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Abolnezhadian F, Iranparast S, Shohan M, Shokati Eshkiki Z, Hamed M, Seyedtabib M, Nashibi R, Assarehzadegan MA, Mard SA, Shayesteh AA, Neisi N, Makvandi M, Alavi SM, Shariati G. Evaluation the frequencies of HLA alleles in moderate and severe COVID-19 patients in Iran: A molecular HLA typing study. Heliyon 2024; 10:e28528. [PMID: 38590857 PMCID: PMC10999921 DOI: 10.1016/j.heliyon.2024.e28528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/16/2023] [Accepted: 03/20/2024] [Indexed: 04/10/2024] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 was first reported in December 2019 and it has spread globally ever since. The HLA system is crucial in directing anti-viral immunity and recent studies are investigating the possible involvement of the HLA genes on the severity of immune inflammation in different phases of COVID-19. Methods In this cross-sectional study, peripheral blood-extracted genomic DNAs of 109 COVID-19 patients and 70 healthy controls were genotyped for different alleles of HLA-A, HLA-B, and HLA-DRB1 loci using sequence-specific primer PCR method. Results The results indicated that frequencies of HLA-DRB1*11:01 and HLA-DRB1*04:03 were significantly higher in severe patients rather than moderates (p: <0.001 and 0.004, respectively). Also, it was observed that HLA-DRB1*04:01 was more frequent in moderate patients and healthy controls (p:0.002). In addition, HLA-B*07:35, and HLA-DRB1*07:01 showed higher frequencies in patients compared with controls (p: 0.031 and 0.003 respectively). Inversely, due to the higher frequencies of HLA-B*51:01 (p:0.027), HLA-DRB1*11:05 (p:0.003), HLA-DRB1*13:05 (p:0.022), and HLA-DRB1*14:01 (p:0.006) in healthy individuals rather than patients, they may be associated with COVID-19 resistance. Conclusion The results show that, based on the population differences, the type of alleles related to the severity of COVID-19 is different, which should be clarified by designing large-scale studies in order to develop HLA-based treatments and vaccines.
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Affiliation(s)
- Farhad Abolnezhadian
- Department of Pediatrics, Abuzar Children's Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sara Iranparast
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Mojtaba Shohan
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Zahra Shokati Eshkiki
- Alimentary Tract Research Center, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mahtab Hamed
- Immunobiology Center of Pasteur Medical Laboratory, Ahvaz, Iran
| | - Maryam Seyedtabib
- Department of Biostatistics & Epidemiology, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Roohangiz Nashibi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad-Ali Assarehzadegan
- Immunology Research Center, Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Ali Mard
- Physiology Research Center, Research Institute for Infectious Diseases of Digestive System and Department of Physiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Akbar Shayesteh
- Alimentary Tract Research Center, Imam Khomeini Hospital Clinical Research Development Unit, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Niloofar Neisi
- Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Manoochehr Makvandi
- Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Seyed Mohammad Alavi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Gholamreza Shariati
- Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Ravazzi-Gauch C, Marzochi LL, Bajay MM, Medeiros MP, Caldas HC, Abbud-Filho M. Influence of HLA-A, B, and -DRB1 genes and panel-reactive antibodies on the waitlist time for kidney transplantation in the state of Sao Paulo-Brazil. Transpl Immunol 2024; 83:101981. [PMID: 38184218 DOI: 10.1016/j.trim.2023.101981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/19/2023] [Accepted: 12/31/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND Brazil ranks second in the absolute number of transplants. However, the supply remains insufficient to meet the demands, resulting in a lengthy waitlist. This study aimed to analyze whether the frequency of human leukocyte antigen (HLA) and the value of calculated panel reactive antibody (cPRA) would influence the waiting time for kidney transplantation. METHODS The HLA-A, B, and -DRB1 frequencies and the cPRA value were analyzed in 11,186 kidney transplant candidates included in the waitlist from 2006 to 2016. RESULTS The most frequent alleles were HLA-A*02, HLA-B*35, and HLA-DRB1*13. The overall mean length of stay on the list was 986 ± 1001 days. The mean waiting time for the three most frequent alleles of the HLA-A and B loci showed no significant difference when compared with the least frequent alleles; however, for the HLA-DRB1 locus, the most frequent alleles showed a shorter waiting time. In the association between HLA and PRA, the average length of stay on the list increased according to the candidate's degree of sensitization, regardless of the analyzed HLA frequency. CONCLUSION The length of stay on the waitlist is influenced by the frequency of the HLA alleles of the DRB1 locus and the degree of sensitization.
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Affiliation(s)
- Camila Ravazzi-Gauch
- Laboratory of Immunology and Experimental Transplantation-LITEX, Medical School of São José do Rio Preto-FAMERP, SP, Brazil
| | - Ludimila Leite Marzochi
- Laboratory of Immunology and Experimental Transplantation-LITEX, Medical School of São José do Rio Preto-FAMERP, SP, Brazil
| | | | | | - Heloisa Cristina Caldas
- Laboratory of Immunology and Experimental Transplantation-LITEX, Medical School of São José do Rio Preto-FAMERP, SP, Brazil
| | - Mario Abbud-Filho
- Laboratory of Immunology and Experimental Transplantation-LITEX, Medical School of São José do Rio Preto-FAMERP, SP, Brazil.
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Saenz Hinojosa S, Adrian Jinam T, Hosomichi K, Romero VI. HLA allelic diversity in the Waorani population of Ecuador: Its significance to their ancestry and migration. Hum Immunol 2024:110771. [PMID: 38443236 DOI: 10.1016/j.humimm.2024.110771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/09/2024] [Accepted: 02/28/2024] [Indexed: 03/07/2024]
Abstract
The Waorani, an isolated indigenous tribe in Ecuador, have long been characterized by limited genetic diversity, with few studies delving into their genetic background. Human Leukocyte Antigen (HLA) genes which are located in the human major histocompatibility complex (MHC) provides valuable insights into population evolution due to its highly polymorphic nature. However, little is known about the HLA diversity and ancestry of the Waorani population. In this study, we sequenced eight HLA genes using Next Generation Sequencing (NGS) from 134 Waorani individuals and obtained up to four-field HLA allele resolution. Cluster and phylogenetic analysis show that the Waorani are genetically distant from other Ecuador populations, but instead show genetic affinities with the Puyanawa and Terena tribes from Brazil, as well as the Mixe tribe from Mexico. The identification of alleles common within the Waorani population, previously linked to specific health conditions, notably paves the way for future association analyses. This extensive study, employing Next-Generation Sequencing (NGS) technology, significantly enriches the sparse and segmented understanding of HLA diversity in the South American region. Our findings enhance the global comprehension of human genetic diversity and underscore the value of studying indigenous populations. Such research is vital for deepening our insights into human migration patterns and evolutionary processes.
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Affiliation(s)
| | - Timothy Adrian Jinam
- Department of Para-Clinical Sciences, Faculty of Medicine & Health Sciences, University Malaysia Sarawak, Malaysia
| | - Kazuyoshi Hosomichi
- Laboratory of Computational Genomics, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Vanessa I Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador.
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Kouniaki DI, Fotopoulos KV, Tarassi K, Tsirogianni A. Utilizing Massively Parallel Sequencing (MPS) of Human Leukocyte Antigen (HLA) Gene Polymorphism to Assess Relatedness in Deficiency Parentage Testing. Genes (Basel) 2024; 15:150. [PMID: 38397140 PMCID: PMC10888046 DOI: 10.3390/genes15020150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/13/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
In the realm of DNA testing with legal implications, the reliability and precision of genetic markers play a pivotal role in confirming or negating paternity claims. This study aimed to assess the potential utility of human leukocyte antigen (HLA) gene polymorphism through massively parallel sequencing (MPS) technology as robust forensic markers for parentage testing involving genetic deficiencies. It sought to redefine the significance of HLA genes in this context. Data on autosomal short tandem repeat (aSTR) mutational events across 18 paternity cases involving 16 commonly employed microsatellite loci were presented. In instances where traditional aSTR analysis failed to establish statistical certainty, kinship determination was pursued via HLA genotyping, encompassing the amplification of 17 linked HLA loci. Within the framework of this investigation, phase-resolved genotypes for HLA genes were meticulously generated, resulting in the definition of 34 inherited HLA haplotypes. An impressive total of 274 unique HLA alleles, which were classified at either the field 3 or 4 level, were identified, including the discovery of four novel HLA alleles. Likelihood ratio (LR) values, which indicated the likelihood of the observed data under a true biological relationship versus no relationship, were subsequently calculated. The analysis of the LR values demonstrated that the HLA genes significantly enhanced kinship determination compared with the aSTR analysis. Combining LR values from aSTR markers and HLA loci yielded conclusive outcomes in duo paternity cases, showcasing the potential of HLA genes and MPS technology for deeper insights and diversity in genetic testing. Comprehensive reference databases and high-resolution HLA typing across diverse populations are essential. Reintegrating HLA alleles into forensic identification complements existing markers, creating a potent method for future forensic analysis.
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Affiliation(s)
- Diamanto I. Kouniaki
- Immunology and Histocompatibility Department, Evangelismos General Hospital, 10676 Athens, Greece; (D.I.K.); (K.T.)
| | - Konstantinos V. Fotopoulos
- School of Electrical and Computer Engineering, National Technical University of Athens (ECE-NTUA), 15772 Zografou, Greece;
| | - Katerina Tarassi
- Immunology and Histocompatibility Department, Evangelismos General Hospital, 10676 Athens, Greece; (D.I.K.); (K.T.)
| | - Alexandra Tsirogianni
- Immunology and Histocompatibility Department, Evangelismos General Hospital, 10676 Athens, Greece; (D.I.K.); (K.T.)
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Hoseinnezhad T, Soltani N, Ziarati S, Behboudi E, Mousavi MJ. The role of HLA genetic variants in COVID-19 susceptibility, severity, and mortality: A global review. J Clin Lab Anal 2024; 38:e25005. [PMID: 38251811 PMCID: PMC10829690 DOI: 10.1002/jcla.25005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic has had a profound global impact, with variations in susceptibility, severity, and mortality rates across different regions. While many factors can contribute to the spread and impact of the disease, specifically human leukocyte antigen (HLA) genetic variants have emerged as potential contributors to COVID-19 outcomes. METHODS In this comprehensive narrative review, we conducted a thorough literature search to identify relevant studies investigating the association between HLA genetic variants and COVID-19 outcomes. Additionally, we analyzed allelic frequency data from diverse populations to assess differences in COVID-19 incidence and severity. RESULTS Our review provides insights into the immunological mechanisms involving HLA-mediated responses to COVID-19 and highlights potential research directions and therapeutic interventions. We found evidence suggesting that certain HLA alleles, such as HLA-A02, may confer a lower risk of COVID-19, while others, like HLA-C04, may increase the risk of severe symptoms and mortality. Furthermore, our analysis of allele frequency distributions revealed significant variations among different populations. CONCLUSION Considering host genetic variations, particularly HLA genetic variants, is crucial for understanding COVID-19 susceptibility and severity. These findings have implications for personalized treatment and interventions based on an individual's genetic profile. However, further research is needed to unravel the precise mechanisms underlying the observed associations and explore the potential for targeted therapies or preventive measures based on HLA genetic variants.
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Affiliation(s)
- Taraneh Hoseinnezhad
- Student Research CommitteeBushehr University of Medical SciencesBushehrIran
- Department of Hematology, School of Para‐MedicineBushehr University of Medical SciencesBushehrIran
| | - Nasrin Soltani
- Student Research CommitteeBushehr University of Medical SciencesBushehrIran
- Department of Hematology, School of Para‐MedicineBushehr University of Medical SciencesBushehrIran
| | - Sarina Ziarati
- Student Research CommitteeBushehr University of Medical SciencesBushehrIran
| | - Emad Behboudi
- Department of Basic Medical SciencesKhoy University of Medical SciencesKhoyIran
| | - Mohammad Javad Mousavi
- Department of Hematology, School of Para‐MedicineBushehr University of Medical SciencesBushehrIran
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Chang SL, Lai CH, Lin GC, Chen YM, Lee MH, Hsu HS, Chen IC. Genetic Susceptibility of HLA Alleles to Non-Steroidal Anti-Inflammatory Drug Hypersensitivity in the Taiwanese Population. Biomedicines 2023; 11:3273. [PMID: 38137494 PMCID: PMC10741656 DOI: 10.3390/biomedicines11123273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Human leukocyte antigen (HLA) genes are important in many immune processes and contribute to many adverse drug reactions. Whether genetic variations in the HLA region are associated with non-steroid anti-inflammatory drug (NSAID) hypersensitivity remains uncertain. Therefore, the aim of our study was to identify HLA genetic variations in patients with NSAID hypersensitivity in the Taiwanese population. METHODS This hospital-based, retrospective case-control study enrolled 37,156 participants with NSAID exposure from the Taiwan Precision Medicine Initiative (TPMI), who were all genotyped and imputed to fine map HLA typing. Our study assigned 1217 cases to the NSAID allergy group and 12,170 controls to a matched group. Logistic regression analyses were utilized to explore associations between HLA alleles and NSAID hypersensitivity. RESULTS Overall, 13,387 patients were genotyped for eight major HLA alleles. Allele frequencies were different between the two groups. In the NSAID allergy group, the genotype frequencies of HLA-A*02:01, HLA-A*34:01, and HLA-DQA1*06:01 were found to be markedly elevated compared to the control group, a significance that persisted even after applying the Bonferroni correction. Furthermore, the risk of NSAID allergy demonstrated a significant association with HLA-A*02:01 (OR = 1.29, p < 0.001) and HLA-A*34:01 (OR = 9.90, p = 0.001), in comparison to their respective counterparts. Notably, the genotype frequency of HLA-B*46:01 exhibited a significant increase in the severe allergy group when compared with the mild allergy group. CONCLUSIONS We identified HLA genotypes linked to the onset and severity of NSAID hypersensitivity. Our findings establish a basis for precision prescription in future clinical applications.
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Affiliation(s)
- Szu-Ling Chang
- Department of Anesthesiology, Taichung Veterans General Hospital, Taichung 407219, Taiwan;
- Department of Postbaccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402202, Taiwan; (C.-H.L.); (Y.-M.C.)
- Institute of Emergency and Critical Care Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Chih-Hung Lai
- Department of Postbaccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402202, Taiwan; (C.-H.L.); (Y.-M.C.)
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medicine and Cardiovascular Center, Taichung Veterans General Hospital, Taichung 407219, Taiwan
| | - Guan-Cheng Lin
- Department of Medical Research, Taichung Veterans General Hospital, Taichung 407219, Taiwan;
| | - Yi-Ming Chen
- Department of Postbaccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402202, Taiwan; (C.-H.L.); (Y.-M.C.)
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taichung Veterans General Hospital, Taichung 407219, Taiwan;
- Division of Allergy, Immunology and Rheumatology, Department of Medical Research, Taichung Veterans General Hospital, Taichung 407219, Taiwan
- Institute of Biomedical Science and Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 402202, Taiwan
| | - Mei-Hsuan Lee
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan;
| | - Han-Shui Hsu
- Institute of Emergency and Critical Care Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Division of Thoracic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 112201, Taiwan
| | - I-Chieh Chen
- Department of Medical Research, Taichung Veterans General Hospital, Taichung 407219, Taiwan;
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Tahamoli-Roudsari A, Rahmani F, Afshar S, Hajilooi M, Solgi G. Expression patterns of T cells-specific long noncoding RNAs in systemic lupus erythematosus patients carrying HLA risk/nonrisk alleles. Lupus 2023; 32:1188-1198. [PMID: 37610356 DOI: 10.1177/09612033231196626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
BACKGROUND Long noncoding RNAs (LncRNAs) play key roles in the regulation of gene expression and subsequently in the pathogenesis of several autoimmune diseases. This study aimed to explore the peripheral expression levels of T-cells-specific LncRNAs and transcription factors in systemic lupus erythematosus (SLE) patients carrying either human leukocyte antigens (HLA) risk or non-risk alleles. METHODS Genotypes of HLA-DRB1 and HLA-DQB1 loci for 106 SLE patients were determined by PCR-SSP. In the next step, patients were stratified based on the presence of HLA-DRB1*03 and/or DRB1*16 allele groups (HLA risk alleles positive or HLA-RPos) or carrying other DRB1 allele groups (HLA-RNeg). Then, transcript levels of LncRNAs (IFNG-AS1, RMRP, Th2LCR, and DQ786243) and mRNAs for transcription factors (Foxp3, Gata3, and Tbx21) were measured using qRT-PCR and compared between two subgroups of patients. RESULTS Totally, 47 cases were classified as HLA-RPos and 59 cases as HLA-RNeg patients. The HLA-RPos patients showed decreased transcript levels of DQ786243 (p = .001) and elevated expression of IFNG-AS1 (p = .06) and T-bet mRNA (p = .03) compared to the HLA-RNeg group. We observed significantly lower expression of Th2LCR (p < .0001) and DQ786243 (p = .001) and higher expression of Tbx21 (p = .009) and Foxp3 (p = .02) in DR3-positive versus DR3-negative patients. Likewise, decreased transcript levels of DQ786243 (p = .02) and RMRP (p = .003) were observed in DR16-positive versus DR16-negative patients. ROC curve analysis revealed the potential of DQ786243 and RMRP as biomarkers in SLE disease based on the carriage of HLA risk alleles. CONCLUSIONS Our results indicate that the contribution of multiple T cell subsets in SLE disease progression as judged by expression analysis of LncRNAs and transcription factors can be inspired by the inheritance of HLA risk/nonrisk alleles is SLE patients.
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Affiliation(s)
- Ahmad Tahamoli-Roudsari
- School of Medicine, Department of Internal Diseases Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Fatemeh Rahmani
- School of Medicine, Department of Immunology, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Saeid Afshar
- School of Medicine, Department of Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mehrdad Hajilooi
- School of Medicine, Department of Immunology, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ghasem Solgi
- School of Medicine, Department of Immunology, Hamadan University of Medical Sciences, Hamadan, Iran
- Cancer Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
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Grubic Z, Maskalan M, Burek Kamenaric M, Desnica L, Mikulic M, Stingl Jankovic K, Durakovic N, Serventi Seiwerth R, Vrhovac R, Zunec R. Alternative donor strategy in unrelated hematopoietic stem cell transplantation - outcome with mismatched donors. Adv Med Sci 2023; 68:332-340. [PMID: 37741003 DOI: 10.1016/j.advms.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 04/06/2023] [Accepted: 09/06/2023] [Indexed: 09/25/2023]
Abstract
PURPOSE This study retrospectively investigated the association between the level of human leukocyte antigen (HLA) mismatches (MMs), direction of disparities and differences at particular HLA locus on clinical outcomes of hematopoietic stem cell transplantation (HSCT). Investigated outcomes were overall survival (OS) and disease-free survival (DFS), graft-versus-host disease (GvHD), relapse and non-relapse mortality (NRM). PATIENTS AND METHODS Study cohort included 108 adult patients transplanted between 2011 and 2021 and their 9/10 mismatched unrelated donors (MMUD). All individuals were typed for HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 loci using Polymerase Chain Reaction-Sequence Specific Primers, PCR-Sequence Based Typing and Next-Generation Sequencing. All statistical analyses were done in the MedCalc software, version 19.2.6. RESULTS Patients with MMs at HLA-B locus demonstrated worse OS (P = 0.0440, HR = 2.00, n = 20). Absence of HLA-DRB5 was associated with a higher incidence of GvHD (P = 0.0112, HR = 1.93, n = 67). A lower incidence of GvHD was observed in patients with HLA class II MMs compared to patients with HLA class I MMs (P = 0.0166, HR = 1.94, n = 29). Finally, analysis of PIRCHE score (PS) impact revealed that patients with HLA class II PS > 10 in GvH direction showed higher incidence of GvHD compared to patients with HLA class II PS < 10 (P = 0.0073, HR = 2.01, n = 55). CONCLUSION Obtained results undisputedly indicate the necessity to further investigate this matter on a larger patient group, with focus on specific HLA alleles to define precisely priority criteria for selecting the best donor for all patients, thus improving the outcome of HSCT with an MMUD.
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Affiliation(s)
- Zorana Grubic
- Tissue Typing Centre, Clinical Department for Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia.
| | - Marija Maskalan
- Tissue Typing Centre, Clinical Department for Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Marija Burek Kamenaric
- Tissue Typing Centre, Clinical Department for Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Lana Desnica
- Department of Hematology, Internal Clinic, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Mirta Mikulic
- Department of Hematology, Internal Clinic, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Katarina Stingl Jankovic
- Tissue Typing Centre, Clinical Department for Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Nadira Durakovic
- Department of Hematology, Internal Clinic, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Ranka Serventi Seiwerth
- Department of Hematology, Internal Clinic, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Radovan Vrhovac
- Department of Hematology, Internal Clinic, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Renata Zunec
- Tissue Typing Centre, Clinical Department for Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
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Angelakakis G, Serraneau KS, Barker VR, Callahan BM, Tong WL, Zaman S, Huda TI, Blanck G. TCR gene segment usage and HLA alleles that are associated with cancer survival rates also represent racial disparities. Int J Immunogenet 2023; 50:41-47. [PMID: 36585798 DOI: 10.1111/iji.12610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 01/01/2023]
Abstract
Understanding racial disparities in cancer outcomes continues to be a challenge, with likely many factors at play, including socioeconomic factors and genetic polymorphisms impacting basic cellular and molecular functions. Additionally, it is possible that specific combinations of environment and genetics have specific impacts. T-cell receptor (TCR) gene segment usage, HLA allele combinations have been associated with autoimmune and infectious disease courses, and more recently, TCR gene segment usage, HLA allele combinations have been associated with distinct survival outcomes in cancer as well. We examined several such, previously reported cancer-related TCR gene segment usage, HLA allele combinations for evidence of racial disparities, with regard to the prevalence of the combination in different racial groups. Results indicated that TCR gene segment usage, potentially reflecting environmental factors related to previous pathogen exposure, in combination with certain HLA alleles or independently, may represent a novel explanation for racial disparities in cancer outcomes. Overall, at this point, a genetic connection to racial disparities in cancer outcomes is detectable but remains modest, suggesting that other factors, such as socioeconomic factors, remain as important considerations.
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Affiliation(s)
- George Angelakakis
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Karisa S Serraneau
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Vayda R Barker
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Blake M Callahan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Wei Lue Tong
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Saif Zaman
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Taha I Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA.,Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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Fakhkhari M, Caidi H, Sadki K. HLA alleles associated with COVID-19 susceptibility and severity in different populations: a systematic review. Egypt J Med Hum Genet 2023; 24:10. [PMID: 36710951 PMCID: PMC9867832 DOI: 10.1186/s43042-023-00390-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/15/2023] [Indexed: 01/23/2023] Open
Abstract
Background COVID-19 is a respiratory disease caused by a novel coronavirus called as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Detected for the first time in December 2019 in Wuhan and it has quickly spread all over the world in a couple of months and becoming a world pandemic. Symptoms of the disease and clinical outcomes are very different in infected people. These differences highlight the paramount need to study and understand the human genetic variation that occurring viral infections. Human leukocyte antigen (HLA) is an important component of the viral antigen presentation pathway, and it plays an essential role in conferring differential viral susceptibility and severity of diseases. HLA alleles have been involved in the immune response to viral diseases such as SARS-CoV-2. Main body of the abstract Herein, we sought to evaluate this hypothesis by summarizing the association between HLA class I and class II alleles with COVID-19 susceptibility and/or severity reported in previous studies among different populations (Chinese, Italian, Iranian, Japanese, Spanish, etc.). The findings of all selected articles showed that several alleles have been found associated with COVID-19 susceptibility and severity. Even results across articles have been inconsistent and, in some cases, conflicting, highlighting that the association between the HLA system and the COVID-19 outcome might be ethnic-dependent, there were some alleles in common between some populations such as HLA-DRB1*15 and HLA-A*30:02. Conclusion These contradictory findings warrant further large, and reproducible studies to decipher any possible genetic predisposition underlying susceptibility to SARS-COV-2 and disease progression and host immune response.
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Affiliation(s)
- Meryem Fakhkhari
- grid.31143.340000 0001 2168 4024Research Laboratory in Oral Biology and Biotechnology, Faculty of Dental Medicine, Mohammed V University in Rabat, Rabat, Morocco
| | - Hayat Caidi
- grid.416738.f0000 0001 2163 0069NARST Surveillance Unit, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Khalid Sadki
- grid.31143.340000 0001 2168 4024Research Laboratory in Oral Biology and Biotechnology, Faculty of Dental Medicine, Mohammed V University in Rabat, Rabat, Morocco
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Prem S, Remberger M, Alotaibi A, Lam W, Law AD, Kim DDH, Michelis FV, Al-Shaibani Z, Lipton JH, Mattsson J, Viswabandya A, Kumar R, Ellison C. Relationship between certain HLA alleles and the risk of cytomegalovirus reactivation following allogeneic hematopoietic stem cell transplantation. Transpl Infect Dis 2022; 24:e13879. [PMID: 35706108 DOI: 10.1111/tid.13879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/20/2022] [Accepted: 05/31/2022] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Evidence is emerging to support an association between certain HLA alleles and the risk of cytomegalovirus (CMV) reactivation following allogeneic HSCT (allo-HSCT). The primary aim of this study was to identify HLA alleles associated with resistance or susceptibility to CMV reactivation. METHODS We studied 586 adults who underwent allo-HSCT for high-risk hematological malignancies. High resolution HLA typing data was available for recipient and donor. HLA Class I and II alleles observed at a frequency of > 5% in our population, were included in the analysis. A CMV viremia level of more than 200 IU/ml on weekly monitoring was considered to be indicative of CMV reactivation. RESULTS The median follow-up time in surviving patients was 21 months (range 4-74 months). The cumulative incidence of CMV reactivation at 6 months in the entire cohort was 55% (95% CI 50.8%-59.2%). Mismatched donor, increasing recipient age, occurrence of AGVHD and recipient CMV seropositivity were associated with increased risk of CMV reactivation. HLA B*07:02 (HR 0.59, 95% CI 0.40-0.83) was associated with decreased risk of CMV reactivation. Patients who developed CMV reactivation had a lower incidence of relapse, higher transplant related mortality (TRM) and lower overall survival (OS) compared to those without CMV reactivation. There was an adverse correlation of OS and TRM with increasing numbers of CMV reactivations. CONCLUSION We observed that HLA B*07:02 was associated with decreased risk of CMV reactivation. CMV reactivation was associated with lower relapse post-transplant, but this did not translate into a survival benefit due to higher transplant related mortality. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shruti Prem
- University of Toronto, Department of Medicine, Section of Medical Oncology and Hematology.,Hans Messner Allogeneic Blood and Marrow Transplantation Program, Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mats Remberger
- Department of Medical Sciences, Uppsala University and KFUE, Uppsala University Hospital, Uppsala, Sweden
| | - Ahmad Alotaibi
- University of Toronto, Department of Medicine, Section of Medical Oncology and Hematology.,Hans Messner Allogeneic Blood and Marrow Transplantation Program, Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Wilson Lam
- University of Toronto, Department of Medicine, Section of Medical Oncology and Hematology.,Hans Messner Allogeneic Blood and Marrow Transplantation Program, Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Arjun Datt Law
- University of Toronto, Department of Medicine, Section of Medical Oncology and Hematology.,Hans Messner Allogeneic Blood and Marrow Transplantation Program, Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Dennis Dong Hwan Kim
- University of Toronto, Department of Medicine, Section of Medical Oncology and Hematology.,Hans Messner Allogeneic Blood and Marrow Transplantation Program, Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Fotios V Michelis
- University of Toronto, Department of Medicine, Section of Medical Oncology and Hematology.,Hans Messner Allogeneic Blood and Marrow Transplantation Program, Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Zeyad Al-Shaibani
- University of Toronto, Department of Medicine, Section of Medical Oncology and Hematology.,Hans Messner Allogeneic Blood and Marrow Transplantation Program, Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jeffrey Howard Lipton
- University of Toronto, Department of Medicine, Section of Medical Oncology and Hematology.,Hans Messner Allogeneic Blood and Marrow Transplantation Program, Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jonas Mattsson
- University of Toronto, Department of Medicine, Section of Medical Oncology and Hematology.,Hans Messner Allogeneic Blood and Marrow Transplantation Program, Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Auro Viswabandya
- University of Toronto, Department of Medicine, Section of Medical Oncology and Hematology.,Hans Messner Allogeneic Blood and Marrow Transplantation Program, Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rajat Kumar
- University of Toronto, Department of Medicine, Section of Medical Oncology and Hematology.,Hans Messner Allogeneic Blood and Marrow Transplantation Program, Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Cynthia Ellison
- HLA Laboratory, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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12
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Cios KJ, Huda TI, Eakins RA, Mihyu MM, Blanck G. Specific TCR V-J gene segment recombinations leading to the identification pan-V-J CDR3s associated with survival distinctions: diffuse large B-cell lymphoma. Leuk Lymphoma 2022; 63:1314-1322. [PMID: 35019822 DOI: 10.1080/10428194.2021.2020781] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In the diffuse large B-cell lymphoma (DLBCL) setting, we examined lymph node biopsy, T-cell receptor features, and the DLBLC patient human leukocyte antigen (HLA) alleles, to provide a basis for assessing survival distinctions represented by the National Cancer Institute Center for Cancer Research (NCICCR) dataset. While previous analyses of other cancer datasets have indicated that specific T-cell receptor (TCR) V or J gene segments, independently, can be associated with a survival distinction, we have here identified V-J recombinations, representing specific V and J gene segments associated with survival distinctions. As specific V-J recombinations represent relatively conserved complementarity determining region-3 (CDR3) amino acid sequences, we assessed the entire DLBCL NCICCR dataset for such conserved CDR3 features. Overall, this approach indicated the opportunity of identifying DLBCL patient subpopulations with TCR CDR3 features, and HLA alleles, with significant survival distinctions, possibly identifying cohorts more likely to benefit from a given immunotherapy.
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Affiliation(s)
- Konrad J Cios
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Taha I Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Rachel A Eakins
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Moody M Mihyu
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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13
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Dholakia D, Kalra A, Misir BR, Kanga U, Mukerji M. HLA-SPREAD: a natural language processing based resource for curating HLA association from PubMed abstracts. BMC Genomics 2022; 23:10. [PMID: 34991484 PMCID: PMC8740486 DOI: 10.1186/s12864-021-08239-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022] Open
Abstract
Extreme complexity in the Human Leukocyte Antigens (HLA) system and its nomenclature makes it difficult to interpret and integrate relevant information for HLA associations with diseases, Adverse Drug Reactions (ADR) and Transplantation. PubMed search displays ~ 146,000 studies on HLA reported from diverse locations. Currently, IPD-IMGT/HLA (Robinson et al., Nucleic Acids Research 48:D948-D955, 2019) database houses data on 28,320 HLA alleles. We developed an automated pipeline with a unified graphical user interface HLA-SPREAD that provides a structured information on SNPs, Populations, REsources, ADRs and Diseases information. Information on HLA was extracted from ~ 28 million PubMed abstracts extracted using Natural Language Processing (NLP). Python scripts were used to mine and curate information on diseases, filter false positives and categorize to 24 tree hierarchical groups and named Entity Recognition (NER) algorithms followed by semantic analysis to infer HLA association(s). This resource from 109 countries and 40 ethnic groups provides interesting insights on: markers associated with allelic/haplotypic association in autoimmune, cancer, viral and skin diseases, transplantation outcome and ADRs for hypersensitivity. Summary information on clinically relevant biomarkers related to HLA disease associations with mapped susceptible/risk alleles are readily retrievable from HLASPREAD. The resource is available at URL http://hla-spread.igib.res.in/ . This resource is first of its kind that can help uncover novel patterns in HLA gene-disease associations.
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Affiliation(s)
- Dhwani Dholakia
- Institute of Genomics and Integrative Biology-Council of Scientific and Industrial Research, New Delhi, 110025, India.
- Academy of Scientific and Innovative Research, Ghaziabad, 201002, India.
| | - Ankit Kalra
- Netaji Subhas University of Technology, New Delhi, 110078, India
| | - Bishnu Raman Misir
- Centre of Excellence for Applied Development of Ayurveda, Prakriti and Genomics, CSIR- IGIB, Delhi, 110007, India
| | - Uma Kanga
- All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Mitali Mukerji
- Institute of Genomics and Integrative Biology-Council of Scientific and Industrial Research, New Delhi, 110025, India.
- Centre of Excellence for Applied Development of Ayurveda, Prakriti and Genomics, CSIR- IGIB, Delhi, 110007, India.
- Present Address: Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, 342037, India.
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14
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Francisco Junior RDS, Temerozo JR, Ferreira CDS, Martins Y, Souza TML, Medina-Acosta E, de Vasconcelos ATR. Differential haplotype expression in class I MHC genes during SARS-CoV-2 infection of human lung cell lines. Front Immunol 2022; 13:1101526. [PMID: 36818472 PMCID: PMC9929942 DOI: 10.3389/fimmu.2022.1101526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/19/2022] [Indexed: 02/05/2023] Open
Abstract
Introduction Cell entry of SARS-CoV-2 causes genome-wide disruption of the transcriptional profiles of genes and biological pathways involved in the pathogenesis of COVID-19. Expression allelic imbalance is characterized by a deviation from the Mendelian expected 1:1 expression ratio and is an important source of allele-specific heterogeneity. Expression allelic imbalance can be measured by allele-specific expression analysis (ASE) across heterozygous informative expressed single nucleotide variants (eSNVs). ASE reflects many regulatory biological phenomena that can be assessed by combining genome and transcriptome information. ASE contributes to the interindividual variability associated with the disease. We aim to estimate the transcriptome-wide impact of SARS-CoV-2 infection by analyzing eSNVs. Methods We compared ASE profiles in the human lung cell lines Calu-3, A459, and H522 before and after infection with SARS-CoV-2 using RNA-Seq experiments. Results We identified 34 differential ASE (DASE) sites in 13 genes (HLA-A, HLA-B, HLA-C, BRD2, EHD2, GFM2, GSPT1, HAVCR1, MAT2A, NQO2, SUPT6H, TNFRSF11A, UMPS), all of which are enriched in protein binding functions and play a role in COVID-19. Most DASE sites were assigned to the MHC class I locus and were predominantly upregulated upon infection. DASE sites in the MHC class I locus also occur in iPSC-derived airway epithelium basal cells infected with SARS-CoV-2. Using an RNA-Seq haplotype reconstruction approach, we found DASE sites and adjacent eSNVs in phase (i.e., predicted on the same DNA strand), demonstrating differential haplotype expression upon infection. We found a bias towards the expression of the HLA alleles with a higher binding affinity to SARS-CoV-2 epitopes. Discussion Independent of gene expression compensation, SARS-CoV-2 infection of human lung cell lines induces transcriptional allelic switching at the MHC loci. This suggests a response mechanism to SARS-CoV-2 infection that swaps HLA alleles with poor epitope binding affinity, an expectation supported by publicly available proteome data.
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Affiliation(s)
| | - Jairo R Temerozo
- Laboratory on Thymus Research, Oswaldo Cruz Institute (Fiocruz), Rio de Janeiro, Brazil.,National Institute of Science and Technology on Neuroimmunomodulation, Rio de Janeiro, Brazil
| | - Cristina Dos Santos Ferreira
- Bioinformatics Laboratory (LABINFO), National Laboratory of Scientific Computation (LNCC/MCTIC), Petrópolis, Brazil
| | - Yasmmin Martins
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA), Buenos Aires, Argentina
| | - Thiago Moreno L Souza
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil.,Center for Technological Development in Health (CDTS), National Institute for Science and Technology on Innovation on Neglected Diseases Neglected Populations (INCT/IDNP), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - Enrique Medina-Acosta
- Molecular Identification and Diagnostics Unit (NUDIM), Laboratory of Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Brazil
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Savsani K, Jabbour G, Dakshanamurthy S. A New Epitope Selection Method: Application to Design a Multi-Valent Epitope Vaccine Targeting HRAS Oncogene in Squamous Cell Carcinoma. Vaccines (Basel) 2021; 10:vaccines10010063. [PMID: 35062725 PMCID: PMC8778118 DOI: 10.3390/vaccines10010063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 12/22/2022] Open
Abstract
We developed an epitope selection method for the design of MHC targeting peptide vaccines. The method utilizes predictions for several clinical checkpoint filters, including binding affinity, immunogenicity, antigenicity, half-life, toxicity, IFNγ release, and instability. The accuracy of the prediction tools for these filter variables was confirmed using experimental data obtained from the Immune Epitope Database (IEDB). We also developed a graphical user interface computational tool called 'PCOptim' to assess the success of an epitope filtration method. To validate the filtration methods, we used a large data set of experimentally determined, immunogenic SARS-CoV-2 epitopes, which were obtained from a meta-analysis. The validation process proved that placing filters on individual parameters was the most effective method to select top epitopes. For a proof-of-concept, we designed epitope-based vaccine candidates for squamous cell carcinoma, selected from the top mutated epitopes of the HRAS gene. By comparing the filtered epitopes to PCOptim's output, we assessed the success of the epitope selection method. The top 15 mutations in squamous cell carcinoma resulted in 16 CD8 epitopes which passed the clinical checkpoints filters. Notably, the identified HRAS epitopes are the same as the clinical immunogenic HRAS epitope-based vaccine candidates identified by the previous studies. This indicates further validation of our filtration method. We expect a similar turn-around for the other designed HRAS epitopes as a vaccine candidate for squamous cell carcinoma. Furthermore, we obtained a world population coverage of 89.45% for the top MHC Class I epitopes and 98.55% population coverage in the absence of the IFNγ release clinical checkpoint filter. We also identified some of the predicted human epitopes to be strong binders to murine MHC molecules, which provides insight into studying their immunogenicity in preclinical models. Further investigation in murine models could warrant the application of these epitopes for treatment or prevention of squamous cell carcinoma.
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Affiliation(s)
- Kush Savsani
- College of Humanities and Sciences, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Gabriel Jabbour
- School of Medicine, Georgetown University Medical Center, Washington, DC 20057, USA;
| | - Sivanesan Dakshanamurthy
- Molecular and Experimental Therapeutic Research in Oncology Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
- Correspondence: ; Tel.: +1-(202)-687-2347
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16
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Punatar S, Gokarn A, Nayak L, Bonda A, Mirgh S, Chichra A, Singh M, D’silva S, Khattry N. Human leukocyte antigen (HLA) alleles as predictive factors for benefit from lenalidomide in acute myeloid leukemia (AML). Am J Blood Res 2021; 11:564-570. [PMID: 34824888 PMCID: PMC8610794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVES Lenalidomide is an active agent in acute myeloid leukemia (AML); response rates are about 15-30%. There are no well-defined predictive factors for benefit from lenalidomide in AML. One of the mechanisms of lenalidomide is natural killer (NK) cell activation; hence human leukocyte antigen (HLA) class I alleles (serving as killer immunoglobulin-like receptor ligands) could play a predictive role. We here evaluate the same when lenalidomide was used as a bridge to transplant. METHODS Consecutive AML patients started on lenalidomide as bridge to transplant between Aug-2013 to Aug-2018 were included in this single centre retrospective analysis. The starting dose and schedule of lenalidomide were at the discretion of the treating clinician. Lenalidomide was scheduled to be stopped about 2-4 weeks prior to planned transplant admission (or was stopped earlier if there was intolerance). For this study, event was defined as progression/relapse while on lenalidomide or within 4 weeks of stopping the drug. The primary endpoint was event free survival (EFS). Those who underwent transplant without an event were censored on the day of transplant. Toxicities and post-transplant outcomes were secondary endpoints. RESULTS Twelve patients (8 males, median age 29 years) were included. At start of lenalidomide, 7 had complete remission (CR)-1 (measurable residual disease or MRD by flow cytometry was positive in 3, negative in 3, and 1 unknown), 4 CR-2 (all MRD negative) and 1 active disease. In the whole cohort, median EFS was not reached with projected 3 year EFS being 80%. There was a significantly reduced risk of event with HLA A*24 (0% vs 75%, P=0.018) or with HLA B*40 (0% vs 60%, P=0.045). Only 1 patient needed discontinuation due to toxicities (cytopenias). Among patients who underwent transplant, grade II-IV acute graft versus host disease (GVHD) was seen in 83%. CONCLUSIONS This is first study to show that HLA alleles may have a bearing on the effect of lenalidomide in AML and could serve as predictive biomarkers. These findings need to be confirmed in larger prospective studies.
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Affiliation(s)
- Sachin Punatar
- HSCT Unit, Department of Medical Oncology Tata Memorial Centre, HSCT Unit, ACTRECKharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute (HBNI)Anushakti Nagar, Mumbai 410210, India
| | - Anant Gokarn
- HSCT Unit, Department of Medical Oncology Tata Memorial Centre, HSCT Unit, ACTRECKharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute (HBNI)Anushakti Nagar, Mumbai 410210, India
| | - Lingaraj Nayak
- HSCT Unit, Department of Medical Oncology Tata Memorial Centre, HSCT Unit, ACTRECKharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute (HBNI)Anushakti Nagar, Mumbai 410210, India
| | - Avinash Bonda
- HSCT Unit, Department of Medical Oncology Tata Memorial Centre, HSCT Unit, ACTRECKharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute (HBNI)Anushakti Nagar, Mumbai 410210, India
| | - Sumeet Mirgh
- HSCT Unit, Department of Medical Oncology Tata Memorial Centre, HSCT Unit, ACTRECKharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute (HBNI)Anushakti Nagar, Mumbai 410210, India
| | - Akanksha Chichra
- HSCT Unit, Department of Medical Oncology Tata Memorial Centre, HSCT Unit, ACTRECKharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute (HBNI)Anushakti Nagar, Mumbai 410210, India
| | - Meenakshi Singh
- Homi Bhabha National Institute (HBNI)Anushakti Nagar, Mumbai 410210, India
- Transplant Immunology and Immunogenetics, ACTREC, Tata Memorial CentreMumbai 410210, India
| | - Selma D’silva
- Homi Bhabha National Institute (HBNI)Anushakti Nagar, Mumbai 410210, India
- Transplant Immunology and Immunogenetics, ACTREC, Tata Memorial CentreMumbai 410210, India
| | - Navin Khattry
- HSCT Unit, Department of Medical Oncology Tata Memorial Centre, HSCT Unit, ACTRECKharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute (HBNI)Anushakti Nagar, Mumbai 410210, India
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Sacchi N, Ciceri F, Bonifazi F, Algeri M, Gallina A, Pollichieni S, Raggio E, Hadj-Amar B, Lombardini L, Pupella S, Liumbruno G, Cardillo M. Availability of HLA-allele-matched unrelated donors and registry size: Estimation from haplotype frequency in the Italian population. Hum Immunol 2021; 82:758-766. [PMID: 34353675 DOI: 10.1016/j.humimm.2021.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 11/25/2022]
Abstract
In Italy, an HLA-matched unrelated donor is currently the primary donor when a HLA matched sibling is not found for allogeneic haematopoietic stem cell transplantation (HSCT). Better outcomes for transplantation require optimal matching between donor and recipient at least at the HLA-A, -B, -C, and -DRB1 loci; therefore, the availability of HLA-matched unrelated donors is important. The enormous HLA polymorphism has always necessitated registries with a large number of individuals in order to be able to provide well-matched donors to a substantial percentage of patients. In order to increase the efficiency of the Italian Bone Marrow Donor Registry (IBMDR) in providing Italian patients with a suitable donor, the probability of finding an HLA-A, -B, -C, and -DRB1 allele-matched (8/8) or a single mismatch unrelated donor (7/8) was estimated in this study according to IBMDR size. Using a biostatistical approach based on HLA haplotype frequencies of more than 100,000 Italian donors enrolled in the IBMDR and HLA-typed at high-resolution level, the probability of finding an 8/8 HLA-matched donor was 23.8%; 33.4%; and 41.4% in simulated registry sizes of 200,000; 500,000; and 1,000,000 donors; respectively. More than 2 million recruited donors are needed to increase the likelihood of identifying an HLA 8/8 matched donor for 50% of Italian patients. If one single mismatch at HLA I class loci was accepted, the probability of finding a 7/8 HLA-matched donor was 62.8%; 73.7%; and 80.3% in 200,000 donors; 500,000; and 1,000,000 donors; respectively. Using the regional haplotype frequencies of IBMDR donors, the probability of recruiting a donor with a new HLA phenotype, in the different Italian regions, was also calculated. Our findings are highly relevant in estimating the optimal size of the national registry, in planning a cost-effective strategy for donor recruitment in Italy, and determining the regional priority setting of recruitment activity in order to increase the phenotypic variability of IBMDR as well as its efficiency.
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Affiliation(s)
- N Sacchi
- E.O. Galliera, Italian Bone Marrow Donor Registry Genova, Italy.
| | - F Ciceri
- Department of Hematology and Stem Cell Transplantation, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - F Bonifazi
- Istituto di Ematologia "Seràgnoli" IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - M Algeri
- Dipartimento di Oncoematologia Pediatrica, IRCCS, Ospedale Pediatrico Bambino Gesu', Sapienza, Università di Roma, Roma, Italy
| | - A Gallina
- E.O. Galliera, Italian Bone Marrow Donor Registry Genova, Italy
| | - S Pollichieni
- E.O. Galliera, Italian Bone Marrow Donor Registry Genova, Italy
| | - E Raggio
- E.O. Galliera, Italian Bone Marrow Donor Registry Genova, Italy
| | - B Hadj-Amar
- Department of Statistics, Rice University, Houston, TX, USA
| | - L Lombardini
- Italian National Transplant Centre, National Institute of Health, Rome, Italy
| | - S Pupella
- Italian National Blood Centre, National Institute of Health, Rome, Italy
| | - G Liumbruno
- Italian National Blood Centre, National Institute of Health, Rome, Italy
| | - M Cardillo
- Italian National Transplant Centre, National Institute of Health, Rome, Italy
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Sepúlveda N. Impact of genetic variation on the molecular mimicry between Anoctamin-2 and Epstein-Barr virus nuclear antigen 1 in Multiple Sclerosis. Immunol Lett 2021; 238:29-31. [PMID: 34310987 DOI: 10.1016/j.imlet.2021.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Nuno Sepúlveda
- CEAUL - Centro de Estatística e Aplicações da Universidade de Lisboa, Portugal.
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Pushpakumara PD, Madhusanka D, Dhanasekara S, Jeewandara C, Ogg GS, Malavige GN. Identification of Novel Candidate CD8 + T Cell Epitopes of the SARS-CoV2 with Homology to Other Seasonal Coronaviruses. Viruses 2021; 13:972. [PMID: 34073934 DOI: 10.3390/v13060972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/15/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Cross-reactive T cell immunity to seasonal coronaviruses (HCoVs) may lead to immunopathology or protection during SARS-CoV2 infection. To understand the influence of cross-reactive T cell responses, we used IEDB (Immune epitope database) and NetMHCpan (ver. 4.1) to identify candidate CD8+ T cell epitopes, restricted through HLA-A and B alleles. Conservation analysis was carried out for these epitopes with HCoVs, OC43, HKU1, and NL63. 12/18 the candidate CD8+ T cell epitopes (binding score of ≥0.90), which had a high degree of homology (>75%) with the other three HCoVs were within the NSP12 and NSP13 proteins. They were predicted to be restricted through HLA-A*2402, HLA-A*201, HLA-A*206, and HLA-B alleles B*3501. Thirty-one candidate CD8+ T cell epitopes that were specific to SARS-CoV2 virus (<25% homology with other HCoVs) were predominantly identified within the structural proteins (spike, envelop, membrane, and nucleocapsid) and the NSP1, NSP2, and NSP3. They were predominantly restricted through HLA-B*3501 (6/31), HLA-B*4001 (6/31), HLA-B*4403 (7/31), and HLA-A*2402 (8/31). It would be crucial to understand T cell responses that associate with protection, and the differences in the functionality and phenotype of epitope specific T cell responses, presented through different HLA alleles common in different geographical groups, to understand disease pathogenesis.
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Ramosaj-Morina A, Burek Kamenaric M, Keka Syla A, Baloku A, Grubic Z, Zunec R. HLA-A, -C, -B, -DRB1, -DQA1, and -DQB1 Allele and Haplotype Repertoires in the Albanian Population from Kosovo. Immunol Invest 2021; 51:1232-1242. [PMID: 33985400 DOI: 10.1080/08820139.2021.1924772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
To give new insight into the huge polymorphism of HLA system and supplement the existing data, an analysis of HLA alleles and HLA-A~C~B~DRB1~DQA1~DQB1 haplotype distribution in 124 Albanian individuals from Kosovo was performed. All samples were HLA-typed applying the polymerase chain reaction-sequence specific oligonucleotide probing (PCR-SSOP) method and all ambiguous HLA typing results were additionally confirmed by the standard PCR-Sequence Specific Primers (PCR-SSP) high-resolution protocol. Twenty-two HLA-A, 21 HLA-C, 37 HLA-B, 27 HLA-DRB1, 11 HLA-DQA1 and 14 HLA-DQB1 allele groups were detected. Sixteen out of 172 different six-locus estimated haplotypes were found at a frequency higher than 1.00% with a cumulative frequency of 28.82%. The most prevalent haplotype was found to be HLA-A*02:01~C*07:01~B*18:01~DRB1*11:04~DQA1*05:05~DQB1*03:0(5.2%).A total of 13 haplotypes were observed with higher frequency than in populations reported in HaploStats and The Allele Frequency Net Database. The proposed origin of the most frequent haplotypes reflects a basic Euro-Mediterranean background of Albanians in Kosovo. This is the first report of high-resolution HLA-A~C~B~DRB1~DQA1~DQB1 haplotype distribution among the Albanian population from Kosovo, which provides valuable anthropological data and confirms population-specific characteristics.
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Affiliation(s)
- Atifete Ramosaj-Morina
- Pediatric Clinic, University Clinical Centre of Kosovo, Prishtina, Kosovo.,Institute of Anatomy, Faculty of Medicine, University of Prishtina, Prishtina, Kosovo
| | | | - Alije Keka Syla
- Pediatric Clinic, University Clinical Centre of Kosovo, Prishtina, Kosovo.,Tissue Typing Centre, Clinical Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Arbana Baloku
- Tissue Typing Centre, Clinical Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Zorana Grubic
- Institute of Anatomy, Faculty of Medicine, University of Prishtina, Prishtina, Kosovo
| | - Renata Zunec
- Institute of Anatomy, Faculty of Medicine, University of Prishtina, Prishtina, Kosovo
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21
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Alves-Leon SV, Ferreira CDS, Herlinger AL, Fontes-Dantas FL, Rueda-Lopes FC, Francisco RDS, Gonçalves JPDC, de Araújo AD, Rêgo CCDS, Higa LM, Gerber AL, Guimarães APDC, de Menezes MT, de Paula Tôrres MC, Maia RA, Nogueira BMG, França LC, da Silva MM, Naurath C, Correia ASDS, Vasconcelos CCF, Tanuri A, Ferreira OC, Cardoso CC, Aguiar RS, de Vasconcelos ATR. Exome-Wide Search for Genes Associated With Central Nervous System Inflammatory Demyelinating Diseases Following CHIKV Infection: The Tip of the Iceberg. Front Genet 2021; 12:639364. [PMID: 33815474 PMCID: PMC8010313 DOI: 10.3389/fgene.2021.639364] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/08/2021] [Indexed: 12/31/2022] Open
Abstract
Chikungunya virus (CHIKV) is a re-emergent arbovirus that causes a disease characterized primarily by fever, rash and severe persistent polyarthralgia, although <1% of cases develop severe neurological manifestations such as inflammatory demyelinating diseases (IDD) of the central nervous system (CNS) like acute disseminated encephalomyelitis (ADEM) and extensive transverse myelitis. Genetic factors associated with host response and disease severity are still poorly understood. In this study, we performed whole-exome sequencing (WES) to identify HLA alleles, genes and cellular pathways associated with CNS IDD clinical phenotype outcomes following CHIKV infection. The cohort includes 345 patients of which 160 were confirmed for CHIKV. Six cases presented neurological manifestation mimetizing CNS IDD. WES data analysis was performed for 12 patients, including the CNS IDD cases and 6 CHIKV patients without any neurological manifestation. We identified 29 candidate genes harboring rare, pathogenic, or probably pathogenic variants in all exomes analyzed. HLA alleles were also determined and patients who developed CNS IDD shared a common signature with diseases such as Multiple sclerosis (MS) and Neuromyelitis Optica Spectrum Disorders (NMOSD). When these genes were included in Gene Ontology analyses, pathways associated with CNS IDD syndromes were retrieved, suggesting that CHIKV-induced CNS outcomesmay share a genetic background with other neurological disorders. To our knowledge, this study was the first genome-wide investigation of genetic risk factors for CNS phenotypes in CHIKV infection. Our data suggest that HLA-DRB1 alleles associated with demyelinating diseases may also confer risk of CNS IDD outcomes in patients with CHIKV infection.
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Affiliation(s)
- Soniza Vieira Alves-Leon
- Translational Neuroscience Laboratory, Rio de Janeiro State Federal University, Rio de Janeiro, Brazil.,Department of Neurology/Reference and Research Center for Multiple Sclerosis and Other Central Nervous System Idiopathic Demyelinating Inflammatory Diseases, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | | | - João Paulo da Costa Gonçalves
- Translational Neuroscience Laboratory, Rio de Janeiro State Federal University, Rio de Janeiro, Brazil.,Department of Neurology/Reference and Research Center for Multiple Sclerosis and Other Central Nervous System Idiopathic Demyelinating Inflammatory Diseases, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amanda Dutra de Araújo
- Translational Neuroscience Laboratory, Rio de Janeiro State Federal University, Rio de Janeiro, Brazil.,Department of Neurology/Reference and Research Center for Multiple Sclerosis and Other Central Nervous System Idiopathic Demyelinating Inflammatory Diseases, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cláudia Cecília da Silva Rêgo
- Translational Neuroscience Laboratory, Rio de Janeiro State Federal University, Rio de Janeiro, Brazil.,Department of Neurology/Reference and Research Center for Multiple Sclerosis and Other Central Nervous System Idiopathic Demyelinating Inflammatory Diseases, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luiza Mendonça Higa
- Molecular Virology Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | - Richard Araújo Maia
- Molecular Virology Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Laise Carolina França
- Translational Neuroscience Laboratory, Rio de Janeiro State Federal University, Rio de Janeiro, Brazil
| | - Marcos Martins da Silva
- Department of Clinical Medicine, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Christian Naurath
- Federal Hospital Cardoso Fontes, Ministry of Health, Rio de Janeiro, Brazil
| | | | | | - Amilcar Tanuri
- Molecular Virology Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Orlando Costa Ferreira
- Molecular Virology Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Renato Santana Aguiar
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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22
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Seedat F, James I, Loubser S, Waja Z, Mallal SA, Hoffmann C, Tiemessen CT, Chaisson RE, Martinson NA. Human leukocyte antigen associations with protection against tuberculosis infection and disease in human immunodeficiency virus-1 infected individuals, despite household tuberculosis exposure and immune suppression. Tuberculosis (Edinb) 2021; 126:102023. [PMID: 33249336 DOI: 10.1016/j.tube.2020.102023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/04/2020] [Accepted: 11/15/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND To determine the association of human leukocyte antigen (HLA) alleles as correlates of risk for and protection against tuberculin skin test (TST) positivity and active TB disease amongst HIV-infected adults. METHODS Genomic DNA was extracted from 754 HIV-infected adults whole-blood. HLA-A, -B, -C and -DRB1 loci were genotyped by next generation sequencing methods. HLA alleles were analysed by the presence/absence of TST immune conversion and active TB disease and further stratified by exposure to a household TB contact, CD4+ T-cell count and, for active TB disease, TST-positivity. RESULTS HLA-A*29:11 and - B*45:01/07 were associated with TST-positivity, while HLA-A*24:02, -A*29:02 and -B*15:16 with TST-negativity. In participants with a household TB contact, HLA-A*66:01, -A*68:02 and -B*49:01 were associated with TST-negativity. For TB disease, HLA-B*41:01, -C*06:02, -DRB1*04:01 and -DRB1*15:01 were associated with susceptibility, while HLA-B*07:02 and -DRB1*11:01 were protective, even for CD4+ T-cell count <350 cells/mm3. For initial TST-positivity and subsequent TB disease, HLA-A*01:01 and -DRB1*11:01 conveyed protection including for those with CD4+ T-cell count <350 cells/mm3. CONCLUSION Several HLA alleles are noted as correlates of TB infection, risk and natural protection in HIV-infected individuals. HLA associations may enable risk stratification of those with HIV infection. Protective alleles may assist in future TB vaccine development.
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Affiliation(s)
- Faheem Seedat
- Department of Internal Medicine, Klerksdorp Tshepong Hospital Complex, Benji Oliphant Road, North West Province Department of Health, University of the Witwatersrand, South Africa.
| | - Ian James
- Institute for Immunology and Infectious Diseases, 90 South Street, Murdoch University, Western Australia, Australia
| | - Shayne Loubser
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road and Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg, South Africa
| | - Ziyaad Waja
- Perinatal HIV Research Unit (PHRU), MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, Chris Hani Road, Chris Hani Baragwanath Academic Hospital, University of the Witwatersrand, South Africa
| | - Simon A Mallal
- Department of Pathology, Microbiology and Immunology, 2201, West End Avenue, Vanderbilt University, Nashville, TN, USA
| | - Christopher Hoffmann
- Johns Hopkins University Centre for TB Research, Charles Street, John Hopkins University, Baltimore, MD, USA
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road and Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg, South Africa
| | - Richard E Chaisson
- Johns Hopkins University Centre for TB Research, Charles Street, John Hopkins University, Baltimore, MD, USA
| | - Neil A Martinson
- Perinatal HIV Research Unit (PHRU), MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, Chris Hani Road, Chris Hani Baragwanath Academic Hospital, University of the Witwatersrand, South Africa
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23
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Eltayeb-Elsheikh N, Khalil E, Mubasher M, AlJurayyan A, AlHarthi H, Omer WH, Elghazali I, Sherbeeni SM, Alghofely MA, Ilonen J, Elghazali G. Association of HLA-DR-DQ alleles, haplotypes, and diplotypes with type 1 diabetes in Saudis. Diabetes Metab Res Rev 2020; 36:e3345. [PMID: 32418312 DOI: 10.1002/dmrr.3345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/14/2020] [Accepted: 04/22/2020] [Indexed: 12/31/2022]
Abstract
AIMS Type 1 diabetes (T1D) is an autoimmune disease that affects many children worldwide. Genetic factors and environmental triggers play crucial interacting roles in the aetiology. This study aimed to assess the contribution of HLA-DRB1-DQA1-DQB1 alleles, haplotypes, and genotypes to the risk of T1D among Saudis. METHODS A total of 222 children with T1D and 342 controls were genotyped for HLA-DRB1, -DQA1, and -DQB1 using reverse sequence-specific oligonucleotide (rSSO) Lab Type high definition (HD) kits. Alleles, haplotypes, and diplotypes were compared between cases and controls using the SAS statistical package. RESULTS DRB1*03:01-DQA1*05:01-DQB1*02:01 (32.4%; OR = 3.68; Pc < .0001), DRB1*04:05-DQA1*03:02-DQB1*03:02 (6.6%; OR = 6.76; Pc < .0001), DRB1*04:02-DQA1*03:01-DQB1*03:02 (6.0%; OR = 3.10; Pc = .0194), DRB1*04:01-DQA1*03:01-DQB1*03:02 (3.7%; OR = 4.22; Pc = .0335), and DRB1*04:05-DQA1*03:02-DQB1*02:02 (2.7%; OR = 6.31; Pc = .0326) haplotypes were significantly increased in cases compared to controls, whereas DRB1*07:01-DQA1*02:01-DQB1*02:02 (OR = 0.41; Pc = .0001), DRB1*13:01-DQA1*01:03-DQB1*06:03 (OR = 0.05; Pc < .0001), DRB1*15:01-DQA1*01:02-DQB1*06:02 (OR = 0.03; Pc < .0001), and DRB1*11:01-DQA1*05:05-DQB1*03:01 (OR = 0.07; Pc = .0291) were significantly decreased. Homozygous DRB1*03:01-DQA1*05:01-DQB1*02:01 genotypes and combinations of DRB1*03:01-DQA1*05:01-DQB1*02:01 with DRB1*04:05-DQA1*03:02-DQB1*03:02, DRB1*04:02-DQA1*03:01-DQB1*03:02, and DRB1*04:01-DQA1*03:01-DQB1*03:02 were significantly increased in cases than controls. Combinations of DRB1*03:01-DQA1*05:01-DQB1*02:01 with DRB1*07:01-DQA1*02:01-DQB1*02:02 and DRB1*13:02-DQA1*01:02-DQB1*06:04 showed low OR values but did not remain significantly decreased after Bonferroni correction. CONCLUSIONS HLA-DRB1-DQA1-DQB1 alleles, haplotypes, and diplotypes in Saudis with T1D are not markedly different from those observed in Western and Middle-Eastern populations but are quite different than those of East Asians.
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Affiliation(s)
- Nezar Eltayeb-Elsheikh
- Department of Pathology and Clinical Laboratory Medicine, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Eltahir Khalil
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Mohamed Mubasher
- Biostatistics & Data Management Core, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Abdullah AlJurayyan
- Department of Pathology and Clinical Laboratory Medicine, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Hanan AlHarthi
- Department of Pathology and Clinical Laboratory Medicine, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Waleed H Omer
- Division of Human Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Inas Elghazali
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Suphia M Sherbeeni
- Endocrinology Department, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed A Alghofely
- Endocrinology Department, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Jorma Ilonen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku and Clinical Microbiology Laboratory, Turku University Hospital, Turku, Finland
| | - Gehad Elghazali
- Department of Immunology, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
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24
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Dittrich D, Maskalan M, Kastelan Z, Palenkic H, Grubic Z. The role of HLA in Balkan endemic nephropathy. Gene 2020; 767:145179. [PMID: 33002571 DOI: 10.1016/j.gene.2020.145179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 11/16/2022]
Abstract
Balkan endemic nephropathy (BEN), a progressive chronic tubulointerstitial disease, occurs in the endemic focus of Croatia in a population of about 10,000 inhabitants. One of its most peculiar characteristics is a strong association with upper tract urothelial carcinoma (UTUC). Despite a high number of studies, currently there are insufficient data about the association of BEN and HLA genes. The aim of this study was to investigate the polymorphism of HLA-A, -B, and -DRB1 alleles and haplotypes among BEN patients and to determine whether an association between HLA and BEN exists. In this study, we investigated HLA-A, -B, and -DRB1 alleles and haplotypes in a population of patients with BEN (N = 111) and matched healthy controls (N = 190). All individuals were tested by PCR-SSO and PCR-SSP methods to assess the possible contribution of HLA alleles and haplotypes to the development of/protection from BEN. Our results showed a positive association between the presence of HLA-B*35:02 and DRB1*04:02 alleles and BEN (P = 0.0179 and P = 0.0151, respectively) in contrast to the protective effect of HLA-A*01:01, B*27:05 and B*57:01 alleles (P = 0.0111, P = 0.0330 and P = 0.0318, respectively). Moreover, when BEN patients' HLA haplotypes were compared to controls, two haplotypes were associated with BEN susceptibility among Croatians (HLA-A*02:01~B*08:01~DRB1*03:01 and HLA-A*02:01~B*27:02~DRB1*16:01, P = 0.0064 and P = 0.0023, respectively), while haplotypes HLA-A*02:01~B*27:05~DRB1*01:01 and HLA-A*02:01~B*38:01~DRB1*13:01 each showed a possible protective effect (P = 0.0495). Our results point toward genetic susceptibility to BEN and observed differences in both susceptible/protective HLA profiles indicate the necessity of further studies in order to elucidate the pathogenesis of this disease.
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Affiliation(s)
- Damir Dittrich
- Department of Urology, General Hospital "Dr. Josip Bencevic", Slavonski Brod, Croatia
| | - Marija Maskalan
- Tissue Typing Centre, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Zeljko Kastelan
- Department of Urology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Hrvoje Palenkic
- Department of Surgery, General Hospital "Dr. Josip Bencevic", Slavonski Brod, Croatia
| | - Zorana Grubic
- Tissue Typing Centre, University Hospital Centre Zagreb, Zagreb, Croatia.
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25
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Geretz A, Cofer L, Ehrenberg PK, Currier JR, Yoon IK, Alera MTP, Jarman R, Rothman AL, Thomas R. Next-generation sequencing of 11 HLA loci in a large dengue vaccine cohort from the Philippines. Hum Immunol 2020; 81:437-444. [PMID: 32654962 DOI: 10.1016/j.humimm.2020.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/27/2020] [Accepted: 06/17/2020] [Indexed: 01/25/2023]
Abstract
HLA genotyping by next-generation sequencing (NGS) has evolved with significant advancements in the last decade. Here we describe full-length HLA genotyping of 11 loci in 612 individuals comprising a dengue vaccine cohort from Cebu province in the Philippines. The multi-locus individual tagging NGS (MIT-NGS) method that we developed initially for genotyping 4-6 loci in one MiSeq run was expanded to 11 loci including HLA-A, B, C, DPA1, DPB1, DQA1, DQB1, DRB1, and DRB3/4/5. This change did not affect the overall coverage or depth of the sequencing reads. HLA alleles with frequencies greater than 10% were A*11:01:01, A*24:02:01, A*24:07:01, A*34:01:01, B*38:02:01, B*15:35, B*35:05:01, C*07:02:01, C*04:01:01, DPA1*02:02:02, DPB1*05:01:01, DPB1*01:01:01, DQA1*01:02:01, DQA1*06:01:01, DQB1*05:02:01, DQB1*03:01:01, DRB1*15:02:01, DRB1*12:02:01, DRB3*03:01:03, DRB4*01:03:01, and DRB5*01:01:01. Improvements in sequencing library preparation provide uniform and even coverage across all exons and introns. This has led to a marked reduction in allele imbalance and dropout. Furthermore, including more loci, such as DRB3/4/5, decreases cross-mapping and incorrect allele assignment at the DRB1 locus. The increased number of loci sequenced for each sample does not reduce the number of samples that can be multiplexed on a single MiSeq run and is therefore more cost-efficient. We believe that such improvements will help HLA genotyping by NGS to gain momentum over other conventional methods by increasing confidence in the calls.
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Affiliation(s)
- Aviva Geretz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Lauryn Cofer
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jeffrey R Currier
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - In-Kyu Yoon
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Maria T P Alera
- Philippines-AFRIMS Virology Research Unit, Cebu City, Philippines
| | - Richard Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Alan L Rothman
- Institute for Immunology and Informatics and Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
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26
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Gong JJ, Margolis DJ, Monos DS. Predictive in silico binding algorithms reveal HLA specificities and autoallergen peptides associated with atopic dermatitis. Arch Dermatol Res 2020; 312:647-656. [PMID: 32152724 DOI: 10.1007/s00403-020-02059-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 02/26/2020] [Indexed: 12/18/2022]
Abstract
Atopic dermatitis (AD) is a skin disease that results from a combination of skin barrier dysfunction and immune dysregulation. The immune dysregulation is often associated with IgE sensitivity. There is also evidence that autoallergens Hom s 1, 2, 3, and 4 play a role in AD; it is possible that patients with specific HLA subtypes are predisposed to autoreactivity due to increased presentation of autoallergen peptides. The goal of our study was to use in silico epitope prediction platforms as an approach to identify HLA subtypes that may preferentially bind autoallergen peptides and are thus candidates for further study. Considering the previously described association of DRB1 alleles with AD and progression of disease, emphasis was placed on DRB1. Certain DRB1 alleles (08:04, 11:01, and 11:04) were identified by both algorithms to bind a significant percent of the generated autoallergen peptides. Conversely, autoallergen core peptide sequences FRQLSHRFH and IRAKLRLQA (Hom s 1), IRKSKNILF (Hom s 2), FKWVPVTDS and MAAIEKVRK (Hom s 3), and FRYFATLKV (Hom s 4) were predicted to bind many DRB1 alleles and, thus, may play a role in the pathogenesis of AD. Our findings provide candidate DRB1 alleles and autoallergen epitopes that will guide future studies exploring the relationship between DRB1 subtype and autoreactivity in AD. A similar approach can be used for any antigen that has been associated with an IgE response and AD.
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Affiliation(s)
- Jan J Gong
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - David J Margolis
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Department of Dermatology, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Dimitrios S Monos
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
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27
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Nestorowicz K, Bogacz A, Bukowska A, Chraplak M, Czerwiński J, Góralski M, Gronkowski M, Jopek K, Kniżewski Ł, Kolasiński M, Kowalski ML, Nowak J, Sowiński M, Wróblewska-Kabba S, Tymoniuk B, Dudkiewicz M. High-resolution allele frequencies for NGS based HLA-A, B, C, DQB1 and DRB1 typing of 23,595 bone marrow donors recruited for the Polish central potential unrelated bone marrow donor registry. Hum Immunol 2020; 81:49-51. [PMID: 31902540 DOI: 10.1016/j.humimm.2019.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 11/21/2022]
Abstract
Next-generation sequencing (NGS)-based typings of HLA-A, B, C, DQB1 and DRB1 loci were performed from 2018 to 2019 in 23 595 newly recruited or re-typed adult potential bone marrow donors registered in Poltransplant Registry to characterize allele and haplotype frequencies of HLA system for loci important for hematopoietic stem cell transplantation. The donors were recruited for registry and not for any other purpose including controls in a disease association study. The population sample was collected in various regions of Poland including all voivodships. The data regarding the degree of relatedness among individuals in the sample were not collected. Typings were supported by public funds as a part of the Polish National Program for Transplant Medicine Development. HLA frequency data are available in the Allele Frequencies Net Database.
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Correale P, Saladino RE, Nardone V, Giannicola R, Agostino R, Pirtoli L, Caraglia M, Botta C, Tagliaferri P. Could PD-1/PDL1 immune checkpoints be linked to HLA signature? Immunotherapy 2019; 11:1523-1526. [PMID: 31865873 DOI: 10.2217/imt-2019-0160] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Pierpaolo Correale
- Medical Oncology Unit, Grand Metropolitan Hospital "Bianchi-Melacrino-Morelli", Reggio Calabria, Italy
| | - Rita E Saladino
- Tissue Typing Unit, Grand Metropolitan Hospital "Bianchi-Melacrino-Morelli", Reggio Calabria, Italy
| | | | - Rocco Giannicola
- Medical Oncology Unit, Grand Metropolitan Hospital "Bianchi-Melacrino-Morelli", Reggio Calabria, Italy
| | - Rita Agostino
- Medical Oncology Unit, Grand Metropolitan Hospital "Bianchi-Melacrino-Morelli", Reggio Calabria, Italy
| | - Luigi Pirtoli
- Department of Biology, College of Science & Technology, Temple University, Philadelphia, PA, USA
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via L. De Crecchio, 7 80138 Naples, Italy
| | - Ciro Botta
- Hematology Unit, Annunziata Hospital, Cosenza, Italy
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Ozyilmaz E, Akilli R, Berk İ, Deniz A, Ozturk OG, Baydar O, Saygideger Y, Seydaoglu G, Erken E. The frequency of diastolic dysfunction in patients with sarcoidosis and it's relationship with HLA DRB1* alleles. Sarcoidosis Vasc Diffuse Lung Dis 2019; 36:285-293. [PMID: 32476964 PMCID: PMC7247094 DOI: 10.36141/svdld.v36i4.8606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 11/25/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Impaired systolic function is common in sarcoidosis however the frequency of diastolic dysfunction (DD) and it's possible genetic basis has not been fully elucidated yet. The aim of this study is to evaluate the frequency of left ventricular DD(LVDD) and right ventricular DD(RVDD) and it's possible relationship between Human Leukocyte Antigen(HLA)-DRB1* alleles in patients with sarcoidosis. METHODS Seventy seven patients (51 females, mean age 41.1±8.2yrs) without known sarcoid related or any other structured heart disease and 77 healthy controls with a similar age and gender (38.7±7.8yrs,51 females) were included in the case control study. DD was diagnosed with echocardiography. RVDD was defined as early(E)/late(A) ratio<1 or >2 on tricuspit valve. LVDD was defined as E/A ratio<1 or >2 on mitral valve, with isovolumetric relaxation time(IVRT)>90 miliseconds(msn) or deceleration rate of early diastolic flow(Edec)>220msn respectively. All patients were HLAtyped with the Sequence Specific Oligonucleotide Probe(SSOP) method. RESULTS The frequencies of LVDDs and RVDDs were significantly higher in sarcoidosis patients than the controls (26.0% vs. 2.6% for LVDD; and 42.9% vs. 18.2% for RVDD)(p<0.05). No significant difference was found in patients according to the presence of RVDD and LVDD in terms of age, gender or respiratory function test parameters. Although the frequency of HLA DRB1* alleles were comparable among patients with RVDD, HLA DRB1*14 alleles were more frequent in patients with LVDD. CONCLUSIONS Biventricular DD is common in patients with sarcoidosis without manifest cardiac involvement. HLA DRB1*14 allele seems to be related with LVDD in this study population.
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Affiliation(s)
- Ezgi Ozyilmaz
- Department of Chest Diseases, Cukurova University Faculty of Medicine, Adana, Turkey,Correspondence: Dr. Ezgi Ozyilmaz Department of Chest Diseases, Cukurova University Faculty of Medicine, 01330 Saricam, Adana, Turkey Tel. 0090 505 384 1435 E-mail:
| | - Rabia Akilli
- Department of Cardiology, Cukurova University Faculty of Medicine, Adana, Turkey
| | - İlayda Berk
- Department of Cardiology, Atatürk State Hospital, 07040, Antalya, Turkey
| | - Ali Deniz
- Department of Cardiology, Cukurova University Faculty of Medicine, Adana, Turkey
| | | | - Oya Baydar
- Department of Chest Diseases, Cukurova University Faculty of Medicine, Adana, Turkey
| | - Yasemin Saygideger
- Department of Chest Diseases, Cukurova University Faculty of Medicine, Adana, Turkey
| | - Gulsah Seydaoglu
- Department of Biostatistics, Cukurova University Faculty of Medicine, Adana, Turkey
| | - Eren Erken
- Department of Rheumatology, Cukurova University Faculty of Medicine, Adana, Turkey
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Moore E, Grifoni A, Weiskopf D, Schulten V, Arlehamn CSL, Angelo M, Pham J, Leary S, Sidney J, Broide D, Frazier A, Phillips E, Mallal S, Mack SJ, Sette A. Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 496 adults from San Diego, California, USA. Hum Immunol 2018; 79:821-822. [PMID: 30278218 DOI: 10.1016/j.humimm.2018.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/21/2018] [Accepted: 09/27/2018] [Indexed: 11/26/2022]
Abstract
DNA sequence-based typing at the HLA-A, -B, -C, -DPB1, -DQA1, -DQB1, and -DRB1 loci was performed on 496 healthy adult donors from San Diego, California, to characterize allele frequencies in support of studies of T cell responses to common allergens. Deviations from Hardy Weinberg proportions were detected at each locus except A and C. Several alleles were found in more than 15% of individuals, including the class II alleles DPB1∗02:01, DPB1∗04:01, DQA1∗01:02, DQA1∗05:01, DQB1∗03:01, and the class I allele A∗02:01. Genotype data will be available in the Allele Frequencies Net Database (AFND 3562).
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Affiliation(s)
- Eugene Moore
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA.
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - Veronique Schulten
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | | | - Michael Angelo
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - John Pham
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - David Broide
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - April Frazier
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Steven J Mack
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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31
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Geretz A, Ehrenberg PK, Bouckenooghe A, Fernández Viña MA, Michael NL, Chansinghakule D, Limkittikul K, Thomas R. Full-length next-generation sequencing of HLA class I and II genes in a cohort from Thailand. Hum Immunol 2018; 79:773-780. [PMID: 30243890 DOI: 10.1016/j.humimm.2018.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/17/2018] [Accepted: 09/18/2018] [Indexed: 01/02/2023]
Abstract
The human leukocyte antigen (HLA) genes are highly variable and are known to play an important role in disease outcomes, including infectious diseases. Prior knowledge of HLA polymorphisms in a population usually forms the basis for an effective case-control study design. As a prelude to future disease association analyses, we report HLA class I and II diversity in 334 unrelated donors from a Dengue vaccine efficacy trial conducted in Thailand. Long-range PCR amplification of six HLA loci was performed on DNA extracted from saliva samples. HLA-A, -B, -C, -DPB1, -DQB1 and -DRB1 were genotyped using a next-generation sequencing method presented at the 17th International HLA and Immunogenetics Workshop. In total, we identified 201 HLA alleles, including 35 HLA-A, 57 HLA-B, 28 HLA-C, 24 HLA-DPB1, 21 HLA-DQB1 and 36 HLA-DRB1 alleles. Very common HLA alleles with frequencies greater than 10 percent were A∗11:01:01, A∗33:03:01, A∗24:02:01, B∗46:01:01, C∗07:02:01, C∗01:02:01, C∗08:01:01, DPB1∗05:01:01, DPB1∗13:01:01, DPB1∗04:01:01, DPB1∗02:01:02, DQB1∗03:01:01, DQB1∗05:02:01, DQB1∗03:03:02, DRB1∗12:02:01, DRB1∗09:01:02, and DRB1∗15:02:01. A novel HLA allele, B∗15:450, had a non-synonymous substitution and occurred in more than one donor. Population-based full-length NGS HLA typing is more conclusive and provides a sound foundation for exploring disease association in a given population.
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Affiliation(s)
- Aviva Geretz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | | | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Kriengsak Limkittikul
- Department of Tropical Pediatrics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
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Grifoni A, Sidney J, Carpenter C, Phillips E, Mallal S, Scriba TJ, Sette A, Lindestam Arlehamn CS. Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 159 individuals from the Worcester region of the Western Cape province of South Africa. Hum Immunol 2018; 79:143-144. [PMID: 29398200 DOI: 10.1016/j.humimm.2018.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 01/05/2018] [Accepted: 01/10/2018] [Indexed: 11/17/2022]
Abstract
DNA sequence-based typing at the HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, and -DRB3/4/5 loci was performed on samples provided by 159 individuals from the Worcester region of the Western Cape province of South Africa. The purpose of the study was to characterize allele frequencies in the local population, to support studies of T cell immunity against pathogens, including Mycobacterium tuberculosis. There are no detectable deviations from Hardy Weinberg proportions for the HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, and -DRB1 loci. A minor deviation was detected at the HLA-DQB1 locus due to an excess of homozygotes. The genotype data are available in the Allele Frequencies Net Database under identifier 3425.
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Affiliation(s)
- Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Chelsea Carpenter
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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Voorter CEM, Matern B, Tran TH, Fink A, Vidan-Jeras B, Montanic S, Fischer G, Fae I, de Santis D, Whidborne R, Andreani M, Testi M, Groeneweg M, Tilanus MGJ. Full-length extension of HLA allele sequences by HLA allele-specific hemizygous Sanger sequencing (SSBT). Hum Immunol 2018; 79:763-772. [PMID: 30107213 DOI: 10.1016/j.humimm.2018.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 12/27/2022]
Abstract
The gold standard for typing at the allele level of the highly polymorphic Human Leucocyte Antigen (HLA) gene system is sequence based typing. Since sequencing strategies have mainly focused on identification of the peptide binding groove, full-length sequence information is lacking for >90% of the HLA alleles. One of the goals of the 17th IHIWS workshop is to establish full-length sequences for as many HLA alleles as possible. In our component "Extension of HLA sequences by full-length HLA allele-specific hemizygous Sanger sequencing" we have used full-length hemizygous Sanger Sequence Based Typing to achieve this goal. We selected samples of which full length sequences were not available in the IPD-IMGT/HLA database. In total we have generated the full-length sequences of 48 HLA-A, 45 -B and 31 -C alleles. For HLA-A extended alleles, 39/48 showed no intron differences compared to the first allele of the corresponding allele group, for HLA-B this was 26/45 and for HLA-C 20/31. Comparing the intron sequences to other alleles of the same allele group revealed that in 5/48 HLA-A, 16/45 HLA-B and 8/31 HLA-C alleles the intron sequence was identical to another allele of the same allele group. In the remaining 10 cases, the sequence either showed polymorphism at a conserved nucleotide or was the result of a gene conversion event. Elucidation of the full-length sequence gives insight in the polymorphic content of the alleles and facilitates the identification of its evolutionary origin.
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Affiliation(s)
- Christina E M Voorter
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands.
| | - Ben Matern
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Thuong Hien Tran
- Transplantation Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Annette Fink
- Transplantation Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Blanka Vidan-Jeras
- Tissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Sendi Montanic
- Tissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Gottfried Fischer
- Department for Blood Group Serology and Blood Transfusion Medicine, Medical University Vienna, Vienna, Austria
| | - Ingrid Fae
- Department for Blood Group Serology and Blood Transfusion Medicine, Medical University Vienna, Vienna, Austria
| | - Dianne de Santis
- Department of Clinical Immunology, PathWest, Royal Perth Hospital, Perth, Australia
| | - Rebecca Whidborne
- Department of Clinical Immunology, PathWest, Royal Perth Hospital, Perth, Australia
| | - Marco Andreani
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Manuela Testi
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Mathijs Groeneweg
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marcel G J Tilanus
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
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Gambino CM, Aiello A, Accardi G, Caruso C, Candore G. Autoimmune diseases and 8.1 ancestral haplotype: An update. HLA 2018; 92:137-143. [PMID: 29877054 DOI: 10.1111/tan.13305] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/08/2018] [Accepted: 06/01/2018] [Indexed: 12/11/2022]
Abstract
The aim of the present review is to provide an update of the current research into the pathogenesis of autoimmune diseases associated with 8.1 ancestral haplotype. This is a common Caucasoid haplotype carried by most people who type for HLA-B8, DR3. Numerous genetic studies reported that individuals with certain HLA alleles have a higher risk of specific autoimmune disorders than those without these alleles. However, much remains to be learned about the heritability of autoimmune conditions. Recently, progress and advances in the field of genome-wide-association studies have revolutionized the capacity to perform large, economically feasible, and statistically robust analyses of HLA within 8.1 ancestral haplotype, and understand its contribute to autoimmune events. In this paper, the characteristic features of this haplotype that might give rise to diverse autoimmune phenotypes are reviewed, focusing on the contribution of the HLA-DRB1 gene, the most polymorphic sequence within the HLA II region.
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Affiliation(s)
- C M Gambino
- Department of Pathobiology and Medical Biotechnologies (Di.Bi.Med.), University of Palermo, Palermo, Italy
| | - A Aiello
- Department of Pathobiology and Medical Biotechnologies (Di.Bi.Med.), University of Palermo, Palermo, Italy
| | - G Accardi
- Department of Pathobiology and Medical Biotechnologies (Di.Bi.Med.), University of Palermo, Palermo, Italy
| | - C Caruso
- Department of Pathobiology and Medical Biotechnologies (Di.Bi.Med.), University of Palermo, Palermo, Italy
| | - G Candore
- Department of Pathobiology and Medical Biotechnologies (Di.Bi.Med.), University of Palermo, Palermo, Italy
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Pasinszki T, Krebsz M. Biosensors for Non-Invasive Detection of Celiac Disease Biomarkers in Body Fluids. Biosensors (Basel) 2018; 8:E55. [PMID: 29914179 DOI: 10.3390/bios8020055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 01/10/2023]
Abstract
Celiac disease is a chronic gluten-initiated autoimmune disorder that predominantly damages the mucosa of the small intestine in genetically-susceptible individuals. It affects a large and increasing number of the world’s population. The diagnosis of this disease and monitoring the response of patients to the therapy, which is currently a life-long gluten-free diet, require the application of reliable, rapid, sensitive, selective, simple, and cost-effective analytical tools. Celiac disease biomarker detection in full blood, serum, or plasma offers a non-invasive way to do this and is well-suited to being the first step of diagnosis. Biosensors provide a novel and alternative way to perform conventional techniques in biomarker sensing, in which electrode material and architecture play important roles in achieving sensitive, selective, and stable detection. There are many opportunities to build and modify biosensor platforms using various materials and detection methods, and the aim of the present review is to summarize developments in this field.
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Sanchez-Mazas A, Nunes JM, Middleton D, Sauter J, Buhler S, McCabe A, Hofmann J, Baier DM, Schmidt AH, Nicoloso G, Andreani M, Grubic Z, Tiercy JM, Fleischhauer K. Common and well-documented HLA alleles over all of Europe and within European sub-regions: A catalogue from the European Federation for Immunogenetics. HLA 2018; 89:104-113. [PMID: 28102034 DOI: 10.1111/tan.12956] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 11/30/2016] [Accepted: 12/19/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND A catalogue of common and well-documented (CWD) human leukocyte antigen (HLA), previously established by the American Society for Histocompatibility and Immunogenetics (ASHI), is widely used as indicator for typing ambiguities to be resolved in tissue transplantation or for checking the universality of any HLA allele in the world. However, European population samples, which are characterized by a substantial level of genetic variation, are underrepresented in the ASHI catalogue. Therefore, the Population Genetics Working Group of the European Federation for Immunogenetics (EFI) has facilitated data collection for an European CWD catalogue. MATERIALS AND METHODS To this end, 2nd-field HLA-A, -B, -C,- DRB1,- DQA1,- DQB1 and -DPB1 data of 77 to 121 European population samples (21 571-3 966 984 individuals) from 3 large databases, HLA-net/Gene[VA], allelefrequencies.net and DKMS, were analysed. RESULTS The total number of CWD alleles is similar in the EFI (N = 1048) and ASHI (N = 1031) catalogues, but the former counts less common (N = 236 vs 377) and more well-documented (N = 812 vs 654) alleles than the latter, possibly reflecting differences in sample numbers and sizes. Interestingly, approximately half of the CWD alleles reported by EFI were not reported by ASHI and vice-versa, underlining the distinct features of the two catalogues. Also, although 78 common alleles are widely distributed across Europe, some alleles are only common within specific sub-regions, showing regional variability. CONCLUSION Although the definition of CWD alleles itself is affected by different parameters, calling for current updates of the list, the EFI CWD catalogue provides new insights into European population genetics and will be a very useful tool for tissue-typing laboratories in and beyond Europe.
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Affiliation(s)
- A Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling history (AGP), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Center (CMU), Geneva, Switzerland.,Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands
| | - J M Nunes
- Laboratory of Anthropology, Genetics and Peopling history (AGP), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Center (CMU), Geneva, Switzerland.,Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands
| | - D Middleton
- Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands.,Transplant Immunology Laboratory, Royal Liverpool and Broadgreen University Hospital, Liverpool, UK
| | - J Sauter
- DKMS, German Bone Marrow Center, Tübingen, Germany
| | - S Buhler
- Laboratory of Anthropology, Genetics and Peopling history (AGP), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Department of Genetic and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - A McCabe
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - J Hofmann
- DKMS, German Bone Marrow Center, Tübingen, Germany
| | - D M Baier
- DKMS, German Bone Marrow Center, Tübingen, Germany
| | - A H Schmidt
- DKMS, German Bone Marrow Center, Tübingen, Germany
| | - G Nicoloso
- Swiss Transfusion Swiss Red Cross (SRC)/Swiss Blood Stem Cells, Bern, Switzerland
| | - M Andreani
- Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands.,Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Z Grubic
- Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands.,Tissue Typing Center, University Hospital Center Zagreb, Zagreb, Croatia
| | - J-M Tiercy
- Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Department of Genetic and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - K Fleischhauer
- Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands.,Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
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Rostami-Nejad M, Hejazi SH, Peña AS, Asadzadeh-Aghdaei H, Rostami K, Volta U, Zali MR. Contributions of HLA haplotypes, IL8 level and Toxoplasma gondii infection in defining celiac disease's phenotypes. BMC Gastroenterol 2018; 18:66. [PMID: 29776388 PMCID: PMC5960085 DOI: 10.1186/s12876-018-0796-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/08/2018] [Indexed: 12/13/2022] Open
Abstract
Background It is not clear why some patients with coeliac disease (CD) present with severe symptoms and small intestinal mucosal damages while others present with milder symptoms and no frank enteropathy. There is no study to assess the associated factors with mild/severe symptoms and enteropathy. The terminologies like latent, silent and potential are difficult to use and are unrepresentative. In the present study we describe coeliac disease’s phenotypes based on HLA haplotypes, IL8 production and past infection with Toxoplasma gondii (T. gondii) infection. Methods In this case-control study, sera originating from 150 healthy subjects and 150 patients diagnosed with CD during the years 2013–14 were analyzed for the presence of antibodies specific T. gondii of the IgG and IgM subclasses. The level of IL8 were measured and HLA-DQ2 and HLA-DQ8 alleles were genotyped. The correlation between these parameters and the damages in intestinal mucosal were assessed using an accepted histopathological classification. Results High levels of IgG antibodies against T. gondii were found in the sera of control group compared to the CD group (52.6% vs. 39.4%, P = 0.02). Mean serum levels of IL8 was significantly higher in CD patients compared with control (P ≤ 0.05). By comparing the level of anti- T. gondii IgG and mucosal damage in celiac disease, we found a significant relationship between the severity of mucosal damages and anti- T. gondii IgG level (P = 0.02). No correlation was detected between Toxoplasma gondii infection and types of HLA (P > 0.05). However, patients with severely abnormal histology carried HLA-DQ2 risk alleles (92 patients (61%)) more often than the controls and those with mild histological abnormalities. Conclusions CD patients with severe histological changes had more often Toxoplasma gondii infection than those affected with mild histological features. This suggests that CD’s phenotypes are correlated to additional factors like infections and to particular HLA DQ2 alleles that may need additional investigations and potentially will require additional treatment. Electronic supplementary material The online version of this article (10.1186/s12876-018-0796-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mohammad Rostami-Nejad
- Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Hossein Hejazi
- Skin Diseases and Leishmaniasis Research Center, Isfahan University of Medical sciences, Isfahan, Iran
| | - Amado Salvador Peña
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, Vrije Universiteit Medical Center (VUmc), Amsterdam, the Netherlands
| | - Hamid Asadzadeh-Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kamran Rostami
- Department of Gastroenterology, Milton Keynes University Hospital, Milton Keynes, UK.
| | - Umberto Volta
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Mohammad Reza Zali
- Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Ozyilmaz E, Goruroglu Ozturk O, Durmaz A, Othman Hasan O, Guzelbaba B, Seydaoglu G, Kuleci S, Hanta I, Erken E, Kocabas A. Early prediction of sarcoidosis prognosis with HLA typing: a 5 year follow-up study. Sarcoidosis Vasc Diffuse Lung Dis 2018; 35:184-191. [PMID: 32476901 PMCID: PMC7170163 DOI: 10.36141/svdld.v35i3.6781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 03/02/2018] [Indexed: 01/23/2023]
Abstract
Background: A wide range of HLA-DR alleles have been associated with sarcoidosis either in terms of disease phenotype or extra pulmonary involvement, however the effect on non-resolution in different ethnic groups is not fully understood. The aim of this study was to investigate whether disease characterics and HLA-DRB1 alleles may early reflect non resolution in sarcoidosis. Methods: 91 patients who were diagnosed in Cukurova University Faculty of Medicine Department of Chest Diseases between 1993-2012 and were followed up until June 2017 were included in the study. All patients underwent HLA analysis by the Sequence Specific Oligonucleotide Prob (SSOP) method. Fifteen of them were excluded from the study group due to lost of follow-up (n=6) and not yet passed 5 years since diagnosis (n=9). Complete resolution at 5th year was defined according to the predefined standard criteria (ACCESS). Results: The resolution rate was 51.3%. The HLA-DRB1*14 allele was significantly higher in patients without resolution (11.8 vs 1.3%)(p=0.006). According to multivariate logistic regression analysis the independent risk factors of non resolution were female gender (OR: 12.6; 95%CI: 2.1-74.9, p=0.005), HLA DRB1*14 allele (OR:51.9; 95%CI: 3.6-735.8, p=0.000), baseline TLCO<75%(predicted) (OR:3.8; 95%CI: 1.1-13.7, p=0.028), extra-pulmonary involvement (OR:3.7; 95%CI: 1.0-13.1, p=0.038) and advanced stage at baseline (OR: 8.3; 95%CI: 1.9-35.4, p=0.001). Conclusions: HLA-DRB1*14 alleles, lower baseline TLCO, advanced stage, female gender or the presence of extra-pulmonary involvement could predict long term non-resolution in sarcoidosis. Early prediction of long term prognosis may affect treatment decisions and avoid further deterioration in these patient groups. (Sarcoidosis Vasc Diffuse Lung Dis 2018; 35: 184-191).
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Affiliation(s)
- Ezgi Ozyilmaz
- Cukurova University Faculty of Medicine, Department of Pulmonary Disease, Adana, Turkey,Correspondence: Dr. Ezgi Ozyilmaz Cukurova University Faculty of Medicine Department of Pulmonary Disease, Balcali, Adana, Turkey Tel. 0090 505 384 1435 E-mail:
| | - Ozlem Goruroglu Ozturk
- Cukurova University Faculty of Medicine, Department of Medical Biochemistry, Adana, Turkey
| | - Ali Durmaz
- Cukurova University Faculty of Medicine, Department of Pulmonary Disease, Adana, Turkey
| | - Orhan Othman Hasan
- Cukurova University Faculty of Medicine, Department of Pulmonary Disease, Adana, Turkey
| | - Bugra Guzelbaba
- Cukurova University Faculty of Medicine, Department of Pulmonary Disease, Adana, Turkey
| | - Gulsah Seydaoglu
- Cukurova University Faculty of Medicine, Department of Biostatistics, Adana, Turkey
| | - Sedat Kuleci
- Cukurova University Faculty of Medicine, Department of Pulmonary Disease, Adana, Turkey
| | - Ismail Hanta
- Cukurova University Faculty of Medicine, Department of Pulmonary Disease, Adana, Turkey
| | - Eren Erken
- Cukurova University Faculty of Medicine, Department of Rheumatology and Immunology, Adana, Turkey
| | - Ali Kocabas
- Cukurova University Faculty of Medicine, Department of Pulmonary Disease, Adana, Turkey
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Fleury H, Tumiotto C, Bellecave P, Recordon-Pinson P. Therapeutic Vaccine Against HIV, Viral Variability, Cytotoxic T Lymphocyte Epitopes, and Genetics of Patients. AIDS Res Hum Retroviruses 2018; 34:27-30. [PMID: 28899104 DOI: 10.1089/aid.2017.0175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The scientific and medical community is seeking to cure HIV. Several pathways have been or are being explored including therapeutic vaccination. Viroimmunological studies on primary infection as well as on elite controllers have demonstrated the importance of the cytotoxic CD8 response and have mainly oriented research on vaccine constructs toward this type of response. The results of these trials are clearly not commensurate with the hope placed in them. Might there be one or more uncontrolled variables? The genetics of patients need to be taken into consideration, especially their human lymphocyte antigen (HLA) alleles. There is a need to find a balance between the conservation of cytotoxic T lymphocyte (CTL) epitopes and presentation by HLA alleles. The pathway is a narrow one between adaptation of the virus to HLA I restriction and the definition of conserved proviral CTL epitopes presentable by HLA I alleles. It is likely that the genetics of patients will need to be considered for HIV-1 vaccine studies and that multidisciplinary collaboration will be essential in this field of infectious diseases.
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Affiliation(s)
- Herve Fleury
- Laboratoire de Virologie, CHU de Bordeaux et CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Camille Tumiotto
- Laboratoire de Virologie, CHU de Bordeaux et CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Pantxika Bellecave
- Laboratoire de Virologie, CHU de Bordeaux et CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Patricia Recordon-Pinson
- Laboratoire de Virologie, CHU de Bordeaux et CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
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Grifoni A, Weiskopf D, Lindestam Arlehamn CS, Angelo M, Leary S, Sidney J, Frazier A, Phillips E, Mallal S, Mack SJ, Tippalagama R, Goonewardana S, Premawansa S, Premawansa G, Wijewickrama A, De Silva AD, Sette A. Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 714 adults from Colombo, Sri Lanka. Hum Immunol 2017; 79:87-88. [PMID: 29289740 DOI: 10.1016/j.humimm.2017.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 12/15/2017] [Accepted: 12/15/2017] [Indexed: 10/18/2022]
Abstract
DNA sequence-based typing at the HLA-A, -B, -C, -DPB1, -DQA1, -DQB1, and -DRB1 loci was performed on 714 healthy adult blood bank donors from Colombo, Sri Lanka, to characterize allele frequencies in support of studies on T cell immunity against pathogens, including Dengue virus. Deviations from Hardy Weinberg proportions were not detected at any locus. Several alleles were found in >30% of individuals, including the class II alleles DPB1 * 04:01, DPB1 * 02:01, DQB1 * 06:01 and DRB1 * 07:01, and the class I alleles A * 33:03 and A * 24:02. Genotype data will be available in the Allele Frequencies Net Database.
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Affiliation(s)
- Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | | | - Michael Angelo
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - April Frazier
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Steven J Mack
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | | | | | - Sunil Premawansa
- Department of Zoology and Environmental Science, Science Faculty, University of Colombo, Sri Lanka
| | | | | | - Aruna D De Silva
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA; Genetech Research Institute, Colombo, Sri Lanka(1)
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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Weiskopf D, Grifoni A, Arlehamn CSL, Angelo M, Leary S, Sidney J, Frazier A, Mack SJ, Phillips E, Mallal S, Cerpas C, Balmaseda A, Harris E, Sette A. Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 339 adults from Managua, Nicaragua. Hum Immunol 2017; 79:1-2. [PMID: 29122684 DOI: 10.1016/j.humimm.2017.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 10/27/2017] [Accepted: 11/03/2017] [Indexed: 11/26/2022]
Abstract
DNA sequence-based typing at the HLA-A, -B, -C, -DPB1, -DQA1, -DQB1, and -DRB1 loci was performed on anonymized samples provided by 339 healthy adult blood bank donors in Managua, Nicaragua. The purpose of the study was to characterize allele frequencies in the local population to support studies of T cell immunity against pathogens, including Dengue virus. Deviations from Hardy Weinberg proportions were detected for all class II loci (HLA-DPB1, -DQA1, -DQB1 and -DRB1), and at the class I C locus, but not at the class I A and B loci. The genotype data will be available in the Allele Frequencies Net Database.
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Affiliation(s)
- Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology (LJI), La Jolla, CA 92037, USA
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology (LJI), La Jolla, CA 92037, USA
| | | | - Michael Angelo
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology (LJI), La Jolla, CA 92037, USA
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology (LJI), La Jolla, CA 92037, USA.
| | - April Frazier
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology (LJI), La Jolla, CA 92037, USA
| | - Steven J Mack
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Cristhiam Cerpas
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
| | - Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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Gentle NL, Loubser S, Paximadis M, Puren A, Tiemessen CT. Killer-cell immunoglobulin-like receptor (KIR) and human leukocyte antigen (HLA) class I genetic diversity in four South African populations. Hum Immunol 2017; 78:503-509. [PMID: 28571758 DOI: 10.1016/j.humimm.2017.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 11/29/2022]
Abstract
Killer-cell Immunoglobulin-like Receptor (KIR) and Human Leukocyte Antigen (HLA) genotypes vary considerably between individuals and populations due to KIR/HLA allelic variation and variable haplotype configurations of KIR. HLA mediate natural killer cell activity by serving as KIR ligands. KIR/HLA polymorphisms associate with both disease susceptibility and severity. We determined the frequencies of KIR, KIR genotypes and KIR-HLA combinations in 364 healthy individuals from four South African populations. Study participants included black African (n=167), Caucasian (n=97), Mixed ancestry (n=50) and Indian (n=50) individuals. We identified 48 KIR genotypes that included two genotypes not previously reported. Based on KIR gene content, Indian individuals represented the most distinct group, showing the highest frequencies of KIR2DL2, KIR2DL5, KIR2DS1, KIR2DS2, KIR2DS3 and KIR3DS1, the lowest frequencies of KIR2DL3, KIR2DS4 and KIR3DL1; and a KIR2DL4-negative individual. KIR2DS1 and KIR3DS1 were infrequent in black African populations. HLA-C2 was more common in black African individuals, while HLA-C1 predominated in the other populations. Indian individuals were more likely to possess KIR2DL2 paired with HLA-C1, while Caucasian individuals exhibited the highest frequencies of KIR2DL3 paired with HLA-C1. This report provides comprehensive reference data for further study of the roles of KIR/HLA in non-communicable and infectious diseases in South African populations.
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Affiliation(s)
- Nikki L Gentle
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2000, South Africa
| | - Shayne Loubser
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2000, South Africa
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2000, South Africa
| | - Adrian Puren
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2000, South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2000, South Africa.
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Loubser S, Paximadis M, Tiemessen CT. Human leukocyte antigen class I (A, B and C) allele and haplotype variation in a South African Indian population. Hum Immunol 2017; 78:468-470. [PMID: 28465172 DOI: 10.1016/j.humimm.2017.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 11/25/2022]
Abstract
In 2013, ∼1,329,300 individuals made up the South African Indian population, which constituted ∼2.5% of the total population of ∼53 million. Historically, from 1860 to 1911, indentured labourers were imported from India, to work in the sugar-cane plantations in the KwaZulu-Natal Province. The local Indian community was further augmented by "passenger" immigrants who paid for passage to South Africa. Extensive HLA allelic variability exists in mainland Indian populations. We investigated HLA-A, -B and -C allele and haplotype diversity in 50 healthy, unrelated individuals recruited from the South African Indian population for comparison to data from mainland India.
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Affiliation(s)
- Shayne Loubser
- Centre for HIV-1 and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maria Paximadis
- Centre for HIV-1 and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T Tiemessen
- Centre for HIV-1 and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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Loubser S, Paximadis M, Tiemessen CT. Human leukocyte antigen class I (A, B and C) allele and haplotype variation in a South African Mixed ancestry population. Hum Immunol 2017; 78:399-400. [PMID: 28438553 DOI: 10.1016/j.humimm.2017.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/13/2017] [Accepted: 04/19/2017] [Indexed: 11/20/2022]
Abstract
South Africa has a large (∼53million), ethnically diverse population (black African, Caucasian, Indian/Asian and Mixed ancestry) and a high disease burden (particularly HIV-1 and Mycobacterium tuberculosis). The Mixed ancestry population constitutes ∼9% of the total population and was established ∼365years ago in the Western Cape region through interracial mixing of black Africans, Europeans and Asians. Admixed populations present unique opportunities to identify genetic factors involved in disease susceptibility. Since HLA genes are important mediators of host immunity, we investigated HLA-A, -B and -C allele and haplotype diversity in 50 healthy, unrelated individuals recruited from the Mixed ancestry population.
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Arlehamn CSL, Copin R, Leary S, Mack SJ, Phillips E, Mallal S, Sette A, Blatner G, Siefers H, Ernst JD. Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 100 Luo infants from the Boro area of Nyanza Province, Kenya. Hum Immunol 2017; 78:325-326. [PMID: 28315719 DOI: 10.1016/j.humimm.2017.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 03/14/2017] [Accepted: 03/14/2017] [Indexed: 11/16/2022]
Abstract
One hundred healthy infants enrolled as controls in a tuberculosis vaccine study in Nyanza Province, Kenya provided anonymized samples for DNA sequence-based typing at the HLA-A, -B, -C, -DPB1, -DQA1, -DQB1, -DRB1, and -DRB3/4/5 loci. The purpose of the study was to characterize allele frequencies in the local population, to support studies of T cell immunity against pathogens, including Mycobacterium tuberculosis. There are no detectable deviations from Hardy Weinberg proportions for the HLA-B, -C, -DRB1, -DPB1, -DQA1 and -DQB1 loci. A minor deviation was detected at the HLA-A locus due to an excess of HLA-A*02:02, 29:02, 30:02, and 68:02 homozygotes. The genotype data are available in the Allele Frequencies Net Database under identifier 3393.
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Affiliation(s)
- Cecilia S Lindestam Arlehamn
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology (LJI), La Jolla, CA 92037, USA; TBRU-ASTRa, USA
| | - Richard Copin
- Division of Infectious Diseases and Immunology, New York University School of Medicine, New York, NY 10016, USA
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia
| | - Steven J Mack
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology (LJI), La Jolla, CA 92037, USA; TBRU-ASTRa, USA
| | | | | | - Joel D Ernst
- Division of Infectious Diseases and Immunology, New York University School of Medicine, New York, NY 10016, USA; TBRU-ASTRa, USA.
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Zu Y, Tan MH, Ren EC, Ying JY. Facile and phase-defined determination of HLA alleles with morpholino-functionalized nanoparticle probes. Nanomedicine 2016; 13:611-618. [PMID: 27720927 DOI: 10.1016/j.nano.2016.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 08/31/2016] [Accepted: 09/18/2016] [Indexed: 11/15/2022]
Abstract
A number of human leukocyte antigen (HLA) gene alleles have been found to be genetic risk markers for immunologically mediated drug hypersensitivity. Clinical adoption of HLA pharmacogenomics requires facile and accurate allele screening assays. As HLA genes are highly polymorphic, currently available methods are usually labor-intensive and liable to generate false positives. Herein we report a general strategy for screening HLA alleles with nanoparticle probes. Specific HLA alleles can be identified by gauging three to five sequence variants. Single-polymerase chain reaction (PCR) and dual-PCR methods have been proposed to achieve phase-defined determination of the sequence variants. Morpholino-functionalized gold nanoparticle probes allow for colorimetric and highly specific detection. Assays for HLA-B*58:01 and HLA-B*15:02 have been developed and validated with 49 selected human genomic DNA samples. The facile nanoparticle probe-based assays can be implemented easily in molecular diagnostic laboratories for accurate and cost-effective screening of HLA alleles.
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Affiliation(s)
- Yanbing Zu
- Institute of Bioengineering and Nanotechnology, Singapore, Singapore
| | - Min-Han Tan
- Institute of Bioengineering and Nanotechnology, Singapore, Singapore
| | - Ee Chee Ren
- Singapore Immunology Network, 8A Biomedical Grove, Immunos, Singapore, Singapore
| | - Jackie Y Ying
- Institute of Bioengineering and Nanotechnology, Singapore, Singapore.
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Han H, Yuan F, Sun Y, Liu J, Liu S, Luo Y, Liang F, Liu N, Long J, Zhao X, Kong F, Xi Y. Three-dimensional structure discrepancy between HLA alleles for effective prediction of aGVHD severity and optimal selection of recipient-donor pairs: a proof-of-concept study. Oncotarget 2016; 6:40337-59. [PMID: 26498683 PMCID: PMC4741899 DOI: 10.18632/oncotarget.5378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 10/05/2015] [Indexed: 12/04/2022] Open
Abstract
The optimal selection of recipient-donor pair and accurate prediction of acute graft-versus-host disease (aGVHD) severity are always the two most crucial works in allogeneic hematopoietic stem cell transplantation (allo-HSCT), which currently rests mostly with HLA compatibility, the most polymorphic loci in the human genome, in clinic. Thus, there is an urgent need for a rapid and reliable quantitative system for optimal recipient-donor pairs selection and accurate prediction of aGVHD severity prior to allo-HSCT. For these reasons, we have developed a new selection/prediction system for optimal recipient-donor selection and effective prediction of aGVHD severity based on HLA three-dimensional (3D) structure modeling (HLA-TDSM) discrepancy, and applied this system in a pilot randomized clinical allo-HSCT study. The 37 patient-donor pairs in the study were typed at low- and high-resolution levels for HLA-A/-B/-DRB1/-DQB1 loci. HLA-TDSM system covering the 10000 alleles in HLA class I and II consists of the revised local and coordinate root-mean-square deviation (RMSD) values for each locus. Its accuracy and reliability were confirmed using stably transfected Hmy2.CIR–HLA-B cells, TCR Vβ gene scan, and antigen-specific alloreactive cytotoxic lymphocytes. Based on the preliminary results, we theoretically defined all HLA acceptable versus unacceptable mismatched alleles. More importantly, HLA-TDSM enabled a successful retrospective verification and prospective prediction for aGVHD severity in a pilot randomized clinical allo-HSCT study of 32 recipient-donor transplant pairs. There was a strong direct correlation between single/total revised RMSD and aGVHD severity (92% in retrospective group vs 95% in prospective group). These results seem to be closely related to the 3D structure discrepancy of mismatched HLA-alleles, but not the number or loci of mismatched HLA-alleles. Our data first provide the proof-of-concept that HLA-TDSM is essential for optimal selection of recipient-donor pairs and effective prediction of aGVHD severity before allo-HSCT.
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Affiliation(s)
- Hongxing Han
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital Affiliated to Academy of Military Medical Sciences, Beijing, China
| | - Fang Yuan
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital Affiliated to Academy of Military Medical Sciences, Beijing, China
| | - Yuying Sun
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital Affiliated to Academy of Military Medical Sciences, Beijing, China
| | - Jinfeng Liu
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital Affiliated to Academy of Military Medical Sciences, Beijing, China
| | - Shuguang Liu
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital Affiliated to Academy of Military Medical Sciences, Beijing, China
| | - Yuan Luo
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital Affiliated to Academy of Military Medical Sciences, Beijing, China
| | - Fei Liang
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital Affiliated to Academy of Military Medical Sciences, Beijing, China
| | - Nan Liu
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital Affiliated to Academy of Military Medical Sciences, Beijing, China
| | - Juan Long
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital Affiliated to Academy of Military Medical Sciences, Beijing, China
| | - Xiao Zhao
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital Affiliated to Academy of Military Medical Sciences, Beijing, China
| | - Fanhua Kong
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital Affiliated to Academy of Military Medical Sciences, Beijing, China
| | - Yongzhi Xi
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital Affiliated to Academy of Military Medical Sciences, Beijing, China
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Tan LK, Mohd-Farid B, Salsabil S, Heselynn H, Wahinuddin S, Lau IS, Gun SC, Nor-Suhaila S, Eashwary M, Mohd-Shahrir MS, Ainon MM, Azmillah R, Muhaini O, Shahnaz M, Too CL. HLA-A, -B, -C, -DRB1 and -DQB1 alleles and haplotypes in 951 Southeast Asia Malays from Peninsular Malaysia. Hum Immunol 2016; 77:818-819. [PMID: 27370684 DOI: 10.1016/j.humimm.2016.06.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 06/26/2016] [Accepted: 06/28/2016] [Indexed: 10/21/2022]
Abstract
A total of 951 Southeast Asia Malays from Peninsular Malaysia were genotyped for HLA-A, -B, -C -DRB1, and -DQB1 loci using polymerase chain reaction sequence-specific oligonucleotide probe hybridization methods. In this report, there were significant deviation from Hardy-Weinberg proportions for the HLA-A (p<0.0001), -B (p<0.0001), -DRB1 (p<0.0001) and -DQB1 (p<0.01) loci. Minor deviations from HWEP were detected for HLA-C (p=0.01). This genotype data was available in Allele Frequencies Network Database (AFND) Gonzalez-Galarza et al. (2015).
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Affiliation(s)
- Lay-Kim Tan
- Allergy and Immunology Research Center, Institute for Medical Research, Kuala Lumpur, Malaysia.
| | - Baharin Mohd-Farid
- Allergy and Immunology Research Center, Institute for Medical Research, Kuala Lumpur, Malaysia
| | - Sulaiman Salsabil
- Allergy and Immunology Research Center, Institute for Medical Research, Kuala Lumpur, Malaysia
| | - Hussein Heselynn
- Department of Medicine, Putrajaya Hospital, Wilayah Persekutuan Putrajaya, Malaysia
| | - Sulaiman Wahinuddin
- Department of Medicine, Hospital Raja Perempuan Bainun, Ipoh, Perak, Malaysia; Universiti Kuala Lumpur, Royal College of Medicine Perak, No 3, Jalan Greentown, 30450 Ipoh, Perak, Malaysia
| | - Ing-Soo Lau
- Department of Medicine, Hospital Selayang, Selangor, Malaysia
| | - Suk-Chyn Gun
- Department of Medicine, Hospital Tunku Ja'afar Seremban, Negari Sembilan, Malaysia
| | - Sharil Nor-Suhaila
- Department of Medicine, Putrajaya Hospital, Wilayah Persekutuan Putrajaya, Malaysia
| | - M Eashwary
- Department of Medicine, Putrajaya Hospital, Wilayah Persekutuan Putrajaya, Malaysia
| | | | - Mohd-Mokhtar Ainon
- Department of Medicine, Tengku Ampuan Afzan Hospital, Kuantan, Pahang, Malaysia
| | - Rosman Azmillah
- Department of Medicine, Hospital Selayang, Selangor, Malaysia
| | - Othman Muhaini
- Department of Medicine, Hospital Raja Perempuan Bainun, Ipoh, Perak, Malaysia
| | - Murad Shahnaz
- Allergy and Immunology Research Center, Institute for Medical Research, Kuala Lumpur, Malaysia
| | - Chun-Lai Too
- Allergy and Immunology Research Center, Institute for Medical Research, Kuala Lumpur, Malaysia; Rheumatology Unit, Department of Medicine, CMM L8:O4, Karolinska University Hospital and Karolinska Institutet, 17176 Stockholm, Sweden.
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49
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Chandra H, Yadav JS. T-cell antigens of Mycobacterium immunogenum, an etiological agent of occupational hypersensitivity pneumonitis. Mol Immunol 2016; 75:168-77. [PMID: 27294559 DOI: 10.1016/j.molimm.2016.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/25/2016] [Accepted: 05/27/2016] [Indexed: 11/17/2022]
Abstract
The T lymphocyte-mediated immune lung disease hypersensitivity pneumonitis (HP) in machinists is poorly understood for disease mechanisms and diagnosis due in part to lack of information on causative T-cell antigens of the etiological agent Mycobacterium immunogenum (MI). Therefore, overall objective of the current study was to identify T-cell reactive antigens of this recently recognized pathogen. In this direction, purified recombinant form of five of the seroreactive proteins (reported in our initial study), including three cell wall-associated (arbitrarily designated as antigens A through C) and two secretory (AgD & AgE), were examined for their potential to activate antigen-presenting cells (APCs) viz. alveolar macrophages and human monocyte-derived dendritic cells (DCs) and for T-cell reactivity. All five proteins strongly activated APCs by inducing inflammatory cytokines (TNF-α, IL-6 & IL-1α) and nitric oxide (NO), albeit to a varying extent (AgE≥AgD>AgB≥AgA≥AgC), implying their differential potential for activation of APCs. However, only two of the five proteins (AgA, AgD) showed significant T-cell response (T lymphocyte proliferation and IFN-γ secretion) when tested using sensitized T-cells from MI-induced HP mouse model. These antigens also activated the human naïve CD4(+) T cells in presence of autologous DCs as measured using ELISPOT for IFN-γ. Immuno-informatic analysis predicted that the identified T-cell antigens (AgA and AgD) bind more number of class I and class II HLA alleles as compared with the reference immuno-dominant antigens ESAT-6 and CFP-10 from the tuberculous mycobacterial species M. tuberculosis. Predicted human population coverage for the epitopes of AgA (90.87%) and AgD (88.09%) was also higher as compared to those for the reference antigens ESAT-6 (82.42%) and CFP-10 (80.21%). These two antigens were further predicted to be highly immunogenic for class I peptide MHC (pMHC) complex as compared to the reference antigens. Collectively, our results imply that AgA and AgD are T-cell antigens with a high HLA binding frequency as well as population coverage for HLA alleles. This first report on T-cell antigens and epitopes of M. immunogenum is significant as it is expected to open up avenues for understanding pathogenesis mechanisms and developing T-cell-based immunodiagnostic tools for this poorly investigated occupational lung disease.
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Affiliation(s)
- Harish Chandra
- Microbial Pathogenesis and Toxicogenomics Laboratory, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, United States of America
| | - Jagjit S Yadav
- Microbial Pathogenesis and Toxicogenomics Laboratory, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, United States of America.
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50
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Kizawa T, Yoto Y, Mizukami M, Tsugawa T, Takeuchi T, Kamasaki H, Ishii-Osai Y, Yamashita T, Nagai K, Hori T, Tsutsumi H. A case report of cutaneous polyarteritis nodosa in siblings. Mod Rheumatol 2016; 28:1049-1052. [PMID: 27299947 DOI: 10.1080/14397595.2016.1189139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Cutaneous polyarteritis nodosa (CPAN) is characterized by a necrotizing vasculitis of small and medium-sized arteries in the skin, which can be associated with fever, arthralgia, myalgia, and neuropathy, but, unlike polyarteritis nodosa (PAN), there is no visceral involvement. CPAN is rare in childhood. We report two siblings who developed CPAN during childhood. Interestingly, both had Mediterranean fever gene (MEFV) mutation, i.e. heterozygous E148Q. They also shared HLA-A24, -DR15 alleles. Simultaneous occurrence of MEFV mutation and HLA alleles with CPAN has never been reported in Japan. These cases could provide some hereditary clue for the development of CPAN.
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Affiliation(s)
- Toshitaka Kizawa
- a Department of Pediatrics , JCHO Sapporo Hokushin Hospital , Sapporo , Japan.,b Department of Pediatrics and
| | | | | | | | | | | | - Yasue Ishii-Osai
- c Department of Dermatology , Sapporo Medical University School of Medicine , Sapporo , Japan , and
| | - Toshiharu Yamashita
- c Department of Dermatology , Sapporo Medical University School of Medicine , Sapporo , Japan , and
| | - Kazushige Nagai
- d Department of Pediatrics , Takikawa Municipal Hospital , Takikawa , Japan
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