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Feng Q, Zhou M, Li S, Morimoto L, Hansen H, Myint SS, Wang R, Metayer C, Kang A, Fear AL, Pappas D, Erlich H, Hollenbach JA, Mancuso N, Trachtenberg E, de Smith AJ, Ma X, Wiemels JL. Interaction between maternal killer immunoglobulin-like receptors and offspring HLAs and susceptibility of childhood ALL. Blood Adv 2022; 6:3756-3766. [PMID: 35500222 PMCID: PMC9631572 DOI: 10.1182/bloodadvances.2021006821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/08/2022] [Indexed: 11/20/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) in children is associated with a distinct neonatal cytokine profile. The basis of this neonatal immune phenotype is unknown but potentially related to maternal-fetal immune receptor interactions. We conducted a case-control study of 226 case child-mother pairs and 404 control child-mother pairs to evaluate the role of interaction between HLA genotypes in the offspring and maternal killer immunoglobulin-like receptor (KIR) genotypes in the etiology of childhood ALL, while considering potential mediation by neonatal cytokines and the immune-modulating enzyme arginase-II (ARG-II). We observed different associations between offspring HLA-maternal KIR activating profiles and the risk of ALL in different predicted genetic ancestry groups. For instance, in Latino subjects who experience the highest risk of childhood leukemia, activating profiles were significantly associated with a lower risk of childhood ALL (odds ratio [OR] = 0.59; 95% confidence interval [CI], 0.49-0.71) and a higher level of ARG-II at birth (coefficient = 0.13; 95% CI, 0.04-0.22). HLA-KIR activating profiles were also associated with a lower risk of ALL in non-Latino Asians (OR = 0.63; 95% CI, 0.38-1.01), although they had a lower tumor necrosis factor-α level (coefficient = -0.27; 95% CI, -0.49 to -0.06). Among non-Latino White subjects, no significant association was observed between offspring HLA-maternal KIR interaction and ALL risk or cytokine levels. The current study reports the association between offspring HLA-maternal KIR interaction and the development of childhood ALL with variation by predicted genetic ancestry. We also observed some associations between activating profiles and immune factors related to cytokine control; however, cytokines did not demonstrate causal mediation of the activating profiles on ALL risk.
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Affiliation(s)
- Qianxi Feng
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA
| | - Mi Zhou
- Department of Laboratory Medicine, University of California, San Francisco, CA
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA
| | - Libby Morimoto
- School of Public Health, University of California, Berkeley, CA
| | - Helen Hansen
- Department of Neurosurgery, University of California, San Francisco, CA
| | - Swe Swe Myint
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA
| | - Rong Wang
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Yale University, New Haven, CT
| | | | - Alice Kang
- School of Public Health, University of California, Berkeley, CA
| | - Anna Lisa Fear
- Children’s Hospital Oakland Research Institute, Oakland, CA; and
| | - Derek Pappas
- Children’s Hospital Oakland Research Institute, Oakland, CA; and
| | - Henry Erlich
- Children’s Hospital Oakland Research Institute, Oakland, CA; and
| | - Jill A. Hollenbach
- Department of Neurology and Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA
| | | | - Adam J. de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Yale University, New Haven, CT
| | - Joseph L. Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA
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2
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Saigusa R, Roy P, Freuchet A, Gulati R, Ghosheh Y, Suthahar SSA, Durant CP, Hanna DB, Kiosses WB, Orecchioni M, Wen L, Wu R, Kuniholm MH, Landay AL, Anastos K, Tien PC, Gange SJ, Kassaye S, Vallejo J, Hedrick CC, Kwok WW, Sette A, Hodis HN, Kaplan RC, Ley K. Single cell transcriptomics and TCR reconstruction reveal CD4 T cell response to MHC-II-restricted APOB epitope in human cardiovascular disease. NATURE CARDIOVASCULAR RESEARCH 2022; 1:462-475. [PMID: 35990517 PMCID: PMC9383695 DOI: 10.1038/s44161-022-00063-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 04/04/2022] [Indexed: 02/02/2023]
Abstract
Atherosclerosis is accompanied by a CD4 T cell response to apolipoprotein B (APOB). Major Histocompatibility Complex (MHC)-II tetramers can be used to isolate antigen-specific CD4 T cells by flow sorting. Here, we produce, validate and use an MHC-II tetramer, DRB1*07:01 APOB-p18, to sort APOB-p18-specific cells from peripheral blood mononuclear cell samples from 8 DRB1*07:01+ women with and without subclinical cardiovascular disease (sCVD). Single cell RNA sequencing showed that transcriptomes of tetramer+ cells were between regulatory and memory T cells in healthy women and moved closer to memory T cells in women with sCVD. TCR sequencing of tetramer+ cells showed clonal expansion and V and J segment usage similar to those found in regulatory T cells. These findings suggest that APOB-specific regulatory T cells may switch to a more memory-like phenotype in women with atherosclerosis. Mouse studies showed that such switched cells promote atherosclerosis.
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Affiliation(s)
| | - Payel Roy
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Rishab Gulati
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Yanal Ghosheh
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | | | - David B. Hanna
- Albert Einstein College of Medicine, Department of Epidemiology and Population Health, Bronx, NY, USA
| | | | | | - Lai Wen
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Runpei Wu
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Mark H. Kuniholm
- University at Albany, Department of Epidemiology and Biostatistics, Rensselaer, NY, USA
| | - Alan L. Landay
- Rush University Medical Center, Department of Internal Medicine, Chicago, IL, USA
| | - Kathryn Anastos
- Albert Einstein College of Medicine, Departments of Medicine and Epidemiology & Population Health, Bronx NY, USA
| | - Phyllis C. Tien
- Department of Medicine, University of California, San Francisco, San Francisco, CA; Department of Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Stephen J. Gange
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore MD, USA
| | - Seble Kassaye
- Georgetown University, Georgetown University Medical Center, Washington, DC, USA
| | | | | | - William W. Kwok
- Benaroya Research Institute at Virginia Mason, Tetramer Core Laboratory, Seattle, WA, USA
| | | | - Howard N. Hodis
- Keck School of Medicine, University of Southern California Departments of Medicine and Population and Public Health Sciences, Los Angeles, CA, USA
- Atherosclerosis Research Unit, University of Southern California, Los Angeles, CA, USA
| | - Robert C. Kaplan
- Albert Einstein College of Medicine, Department of Epidemiology and Population Health, Bronx, NY, USA
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA, USA
| | - Klaus Ley
- La Jolla Institute for Immunology, La Jolla, CA, USA
- University of California San Diego, San Diego, CA, USA
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3
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Douillard V, Castelli EC, Mack SJ, Hollenbach JA, Gourraud PA, Vince N, Limou S. Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research. Front Genet 2021; 12:774916. [PMID: 34925459 PMCID: PMC8677840 DOI: 10.3389/fgene.2021.774916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 01/11/2023] Open
Abstract
The current SARS-CoV-2 pandemic era launched an immediate and broad response of the research community with studies both about the virus and host genetics. Research in genetics investigated HLA association with COVID-19 based on in silico, population, and individual data. However, they were conducted with variable scale and success; convincing results were mostly obtained with broader whole-genome association studies. Here, we propose a technical review of HLA analysis, including basic HLA knowledge as well as available tools and advice. We notably describe recent algorithms to infer and call HLA genotypes from GWAS SNPs and NGS data, respectively, which opens the possibility to investigate HLA from large datasets without a specific initial focus on this region. We thus hope this overview will empower geneticists who were unfamiliar with HLA to run MHC-focused analyses following the footsteps of the Covid-19|HLA & Immunogenetics Consortium.
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Affiliation(s)
- Venceslas Douillard
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | | | - Steven J. Mack
- Division of Allergy, Immunology and Bone Marrow Transplantation, Department of Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Pierre-Antoine Gourraud
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
- Ecole Centrale de Nantes, Department of Computer Sciences and Mathematics in Biology, Nantes, France
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4
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Nunes K, Aguiar VRC, Silva M, Sena AC, de Oliveira DCM, Dinardo CL, Kehdy FSG, Tarazona-Santos E, Rocha VG, Carneiro-Proietti ABF, Loureiro P, Flor-Park MV, Maximo C, Kelly S, Custer B, Weir BS, Sabino EC, Porto LC, Meyer D. How Ancestry Influences the Chances of Finding Unrelated Donors: An Investigation in Admixed Brazilians. Front Immunol 2020; 11:584950. [PMID: 33240273 PMCID: PMC7677137 DOI: 10.3389/fimmu.2020.584950] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022] Open
Abstract
A match of HLA loci between patients and donors is critical for successful hematopoietic stem cell transplantation. However, the extreme polymorphism of HLA loci - an outcome of millions of years of natural selection - reduces the chances that two individuals will carry identical combinations of multilocus HLA genotypes. Further, HLA variability is not homogeneously distributed throughout the world: African populations on average have greater variability than non-Africans, reducing the chances that two unrelated African individuals are HLA identical. Here, we explore how self-identification (often equated with "ethnicity" or "race") and genetic ancestry are related to the chances of finding HLA compatible donors in a large sample from Brazil, a highly admixed country. We query REDOME, Brazil's Bone Marrow Registry, and investigate how different criteria for identifying ancestry influence the chances of finding a match. We find that individuals who self-identify as "Black" and "Mixed" on average have lower chances of finding matches than those who self-identify as "White" (up to 57% reduction). We next show that an individual's African genetic ancestry, estimated using molecular markers and quantified as the proportion of an individual's genome that traces its ancestry to Africa, is strongly associated with reduced chances of finding a match (up to 60% reduction). Finally, we document that the strongest reduction in chances of finding a match is associated with having an MHC region of exclusively African ancestry (up to 75% reduction). We apply our findings to a specific condition, for which there is a clinical indication for transplantation: sickle-cell disease. We show that the increased African ancestry in patients with this disease leads to reduced chances of finding a match, when compared to the remainder of the sample, without the condition. Our results underscore the influence of ancestry on chances of finding compatible HLA matches, and indicate that efforts guided to increasing the African component of registries are necessary.
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Affiliation(s)
- Kelly Nunes
- Laboratory of Evolutionary Genetics, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Vitor R. C. Aguiar
- Laboratory of Evolutionary Genetics, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Márcio Silva
- Instituto de Matemática e Estatística, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre C. Sena
- Instituto de Matemática e Estatística, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Danielli C. M. de Oliveira
- Registro Nacional de Doadores Voluntários de Medula Óssea—REDOME, Instituto Nacional do Câncer, Ministério da Saúde, Rio de Janeiro, Brazil
| | | | | | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vanderson G. Rocha
- Fundação Pró Sangue, Hemocentro de São Paulo, São Paulo, Brazil
- Serviço de Hematologia, Hemoterapia e Terapia Celular, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Paula Loureiro
- Fundação Hemominas, Belo Horizonte, Brazil
- Fundação de Hematologia e Hemoterapia de Pernambuco, HEMOPE, Recife, Brazil
| | - Miriam V. Flor-Park
- Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Instituto da Criança, São Paulo, Brazil
| | | | - Shannon Kelly
- Epidemiology, Vitalant Research Institute, San Francisco, CA, United States
- University of California San Francisco Benioff Children’s Hospital Oakland, Oakland, CA, United States
| | - Brian Custer
- Epidemiology, Vitalant Research Institute, San Francisco, CA, United States
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Bruce S. Weir
- Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Departamento de Moléstias Infecciosas e Parasitárias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Luís Cristóvão Porto
- Laboratório de Histocompatibilidade e Criopreservação, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Diogo Meyer
- Laboratory of Evolutionary Genetics, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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5
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Ritari J, Hyvärinen K, Clancy J, Partanen J, Koskela S. Increasing accuracy of HLA imputation by a population-specific reference panel in a FinnGen biobank cohort. NAR Genom Bioinform 2020; 2:lqaa030. [PMID: 33575586 PMCID: PMC7671345 DOI: 10.1093/nargab/lqaa030] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/20/2020] [Accepted: 04/26/2020] [Indexed: 01/02/2023] Open
Abstract
The HLA genes, the most polymorphic genes in the human genome, constitute the strongest single genetic susceptibility factor for autoimmune diseases, transplantation alloimmunity and infections. HLA imputation via statistical inference of alleles based on single-nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with alleles is a powerful first-step screening tool. Due to different LD structures between populations, the accuracy of HLA imputation may benefit from matching the imputation reference with the study population. To evaluate the potential advantage of using population-specific reference in HLA imputation, we constructed an HLA reference panel consisting of 1150 Finns with 5365 major histocompatibility complex region SNPs consistent between genome builds. We evaluated the accuracy of the panel against a European panel in an independent test set of 213 Finnish subjects. We show that the Finnish panel yields a lower imputation error rate (1.24% versus 1.79%). More than 30% of imputation errors occurred in haplotypes enriched in Finland. The frequencies of imputed HLA alleles were highly correlated with clinical-grade HLA allele frequencies and allowed accurate replication of established HLA–disease associations in ∼102 000 biobank participants. The results show that a population-specific reference increases imputation accuracy in a relatively isolated population within Europe and can be successfully applied to biobank-scale genome data collections.
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Affiliation(s)
- Jarmo Ritari
- Research and Development, Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
| | - Kati Hyvärinen
- Research and Development, Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
| | - Jonna Clancy
- Research and Development, Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
| | | | - Jukka Partanen
- Research and Development, Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
| | - Satu Koskela
- Research and Development, Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
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6
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Kovacs AAZ, Kono N, Wang CH, Wang D, Frederick T, Operskalski E, Tien PC, French AL, Minkoff H, Kassaye S, T. Golub E, Aouizerat BE, Kuniholm MH, Millstein J. Association of HLA Genotype With T-Cell Activation in Human Immunodeficiency Virus (HIV) and HIV/Hepatitis C Virus-Coinfected Women. J Infect Dis 2020; 221:1156-1166. [PMID: 31802115 PMCID: PMC7325713 DOI: 10.1093/infdis/jiz589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/06/2019] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Global immune activation and HLA alleles are each associated with the pathogenesis of human immunodeficiency virus (HIV) and hepatitis C virus . METHODS We evaluated the relationship between 44 HLA class I and 28 class II alleles and percentages of activated CD8 (CD8+CD38+DR+) and CD4 (CD4+CD38+DR+) T cells in 586 women who were naive to highly active antiretroviral therapy. We used linear generalized estimating equation regression models, adjusting for race/ethnicity, age, HIV load, and hepatitis C virus infection and controlling for multiplicity using a false discovery rate threshold of 0.10. RESULTS Ten HLA alleles were associated with CD8 and/or CD4 T-cell activation. Lower percentages of activated CD8 and/or CD4 T cells were associated with protective alleles B*57:03 (CD8 T cells, -6.6% [P = .002]; CD4 T cells, -2.7% [P = .007]), C*18:01 (CD8 T cells, -6.6%; P < .0008) and DRB1*13:01 (CD4 T cells, -2.7%; P < .0004), and higher percentages were found with B*18:01 (CD8 T cells, 6.2%; P < .0003), a detrimental allele. Other alleles/allele groups associated with activation included C*12:03, group DQA1*01:00, DQB1*03:01, DQB1*03:02, DQB1*06:02, and DQB1*06:03. CONCLUSION These findings suggest that a person's HLA type may play a role in modulating T-cell activation independent of viral load and sheds light on the relationship between HLA, T-cell activation, immune control, and HIV pathogenesis.
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Affiliation(s)
- Andrea A Z Kovacs
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Naoko Kono
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Chia-Hao Wang
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, Keck School of Medicine, University of Southern California, Los Angeles, California
- City of Hope National Medical Center, Duarte, California
| | - Daidong Wang
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Toni Frederick
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Eva Operskalski
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Phyllis C Tien
- Department of Medicine, University of California, San Francisco and Department of Veterans Affairs, San Francisco, California
| | - Audrey L French
- Department of Medicine, Stroger Hospital of Cook County/CORE Center, Rush Medical School, Chicago, Illinois
| | - Howard Minkoff
- Departments of Obstetrics and Gynecology Maimonides Medical Center and SUNY Downstate, Brooklyn, New York
| | - Seble Kassaye
- Department of Medicine, Georgetown University School of Medicine, Washington, DC
| | - Elizabeth T. Golub
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, New York University, New York, New York
- Department of Oral and Maxillofacial Surgery, New York University, New York, New York
| | - Mark H Kuniholm
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York
| | - Joshua Millstein
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
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7
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Katrinli S, Lori A, Kilaru V, Carter S, Powers A, Gillespie CF, Wingo AP, Michopoulos V, Jovanovic T, Ressler KJ, Smith AK. Association of HLA locus alleles with posttraumatic stress disorder. Brain Behav Immun 2019; 81:655-658. [PMID: 31310798 PMCID: PMC6754776 DOI: 10.1016/j.bbi.2019.07.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 07/09/2019] [Accepted: 07/12/2019] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Immune dysregulation has been widely observed in those with posttraumatic stress disorder (PTSD). An individual's immune response is shaped, in part, by the highly polymorphic Human Leukocyte Antigen (HLA) locus that is associated with major psychiatric disorders such as schizophrenia, major depression and bipolar disorder. The aim of the current study was to investigate the association between common HLA alleles and PTSD. METHODS Genome-wide association data was used to predict alleles of 7 classical polymorphic HLA genes (A, B, C, DRB1, DQA1, DQB1, DPB1) in 403 lifetime PTSD cases and 369 trauma exposed controls of African ancestry. Association of HLA allelic variations with lifetime PTSD was analyzed using logistic regression, controlling for ancestry, sex and multiple comparisons. The effect of HLA alleles on gene expression was assessed by weighted correlation network analysis (WGCNA), using 353 subjects with available expression data. Enrichment analysis was performed using anRichment to identify associated pathways of each module. RESULTS HLA-B*58:01 (p = 0.035), HLA-C*07:01 (p = 0.035), HLA-DQA1*01:01 (p = 0.003), HLA-DQB1*05:01 (p = 0.009) and HLA-DPB1*17:01 (p = 0.017) were more common in PTSD cases, while HLA-A*02:01 (p = 0.026), HLA-DQA1*05:05 (p = 0.011) and HLA-DRB1*11:01 (p < 0.001) were more frequent in controls. WGCNA was used to explore expression patterns of the PTSD related alleles. Gene expression modules of PTSD-related HLA alleles were enriched in various pathways, including pathways related to immune and neural activity. CONCLUSIONS To the best of our knowledge, this is the first study to report an association of HLA alleles with PTSD. Altogether, our results support the link between the immune system, brain and PTSD.
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Affiliation(s)
- Seyma Katrinli
- Emory University, Department of Gynecology and Obstetrics, Atlanta, Georgia, USA
| | - Adriana Lori
- Emory University, Department of Psychiatry & Behavioral Sciences, Atlanta, GA, USA
| | - Varun Kilaru
- Emory University, Department of Gynecology and Obstetrics, Atlanta, Georgia, USA
| | - Sierra Carter
- Department of Psychology, Georgia State University, Atlanta, Georgia, USA
| | - Abigail Powers
- Emory University, Department of Psychiatry & Behavioral Sciences, Atlanta, GA, USA
| | - Charles F. Gillespie
- Emory University, Department of Psychiatry & Behavioral Sciences, Atlanta, GA, USA
| | - Aliza P. Wingo
- Emory University, Department of Psychiatry & Behavioral Sciences, Atlanta, GA, USA,Division of Mental Health, Atlanta VA Medical Center, Decatur, GA, USA
| | - Vasiliki Michopoulos
- Emory University, Department of Psychiatry & Behavioral Sciences, Atlanta, GA, USA
| | - Tanja Jovanovic
- Emory University, Department of Psychiatry & Behavioral Sciences, Atlanta, GA, USA
| | - Kerry J. Ressler
- Emory University, Department of Psychiatry & Behavioral Sciences, Atlanta, GA, USA,Department of Psychiatry, Harvard Medical School and McLean Hospital, Belmont, MA, USA
| | - Alicia K. Smith
- Emory University, Department of Gynecology and Obstetrics, Atlanta, Georgia, USA,Emory University, Department of Psychiatry & Behavioral Sciences, Atlanta, GA, USA,Corresponding author: Dr Alicia K Smith,
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8
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Kuniholm MH, Strickler HD, Anastos K, Prokunina-Olsson L, Aouizerat BE, O'Brien TR. Relationship of Genotype for HLA B*57 and IFNL4 With Disease Progression in Female HIV Controllers. Clin Infect Dis 2019; 65:1243-1244. [PMID: 28541547 DOI: 10.1093/cid/cix481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mark H Kuniholm
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, Departments of
| | | | - Kathryn Anastos
- Epidemiology and Population Health and.,Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research and.,Department of Oral and Maxillofacial Surgery, New York University ; and
| | - Thomas R O'Brien
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
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9
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Racial differences in human papilloma virus types amongst United States women with HIV and cervical precancer. AIDS 2018; 32:2821-2826. [PMID: 30234608 DOI: 10.1097/qad.0000000000002005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Recent studies reported a lower human papillomavirus 16 (HPV16) prevalence in cervical precancer among African American than Caucasian women in the general population. We assessed this relationship in women with HIV. DESIGN Women living with or at risk for HIV in the Women's Interagency HIV Study were followed semi-annually with Pap tests, colposcopy/histology (if indicated), and collection of cervicovaginal lavage samples for HPV testing by PCR. Racial and ethnic groups were defined using genomic Ancestry Informative Markers (AIMs). RESULTS Among 175 cases of cervical intraepithelial neoplasia 3 or worse (CIN-3+), 154 were diagnosed in women with HIV. African American (27%) and Hispanic (37%) cases were significantly less likely than Caucasian (62%) women to test positive for HPV16 (P = 0.01). In multivariate logistic regression models, these associations remained significant for African Americans (odds ratio = 0.13; 95% confidence interval (CI) 0.04-0.44; P = 0.001) but not Hispanics, after controlling for HIV status, CD4 count, history of AIDS, age, smoking, and sexual behavior. Limiting the analysis to women with HIV did not change the findings. CONCLUSION HPV16 prevalence is lower in African American compared with Caucasian women with HIV and cervical precancer, independent of immune status. Future studies to determine why these racial differences exist are warranted, and whether there are similar associations between race and invasive cervical cancer in women with HIV. Further, HPV types not covered by quadrivalent and bivalent vaccines may play an especially important role in cervical precancer among HIV-positive African American women, a possible advantage to using nonavalent HPV vaccine in this population.
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Hillary RP, Ollila HM, Lin L, Desestret V, Rogemond V, Picard G, Small M, Arnulf I, Dauvilliers Y, Honnorat J, Mignot E. Complex HLA association in paraneoplastic cerebellar ataxia with anti-Yo antibodies. J Neuroimmunol 2018; 315:28-32. [DOI: 10.1016/j.jneuroim.2017.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 12/17/2017] [Accepted: 12/17/2017] [Indexed: 12/18/2022]
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Association of a 3' untranslated region polymorphism in proprotein convertase subtilisin/kexin type 9 with HIV viral load and CD4+ levels in HIV/hepatitis C virus coinfected women. AIDS 2017; 31:2483-2492. [PMID: 29120899 DOI: 10.1097/qad.0000000000001648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVE To assess variation in genes that regulate cholesterol metabolism in relation to the natural history of HIV infection. DESIGN Cross-sectional and longitudinal analysis of the Women's Interagency HIV Study. METHODS We examined 2050 single nucleotide polymorphisms (SNPs) in 19 genes known to regulate cholesterol metabolism in relation to HIV viral load and CD4 T-cell levels in a multiracial cohort of 1066 antiretroviral therapy-naive women. RESULTS Six SNPs were associated with both HIV viral load and CD4 T-cell levels at a false discovery rate of 0.01. Bioinformatics tools did not predict functional activity for five SNPs, located in introns of nuclear receptor corepressor 2, retinoid X receptor alpha (RXRA), and tetratricopeptide repeat domain 39B. Rs17111557 located in the 3' untranslated region of proprotein convertase subtilisin/kexin type 9 (PCSK9) putatively affects binding of hsa-miR-548t-5p and hsa-miR-4796-3p, which could regulate PCSK9 expression levels. Interrogation of rs17111557 revealed stronger associations in the subset of women with HIV/hepatitis C virus (HCV) coinfection (n = 408, 38% of women). Rs17111557 was also associated with low-density lipoprotein cholesterol levels in HIV/HCV coinfected (β: -10.4; 95% confidence interval: -17.9, -2.9; P = 0.007), but not in HIV monoinfected (β:1.2; 95% confidence interval: -6.3, 8.6; P = 0.76) women in adjusted analysis. CONCLUSION PCSK9 polymorphism may affect HIV pathogenesis, particularly in HIV/HCV coinfected women. A likely mechanism for this effect is PCSK9-mediated regulation of cholesterol metabolism. Replication in independent cohorts is needed to clarify the generalizability of the observed associations.
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Significant variation between SNP-based HLA imputations in diverse populations: the last mile is the hardest. THE PHARMACOGENOMICS JOURNAL 2017; 18:367-376. [PMID: 28440342 DOI: 10.1038/tpj.2017.7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 12/07/2016] [Accepted: 02/14/2017] [Indexed: 12/17/2022]
Abstract
Four single nucleotide polymorphism (SNP)-based human leukocyte antigen (HLA) imputation methods (e-HLA, HIBAG, HLA*IMP:02 and MAGPrediction) were trained using 1000 Genomes SNP and HLA genotypes and assessed for their ability to accurately impute molecular HLA-A, -B, -C and -DRB1 genotypes in the Human Genome Diversity Project cell panel. Imputation concordance was high (>89%) across all methods for both HLA-A and HLA-C, but HLA-B and HLA-DRB1 proved generally difficult to impute. Overall, <27.8% of subjects were correctly imputed for all HLA loci by any method. Concordance across all loci was not enhanced via the application of confidence thresholds; reliance on confidence scores across methods only led to noticeable improvement (+3.2%) for HLA-DRB1. As the HLA complex is highly relevant to the study of human health and disease, a standardized assessment of SNP-based HLA imputation methods is crucial for advancing genomic research. Considerable room remains for the improvement of HLA-B and especially HLA-DRB1 imputation methods, and no imputation method is as accurate as molecular genotyping. The application of large, ancestrally diverse HLA and SNP reference data sets and multiple imputation methods has the potential to make SNP-based HLA imputation methods a tractable option for determining HLA genotypes.
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