belonging to different linguistic families. We showed that the Munda from Northeast India exhibit a peculiar genetic profile with a reduced level of HLA diversity compared to surrounding Indian populations. They also exhibit less diversity than Southeast Asian populations except at locus DRB1. Several analyses using genetic distances indicate that the Munda are much more closely related to populations from the Indian subcontinent than to Southeast Asian populations speaking languages of the same Austroasiatic linguistic family. On the other hand, they do not share a closer relationship with Dravidians compared with Indo-Europeans, thus arguing against the idea that the Munda share a common and ancient Indian origin with Dravidians. Our results do not favor either a scenario where the Munda would be representative of an ancestral Austroasiatic population giving rise to an eastward Austroasiatic expansion to Southeast Asia. Rather, their peculiar genetic profile is better explained by a decrease in genetic diversity through genetic drift from an ancestral population having a genetic profile similar to present-day Austroasiatic populations from Southeast Asia (thus suggesting a possible southeastern origin), followed by intensive gene flow with neighboring Indian populations. This conclusion is in agreement with archaeological and linguistic information. The history of the Austroasiatic family represents a fascinating example where complex interactions among culturally distinct human populations occurred in the past.
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Affiliation(s)
- Maria Eugenia Riccio
- Laboratory of Anthropology, Genetics, and Peopling History (AGP), Laboratory of Anthropology, Genetics, and Peopling History (AGP), Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Switzerland.
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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.
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Affiliation(s)
- Kouichi Kurose
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
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18
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Ali S, Chopra R, Aggarwal S, Srivastava AK, Kalaiarasan P, Malhotra D, Gochhait S, Garg VK, Bhattacharya SN, Bamezai RNK. Association of variants in BAT1-LTA-TNF-BTNL2 genes within 6p21.3 region show graded risk to leprosy in unrelated cohorts of Indian population. Hum Genet 2011; 131:703-16. [DOI: 10.1007/s00439-011-1114-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 10/29/2011] [Indexed: 12/19/2022]
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Chhaya S, Desai S, Saranath D. HLA polymorphisms in Sindhi community in Mumbai, India. Int J Immunogenet 2010; 37:373-7. [DOI: 10.1111/j.1744-313x.2010.00936.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Williams R, Chen YF, Endres R, Middleton D, Trucco M, Williams JD, Knowler W. Molecular variation at the HLA-A, B, C, DRB1, DQA1, and DQB1 loci in full heritage American Indians in Arizona: private haplotypes and their evolution. ACTA ACUST UNITED AC 2009; 74:520-33. [PMID: 19845915 DOI: 10.1111/j.1399-0039.2009.01381.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A sample of 492 full heritage, unrelated residents of the Gila River Indian Community (GRIC) of Arizona were characterized for their high-resolution DNA alleles at the HLA-A, B, C, DRB1, DQA1, and DQB1 loci. Only five allelic categories are found at HLA-A, 10 at HLA-B, 8 at HLA-C and HLA-DR, and 4 at DQA1 and DQB1. There is little evidence for population structure at the 6 loci. Two 'private' alleles, B*5102 and B*4005, which are found nearly exclusively in American Indian populations in the desert southwest and northern Mexico, are likely new mutations after the first inhabitation of the area, the evolution of which are reflected in the contemporary distribution of their respective haplotypes. DRB1*1402 has the highest reported frequency of any specificity at the DRB1 locus, 0.7461, and serves as a sensitive probe for locating related east Asian populations. The haplotypes in this population also exhibit a highly restricted distribution and strong genetic disequilibria, which has important implications for matching solid organ and bone marrow allografts. It is shown that, when one considers HLA-A-B-DRB1 homozygotes as allograft donors for all full heritage members of the GRIC, 50% of the community would find a non-mismatched organ within the homozygotes for the six most common haplotypes. This raises questions about transplantation policy and whether, in the presence of high-frequency private alleles and a restricted number of haplotypes, the full heritage American Indian community of the desert southwest should act as its own pool of donors for its affected members.
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Affiliation(s)
- R Williams
- National Institutes of Health, Institute of Diabetes and Digestive and Kidney Diseases, Diabetes Epidemiology and Clinical Research Section, Phoenix, AZ, USA.
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Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies. Hum Immunol 2008; 69:443-64. [PMID: 18638659 DOI: 10.1016/j.humimm.2008.05.001] [Citation(s) in RCA: 260] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 05/03/2008] [Accepted: 05/07/2008] [Indexed: 12/21/2022]
Abstract
This paper presents a meta-analysis of high-resolution human leukocyte antigen (HLA) allele frequency data describing 497 population samples. Most of the datasets were compiled from studies published in eight journals from 1990 to 2007; additional datasets came from the International Histocompatibility Workshops and from the AlleleFrequencies.net database. In all, these data represent approximately 66,800 individuals from throughout the world, providing an opportunity to observe trends that may not have been evident at the time the data were originally analyzed, especially with regard to the relative importance of balancing selection among the HLA loci. Population genetic measures of allele frequency distributions were summarized across populations by locus and geographic region. A role for balancing selection maintaining much of HLA variation was confirmed. Further, the breadth of this meta-analysis allowed the ranking of the HLA loci, with DQA1 and HLA-C showing the strongest balancing selection and DPB1 being compatible with neutrality. Comparisons of the allelic spectra reported by studies since 1990 indicate that most of the HLA alleles identified since 2000 are very-low-frequency alleles. The literature-based allele-count data, as well as maps summarizing the geographic distributions for each allele, are available online.
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