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de Araújo JLF, Bonifácio VF, Batista LM, de Ávila RE, Aguiar RS, Bastos-Rodrigues L, de Souza RP. Association of 3p21.31 Locus (CXCR6 and LZTFL1) with COVID-19 Outcomes in Brazilian Hospitalyzed Subjects. Curr Microbiol 2023; 80:319. [PMID: 37578643 DOI: 10.1007/s00284-023-03437-3] [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: 03/21/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
The 3p21.31 locus has been associated with severe COVID-19 prognosis in GWAS studies. Here, we evaluated whether three polymorphisms (LZTFL1 rs10490770, CXCR6 rs2234355 and rs2234358) in the reported locus were associated with the need for mechanical ventilation, hospitalization length and death in 102 COVID-19 hospitalized Brazilian subjects. No genetic association was found with the need for mechanical ventilation and hospitalization length. CXCR6 rs2234355 was associated with mortality under the codominance model, with carriers of the A/A genotype having a greater chance of death than A/G (OR: 10.5; 95% CI: 1.55-70.76). Our results further suggest that the CXCR6 genetic variant contributes to COVID-19 outcomes.
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Affiliation(s)
- João Locke Ferreira de Araújo
- Grupo de Pesquisa em Bioestatística e Epidemiologia Molecular, Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Victória Frigério Bonifácio
- Departamento de Nutrição, Escola de Enfermagem, Universidade Federal de Minas Gerais, Minas Gerais - Brazil, Belo Horizonte, MG, Brazil
| | - Lorena Medeiros Batista
- Departamento de Nutrição, Escola de Enfermagem, Universidade Federal de Minas Gerais, Minas Gerais - Brazil, Belo Horizonte, MG, Brazil
| | | | - Renato Santana Aguiar
- Grupo de Pesquisa em Bioestatística e Epidemiologia Molecular, Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
- Instituto D'OR de Pesquisa e Ensino, Rio de Janeiro, RJ, Brazil
| | - Luciana Bastos-Rodrigues
- Departamento de Nutrição, Escola de Enfermagem, Universidade Federal de Minas Gerais, Minas Gerais - Brazil, Belo Horizonte, MG, Brazil.
| | - Renan Pedra de Souza
- Grupo de Pesquisa em Bioestatística e Epidemiologia Molecular, Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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Real LM, Sáez ME, Corma-Gómez A, Gonzalez-Pérez A, Thorball C, Ruiz R, Jimenez-Leon MR, Gonzalez-Serna A, Gasca-Capote C, Bravo MJ, Royo JL, Perez-Gomez A, Camacho-Sojo MI, Gallego I, Vitalle J, Bachiller S, Gutierrez-Valencia A, Vidal F, Fellay J, Lichterfeld M, Ruiz-Mateos E. A metagenome-wide association study of HIV disease progression in HIV controllers. iScience 2023; 26:107214. [PMID: 37456859 PMCID: PMC10339206 DOI: 10.1016/j.isci.2023.107214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/19/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
Some HIV controllers experience immunologic progression with CD4+ T cell decline. We aimed to identify genetic factors associated with CD4+ T cell lost in HIV controllers. A total of 561 HIV controllers were included, 442 and 119 from the International HIV controllers Study Cohort and the Swiss HIV Cohort Study, respectively. No SNP or gene was associated with the long-term non-progressor HIV spontaneous control phenotype in the individual GWAS or in the meta-analysis. However, SNPs previously associated with natural HIV control linked to HLA-B (rs2395029 [p = 0.005; OR = 1.70], rs59440261 [p = 0.003; OR = 1.78]), MICA (rs112243036 [p = 0.011; OR = 1.45]), and PSORS1C1 loci (rs3815087 [p = 0.017; OR = 1.39]) showed nominal association with this phenotype. Genetic factors associated with the long-term HIV controllers without risk of immunologic progression are those previously related to the overall HIV controller phenotype.
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Affiliation(s)
- Luis Miguel Real
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de Valme, Instituto de Biomedicina de Sevilla, IBIS, Sevilla, Spain
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Facultad de Medicina, Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC)-Instituto de Salud Carlos III, Madrid, Spain
| | - María E. Sáez
- Centro Andaluz de Estudios Bioinformáticos (CAEBI, SL), Sevilla, Spain
| | - Anais Corma-Gómez
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de Valme, Instituto de Biomedicina de Sevilla, IBIS, Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC)-Instituto de Salud Carlos III, Madrid, Spain
| | | | - Christian Thorball
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Rocío Ruiz
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla/Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41012 Sevilla, Spain
| | - María Reyes Jimenez-Leon
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
| | - Alejandro Gonzalez-Serna
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de Valme, Instituto de Biomedicina de Sevilla, IBIS, Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC)-Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Gasca-Capote
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
| | - María José Bravo
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Facultad de Medicina, Universidad de Málaga, Málaga, Spain
| | - José Luis Royo
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Facultad de Medicina, Universidad de Málaga, Málaga, Spain
| | - Alberto Perez-Gomez
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
| | - María Inés Camacho-Sojo
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
| | - Isabel Gallego
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
| | - Joana Vitalle
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
| | - Sara Bachiller
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
- Department of Medical Biochemistry, Molecular Biology and Immunology, School of Medicine, University of Seville, Seville, Spain
| | - Alicia Gutierrez-Valencia
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
| | - Francisco Vidal
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC)-Instituto de Salud Carlos III, Madrid, Spain
- Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ezequiel Ruiz-Mateos
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
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Nosik M, Berezhnya E, Bystritskaya E, Kiseleva I, Lobach O, Kireev D, Svitich O. Female Sex Hormones Upregulate the Replication Activity of HIV-1 Sub-Subtype A6 and CRF02_AG but Not HIV-1 Subtype B. Pathogens 2023; 12:880. [PMID: 37513727 PMCID: PMC10383583 DOI: 10.3390/pathogens12070880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/18/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
More than 50% of all people living with HIV worldwide are women. Globally, HIV/AIDS is the leading cause of death among women aged 15 to 44. The safe and effective methods of hormonal contraception are an essential component of preventive medical care in order to reduce maternal and infant mortality. However, there is limited knowledge regarding the effect of hormones on the rate of viral replication in HIV infection, especially non-B subtypes. The goal of the present work was to study in vitro how the female hormones β-estradiol and progesterone affect the replication of the HIV-1 subtypes A6, CRF02_AG, and B. The findings show that high doses of hormones enhanced the replication of HIV-1 sub-subtype A6 by an average of 1.75 times and the recombinant variant CRF02_AG by 1.4 times but did not affect the replication of HIV-1 subtype B. No difference was detected in the expression of CCR5 and CXCR4 co-receptors on the cell surface, either in the presence or absence of hormones. However, one of the reasons for the increased viral replication could be the modulated TLRs secretion, as it was found that high doses of estradiol and progesterone upregulated, to varying degrees, the expression of TLR2 and TLR9 genes in the PBMCs of female donors infected with HIV-1 sub-subtype A6.
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Affiliation(s)
- Marina Nosik
- I.I. Mechnikov Institute of Vaccines and Sera, 105064 Moscow, Russia
| | - Elena Berezhnya
- I.I. Mechnikov Institute of Vaccines and Sera, 105064 Moscow, Russia
| | | | - Irina Kiseleva
- I.I. Mechnikov Institute of Vaccines and Sera, 105064 Moscow, Russia
| | - Olga Lobach
- I.I. Mechnikov Institute of Vaccines and Sera, 105064 Moscow, Russia
| | - Dmitry Kireev
- Central Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Oxana Svitich
- I.I. Mechnikov Institute of Vaccines and Sera, 105064 Moscow, Russia
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Inderbitzin A, Loosli T, Opitz L, Rusert P, Metzner KJ. Transcriptome profiles of latently- and reactivated HIV-1 infected primary CD4+ T cells: A pooled data-analysis. Front Immunol 2022; 13:915805. [PMID: 36090997 PMCID: PMC9459035 DOI: 10.3389/fimmu.2022.915805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
The main obstacle to cure HIV-1 is the latent reservoir. Antiretroviral therapy effectively controls viral replication, however, it does not eradicate the latent reservoir. Latent CD4+ T cells are extremely rare in HIV-1 infected patients, making primary CD4+ T cell models of HIV-1 latency key to understanding latency and thus finding a cure. In recent years several primary CD4+ T cell models of HIV-1 latency were developed to study the underlying mechanism of establishing, maintaining and reversing HIV-1 latency. In the search of biomarkers, primary CD4+ T cell models of HIV-1 latency were used for bulk and single-cell transcriptomics. A wealth of information was generated from transcriptome analyses of different primary CD4+ T cell models of HIV-1 latency using latently- and reactivated HIV-1 infected primary CD4+ T cells. Here, we performed a pooled data-analysis comparing the transcriptome profiles of latently- and reactivated HIV-1 infected cells of 5 in vitro primary CD4+ T cell models of HIV-1 latency and 2 ex vivo studies of reactivated HIV-1 infected primary CD4+ T cells from HIV-1 infected individuals. Identifying genes that are differentially expressed between latently- and reactivated HIV-1 infected primary CD4+ T cells could be a more successful strategy to better understand and characterize HIV-1 latency and reactivation. We observed that natural ligands and coreceptors were predominantly downregulated in latently HIV-1 infected primary CD4+ T cells, whereas genes associated with apoptosis, cell cycle and HLA class II were upregulated in reactivated HIV-1 infected primary CD4+ T cells. In addition, we observed 5 differentially expressed genes that co-occurred in latently- and reactivated HIV-1 infected primary CD4+ T cells, one of which, MSRB2, was found to be differentially expressed between latently- and reactivated HIV-1 infected cells. Investigation of primary CD4+ T cell models of HIV-1 latency that mimic the in vivo state remains essential for the study of HIV-1 latency and thus providing the opportunity to compare the transcriptome profile of latently- and reactivated HIV-1 infected cells to gain insights into differentially expressed genes, which might contribute to HIV-1 latency.
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Affiliation(s)
- Anne Inderbitzin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Lennart Opitz
- Functional Genomics Center Zurich, Eidgenössische Technische Hochschule (ETH) Zürich/University of Zurich, Zurich, Switzerland
| | - Peter Rusert
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J. Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- *Correspondence: Karin J. Metzner,
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De La Torre-Tarazona E, Ayala-Suárez R, Díez-Fuertes F, Alcamí J. Omic Technologies in HIV: Searching Transcriptional Signatures Involved in Long-Term Non-Progressor and HIV Controller Phenotypes. Front Immunol 2022; 13:926499. [PMID: 35844607 PMCID: PMC9284212 DOI: 10.3389/fimmu.2022.926499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
This article reviews the main discoveries achieved by transcriptomic approaches on HIV controller (HIC) and long-term non-progressor (LTNP) individuals, who are able to suppress HIV replication and maintain high CD4+ T cell levels, respectively, in the absence of antiretroviral therapy. Different studies using high throughput techniques have elucidated multifactorial causes implied in natural control of HIV infection. Genes related to IFN response, calcium metabolism, ribosome biogenesis, among others, are commonly differentially expressed in LTNP/HIC individuals. Additionally, pathways related with activation, survival, proliferation, apoptosis and inflammation, can be deregulated in these individuals. Likewise, recent transcriptomic studies include high-throughput sequencing in specific immune cell subpopulations, finding additional gene expression patterns associated to viral control and/or non-progression in immune cell subsets. Herein, we provide an overview of the main differentially expressed genes and biological routes commonly observed on immune cells involved in HIV infection from HIC and LTNP individuals, analyzing also different technical aspects that could affect the data analysis and the future perspectives and gaps to be addressed in this field.
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Affiliation(s)
- Erick De La Torre-Tarazona
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Rubén Ayala-Suárez
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Francisco Díez-Fuertes
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- *Correspondence: Francisco Díez-Fuertes,
| | - José Alcamí
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Human Immunodeficiency Virus (HIV) Unit, Hospital Clínic de Barcelona, Barcelona, Spain
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Mechanism of Viral Suppression among HIV Elite Controllers and Long-Term Nonprogressors in Nigeria and South Africa. Viruses 2022; 14:v14061270. [PMID: 35746741 PMCID: PMC9228396 DOI: 10.3390/v14061270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 12/30/2022] Open
Abstract
A subgroup among people living with HIV (PLHIV) experience viral suppression, sometimes to an undetectable level in the blood and/or are able to maintain a healthy CD4+ T-cell count without the influence of antiretroviral (ARV) therapy. One out of three hundred PLHIV fall into this category, and a large sample of this group can be found in areas with a high prevalence of HIV infection such as Nigeria and South Africa. Understanding the mechanism underpinning the nonprogressive phenotype in this subgroup may provide insights into the control of the global HIV epidemic. This work provides mechanisms of the elite control and nonprogressive phenotype among PLHIV in Nigeria and South Africa and identifies research gaps that will contribute to a better understanding on HIV controllers among PLHIV.
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Qiu K, Zeng T, Liao Y, Min J, Zhang N, Peng M, Kong W, Chen LL. Identification of Inflammation-Related Biomarker Pro-ADM for Male Patients With Gout by Comprehensive Analysis. Front Immunol 2022; 12:798719. [PMID: 35116032 PMCID: PMC8803656 DOI: 10.3389/fimmu.2021.798719] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/28/2021] [Indexed: 11/22/2022] Open
Abstract
Objective Gout is a local inflammatory disease caused by the deposition of monosodium urate (MSU) crystals in joints or adjacent tissues. When some gout occurs without hyperuricemia, or its clinical symptoms and signs are not typical, the diagnosis of gout will be delayed, so there is an urgent need to find a new biomarker to predict and diagnose of gout flare. Our research attempts to find the key genes and potential molecular mechanisms of gout through bioinformatics analysis, and collected general data and blood biochemical samples of patients with gout and healthy, then analyzed and compared the expression of factors regulated by key genes. Method GSE160170 were downloaded from GEO database for analysis. The data were normalized to identify the differentially expressed genes (DEGs), then GO and KEGG enrichment analysis were applied. Protein-protein interaction (PPI) networks and hub genes between DEGs were identified. Then collect general information and blood samples from male patients with acute gout, hyperuricemia and healthy. ELISA method was used to detect pro-ADM levels of different groups, and the data was input into SPSS statistical software for analysis. Result We identified 266 DEGs (179 up-regulated and 87 down-regulated) between gout patients and healthy controls. GO analysis results show that DEGs are mostly enriched in inflammatory response, growth factor activity, cytokine activity, chemokine activity, S100 protein binding and CXCR chemokine receptor binding. KEGG pathway analysis showed that DEGs are mainly related to Chemokine signaling pathway and Cytokine-cytokine receptor interaction. ADM, CXCR1, CXCR6, CXCL3, CCL3, CCL18, CCL3L3, CCL4L1, CD69, CD83, AREG, EREG, B7RP1, HBEGF, NAMPT and S100B are the most important hub genes in the PPI network. We found that the expression of pro-ADM in the gout group and hyperuricemia group was higher than that in the healthy group, and the difference was statistically significant. Conclusion In this study, a series of bioinformatics analyses were performed on DEGs to identify key genes and pathways related to gout. Through clinical verification, we found that pro-ADM can be used as an inflammation-related biomarker for acute attacks of gout, providing new ideas for the diagnosis and treatment of gout.
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Affiliation(s)
- Kangli Qiu
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Clinical Research Center for Diabetes and Metabolic Disorders, Wuhan, China
| | - Tianshu Zeng
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Clinical Research Center for Diabetes and Metabolic Disorders, Wuhan, China
| | - Yunfei Liao
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Clinical Research Center for Diabetes and Metabolic Disorders, Wuhan, China
| | - Jie Min
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Clinical Research Center for Diabetes and Metabolic Disorders, Wuhan, China
| | - Nan Zhang
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Clinical Research Center for Diabetes and Metabolic Disorders, Wuhan, China
| | - Miaomiao Peng
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Clinical Research Center for Diabetes and Metabolic Disorders, Wuhan, China
| | - Wen Kong
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Clinical Research Center for Diabetes and Metabolic Disorders, Wuhan, China
| | - Lu-lu Chen
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Clinical Research Center for Diabetes and Metabolic Disorders, Wuhan, China
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Viral and Cellular factors leading to the Loss of CD4 Homeostasis in HIV-1 Viremic Nonprogressors. J Virol 2021; 96:e0149921. [PMID: 34668779 PMCID: PMC8754213 DOI: 10.1128/jvi.01499-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) viremic nonprogressors (VNPs) represent a very rare HIV-1 extreme phenotype. VNPs are characterized by persistent high plasma viremia and maintenance of CD4+ T-cell counts in the absence of treatment. However, the causes of nonpathogenic HIV-1 infection in VNPs remain elusive. Here, we identified for the first time two VNPs who experienced the loss of CD4+ homeostasis (LoH) after more than 13 years. We characterized in deep detail viral and host factors associated with the LoH and compared with standard VNPs and healthy controls. The viral factors determined included HIV-1 coreceptor usage and replicative capacity. Changes in CD4+ and CD8+ T-cell activation, maturational phenotype, and expression of CCR5 and CXCR6 in CD4+ T-cells were also evaluated as host-related factors. Consistently, we determined a switch in HIV-1 coreceptor use to CXCR4 concomitant with an increase in replicative capacity at the LoH for the two VNPs. Moreover, we delineated an increase in the frequency of HLA-DR+CD38+ CD4+ and CD8+ T cells and traced the augment of naive T-cells upon polyclonal activation with LoH. Remarkably, very low and stable levels of CCR5 and CXCR6 expression in CD4+ T-cells were measured over time. Overall, our results demonstrated HIV-1 evolution toward highly pathogenic CXCR4 strains in the context of very limited and stable expression of CCR5 and CXCR6 in CD4+ T cells as potential drivers of LoH in VNPs. These data bring novel insights into the correlates of nonpathogenic HIV-1 infection. IMPORTANCE The mechanism behind nonpathogenic human immunodeficiency virus type 1 (HIV-1) infection remains poorly understood, mainly because of the very low frequency of viremic nonprogressors (VNPs). Here, we report two cases of VNPs who experienced the loss of CD4+ T-cell homeostasis (LoH) after more than 13 years of HIV-1 infection. The deep characterization of viral and host factors supports the contribution of viral and host factors to the LoH in VNPs. Thus, HIV-1 evolution toward highly replicative CXCR4 strains together with changes in T-cell activation and maturational phenotypes were found. Moreover, we measured very low and stable levels of CCR5 and CXCR6 in CD4+ T-cells over time. These findings support viral evolution toward X4 strains limited by coreceptor expression to control HIV-1 pathogenesis and demonstrate the potential of host-dependent factors, yet to be fully elucidated in VNPs, to control HIV-1 pathogenesis.
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Xu L, Liu Y, Song X, Li Y, Han Y, Zhu T, Cao W, Li T. Naïve CD4 + cell counts significantly decay and high HIV RNA levels contribute to immunological progression in long-term non-progressors infected with HIV by blood products: a cohort study. BMC Immunol 2021; 22:36. [PMID: 34082709 PMCID: PMC8173962 DOI: 10.1186/s12865-021-00426-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Some long-term non-progressors (LTNPs) have decreasing CD4+ T cell counts and progress to AIDS. Exploring which subsets of CD4+ T cell decreasing and the determinants associated with the decay in these patients will improve disease progression surveillance and provide further understanding of HIV pathogenesis. METHODS Twenty-five LTNPs infected with HIV by blood products were classified as decreased (DG) if their CD4+ cell count dropped to < 400 cells/μL during follow-up or as non-decreased (non-DG) if their CD4+ cell count was ≥400 cells/μL. Laboratory and clinical assessments were conducted at 6 consecutive visits to identify DG characteristics. RESULTS The LTNPs were infected with HIV for 12 (IQR: 11.5-14) years, and 23 were classified as the B' subtype. Six individuals lost LTNP status 14.5 (IQR: 12.5-17.5) years after infection (DG), and the CD4+ T cell count decreased to 237 (IQR: 213-320) cells/μL at the latest visit. The naïve CD4+ T cell count decrease was greater than that of memory CD4+ T cells [- 128 (IQR: - 196, - 107) vs - 64 (IQR: - 182, - 25) cells/μL)]. Nineteen individuals retained LTNP status (non-DG). At enrolment, the viral load (VL) level (p = 0.03) and CD8+CD38+ percentage (p = 0.03) were higher in DG than non-DG individuals. During follow-up, viral load and CD8+CD38+ percentage were significantly increased and negatively associated with CD4+ cell count [(r = - 0.529, p = 0.008), (r = - 0.476, p = 0.019), respectively]. However, the CD8+CD28+ percentage and B cell count dropped in DG and were positively correlated with CD4+ T cell count [(r = 0.448, p = 0.028), (r = 0.785, p < 0.001)]. CONCLUSION Immunological progression was mainly characterized by the decrease of naïve CD4+ T cell in LTNPs infected with HIV by blood products and it may be associated with high HIV RNA levels.
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Affiliation(s)
- Ling Xu
- Department of Infectious Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yubin Liu
- Department of Infectious Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaojing Song
- Department of Infectious Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yanling Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yang Han
- Department of Infectious Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ting Zhu
- Department of Infectious Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Cao
- Department of Infectious Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Taisheng Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China. .,Clinical Immunology Center, Chinese Academy of Medical Sciences, Beijing, China. .,Tsinghua University Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China.
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10
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Kousa YA, Hossain RA. Causes of Phenotypic Variability and Disabilities after Prenatal Viral Infections. Trop Med Infect Dis 2021; 6:tropicalmed6020095. [PMID: 34205913 PMCID: PMC8293342 DOI: 10.3390/tropicalmed6020095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/25/2021] [Accepted: 05/29/2021] [Indexed: 12/14/2022] Open
Abstract
Prenatal viral infection can lead to a spectrum of neurodevelopmental disabilities or fetal demise. These can include microencephaly, global developmental delay, intellectual disability, refractory epilepsy, deafness, retinal defects, and cortical-visual impairment. Each of these clinical conditions can occur on a semi-quantitative to continuous spectrum, from mild to severe disease, and often as a collective of phenotypes. Such serious outcomes result from viruses’ overlapping neuropathology and hosts’ common neuronal and gene regulatory response to infections. The etiology of variability in clinical outcomes is not yet clear, but it may be related to viral, host, vector, and/or environmental risk and protective factors that likely interact in multiple ways. In this perspective of the literature, we work toward understanding the causes of phenotypic variability after prenatal viral infections by highlighting key aspects of the viral lifecycle that can affect human disease, with special attention to the 2015 Zika pandemic. Therefore, this work offers important insights into how viral infections and environmental teratogens affect the prenatal brain, toward our ultimate goal of preventing neurodevelopmental disabilities.
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Affiliation(s)
- Youssef A. Kousa
- Division of Neurology, Children’s National Hospital, Washington, DC 20010, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC 20052, USA
- Correspondence:
| | - Reafa A. Hossain
- Structural Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20892, USA;
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11
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The Role of CXCL16 in the Pathogenesis of Cancer and Other Diseases. Int J Mol Sci 2021; 22:ijms22073490. [PMID: 33800554 PMCID: PMC8036711 DOI: 10.3390/ijms22073490] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 12/15/2022] Open
Abstract
CXCL16 is a chemotactic cytokine belonging to the α-chemokine subfamily. It plays a significant role in the progression of cancer, as well as the course of atherosclerosis, renal fibrosis, and non-alcoholic fatty liver disease (NAFLD). Since there has been no review paper discussing the importance of this chemokine in various diseases, we have collected all available knowledge about CXCL16 in this review. In the first part of the paper, we discuss background information about CXCL16 and its receptor, CXCR6. Next, we focus on the importance of CXCL16 in a variety of diseases, with an emphasis on cancer. We discuss the role of CXCL16 in tumor cell proliferation, migration, invasion, and metastasis. Next, we describe the role of CXCL16 in the tumor microenvironment, including involvement in angiogenesis, and its significance in tumor-associated cells (cancer associated fibroblasts (CAF), microglia, tumor-associated macrophages (TAM), tumor-associated neutrophils (TAN), mesenchymal stem cells (MSC), myeloid suppressor cells (MDSC), and regulatory T cells (Treg)). Finally, we focus on the antitumor properties of CXCL16, which are mainly caused by natural killer T (NKT) cells. At the end of the article, we summarize the importance of CXCL16 in cancer therapy.
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12
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Berg MG, Olivo A, Harris BJ, Rodgers MA, James L, Mampunza S, Niles J, Baer F, Yamaguchi J, Kaptue L, Laeyendecker O, Quinn TC, McArthur C, Cloherty GA. A high prevalence of potential HIV elite controllers identified over 30 years in Democratic Republic of Congo. EBioMedicine 2021; 65:103258. [PMID: 33674212 PMCID: PMC7992073 DOI: 10.1016/j.ebiom.2021.103258] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 11/22/2022] Open
Abstract
Background In-depth analysis of the HIV pandemic at its epicenter in the Congo basin has been hampered by 40 years of political unrest and lack of functional public health infrastructure. In recent surveillance studies (2017-18), we found that the prevalence of HIV in Kinshasa, Democratic Republic of Congo (11%) far exceeded previous estimates. Methods 10,457 participants were screened in Kinshasa with rapid tests from 2017-2019. Individuals confirmed as reactive by the Abbott ARCHITECT HIV Ag/Ab Combo assay (n=1968) were measured by the Abbott RealTime HIV-1 viral load assay. Follow up characterization of samples was performed with alternate manufacturer viral load assays, qPCR for additional blood borne viruses, unbiased next generation sequencing, and HIV Western blotting. Findings Our data suggested the existence of a significant cohort (n=429) of HIV antibody positive/viral load negative individuals. We systematically eliminated collection site bias, sample integrity, and viral genetic diversity as alternative explanations for undetectable viral loads. Mass spectroscopy unexpectedly detected the presence of 3TC antiviral medication in approximately 60% of those tested (209/354), and negative Western blot results indicated false positive serology in 12% (49/404). From the remaining Western blot positives (n=53) and indeterminates (n=31) with reactive Combo and rapid test results, we estimate 2.7-4.3% of infections in DRC to be potential elite controllers. We also analyzed samples from the DRC collected in 1987 and 2001-03, when antiretroviral drugs were not available, and found similarly elevated trends. Interpretation Viral suppression to undetectable viral loads without therapy occurs infrequently in HIV-1 infected patients around the world. Mining of global data suggests a unique ability to control HIV infection arose early in central Africa and occurs in <1% of founder populations. Identification of this group of elite controllers presents a unique opportunity to study potentially novel genetic mechanisms of viral suppression. Funding Abbott Laboratories funded surveillance in DRC and subsequent research efforts. Additional funding was received from a MIZZOU Award from the University of Missouri. Research was supported in part by the Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH.
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Affiliation(s)
- Michael G Berg
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, IL, United States.
| | - Ana Olivo
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, IL, United States
| | - Barbara J Harris
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, IL, United States
| | - Mary A Rodgers
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, IL, United States
| | - Linda James
- Université Protestante au Congo, Croisement de l'avenue de Libération et du Boulevard Triomphal, Kinshasa, Democratic Republic of Congo; IMA World Health, 1730 M St NW Suite 1100, Washington DC, United States
| | - Samuel Mampunza
- Université Protestante au Congo, Croisement de l'avenue de Libération et du Boulevard Triomphal, Kinshasa, Democratic Republic of Congo
| | - Jonathan Niles
- IMA World Health, 1730 M St NW Suite 1100, Washington DC, United States
| | - Franklin Baer
- SANRU NGO, 76 Ave. de la Justice, Kinshasa-Gombe, Democratic Republic of Congo
| | - Julie Yamaguchi
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, IL, United States
| | | | - Oliver Laeyendecker
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Baltimore MD, United States; Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Baltimore MD, United States; Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Carole McArthur
- Pathology Department, Truman Medical Center, Kansas City, MO, United States; Department of Oral and Craniofacial Sciences, University of Missouri-Kansas City School of Dentistry, Kansas City, MO, United States; University of Missouri-Kansas City School of Medicine, Kansas City, MO, United States
| | - Gavin A Cloherty
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, IL, United States
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13
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Jabalameli N, Rajabi F, Firooz A, Rezaei N. The Overlap between Genetic Susceptibility to COVID-19 and Skin Diseases. Immunol Invest 2021; 51:1087-1094. [DOI: 10.1080/08820139.2021.1876086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Navid Jabalameli
- Network of Dermatology Research (NDR), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Fateme Rajabi
- Network of Dermatology Research (NDR), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Center for Research & Training in Skin Diseases & Leprosy, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Firooz
- Center for Research & Training in Skin Diseases & Leprosy, Tehran University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Sheffield, UK
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14
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Thorball CW, Borghesi A, Bachmann N, Von Siebenthal C, Vongrad V, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Roth V, Kok YL, Parbhoo S, Wieser M, Böni J, Perreau M, Klimkait T, Yerly S, Battegay M, Rauch A, Schmid P, Bernasconi E, Cavassini M, Kouyos RD, Günthard HF, Metzner KJ, Fellay J. Host Genomics of the HIV-1 Reservoir Size and Its Decay Rate During Suppressive Antiretroviral Treatment. J Acquir Immune Defic Syndr 2020; 85:517-524. [PMID: 33136754 DOI: 10.1097/qai.0000000000002473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The primary hurdle for the eradication of HIV-1 is the establishment of a latent viral reservoir early after primary infection. Here, we investigated the potential influence of human genetic variation on the HIV-1 reservoir size and its decay rate during suppressive antiretroviral treatment. SETTING Genome-wide association study and exome sequencing study to look for host genetic determinants of HIV-1 reservoir measurements in patients enrolled in the Swiss HIV Cohort Study, a nation-wide prospective observational study. METHODS We measured total HIV-1 DNA in peripheral blood mononuclear cells from study participants, as a proxy for the reservoir size at 3 time points over a median of 5.4 years, and searched for associations between human genetic variation and 2 phenotypic readouts: the reservoir size at the first time point and its decay rate over the study period. We assessed the contribution of common genetic variants using genome-wide genotyping data from 797 patients with European ancestry enrolled in the Swiss HIV Cohort Study and searched for a potential impact of rare variants and exonic copy number variants using exome sequencing data generated in a subset of 194 study participants. RESULTS Genome-wide and exome-wide analyses did not reveal any significant association with the size of the HIV-1 reservoir or its decay rate on suppressive antiretroviral treatment. CONCLUSIONS Our results point to a limited influence of human genetics on the size of the HIV-1 reservoir and its long-term dynamics in successfully treated individuals.
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Affiliation(s)
- Christian W Thorball
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alessandro Borghesi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Nadine Bachmann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Chantal Von Siebenthal
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Valentina Vongrad
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Teja Turk
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Volker Roth
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
| | - Yik Lim Kok
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sonali Parbhoo
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Mario Wieser
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Thomas Klimkait
- Division Infection Diagnostics, Department Biomedicine-Petersplatz, University of Basel, Basel, Switzerland
| | - Sabine Yerly
- Division of Infectious Diseases and Laboratory of Virology, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Manuel Battegay
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, University Hospital Bern, Bern, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital of St. Gallen, St. Gallen, Switzerland
| | - Enos Bernasconi
- Infectious Diseases Service, Regional Hospital of Lugano, Lugano, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland; and
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
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Li BX, Zhang H, Liu Y, Li Y, Zheng JJ, Li WX, Feng K, Sun M, Dai SX. Novel pathways of HIV latency reactivation revealed by integrated analysis of transcriptome and target profile of bryostatin. Sci Rep 2020; 10:3511. [PMID: 32103135 PMCID: PMC7044323 DOI: 10.1038/s41598-020-60614-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 02/12/2020] [Indexed: 01/17/2023] Open
Abstract
The reactivation of HIV latency cell will be necessary to curing HIV infection. Although many latency-reversal agents (LRAs) have proven effective to reactivate the latency cell, there is a lack of any systematic analysis of the molecular targets of these LRAs and related pathways in the context of transcriptome. In this study, we performed an integrated analysis of the target profile of bryostatin and transcriptome of the reactivated CD4+ T cells after exposing to bryostatin. The result showed a distinct gene expression profile between latency cells and bryostatin reactivated cells. We found bryostatin can target multiple types of protein other than only protein kinase C. Functional network analysis of the target profile and differential expressed genes suggested that bryostatin may activate a few novel pathways such as pyrimidine metabolism, purine metabolism and p53 signaling pathway, besides commonly known pathways DNA replication, cell cycle and so on. The results suggest that bryostatin may reactivate the HIV-latent cells through up-regulation of pyrimidine and purine metabolism or through starting the cell-cycle arrest and apoptosis induced by up-regulation of p53 signaling pathway. Our study provides some novel insights into the role of bryostatin and its affected pathways in controlling HIV latency and reactivation.
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Affiliation(s)
- Bing-Xiang Li
- Institute of Medical Biology, Peking Union Medical College and Chinese Academy of Medical Sciences, Kunming, China
| | - Han Zhang
- Institute of Medical Biology, Peking Union Medical College and Chinese Academy of Medical Sciences, Kunming, China
| | - Yubin Liu
- Department of Infectious Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ya Li
- Yunnan Key Laboratory of Laboratory Medicine, Yunnan Institute of Laboratory Diagnosis, Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Jun-Juan Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Wen-Xing Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Kai Feng
- Institute of Medical Biology, Peking Union Medical College and Chinese Academy of Medical Sciences, Kunming, China
| | - Ming Sun
- Institute of Medical Biology, Peking Union Medical College and Chinese Academy of Medical Sciences, Kunming, China.
| | - Shao-Xing Dai
- Yunnan Key Laboratory of Primate Biomedicine Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China.
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16
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Association of HLA-DRB1∗09:01 with tIgE levels among African-ancestry individuals with asthma. J Allergy Clin Immunol 2020; 146:147-155. [PMID: 31981624 DOI: 10.1016/j.jaci.2020.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 12/05/2019] [Accepted: 01/08/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Asthma is a complex chronic inflammatory disease of the airways. Association studies between HLA and asthma were first reported in the 1970s, and yet, the precise role of HLA alleles in asthma is not fully understood. Numerous genome-wide association studies were recently conducted on asthma, but were always limited to simple genetic markers (single nucleotide polymorphisms) and not complex HLA gene polymorphisms (alleles/haplotypes), therefore not capturing the biological relevance of this complex locus for asthma pathogenesis. OBJECTIVE To run the first HLA-centric association study with asthma and specific asthma-related phenotypes in a large cohort of African-ancestry individuals. METHODS We collected high-density genomics data for the Consortium on Asthma among African-ancestry Populations in the Americas (N = 4993) participants. Using computer-intensive machine-learning attribute bagging methods to infer HLA alleles, and Easy-HLA to infer HLA 5-gene haplotypes, we conducted a high-throughput HLA-centric association study of asthma susceptibility and total serum IgE (tIgE) levels in subjects with and without asthma. RESULTS Among the 1607 individuals with asthma, 972 had available tIgE levels, with a mean tIgE level of 198.7 IU/mL. We could not identify any association with asthma susceptibility. However, we showed that HLA-DRB1∗09:01 was associated with increased tIgE levels (P = 8.5 × 10-4; weighted effect size, 0.51 [0.15-0.87]). CONCLUSIONS We identified for the first time an HLA allele associated with tIgE levels in African-ancestry individuals with asthma. Our report emphasizes that by leveraging powerful computational machine-learning methods, specific/extreme phenotypes, and population diversity, we can explore HLA gene polymorphisms in depth and reveal the full extent of complex disease associations.
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17
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23rd Nantes Actualités Transplantation: "Genomics and Immunogenetics of Kidney and Inflammatory Diseases-Lessons for Transplantation". Transplantation 2019; 103:857-861. [PMID: 30399125 DOI: 10.1097/tp.0000000000002517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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18
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Le Clerc S, Limou S, Zagury JF. Large-Scale "OMICS" Studies to Explore the Physiopatholgy of HIV-1 Infection. Front Genet 2019; 10:799. [PMID: 31572435 PMCID: PMC6754074 DOI: 10.3389/fgene.2019.00799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
In this review, we present the main large-scale experimental studies that have been performed in the HIV/AIDS field. These “omics” studies are based on several technologies including genotyping, RNA interference, and transcriptome or epigenome analysis. Due to the direct connection with disease evolution, there has been a large focus on genotyping cohorts of well-characterized patients through genome-wide association studies (GWASs), but there have also been several invitro studies such as small interfering RNA (siRNA) interference or transcriptome analyses of HIV-1–infected cells. After describing the major results obtained with these omics technologies—including some with a high relevance for HIV-1 treatment—we discuss the next steps that the community needs to embrace in order to derive new actionable therapeutic or diagnostic targets. Only integrative approaches that combine all big data results and consider their complex interactions will allow us to capture the global picture of HIV molecular pathogenesis. This novel challenge will require large collaborative efforts and represents a huge open field for innovative bioinformatics approaches.
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Affiliation(s)
- Sigrid Le Clerc
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation en Urologie et Néphrologie (ITUN), CHU de Nantes, Nantes, France.,Computer Sciences and Mathematics Department, Ecole Centrale de Nantes, Nantes, France
| | - Jean-François Zagury
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
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Lee SY, Park YK, Yoon CH, Kim K, Kim KC. Meta-analysis of gene expression profiles in long-term non-progressors infected with HIV-1. BMC Med Genomics 2019; 12:3. [PMID: 30626383 PMCID: PMC6325803 DOI: 10.1186/s12920-018-0443-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/03/2018] [Indexed: 02/08/2023] Open
Abstract
Background In the absence of antiretroviral treatments (ARTs), a small group of individuals infected with HIV, including long-term non-progressors (LTNPs) who maintain high levels of CD4+ T cells for more than 7–10 years in the absence of ART and in particular a subgroup of LTNPs, elite controllers (ECs), who have low levels of viremia, remain clinically and/or immunologically stable for years. However, the mechanism of stable disease progression in LTNPs and ECs needs to be elucidated to help those infected with HIV-1 remain healthy. In this study, to identify the characteristics of gene expression profiles and biomarkers in LTNPs, we performed a meta-analysis using multiple gene expression profiles among LTNPs, individuals infected with HIV-1 without ART, individuals infected with HIV-1 with ART, and healthy controls. Methods The gene expression profiles obtained from the Gene Expression Omnibus (GEO) microarray data repositories were classified into three groups: LTNPs versus healthy controls (first group, 3 studies), LTNPs versus patients infected with HIV-1 without ART (second group, 3 studies), and LTNPs versus patients infected with HIV-1 with ART (third group, 3 studies). In addition, we considered a fourth group, patients infected with HIV-1 without ART versus healthy controls (3 studies), to exclude genes associated with HIV-1 infection in the three groups. For each group, we performed a meta-analysis using the RankProd method to identify and compare the differentially expressed genes (DEGs) in the three groups. Results We identified the 14 common DEGs in the three groups when comparing them with each other. Most belonged to immune responses, antigen processing and presentation, the interferon-gamma-mediated signaling pathway, and T cell co-stimulation. Of these DEGs, PHLDA1 was up-regulated and ACTB and ACTG1 were down-regulated in all three groups. However, the rest of the up- or down-regulated genes were discordant in the three groups. Additionally, ACTB and ACTG1 are known to inhibit viral assembly and production, and THBS1 is known to inhibit HIV-1 infection. Conclusions These results suggest that significant genes identified in a meta-analysis provide clues to the cause of delayed disease progression and give a deeper understanding of HIV pathogenesis in LTNPs. Electronic supplementary material The online version of this article (10.1186/s12920-018-0443-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sun Young Lee
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Yong Kwang Park
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Cheol-Hee Yoon
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Kisoon Kim
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Kyung-Chang Kim
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju, Chungbuk, 28159, Republic of Korea.
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Whole Exome Sequencing of HIV-1 long-term non-progressors identifies rare variants in genes encoding innate immune sensors and signaling molecules. Sci Rep 2018; 8:15253. [PMID: 30323326 PMCID: PMC6189090 DOI: 10.1038/s41598-018-33481-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 08/17/2018] [Indexed: 01/25/2023] Open
Abstract
Common CCR5-∆32 and HLA alleles only explain a minority of the HIV long-term non-progressor (LTNP) and elite controller (EC) phenotypes. To identify rare genetic variants contributing to the slow disease progression phenotypes, we performed whole exome sequencing (WES) on seven LTNPs and four ECs. HLA and CCR5 allele status, total HIV DNA reservoir size, as well as variant-related functional differences between the ECs, LTNPs, and eleven age- and gender-matched HIV-infected non-controllers on antiretroviral therapy (NCARTs) were investigated. Several rare variants were identified in genes involved in innate immune sensing, CD4-dependent infectivity, HIV trafficking, and HIV transcription mainly within the LTNP group. ECs and LTNPs had a significantly lower HIV reservoir compared to NCARTs. Furthermore, three LTNPs with variants affecting HIV nuclear import showed integrated HIV DNA levels below detection limit after in vitro infection. HIV slow progressors with variants in the TLR and NOD2 pathways showed reduced pro-inflammatory responses compared to matched controls. Low-range plasma levels of fibronectin was observed in a LTNP harboring two FN1 variants. Taken together, this study identified rare variants in LTNPs as well as in one EC, which may contribute to understanding of HIV pathogenesis and these slow progressor phenotypes, especially in individuals without protecting CCR5-∆32 and HLA alleles.
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Unique Phenotypic Characteristics of Recently Transmitted HIV-1 Subtype C Envelope Glycoprotein gp120: Use of CXCR6 Coreceptor by Transmitted Founder Viruses. J Virol 2018; 92:JVI.00063-18. [PMID: 29491151 DOI: 10.1128/jvi.00063-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 02/15/2018] [Indexed: 12/13/2022] Open
Abstract
Adequate information on the precise molecular and biological composition of the viral strains that establish HIV infection in the human host will provide effective means of immunization against HIV infection. In an attempt to identify the transmitted founder (TF) virus and differentiate the biological properties and infectious potential of the TF virus from those of the population of the early transmitted viruses, 250 patient-derived gp120 envelope glycoproteins were cloned in pMN-K7-Luc-IRESs-NefΔgp120 to obtain chimeric viruses. Samples were obtained from eight infants who had recently become infected with HIV through mother-to-child transmission (MTCT) and two adults who acquired infection through the heterosexual route and were in the chronic stage of infection. Among the 250 clones tested, 65 chimeric viruses were infectious, and all belonged to HIV-1 subtype C. The 65 clones were analyzed for molecular features of the envelope, per-infectious-particle infectivity, coreceptor tropism, drug sensitivity, and sensitivity to broadly neutralizing antibodies. Based on genotypic and phenotypic analysis of the viral clones, we identified 10 TF viruses from the eight infants. The TF viruses were characterized by shorter V1V2 regions, a reduced number of potential N-linked glycosylation sites, and a higher infectivity titer compared to the virus variants from the adults in the chronic stage of infection. CXCR6 coreceptor usage, in addition to that of the CCR5 coreceptor, which was used by all 65 chimeric viruses, was identified in 13 viruses. The sensitivity of the TF variants to maraviroc and a standard panel of neutralizing monoclonal antibodies (VRC01, PG09, PG16, and PGT121) was found to be much lower than that of the virus variants from the adults in the chronic stage of infection.IMPORTANCE Tremendous progress has been made during the last three and half decades of HIV research, but some significant gaps continue to exist. One of the frontier areas of HIV research which has not seen a breakthrough yet is vaccine research, which is because of the enormous genetic diversity of HIV-1 and the unique infectious fitness of the virus. Among the repertoire of viral variants, the virus that establishes successful infection (transmitted founder [TF] virus) has not been well characterized yet. An insight into the salient features of the TF virus would go a long way toward helping with the design of an effective vaccine against HIV. Here we studied the biological properties of recently transmitted viruses isolated from infants who acquired infection from the mother and have come up with unique characterizations for the TF virus that establishes infection in the human host.
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Human Genomic Loci Important in Common Infectious Diseases: Role of High-Throughput Sequencing and Genome-Wide Association Studies. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2018; 2018:1875217. [PMID: 29755620 PMCID: PMC5884297 DOI: 10.1155/2018/1875217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 03/07/2018] [Indexed: 12/27/2022]
Abstract
HIV/AIDS, tuberculosis (TB), and malaria are 3 major global public health threats that undermine development in many resource-poor settings. Recently, the notion that positive selection during epidemics or longer periods of exposure to common infectious diseases may have had a major effect in modifying the constitution of the human genome is being interrogated at a large scale in many populations around the world. This positive selection from infectious diseases increases power to detect associations in genome-wide association studies (GWASs). High-throughput sequencing (HTS) has transformed both the management of infectious diseases and continues to enable large-scale functional characterization of host resistance/susceptibility alleles and loci; a paradigm shift from single candidate gene studies. Application of genome sequencing technologies and genomics has enabled us to interrogate the host-pathogen interface for improving human health. Human populations are constantly locked in evolutionary arms races with pathogens; therefore, identification of common infectious disease-associated genomic variants/markers is important in therapeutic, vaccine development, and screening susceptible individuals in a population. This review describes a range of host-pathogen genomic loci that have been associated with disease susceptibility and resistant patterns in the era of HTS. We further highlight potential opportunities for these genetic markers.
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CXCR7/ACKR3-targeting ligands interfere with X7 HIV-1 and HIV-2 entry and replication in human host cells. Heliyon 2018; 4:e00557. [PMID: 29560468 PMCID: PMC5857896 DOI: 10.1016/j.heliyon.2018.e00557] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/09/2018] [Accepted: 02/22/2018] [Indexed: 11/20/2022] Open
Abstract
Chemokine receptors CCR5 and CXCR4 are considered the main coreceptors for initial HIV infection, replication and transmission, and subsequent AIDS progression. Over the years, other chemokine receptors, belonging to the family of G protein-coupled receptors, have also been identified as candidate coreceptors for HIV entry into human host cells. Amongst them, CXCR7, also known as atypical chemokine receptor 3 (ACKR3), was suggested as a coreceptor candidate capable of facilitating both HIV-1 and HIV-2 entry in vitro. In this study, a cellular infection model was established to further decipher the role of CXCR7 as an HIV coreceptor. Using this model, CXCR7-mediated viral entry was demonstrated for several clinical HIV isolates as well as laboratory strains. Of interest, the X4-tropic HIV-1 HE strain showed rapid adaptation towards CXCR7-mediated infection after continuous passaging on CD4- and CXCR7-expressing cells. Furthermore, we uncovered anti-CXCR7 monoclonal antibodies, small molecule CXCR7 inhibitors and the natural CXCR7 chemokine ligands as potent inhibitors of CXCR7 receptor-mediated HIV entry and replication. Even though the clinical relevance of CXCR7-mediated HIV infection remains poorly understood, our data suggest that divergent HIV-1 and HIV-2 strains can quickly adapt their coreceptor usage depending on the cellular environment, which warrants further investigation.
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Zhang W, Ambikan AT, Sperk M, van Domselaar R, Nowak P, Noyan K, Russom A, Sönnerborg A, Neogi U. Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune-control Mechanisms of HIV-1 Infected Elite Controllers. EBioMedicine 2018; 27:40-50. [PMID: 29269040 PMCID: PMC5828548 DOI: 10.1016/j.ebiom.2017.11.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/22/2017] [Accepted: 11/30/2017] [Indexed: 12/21/2022] Open
Abstract
A small subset of HIV-1 infected individuals, the "Elite Controllers" (EC), can control viral replication and restrain progression to immunodeficiency without antiretroviral therapy (ART). In this study, a cross-sectional transcriptomics and targeted proteomics analysis were performed in a well-defined Swedish cohort of untreated EC (n=19), treatment naïve patients with viremia (VP, n=32) and HIV-1-negative healthy controls (HC, n=23). The blood transcriptome identified 151 protein-coding genes that were differentially expressed (DE) in VP compared to EC. Genes like CXCR6 and SIGLEC1 were downregulated in EC compared to VP. A definite distinction in gene expression between males and females among all patient-groups were observed. The gene expression profile between female EC and the healthy females was similar but did differ between male EC and healthy males. At targeted proteomics analysis, 90% (29/32) of VPs clustered together while EC and HC clustered separately from VP. Among the soluble factors, 33 were distinctive to be statistically significant (False discovery rate=0.02). Cell surface receptor signaling pathway, programmed cell death, response to cytokine and cytokine-mediated signaling seem to synergistically play an essential role in HIV-1 control in EC.
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Affiliation(s)
- Wang Zhang
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Science for Life Laboratory, Division of Proteomics and Nanobiotechnology, KTH Royal Institute of Technology, Solna, Stockholm, Sweden
| | - Anoop T Ambikan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maike Sperk
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Faculty of Medicine, University of Tuebingen, Tuebingen, Germany
| | - Robert van Domselaar
- Department of Medicine Huddinge, Unit of Infectious Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Piotr Nowak
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Medicine Huddinge, Unit of Infectious Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kajsa Noyan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Aman Russom
- Science for Life Laboratory, Division of Proteomics and Nanobiotechnology, KTH Royal Institute of Technology, Solna, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Medicine Huddinge, Unit of Infectious Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Science for Life Laboratory, Division of Proteomics and Nanobiotechnology, KTH Royal Institute of Technology, Solna, Stockholm, Sweden.
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Genetic and immune determinants of immune activation in HIV-exposed seronegative individuals and their role in protection against HIV infection. INFECTION GENETICS AND EVOLUTION 2017; 66:325-334. [PMID: 29258786 DOI: 10.1016/j.meegid.2017.12.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 12/13/2022]
Abstract
Soon thereafter infection is established, hosts strive for an efficient eradication of microorganisms, with as limited tissue damage as possible, and durable immunological protection against re-infection. On the other hand, pathogens have developed countermeasures to escape host surveillance and to warrant diffusion to other hosts. In this molecular arms race the final results relies on multiple variables, including the genetic and immunologic e correlates of protection available for the host. In the field of HIV-infection, natural protection has been repeatedly associated to the presence of an immune activation state, at least in some cohorts of HESN (HIV-exposed seronegative). Indeed, these subjects, who naturally resist HIV-infection despite repeated exposure to the virus, are characterized by an increased expression of activation markers on circulating cells and greater production of immunological effector molecules both in basal condition and upon specific-stimulation. Although these results are not univocally shared, several publications emphasize the existence of a correlation between polymorphisms in genes associated with increased immune activation and the HESN phenotype. In this review, we will describe some of the genetic variants associated with protection against HIV infection. Understanding the basis of HIV resistance in HESN is mandatory to develop new preventative and therapeutic interventions.
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26
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Planas D, Zhang Y, Monteiro P, Goulet JP, Gosselin A, Grandvaux N, Hope TJ, Fassati A, Routy JP, Ancuta P. HIV-1 selectively targets gut-homing CCR6+CD4+ T cells via mTOR-dependent mechanisms. JCI Insight 2017; 2:93230. [PMID: 28768913 PMCID: PMC5543920 DOI: 10.1172/jci.insight.93230] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/29/2017] [Indexed: 12/30/2022] Open
Abstract
Gut-associated lymphoid tissues are enriched in CCR6+ Th17-polarized CD4+ T cells that contribute to HIV-1 persistence during antiretroviral therapy (ART). This raises the need for Th17-targeted immunotherapies. In an effort to identify mechanisms governing HIV-1 permissiveness/persistence in gut-homing Th17 cells, we analyzed the transcriptome of CCR6+ versus CCR6- T cells exposed to the gut-homing inducer retinoic acid (RA) and performed functional validations in colon biopsies of HIV-infected individuals receiving ART (HIV+ART). Although both CCR6+ and CCR6- T cells acquired gut-homing markers upon RA exposure, the modulation of unique sets of genes coincided with preferential HIV-1 replication in RA-treated CCR6+ T cells. This molecular signature included the upregulation of HIV-dependency factors acting at entry/postentry levels, such as the CCR5 and PI3K/Akt/mTORC1 signaling pathways. Of note, mTOR expression/phosphorylation was distinctively induced by RA in CCR6+ T cells. Consistently, mTOR inhibitors counteracted the effect of RA on HIV replication in vitro and viral reactivation in CD4+ T cells from HIV+ART individuals via postentry mechanisms independent of CCR5. Finally, CCR6+ versus CCR6- T cells infiltrating the colons of HIV+ART individuals expressed unique molecular signatures, including higher levels of CCR5, integrin β7, and mTOR phosphorylation. Together, our results identify mTOR as a druggable key regulator of HIV permissiveness in gut-homing CCR6+ T cells.
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Affiliation(s)
- Delphine Planas
- Centre de recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Québec, Canada
- Département of microbiologie, infectiologie et immunologie, Université de Montréal, Faculté de Médecine, Montreal, Québec, Canada
| | - Yuwei Zhang
- Centre de recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Québec, Canada
- Département of microbiologie, infectiologie et immunologie, Université de Montréal, Faculté de Médecine, Montreal, Québec, Canada
| | - Patricia Monteiro
- Centre de recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Québec, Canada
- Département of microbiologie, infectiologie et immunologie, Université de Montréal, Faculté de Médecine, Montreal, Québec, Canada
| | | | - Annie Gosselin
- Centre de recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Québec, Canada
| | - Nathalie Grandvaux
- Centre de recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Québec, Canada
- Faculté de Médecine, Département of biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec, Canada
| | - Thomas J. Hope
- Department of Cellular and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | | | - Jean-Pierre Routy
- Chronic Viral Illness Service and Research Institute and
- Division of Hematology, McGill University Health Centre, Montreal, Québec, Canada
| | - Petronela Ancuta
- Centre de recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Québec, Canada
- Département of microbiologie, infectiologie et immunologie, Université de Montréal, Faculté de Médecine, Montreal, Québec, Canada
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27
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Novel genetic associations and gene-gene interactions of chemokine receptor and chemokine genetic polymorphisms in HIV/AIDS. AIDS 2017; 31:1235-1243. [PMID: 28358741 DOI: 10.1097/qad.0000000000001491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVE To investigate the influence of candidate polymorphisms on chemokine receptor/ligand genes on HIV infection and AIDS progression (HIV/AIDS). DESIGN Fifteen polymorphisms of the CCR3, CCR4, CCR5, CCR6, CCR8, CXCR3, CXCR6, CCL20, CCL22 and CXCL10 genes were analysed in 206 HIV-positive patients classified as rapid progressors (n = 40), or nonrapid progressors (n = 166), and in 294 HIV-seronegative patients. METHODS The polymorphisms were genotyped using minisequencing. Genetic models were tested using binomial logistic regression; nonparametric multifactor dimensionality reduction (MDR) was used to detect gene-gene interactions. RESULTS The CCR3 rs3091250 [TT, adjusted odds ratio (AOR): 2.147, 95% confidence interval (CI) 1.076-4.287, P = 0.030], CCR8 rs2853699 (GC/CC, AOR: 1.577, 95% CI 1.049-2.371, P = 0.029), CXCL10 rs56061981 (CT/TT, AOR: 1.819, 95% CI 1.074-3.081, P = 0.026) and CCL22 rs4359426 (CA/AA, AOR: 1.887, 95% CI 1.021-3.487, P = 0.043) polymorphisms were associated with susceptibility to HIV infection. The CCL20 rs13034664 (CC, OR: 0.214, 95% CI 0.063-0.730, P = 0.014) and CCL22 rs4359426 (CA/AA, OR: 2.685, 95% CI 1.128-6.392, P = 0.026) variants were associated with rapid progression to AIDS. In MDR analyses revealed that the CXCL10 rs56061981 and CCL22 rs4359426 combination was the best model, with 57% accuracy (P = 0.008) for predicting susceptibility to HIV infection. CONCLUSION Our results provide new insights into the influence of candidate chemokine receptor/ligand polymorphisms and significant evidence for gene-gene interactions on HIV/AIDS susceptibility.
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28
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Chen M, Yao Y, Yue M, Zang F, Liu M, Wang J, Chen H, Zhang Y, Li J, Huang P, Yu R. Polymorphisms of chemokine receptor genes and clearance of hepatitis C virus infection in Chinese population. Gene 2017; 624:1-5. [PMID: 28456591 DOI: 10.1016/j.gene.2017.04.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/19/2017] [Accepted: 04/25/2017] [Indexed: 12/28/2022]
Abstract
BACKGROUND Chemokine genes play an essential role in both spontaneous clearance in acute infection and therapy of HCV. We investigated whether several CXC family-related genes associated with HCV spontaneous clearance and response to treatment. METHODS The current study genotyped four SNPs, respectively are CXCR6 rs2234358, CXCL12 rs1801157, CXCL9 rs10336, rs3733236 to assess their associations with HCV spontaneous clearance and response to treatment in a two stage study (668 chronic and 400 resolvers in discovery group, meanwhile 333 chronic and 199 resolver in replication group), and a treatment cohort of HCV with 282 patients. RESULTS We found that the CXCR6 rs2234358 was associated with HCV spontaneous clearance in Chinese Han population (dominant model: adjusted OR=1.62, 95%CI: 1.30-2.01; additive model: adjusted OR=1.43, 95%CI: 1.20-1.70). Patients carrying GT/TT genotypes had increased sustained virological response compared with patients carrying the GG genotype (dominant model: adjusted OR=2.23, 95%CI: 1.26-3.95). CONCLUSION These results suggest that CXCR6 rs2234358 is associated with spontaneous clearance of HCV and response to IFN-α/RBV therapy, which may be identified as a predictive marker in Chinese Han population of HCV.
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Affiliation(s)
- Mingzhu Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yinan Yao
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Ming Yue
- Department of Infectious Diseases, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Feng Zang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Mei Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jie Wang
- Department of Basic and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing 211166, China
| | - Hongbo Chen
- Department of Infectious Diseases, the Jurong Peoples' Hospital, Jurong 212400, China
| | - Yun Zhang
- Institute of Epidemiology and Microbiology, Huadong Research Institute for Medicine and Biotechnics, Nanjing 210002, China
| | - Jun Li
- Department of Infectious Diseases, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Peng Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Rongbin Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
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29
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Langlais D, Fodil N, Gros P. Genetics of Infectious and Inflammatory Diseases: Overlapping Discoveries from Association and Exome-Sequencing Studies. Annu Rev Immunol 2017; 35:1-30. [DOI: 10.1146/annurev-immunol-051116-052442] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David Langlais
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Nassima Fodil
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Philippe Gros
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
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30
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Picton ACP, Paximadis M, Chaisson RE, Martinson NA, Tiemessen CT. CXCR6 gene characterization in two ethnically distinct South African populations and association with viraemic disease control in HIV-1-infected black South African individuals. Clin Immunol 2017; 180:69-79. [PMID: 28428094 DOI: 10.1016/j.clim.2017.04.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 02/17/2017] [Accepted: 04/15/2017] [Indexed: 12/11/2022]
Abstract
CXCR6 genetic variation was described for HIV-1-uninfected black (n=41) and Caucasian (n=40) South Africans. We also investigated the CXCR6 rs2234358 and rs2234355 single nucleotide polymorphisms in HIV-1 disease control in 124 HIV-1-infected drug-naïve black individuals [elite controllers (n=11), viraemic controllers (VCs, n=30), high viral load long-term nonprogressors (HVL LTNPs, n=11) and progressors (n=72)] compared to healthy controls (HCs; n=232). The rs2234358-T allele was underrepresented in VCs (40.0%) compared to HCs (59%, P=0.006), HVL LTNPs (72.7%, P=0.012) and progressors (59%, P=0.014). The rs2234358-TT genotype was underrepresented in VCs (7%) compared to progressors (32%; OR=6.57, P=0.006) and HCs (35%; OR=7.18, P=0.001, Pbonferroni=0.034). The rs2234355-GA genotype was overrepresented in VCs (80%) compared to HCs (50.4%; OR=0.25, P=0.003) and progressors (29.17%; OR=0.10, P=3.8×10-5, Pbonferroni=0.001). The combination of rs2234355-GA in the absence of rs2234358-TT was overrepresented in VCs (80%) compared to HCs (32.6%, OR=0.12, P=1×10-6, Pbonferroni=3.4×10-5) and to progressors (16.7%; OR=0.05, P<1×10-8, Pbonferroni<1×10-7).
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Affiliation(s)
- Anabela C P Picton
- Centre for HIV and STIs, National Institute for Communicable Diseases, NHLS, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, NHLS, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Richard E Chaisson
- Johns Hopkins University Center for AIDS Research, Baltimore, MD, United States
| | - Neil A Martinson
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa and MRC Soweto Matlosana Centre for HIV/AIDS and TB Research, South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, NHLS, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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31
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Valverde-Villegas JM, de Medeiros RM, Almeida SEM, Chies JAB. Immunogenetic profiling of 23 SNPs of cytokine and chemokine receptor genes through a minisequencing technique: Design, development and validation. Int J Immunogenet 2017; 44:135-144. [PMID: 28374494 DOI: 10.1111/iji.12314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 02/28/2017] [Indexed: 12/15/2022]
Abstract
The minisequencing technique offers accuracy and robustness to genotyping of polymorphic DNA variants, being an excellent option for the identification and analyses of prognostic/susceptibility markers in human diseases. Two multiplex minisequencing assays were designed and standardized to screen 23 candidate SNPs in cytokine, chemokine receptor and ligand genes previously associated with susceptibility to cancer and autoimmune disorders as well as to infectious diseases outcome. The SNPs were displayed in two separate panels (panel 1-IL2 rs2069762, TNFα rs1800629, rs361525; IL4 rs2243250; IL6 rs1800795; IL10 rs1800896, rs1800872; IL17A rs8193036, rs2275913 and panel 2-CCR3 rs309125, CCR4 rs6770096, rs2228428; CCR6 rs968334; CCR8 rs2853699; CXCR3 rs34334103, rs2280964;CXCR6 rs223435, rs2234358; CCL20 rs13034664, rs6749704; CCL22 rs4359426; CXCL10/IP-10 rs3921, rs56061981). A total of 305 DNA samples from healthy individuals were genotyped by minisequencing. To validate the minisequencing technique and to encompass the majority of the potential genotypes for all 23 SNPs, 20 of these samples were genotyped by Sanger sequencing. The results of both techniques were 100% in agreement. The technique of minisequencing showed high accuracy and robustness, avoiding the need for high quantities of DNA template samples. It was easily to be conducted in bulk samples derived from a highly admixed human population, being therefore an excellent option for immunogenetic studies.
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Affiliation(s)
- J M Valverde-Villegas
- Post Graduation Program in Genetic and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - R M de Medeiros
- Post Graduation Program in Genetic and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.,Technological and Scientific Development Center - CDCT, State Foundation in Production and Health Research - FEPPS, Porto Alegre, RS, Brazil
| | - S E M Almeida
- Post Graduation Program in Genetic and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.,Technological and Scientific Development Center - CDCT, State Foundation in Production and Health Research - FEPPS, Porto Alegre, RS, Brazil
| | - J A B Chies
- Post Graduation Program in Genetic and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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Zulfiqar HF, Javed A, Sumbal, Afroze B, Ali Q, Akbar K, Nadeem T, Rana MA, Nazar ZA, Nasir IA, Husnain T. HIV Diagnosis and Treatment through Advanced Technologies. Front Public Health 2017; 5:32. [PMID: 28326304 PMCID: PMC5339269 DOI: 10.3389/fpubh.2017.00032] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/15/2017] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus (HIV) is the chief contributor to global burden of disease. In 2010, HIV was the fifth leading cause of disability-adjusted life years in people of all ages and leading cause for people aged 30-44 years. It is classified as a member of the family Retroviridae and genus Lentivirus based on the biological, morphological, and genetic properties. It infects different cells of the immune system, such as CD4+ T cells (T-helper cells), dendritic cells, and macrophages. HIV has two subtypes: HIV-1 and HIV-2. Among these strains, HIV-1 is the most virulent and pathogenic. Advanced diagnostic methods are exploring new ways of treatment and contributing in the reduction of HIV cases. The diagnostic techniques like PCR, rapid test, EIA, p24 antigen, and western blot have markedly upgraded the diagnosis of HIV. Antiretroviral therapy and vaccines are promising candidates in providing therapeutic and preventive regimes, respectively. Invention of CRISPR/Cas9 is a breakthrough in the field of HIV disease management.
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Affiliation(s)
| | - Aneeqa Javed
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Sumbal
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Bakht Afroze
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Qurban Ali
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Khadija Akbar
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Tariq Nadeem
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | | | - Zaheer Ahmad Nazar
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Idrees Ahmad Nasir
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
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RICH2 is implicated in viraemic control of HIV-1 in black South African individuals. INFECTION GENETICS AND EVOLUTION 2017; 49:78-87. [PMID: 28069446 DOI: 10.1016/j.meegid.2017.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/22/2016] [Accepted: 01/05/2017] [Indexed: 11/22/2022]
Abstract
An intronic single nucleotide polymorphism (SNP) in RICH2 (rs2072255; 255i), in complete linkage disequilibrium (LD) with an exonic SNP (rs2072254; 254e), has been identified in a genome wide association study to be associated with progression to AIDS in Caucasian individuals. RICH2 links tetherin to the cortical actin network and the RICH2/tetherin interaction has been shown to be important for the downstream activation of NF-κβ and the consequential promotion of proinflammatory responses. We investigated the role of these two SNPs in natural control of HIV-1 in black South Africans including healthy controls (HCs; N=102) and antiretroviral-naive HIV-1-infected controllers (HICs; N=52) and progressors (N=74). HICs were stratified as elite controllers (ECs; N=11), viraemic controllers (VCs; N=30), high viral load (VL) long term non-progressors (HVL LTNPs; N=11) and also according to VL<400RNA copies/ml (HICs VL<400; N=20) and VL>400RNA copies/ml (HICs VL>400; N=32). Results showed that in contrast to Caucasians who had very strong LD between these SNPs (r2=0.97), black populations exhibited low LD (r2=0.11-0.27), however a 254e minor allele was always present with a 255i minor allele but not vice versa. The SNPs did not show significant over- or underrepresentation in any particular group, however the combination of 254e major allele homozygosity and 255i heterozygosity (254eAA/255iGA) was underrepresented in HICs (OR=3.26; P=0.04) and VCs (OR=7.77; P=0.02) compared to HCs, and in HICs VL>400 compared to both HCs (P=0.002) and progressors (P=0.02). A lower CD4+ T-cell count was associated with 254eAA/255iGA and 255i (GA+AA) in the total HIV-1-infected group (P=0.043) and progressors (P=0.017), respectively. In silico analysis predicted loss of an exonic splice enhancer site with the 254e-G allele. We postulate that altered splicing of RICH2 will affect levels of RICH2 expression and consequently NF-κβ activation. These findings point to a role for RICH2 and tetherin in viraemic natural control of HIV-1.
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Spadoni JL, Rucart P, Le Clerc S, van Manen D, Coulonges C, Ulveling D, Laville V, Labib T, Taing L, Delaneau O, Montes M, Schuitemaker H, Noirel J, Zagury JF. Identification of Genes Whose Expression Profile Is Associated with Non-Progression towards AIDS Using eQTLs. PLoS One 2015; 10:e0136989. [PMID: 26367535 PMCID: PMC4569262 DOI: 10.1371/journal.pone.0136989] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/12/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Many genome-wide association studies have been performed on progression towards the acquired immune deficiency syndrome (AIDS) and they mainly identified associations within the HLA loci. In this study, we demonstrate that the integration of biological information, namely gene expression data, can enhance the sensitivity of genetic studies to unravel new genetic associations relevant to AIDS. METHODS We collated the biological information compiled from three databases of expression quantitative trait loci (eQTLs) involved in cells of the immune system. We derived a list of single nucleotide polymorphisms (SNPs) that are functional in that they correlate with differential expression of genes in at least two of the databases. We tested the association of those SNPs with AIDS progression in two cohorts, GRIV and ACS. Tests on permuted phenotypes of the GRIV and ACS cohorts or on randomised sets of equivalent SNPs allowed us to assess the statistical robustness of this method and to estimate the true positive rate. RESULTS Eight genes were identified with high confidence (p = 0.001, rate of true positives 75%). Some of those genes had previously been linked with HIV infection. Notably, ENTPD4 belongs to the same family as CD39, whose expression has already been associated with AIDS progression; while DNAJB12 is part of the HSP90 pathway, which is involved in the control of HIV latency. Our study also drew our attention to lesser-known functions such as mitochondrial ribosomal proteins and a zinc finger protein, ZFP57, which could be central to the effectiveness of HIV infection. Interestingly, for six out of those eight genes, down-regulation is associated with non-progression, which makes them appealing targets to develop drugs against HIV.
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Affiliation(s)
- Jean-Louis Spadoni
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Pierre Rucart
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Sigrid Le Clerc
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
- Crucell Holland B.V., Archimedesweg 4–6, 2333 CN, Leiden, The Netherlands
| | - Cédric Coulonges
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Damien Ulveling
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Vincent Laville
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Taoufik Labib
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Lieng Taing
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Olivier Delaneau
- Département de Génétique et Développement, Faculté de Médecine, Université de Genève, Switzerland
| | - Matthieu Montes
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
- Crucell Holland B.V., Archimedesweg 4–6, 2333 CN, Leiden, The Netherlands
| | - Josselin Noirel
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Jean-François Zagury
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
- * E-mail:
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Singh SP, Foley JF, Zhang HH, Hurt DE, Richards JL, Smith CS, Liao F, Farber JM. Selectivity in the Use of Gi/o Proteins Is Determined by the DRF Motif in CXCR6 and Is Cell-Type Specific. Mol Pharmacol 2015; 88:894-910. [PMID: 26316539 DOI: 10.1124/mol.115.099960] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/21/2015] [Indexed: 01/02/2023] Open
Abstract
CXCR6, the receptor for CXCL16, is expressed on multiple cell types and can be a coreceptor for human immunodeficiency virus 1. Except for CXCR6, all human chemokine receptors contain the D(3.49)R(3.50)Y(3.51) sequence, and all but two contain A(3.53) at the cytoplasmic terminus of the third transmembrane helix (H3C), a region within class A G protein-coupled receptors that contacts G proteins. In CXCR6, H3C contains D(3.49)R(3.50)F(3.51)I(3.52)V(3.53) at positions 126-130. We investigated the importance and interdependence of the canonical D126 and the noncanonical F128 and V130 in CXCR6 by mutating D126 to Y, F128 to Y, and V130 to A singly and in combination. For comparison, we mutated the analogous positions D142, Y144, and A146 to Y, F, and V, respectively, in CCR6, a related receptor containing the canonical sequences. Mutants were analyzed in both human embryonic kidney 293T and Jurkat E6-1 cells. Our data show that for CXCR6 and/or CCR6, mutations in H3C can affect both receptor signaling and chemokine binding; noncanonical H3C sequences are functionally linked, with dual changes mitigating the effects of single mutations; mutations in H3C that compromise receptor activity show selective defects in the use of individual Gi/o proteins; and the effects of mutations in H3C on receptor function and selectivity in Gi/o protein use can be cell-type specific. Our findings indicate that the ability of CXCR6 to make promiscuous use of the available Gi/o proteins is exquisitely dependent on sequences within the H3C and suggest that the native sequence allows for preservation of this function across different cellular environments.
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Affiliation(s)
- Satya P Singh
- Laboratory of Molecular Immunology (S.P.S., J.F.F., H.H.Z., J.L.R., C.S.S., F.L., J.M.F.) and Bioinformatics and Scientific IT Program, Office of Technology Information Systems, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland (D.E.H.); and Howard Hughes Medical Institute, National Institutes of Health Research Scholars Program, Bethesda, Maryland (C.S.S.)
| | - John F Foley
- Laboratory of Molecular Immunology (S.P.S., J.F.F., H.H.Z., J.L.R., C.S.S., F.L., J.M.F.) and Bioinformatics and Scientific IT Program, Office of Technology Information Systems, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland (D.E.H.); and Howard Hughes Medical Institute, National Institutes of Health Research Scholars Program, Bethesda, Maryland (C.S.S.)
| | - Hongwei H Zhang
- Laboratory of Molecular Immunology (S.P.S., J.F.F., H.H.Z., J.L.R., C.S.S., F.L., J.M.F.) and Bioinformatics and Scientific IT Program, Office of Technology Information Systems, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland (D.E.H.); and Howard Hughes Medical Institute, National Institutes of Health Research Scholars Program, Bethesda, Maryland (C.S.S.)
| | - Darrell E Hurt
- Laboratory of Molecular Immunology (S.P.S., J.F.F., H.H.Z., J.L.R., C.S.S., F.L., J.M.F.) and Bioinformatics and Scientific IT Program, Office of Technology Information Systems, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland (D.E.H.); and Howard Hughes Medical Institute, National Institutes of Health Research Scholars Program, Bethesda, Maryland (C.S.S.)
| | - Jennifer L Richards
- Laboratory of Molecular Immunology (S.P.S., J.F.F., H.H.Z., J.L.R., C.S.S., F.L., J.M.F.) and Bioinformatics and Scientific IT Program, Office of Technology Information Systems, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland (D.E.H.); and Howard Hughes Medical Institute, National Institutes of Health Research Scholars Program, Bethesda, Maryland (C.S.S.)
| | - Craig S Smith
- Laboratory of Molecular Immunology (S.P.S., J.F.F., H.H.Z., J.L.R., C.S.S., F.L., J.M.F.) and Bioinformatics and Scientific IT Program, Office of Technology Information Systems, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland (D.E.H.); and Howard Hughes Medical Institute, National Institutes of Health Research Scholars Program, Bethesda, Maryland (C.S.S.)
| | - Fang Liao
- Laboratory of Molecular Immunology (S.P.S., J.F.F., H.H.Z., J.L.R., C.S.S., F.L., J.M.F.) and Bioinformatics and Scientific IT Program, Office of Technology Information Systems, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland (D.E.H.); and Howard Hughes Medical Institute, National Institutes of Health Research Scholars Program, Bethesda, Maryland (C.S.S.)
| | - Joshua M Farber
- Laboratory of Molecular Immunology (S.P.S., J.F.F., H.H.Z., J.L.R., C.S.S., F.L., J.M.F.) and Bioinformatics and Scientific IT Program, Office of Technology Information Systems, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland (D.E.H.); and Howard Hughes Medical Institute, National Institutes of Health Research Scholars Program, Bethesda, Maryland (C.S.S.)
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Zabel BA, Rott A, Butcher EC. Leukocyte chemoattractant receptors in human disease pathogenesis. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2014; 10:51-81. [PMID: 25387059 DOI: 10.1146/annurev-pathol-012513-104640] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Combinations of leukocyte attractant ligands and cognate heptahelical receptors specify the systemic recruitment of circulating cells by triggering integrin-dependent adhesion to endothelial cells, supporting extravasation, and directing specific intratissue localization via gradient-driven chemotaxis. Chemoattractant receptors also control leukocyte egress from lymphoid organs and peripheral tissues. In this article, we summarize the fundamental mechanics of leukocyte trafficking, from the evolution of multistep models of leukocyte recruitment and navigation to the regulation of chemoattractant availability and function by atypical heptahelical receptors. To provide a more complete picture of the migratory circuits involved in leukocyte trafficking, we integrate a number of nonchemokine chemoattractant receptors into our discussion. Leukocyte chemoattractant receptors play key roles in the pathogenesis of autoimmune diseases, allergy, inflammatory disorders, and cancer. We review recent advances in our understanding of chemoattractant receptors in disease pathogenesis, with a focus on genome-wide association studies in humans and the translational implications of mechanistic studies in animal disease models.
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Affiliation(s)
- Brian A Zabel
- Palo Alto Veterans Institute for Research and Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304;
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Abstract
OBJECTIVE To evaluate the impact of mitochondrial DNA (mtDNA) haplogroups on virologic and immunological outcomes of HIV infection. DESIGN HAART-naive African American adolescent participants to the Reaching for Excellence in Adolescent Care and Health study. METHODS The mtDNA haplogroups were inferred from sequenced mtDNA hypervariable regions HV1 and HV2 and their predictive value on HIV outcomes were evaluated in linear mixed models, controlled for human leukocyte antigen (HLA)-B27, HLA-B57 and HLA-B35-Px alleles and other covariates. RESULTS We report data showing that the mtDNA L2 lineage, a group composed of L2a, L2b and L2e mtDNA haplogroups in the studied population, is significantly associated (beta = -0.08; Bonferroni-adjusted P = 0.004) with decline of CD4 T cells (median loss of 8 ± 1 cells per month) in HAART-naive HIV-infected individuals of African American descent (n = 133). No significant association (P < 0.05) with set-point viral load was observed with any of the tested mtDNA haplogroups. The present data concur with previous findings in the AIDS Clinical Trials Group study 384, implicating the L2 lineage with slower CD4 T-cell recovery after antiretroviral therapy in African Americans. CONCLUSIONS Whereas the L2 lineage showed an association with unfavorable immunological outcomes of HIV infection, its phylogenetic divergence from J and U5a, two lineages associated with accelerated HIV progression in European Americans, raises the possibility that interactions with common nucleus-encoded variants drive HIV progression. Disentangling the effects of mitochondrial and nuclear gene variants on the outcomes of HIV infection is an important step to be taken toward a better understanding of HIV/AIDS pathogenesis and pharmacogenomics.
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Abel L, Alcaïs A, Schurr E. The dissection of complex susceptibility to infectious disease: bacterial, viral and parasitic infections. Curr Opin Immunol 2014; 30:72-8. [PMID: 25083600 DOI: 10.1016/j.coi.2014.07.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 06/17/2014] [Accepted: 07/06/2014] [Indexed: 01/01/2023]
Abstract
Infectious diseases are the result of the exposure of susceptible hosts to pathogenic microbes. Genetic factors are important determinants of host susceptibility and efforts are being made to establish the molecular identity of such genetic susceptibility variants by genome-wide association studies. Results obtained to date partly confirm already known genetic vulnerabilities, but also point to new and unexpected mechanisms of susceptibility that extend from classical innate and acquired immunity to weaknesses in constitutional resistance. These studies also revealed an overlap in genetic control between infectious disease and other common immune and inflammatory disorders.
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Affiliation(s)
- Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U.980, University Paris Descartes, Necker Enfants-Malades Hospital, Paris 75015, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Alexandre Alcaïs
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U.980, University Paris Descartes, Necker Enfants-Malades Hospital, Paris 75015, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; URC, CIC, Necker and Cochin Hospitals, Paris, France
| | - Erwin Schurr
- McGill International TB Centre & Departments of Human Genetics and Medicine, McGill University, Montreal, Quebec, Canada; Program in Immunology and Infectious Diseases in Global Health, The Research Institute of the McGill University Health Centre, Canada.
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Abstract
The study of individuals at opposite ends of the HIV clinical spectrum can provide invaluable insights into HIV biology. Heterogeneity in criteria used to define these individuals can introduce inconsistencies in results from research and make it difficult to identify biological mechanisms underlying these phenotypes. In this systematic review, we formally quantified the heterogeneity in definitions used for terms referring to extreme phenotypes in the literature, and identified common definitions and components used to describe these phenotypes. We assessed 714 definitions of HIV extreme phenotypes in 501 eligible studies published between 1 January 2000 and 15 March 2012, and identified substantial variation among these. This heterogeneity in definitions may represent important differences in biological endophenotypes and clinical progression profiles of individuals selected by these, suggesting the need for harmonized definitions. In this context, we were able to identify common components in existing definitions that may provide a framework for developing consensus definitions for these phenotypes in HIV infection.
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Bernier A, Cleret-Buhot A, Zhang Y, Goulet JP, Monteiro P, Gosselin A, DaFonseca S, Wacleche VS, Jenabian MA, Routy JP, Tremblay C, Ancuta P. Transcriptional profiling reveals molecular signatures associated with HIV permissiveness in Th1Th17 cells and identifies peroxisome proliferator-activated receptor gamma as an intrinsic negative regulator of viral replication. Retrovirology 2013; 10:160. [PMID: 24359430 PMCID: PMC3898812 DOI: 10.1186/1742-4690-10-160] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/10/2013] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND We previously demonstrated that primary Th1Th17 cells are highly permissive to HIV-1, whereas Th1 cells are relatively resistant. Molecular mechanisms underlying these differences remain unknown. RESULTS Exposure to replication competent and single-round VSV-G pseudotyped HIV strains provide evidence that superior HIV replication in Th1Th17 vs. Th1 cells was regulated by mechanisms located at entry and post-entry levels. Genome-wide transcriptional profiling identified transcripts upregulated (n = 264) and downregulated (n = 235) in Th1Th17 vs. Th1 cells (p-value < 0.05; fold change cut-off 1.3). Gene Set Enrichment Analysis revealed pathways enriched in Th1Th17 (nuclear receptors, trafficking, p38/MAPK, NF-κB, p53/Ras, IL-23) vs. Th1 cells (proteasome, interferon α/β). Differentially expressed genes were classified into biological categories using Gene Ontology. Th1Th17 cells expressed typical Th17 markers (IL-17A/F, IL-22, CCL20, RORC, IL-26, IL-23R, CCR6) and transcripts functionally linked to regulating cell trafficking (CEACAM1, MCAM), activation (CD28, CD40LG, TNFSF13B, TNFSF25, PTPN13, MAP3K4, LTB, CTSH), transcription (PPARγ, RUNX1, ATF5, ARNTL), apoptosis (FASLG), and HIV infection (CXCR6, FURIN). Differential expression of CXCR6, PPARγ, ARNTL, PTPN13, MAP3K4, CTSH, SERPINB6, PTK2, and ISG20 was validated by RT-PCR, flow cytometry and/or confocal microscopy. The nuclear receptor PPARγ was preferentially expressed by Th1Th17 cells. PPARγ RNA interference significantly increased HIV replication at levels post-entry and prior HIV-DNA integration. Finally, the activation of PPARγ pathway via the agonist Rosiglitazone induced the nuclear translocation of PPARγ and a robust inhibition of viral replication. CONCLUSIONS Thus, transcriptional profiling in Th1Th17 vs. Th1 cells demonstrated that HIV permissiveness is associated with a superior state of cellular activation and limited antiviral properties and identified PPARγ as an intrinsic negative regulator of viral replication. Therefore, triggering PPARγ pathway via non-toxic agonists may contribute to limiting covert HIV replication and disease progression during antiretroviral treatment.
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Affiliation(s)
- Annie Bernier
- Department of Microbiology, Infectiology, and Immunology, Université de Montréal, Faculty of Medicine, Montreal Quebec, Canada
- CHUM-Research Centre, 900 rue Saint-Denis, Tour Viger, room R09.416, Montréal, Quebec H2X 0A9, Canada
| | - Aurélie Cleret-Buhot
- Department of Microbiology, Infectiology, and Immunology, Université de Montréal, Faculty of Medicine, Montreal Quebec, Canada
- CHUM-Research Centre, 900 rue Saint-Denis, Tour Viger, room R09.416, Montréal, Quebec H2X 0A9, Canada
| | - Yuwei Zhang
- Department of Microbiology, Infectiology, and Immunology, Université de Montréal, Faculty of Medicine, Montreal Quebec, Canada
- CHUM-Research Centre, 900 rue Saint-Denis, Tour Viger, room R09.416, Montréal, Quebec H2X 0A9, Canada
| | - Jean-Philippe Goulet
- Faculty of Medicine, CARTaGENE, Université de Montréal, Montreal Quebec, Canada
- Department of Pediatrics, Faculty of Medicine, Ste Justine Hospital Research Center, Université de Montréal, Montreal Quebec, Canada
| | - Patricia Monteiro
- Department of Microbiology, Infectiology, and Immunology, Université de Montréal, Faculty of Medicine, Montreal Quebec, Canada
- CHUM-Research Centre, 900 rue Saint-Denis, Tour Viger, room R09.416, Montréal, Quebec H2X 0A9, Canada
| | - Annie Gosselin
- CHUM-Research Centre, 900 rue Saint-Denis, Tour Viger, room R09.416, Montréal, Quebec H2X 0A9, Canada
| | - Sandrina DaFonseca
- Department of Microbiology, Infectiology, and Immunology, Université de Montréal, Faculty of Medicine, Montreal Quebec, Canada
- CHUM-Research Centre, 900 rue Saint-Denis, Tour Viger, room R09.416, Montréal, Quebec H2X 0A9, Canada
| | - Vanessa Sue Wacleche
- Department of Microbiology, Infectiology, and Immunology, Université de Montréal, Faculty of Medicine, Montreal Quebec, Canada
- CHUM-Research Centre, 900 rue Saint-Denis, Tour Viger, room R09.416, Montréal, Quebec H2X 0A9, Canada
| | - Mohammad-Ali Jenabian
- Chronic Viral Illness Service, McGill University Health Centre, Montreal Quebec, Canada
- Research Institute, McGill University Health Centre, Montreal Quebec, Canada
| | - Jean-Pierre Routy
- Chronic Viral Illness Service, McGill University Health Centre, Montreal Quebec, Canada
- Research Institute, McGill University Health Centre, Montreal Quebec, Canada
- Division of Hematology, McGill University Health Centre, Montreal Quebec, Canada
| | - Cécile Tremblay
- Department of Microbiology, Infectiology, and Immunology, Université de Montréal, Faculty of Medicine, Montreal Quebec, Canada
- CHUM-Research Centre, 900 rue Saint-Denis, Tour Viger, room R09.416, Montréal, Quebec H2X 0A9, Canada
| | - Petronela Ancuta
- Department of Microbiology, Infectiology, and Immunology, Université de Montréal, Faculty of Medicine, Montreal Quebec, Canada
- CHUM-Research Centre, 900 rue Saint-Denis, Tour Viger, room R09.416, Montréal, Quebec H2X 0A9, Canada
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Cespedes MS, Kerns SL, Holzman RS, McLaren PJ, Ostrer H, Aberg JA. Genetic predictors of cervical dysplasia in African American HIV-infected women: ACTG DACS 268. HIV CLINICAL TRIALS 2013; 14:292-302. [PMID: 24334182 DOI: 10.1310/hct1406-292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To examine genome-wide associations in HIV-infected women with a history of cervical dysplasia compared with HIV-infected women with no history of abnormal Papanicolaou (Pap) tests. DESIGN Case-control study using data from women analyzed for the HIV Controllers Study and enrolled in HIV treatment-naïve studies in the AIDS Clinical Trials Group (ACTG). METHODS Genotyping utilized Illumina HumanHap 650 Y or 1MDuo platforms. After quality control and principal component analysis, ~610,000 significant single nucleotide polymorphisms (SNPs) were tested for association. Threshold for significance was P < 5 × 10(-8) for genome-wide associations. RESULTS No significant genomic association was observed between women with low-grade dysplasia and controls. The genome-wide association study (GWAS) analysis between women with high-grade dysplasia or invasive cervical cancer and normal controls identified significant SNPs. In the analyses limited to African American women, 11 SNPs were significantly associated with the development of high-grade dysplasia or cancer after correcting for multiple comparisons. The model using significant SNPs alone had improved accuracy in predicting high-grade dysplasia in African American women compared to the use of clinical data (area under the receiver operating characteristic curve for genetic and clinical model = 0.9 and 0.747, respectively). CONCLUSIONS These preliminary data serve as proof of concept that there may be a genetic predisposition to developing high-grade cervical dysplasia in African American HIV-infected women. Given the small sample size, the results need to be validated in a separate cohort.
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Affiliation(s)
| | | | | | - Paul J McLaren
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Harry Ostrer
- Albert Einstein College of Medicine, Bronx, New York
| | - Judith A Aberg
- New York University School of Medicine, New York, New York
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Bachelerie F, Ben-Baruch A, Burkhardt AM, Combadiere C, Farber JM, Graham GJ, Horuk R, Sparre-Ulrich AH, Locati M, Luster AD, Mantovani A, Matsushima K, Murphy PM, Nibbs R, Nomiyama H, Power CA, Proudfoot AEI, Rosenkilde MM, Rot A, Sozzani S, Thelen M, Yoshie O, Zlotnik A. International Union of Basic and Clinical Pharmacology. [corrected]. LXXXIX. Update on the extended family of chemokine receptors and introducing a new nomenclature for atypical chemokine receptors. Pharmacol Rev 2013; 66:1-79. [PMID: 24218476 DOI: 10.1124/pr.113.007724] [Citation(s) in RCA: 645] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Sixteen years ago, the Nomenclature Committee of the International Union of Pharmacology approved a system for naming human seven-transmembrane (7TM) G protein-coupled chemokine receptors, the large family of leukocyte chemoattractant receptors that regulates immune system development and function, in large part by mediating leukocyte trafficking. This was announced in Pharmacological Reviews in a major overview of the first decade of research in this field [Murphy PM, Baggiolini M, Charo IF, Hébert CA, Horuk R, Matsushima K, Miller LH, Oppenheim JJ, and Power CA (2000) Pharmacol Rev 52:145-176]. Since then, several new receptors have been discovered, and major advances have been made for the others in many areas, including structural biology, signal transduction mechanisms, biology, and pharmacology. New and diverse roles have been identified in infection, immunity, inflammation, development, cancer, and other areas. The first two drugs acting at chemokine receptors have been approved by the U.S. Food and Drug Administration (FDA), maraviroc targeting CCR5 in human immunodeficiency virus (HIV)/AIDS, and plerixafor targeting CXCR4 for stem cell mobilization for transplantation in cancer, and other candidates are now undergoing pivotal clinical trials for diverse disease indications. In addition, a subfamily of atypical chemokine receptors has emerged that may signal through arrestins instead of G proteins to act as chemokine scavengers, and many microbial and invertebrate G protein-coupled chemokine receptors and soluble chemokine-binding proteins have been described. Here, we review this extended family of chemokine receptors and chemokine-binding proteins at the basic, translational, and clinical levels, including an update on drug development. We also introduce a new nomenclature for atypical chemokine receptors with the stem ACKR (atypical chemokine receptor) approved by the Nomenclature Committee of the International Union of Pharmacology and the Human Genome Nomenclature Committee.
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Affiliation(s)
- Francoise Bachelerie
- Chair, Subcommittee on Chemokine Receptors, Nomenclature Committee-International Union of Pharmacology, Bldg. 10, Room 11N113, NIH, Bethesda, MD 20892.
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Biasin M, De Luca M, Gnudi F, Clerici M. The genetic basis of resistance to HIV infection and disease progression. Expert Rev Clin Immunol 2013; 9:319-34. [PMID: 23557268 DOI: 10.1586/eci.13.16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Susceptibility to HIV infection and the modulation of disease progression are strictly dependent on inter-individual variability, much of which is secondary to host genetic heterogeneity. The study of host factors that control these phenomena relies not only on candidate gene approaches but also on unbiased genome-wide genetic and functional analyses. Additional new insights stem from the study of mechanisms that control the expression of host and viral genes, such as miRNA. The genetic host factors that have been suggested to be associated either with resistance to HIV-1 infection or with absent/delayed progression to AIDS are nevertheless unable to fully justify the phenomenon of differential susceptibility to HIV. Multidisciplinary approaches are needed to further analyze individuals who deviate from the expected response to HIV exposure/infection. Results of these analyses will facilitate the identification of novel targets that could be exploited in the setting up of innovative therapeutic or vaccine approaches.
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Affiliation(s)
- Mara Biasin
- Department of Biomedical and Clinical Sciences, University of Milan, Via GB Grassi 74, 20157 Milan, Italy.
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Santa-Marta M, de Brito PM, Godinho-Santos A, Goncalves J. Host Factors and HIV-1 Replication: Clinical Evidence and Potential Therapeutic Approaches. Front Immunol 2013; 4:343. [PMID: 24167505 PMCID: PMC3807056 DOI: 10.3389/fimmu.2013.00343] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 10/06/2013] [Indexed: 12/17/2022] Open
Abstract
HIV and human defense mechanisms have co-evolved to counteract each other. In the process of infection, HIV takes advantage of cellular machinery and blocks the action of the host restriction factors (RF). A small subset of HIV+ individuals control HIV infection and progression to AIDS in the absence of treatment. These individuals known as long-term non-progressors (LNTPs) exhibit genetic and immunological characteristics that confer upon them an efficient resistance to infection and/or disease progression. The identification of some of these host factors led to the development of therapeutic approaches that attempted to mimic the natural control of HIV infection. Some of these approaches are currently being tested in clinical trials. While there are many genes which carry mutations and polymorphisms associated with non-progression, this review will be specifically focused on HIV host RF including both the main chemokine receptors and chemokines as well as intracellular RF including, APOBEC, TRIM, tetherin, and SAMHD1. The understanding of molecular profiles and mechanisms present in LTNPs should provide new insights to control HIV infection and contribute to the development of novel therapies against AIDS.
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Affiliation(s)
- Mariana Santa-Marta
- URIA-Centro de Patogénese Molecular, Faculdade de Farmácia, Universidade de Lisboa , Lisboa , Portugal ; Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa , Lisboa , Portugal
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Dahiya S, Irish BP, Nonnemacher MR, Wigdahl B. Genetic variation and HIV-associated neurologic disease. Adv Virus Res 2013; 87:183-240. [PMID: 23809924 DOI: 10.1016/b978-0-12-407698-3.00006-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
HIV-associated neurologic disease continues to be a significant complication in the era of highly active antiretroviral therapy. A substantial subset of the HIV-infected population shows impaired neuropsychological performance as a result of HIV-mediated neuroinflammation and eventual central nervous system (CNS) injury. CNS compartmentalization of HIV, coupled with the evolution of genetically isolated populations in the CNS, is responsible for poor prognosis in patients with AIDS, warranting further investigation and possible additions to the current therapeutic strategy. This chapter reviews key advances in the field of neuropathogenesis and studies that have highlighted how molecular diversity within the HIV genome may impact HIV-associated neurologic disease. We also discuss the possible functional implications of genetic variation within the viral promoter and possibly other regions of the viral genome, especially in the cells of monocyte-macrophage lineage, which are arguably key cellular players in HIV-associated CNS disease.
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Affiliation(s)
- Satinder Dahiya
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Bryan P Irish
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
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Ballana E, Esté JA. Insights from host genomics into HIV infection and disease: Identification of host targets for drug development. Antiviral Res 2013; 100:473-86. [PMID: 24084487 DOI: 10.1016/j.antiviral.2013.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/17/2013] [Accepted: 09/20/2013] [Indexed: 01/11/2023]
Abstract
HIV susceptibility and disease progression show a substantial degree of individual heterogeneity, ranging from fast progressors to long-term non progressors or elite controllers, that is, subjects that control infection in the absence of therapy. Recent years have seen a significant increase in understanding of the host genetic determinants of susceptibility to HIV infection and disease progression, driven in large part by candidate gene studies, genome-wide association studies, genome-wide transcriptome analyses, and large-scale functional screens. These studies have identified common variants in host loci that clearly influence disease progression, characterized the scale and dynamics of gene and protein expression changes in response to infection, and provided the first comprehensive catalogue of genes and pathways involved in viral replication. This review highlights the potential of host genomic influences in antiviral therapy by pointing to promising novel drug targets but also providing the basis of the identification and validation of host mechanisms that might be susceptible targets for novel antiviral therapies.
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Affiliation(s)
- Ester Ballana
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.
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Abstract
Host genetic factors are a major contributing factor to the inter-individual variation observed in response to human immunodeficiency virus (HIV) infection and are linked to resistance to HIV infection among exposed individuals, as well as rate of disease progression and the likelihood of viral transmission. Of the genetic variants that have been shown to affect the natural history of HIV infection, the human leukocyte antigen (HLA) class I genes exhibit the strongest and most consistent association, underscoring a central role for CD8(+) T cells in resistance to the virus. HLA proteins play important roles in T-cell-mediated adaptive immunity by presenting immunodominant HIV epitopes to cytotoxic T lymphocytes (CTLs) and CD4(+) T cells. Genetic and functional data also indicate a function for HLA in natural killer cell-mediated innate immunity against HIV by interacting with killer cell immunoglobulin-like receptors (KIR). We review the HLA and KIR associations with HIV disease and discuss the mechanisms underlying these associations.
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Affiliation(s)
- Maureen P. Martin
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
- Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts, USA
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Limou S, Zagury JF. Immunogenetics: Genome-Wide Association of Non-Progressive HIV and Viral Load Control: HLA Genes and Beyond. Front Immunol 2013; 4:118. [PMID: 23750159 PMCID: PMC3664380 DOI: 10.3389/fimmu.2013.00118] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/04/2013] [Indexed: 01/11/2023] Open
Abstract
Very early after the identification of the human immunodeficiency virus (HIV), host genetics factors were anticipated to play a role in viral control and disease progression. As early as the mid-1990s, candidate gene studies demonstrated a central role for the chemokine co-receptor/ligand (e.g., CCR5) and human leukocyte antigen (HLA) systems. In the last decade, the advent of genome-wide arrays opened a new era for unbiased genetic exploration of the genome and brought big expectations for the identification of new unexpected genes and pathways involved in HIV/AIDS. More than 15 genome-wide association studies targeting various HIV-linked phenotypes have been published since 2007. Surprisingly, only the two HIV-chemokine co-receptors and HLA loci have exhibited consistent and reproducible statistically significant genetic associations. In this chapter, we will review the findings from the genome-wide studies focusing especially on non-progressive and HIV control phenotypes, and discuss the current perspectives.
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Affiliation(s)
- Sophie Limou
- Basic Science Program, Basic Research Laboratory, Frederick National Laboratory for Cancer ResearchFrederick, MD, USA
| | - Jean-François Zagury
- Chaire de Bioinformatique, Laboratoire Génomique Bioinformatique et Applications (EA 4627), Conservatoire National des Arts et MétiersParis, France
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Fareed M, Afzal M. Single nucleotide polymorphism in genome-wide association of human population: A tool for broad spectrum service. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2013. [DOI: 10.1016/j.ejmhg.2012.08.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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50
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A Genome-Wide Association Study in Caucasian Women Points Out a Putative Role of the STXBP5L Gene in Facial Photoaging. J Invest Dermatol 2013; 133:929-35. [DOI: 10.1038/jid.2012.458] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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