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OBrien SJ. Legacy of a magic gene- CCR5-∆32: From discovery to clinical benefit in a generation. Proc Natl Acad Sci U S A 2024; 121:e2321907121. [PMID: 38457490 PMCID: PMC10962972 DOI: 10.1073/pnas.2321907121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/22/2024] [Indexed: 03/10/2024] Open
Abstract
The discovery of the 32-bp deletion allele of the chemokine receptor gene CCR5 showed that homozygous carriers display near-complete resistance to HIV infection, irrespective of exposure. Algorithms of molecular evolutionary theory suggested that the CCR5-∆32 mutation occurred but once in the last millennium and rose by strong selective pressure relatively recently to a ~10% allele frequency in Europeans. Several lines of evidence support the hypothesis that CCR5-∆32 was selected due to its protective influence to resist Yersinia pestis, the agent of the Black Death/bubonic plague of the 14th century. Powerful anti-AIDS entry inhibitors targeting CCR5 were developed as a treatment for HIV patients, particularly those whose systems had developed resistance to powerful anti-retroviral therapies. Homozygous CCR5-∆32/∆32 stem cell transplant donors were used to produce HIV-cleared AIDS patients in at least five "cures" of HIV infection. CCR5 has also been implicated in regulating infection with Staphylococcus aureus, in recovery from stroke, and in ablation of the fatal graft versus host disease (GVHD) in cancer transplant patients. While homozygous CCR5-∆32/32 carriers block HIV infection, alternatively they display an increased risk for encephalomyelitis and death when infected with the West Nile virus.
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Affiliation(s)
- Stephen J. OBrien
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, Ft Lauderdale, FL33004
- Indiana University School of Public Health, Bloomington, IN47405
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2
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Singh H, Jadhav S, Arif Khan A, Aggarwal SK, Choudhari R, Verma S, Aggarwal S, Gupta V, Singh A, Nain S, Maan HS. APOBEC3, TRIM5α, and BST2 polymorphisms in healthy individuals of various populations with special references to its impact on HIV transmission. Microb Pathog 2022; 162:105326. [PMID: 34863878 DOI: 10.1016/j.micpath.2021.105326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 11/30/2022]
Abstract
AIDS restriction genes (ARGs) like APOBEC3, TRIM5α, and BST2 can act as immunological detectors of the innate protective mechanism of the body. ARGs influence the course of viral pathogenesis and progression of the disease. The infection caused by different viruses including HIV activates the innate immune receptors leading to production of proinflammatory cytokines, interferons and signals that recruit and activate cells involved in the process of inflammation following induction of adaptive immunity. Differential expression of genes involved in viral infection decide the fate and subsequent susceptibility to infection and its clinical outcome. Nevertheless, comprehensive reports on the incidence of genetic polymorphism of APOBEC3s, TRIM5α, and BST-2 in the general population and its association with pathological conditions have not been described well. Therefore, the occurrence of APOBEC3, TRIM5α, and BST2 polymorphism in healthy individuals and its impact on HIV transmission was analyzed. We conducted an extensive search using the several databases including, EMBASE, PubMed (Medline), and Google Scholar. APOBEC3-D, -F, -G, and -H out of the seven human APOBEC3s, help in the control of viral infection. Amongst various restriction factors, TRIM5α and BST-2 also restrict the viral infection followed by the development of the disease. In the current review, a brief account of the polymorphism in the APOBEC3G, TRIM5α, and BST2 genes are explored among different populations along with the interaction of APOBEC3G with Vif protein. Furthermore, this review specifically focus on ARGs polymorphism (APOBEC3G, TRIM5α, and BST2) associated with HIV transmission.
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Affiliation(s)
- HariOm Singh
- Department of Molecular Biology, ICMR-National AIDS Research Institute, Pune, India.
| | - Sushama Jadhav
- Department of Molecular Biology, ICMR-National AIDS Research Institute, Pune, India
| | - Abdul Arif Khan
- Department of Microbiology, ICMR-National AIDS Research Institute, Pune, India
| | - Shubham K Aggarwal
- Department of Molecular Biology, ICMR-National AIDS Research Institute, Pune, India
| | - Ranjana Choudhari
- Department of Molecular Biology, ICMR-National AIDS Research Institute, Pune, India
| | - Sheetal Verma
- Department of Microbiology, King George's Medical University, Lucknow, U.P, India
| | - Sumit Aggarwal
- Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Vivek Gupta
- Department of Biochemistry, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Amita Singh
- District Women Hospital, Prayagraj, UP, 211003, India
| | - Sumitra Nain
- Department of Pharmacy, Banasthali Vidyapith, Banasthali Newai, 304022, Rajasthan, India
| | - Harjeet Singh Maan
- State Virology Laboratory, Department of Microbiology Gandhi Medical College, Bhopal, 462001, India
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3
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Genome-wide association study reveals genetic variants associated with HIV-1C infection in a Botswana study population. Proc Natl Acad Sci U S A 2021; 118:2107830118. [PMID: 34782459 DOI: 10.1073/pnas.2107830118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2021] [Indexed: 11/18/2022] Open
Abstract
Although there have been many studies of gene variant association with different stages of HIV/AIDS progression in United States and European cohorts, few gene-association studies have assessed genic determinants in sub-Saharan African populations, which have the highest density of HIV infections worldwide. We carried out genome-wide association studies on 766 study participants at risk for HIV-1 subtype C (HIV-1C) infection in Botswana. Three gene associations (AP3B1, PTPRA, and NEO1) were shown to have significant association with HIV-1C acquisition. Each gene association was replicated within Botswana or in the United States-African American or United States-European American AIDS cohorts or in both. Each associated gene has a prior reported influence on HIV/AIDS pathogenesis. Thirteen previously discovered AIDS restriction genes were further replicated in the Botswana cohorts, extending our confidence in these prior AIDS restriction gene reports. This work presents an early step toward the identification of genetic variants associated with and affecting HIV acquisition or AIDS progression in the understudied HIV-1C afflicted Botswana population.
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O'Brien SJ. A Beautiful Life: High Risk-High Payoff in Genetic Science. Annu Rev Anim Biosci 2020; 8:1-24. [PMID: 31743063 DOI: 10.1146/annurev-animal-021419-083944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This narrative is a personal view of adventures in genetic science and society that have blessed my life and career across five decades. The advances I enjoyed and the lessons I learned derive from educational training, substantial collaboration, and growing up in the genomics age. I parse the stories into six research disciplines my students, fellows, and colleagues have entered and, in some cases, made an important difference. The first is comparative genetics, where evolutionary inference is applied to genome organization, from building gene maps in the 1970s to building whole genome sequences today. The second area tracks the progression of molecular evolutionary advances and applications to resolve the hierarchical relationship among living species in the silence of prehistory. The third endeavor outlines the birth and maturation of genetic studies and application to species conservation. The fourth theme discusses how emerging viruses studied in a genomic sense opened our eyes to host-pathogen interaction and interdependence. The fifth research emphasis outlines the population genetic-based search and discovery of human restriction genes that influence the epidemiological outcome of abrupt outbreaks, notably HIV-AIDS and several cancers. Finally, the last arena explored illustrates how genetic individualization in human and animals has improved forensic evidence in capital crimes. Each discipline has intuitive and technological overlaps, and each has benefitted from the contribution of genetic and genomic principles I learned so long ago from Drosophila. The journey continues.
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Affiliation(s)
- Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004; .,Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, Florida 33004, USA
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5
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Mehlotra RK. Human Genetic Variation and HIV/AIDS in Papua New Guinea: Time to Connect the Dots. Curr HIV/AIDS Rep 2019; 15:431-440. [PMID: 30218255 DOI: 10.1007/s11904-018-0417-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PURPOSE OF REVIEW Human genetic polymorphisms known to influence HIV acquisition and disease progression occur in Papua New Guinea (PNG). However, no genetic association study has been reported so far. In this article, we review research findings, with a view to stimulate genotype-to-phenotype research. RECENT FINDINGS PNG, a country in Oceania, has a high prevalence of HIV and many sexually transmitted infections. While limited data is available from this country regarding the distribution of human genetic polymorphisms known to influence clinical outcomes of HIV/AIDS, genetic association studies are lacking. Our studies, in the past decade, have revealed that polymorphisms in chemokine receptor-ligand (CCR2-CCR5, CXCL12), innate immune (Toll-like receptor, β-defensin), and antiretroviral drug-metabolism enzyme (CYP2B6, UGT2B7) genes are prevalent in PNG. Although our results need to be validated in further studies, it is urgent to pursue large-scale, comprehensive genetic association studies that include these as well as additional genetic polymorphisms.
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Affiliation(s)
- Rajeev K Mehlotra
- Center for Global Health and Diseases, Case Western Reserve University School of Medicine, Biomedical Research Building, #409A, 2109 Adelbert Rd., Cleveland, OH, 44106, USA.
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Tuen M, Bimela JS, Banin AN, Ding S, Harkins GW, Weiss S, Itri V, Durham AR, Porcella SF, Soni S, Mayr L, Meli J, Torimiro JN, Tongo M, Wang X, Kong XP, Nádas A, Kaufmann DE, Brumme ZL, Nanfack AJ, Quinn TC, Zolla-Pazner S, Redd AD, Finzi A, Gorny MK, Nyambi PN, Duerr R. Immune Correlates of Disease Progression in Linked HIV-1 Infection. Front Immunol 2019; 10:1062. [PMID: 31139189 PMCID: PMC6527802 DOI: 10.3389/fimmu.2019.01062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/25/2019] [Indexed: 01/01/2023] Open
Abstract
Genetic and immunologic analyses of epidemiologically-linked HIV transmission enable insights into the impact of immune responses on clinical outcomes. Human vaccine trials and animal studies of HIV-1 infection have suggested immune correlates of protection; however, their role in natural infection in terms of protection from disease progression is mostly unknown. Four HIV-1+ Cameroonian individuals, three of them epidemiologically-linked in a polygamous heterosexual relationship and one incidence-matched case, were studied over 15 years for heterologous and cross-neutralizing antibody responses, antibody binding, IgA/IgG levels, antibody-dependent cellular cytotoxicity (ADCC) against cells expressing wild-type or CD4-bound Env, viral evolution, Env epitopes, and host factors including HLA-I alleles. Despite viral infection with related strains, the members of the transmission cluster experienced contrasting clinical outcomes including cases of rapid progression and long-term non-progression in the absence of strongly protective HLA-I or CCR5Δ32 alleles. Slower progression and higher CD4/CD8 ratios were associated with enhanced IgG antibody binding to native Env and stronger V1V2 antibody binding responses in the presence of viruses with residue K169 in V2. ADCC against cells expressing Env in the CD4-bound conformation in combination with low Env-specific IgA/IgG ratios correlated with better clinical outcome. This data set highlights for the first time that V1V2-directed antibody responses and ADCC against cells expressing open, CD4-exposed Env, in the presence of low plasma IgA/IgG ratios, can correlate with clinical outcome in natural infection. These parameters are comparable to the major correlates of protection, identified post-hoc in the RV144 vaccine trial; thus, they may also modulate the rate of clinical progression once infected. The findings illustrate the potential of immune correlate analysis in natural infection to guide vaccine development.
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Affiliation(s)
- Michael Tuen
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Jude S Bimela
- Department of Pathology, New York University School of Medicine, New York, NY, United States.,Department of Biochemistry, University of Yaoundé 1, Yaoundé, Cameroon
| | - Andrew N Banin
- Department of Pathology, New York University School of Medicine, New York, NY, United States.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Shilei Ding
- Centre de Recherche du CHUM, Montréal, QC, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Gordon W Harkins
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Svenja Weiss
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Vincenza Itri
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Allison R Durham
- Division of Intramural Research, National Institutes of Health-National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, Division of Intramural Research, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT, United States
| | - Sonal Soni
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Luzia Mayr
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Josephine Meli
- Medical Diagnostic Center, Yaoundé, Cameroon.,Yaoundé General Hospital, Yaoundé, Cameroon
| | - Judith N Torimiro
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon.,"Chantal Biya" International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Marcel Tongo
- Center of Research for Emerging and Re-Emerging Diseases, Institute of Medical Research and Study of Medicinal Plants, Yaoundé, Cameroon.,School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, KwaZulu-Natal Research Innovation and Sequencing Platform, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Xiaohong Wang
- Veterans Affairs New York Harbor Healthcare Systems, New York, NY, United States
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States
| | - Arthur Nádas
- New York University School of Medicine, Institute of Environmental Medicine, New York, NY, United States
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Montréal, QC, Canada.,Department of Medicine, Université de Montréal, Montréal, QC, Canada.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, Vancouver, BC, Canada
| | - Aubin J Nanfack
- Department of Pathology, New York University School of Medicine, New York, NY, United States.,Medical Diagnostic Center, Yaoundé, Cameroon.,"Chantal Biya" International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Thomas C Quinn
- Division of Intramural Research, National Institutes of Health-National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States.,Department of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Susan Zolla-Pazner
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Andrew D Redd
- Division of Intramural Research, National Institutes of Health-National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States.,Department of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montréal, QC, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
| | - Miroslaw K Gorny
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Phillipe N Nyambi
- Department of Pathology, New York University School of Medicine, New York, NY, United States.,Veterans Affairs New York Harbor Healthcare Systems, New York, NY, United States
| | - Ralf Duerr
- Department of Pathology, New York University School of Medicine, New York, NY, United States
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Agniel D, Xie W, Essex M, Cai T. FUNCTIONAL PRINCIPAL VARIANCE COMPONENT TESTING FOR A GENETIC ASSOCIATION STUDY OF HIV PROGRESSION. Ann Appl Stat 2018; 12:1871-1893. [PMID: 32256927 PMCID: PMC7111467 DOI: 10.1214/18-aoas1135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
HIV-1C is the most prevalent subtype of HIV-1 and accounts for over half of HIV-1 infections worldwide. Host genetic influence of HIV infection has been previously studied in HIV-1B, but little attention has been paid to the more prevalent subtype C. To understand the role of host genetics in HIV-1C disease progression, we perform a study to assess the association between longitudinally collected measures of disease and more than 100,000 genetic markers located on chromosome 6. The most common approach to analyzing longitudinal data in this context is linear mixed effects models, which may be overly simplistic in this case. On the other hand, existing flexible and nonparametric methods either require densely sampled points, restrict attention to a single SNP, lack testing procedures, or are cumbersome to fit on the genome-wide scale. We propose a functional principal variance component (FPVC) testing framework which captures the nonlinearity in the CD4 and viral load with low degrees of freedom and is fast enough to carry out thousands or millions of times. The FPVC testing unfolds in two stages. In the first stage, we summarize the markers of disease progression according to their major patterns of variation via functional principal components analysis (FPCA). In the second stage, we employ a simple working model and variance component testing to examine the association between the summaries of disease progression and a set of single nucleotide polymorphisms. We supplement this analysis with simulation results which indicate that FPVC testing can offer large power gains over the standard linear mixed effects model.
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Affiliation(s)
- Denis Agniel
- RAND Corporation, 1776 Main St., Santa Monica, California 90401, USA
| | - Wen Xie
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, Massachusetts 02115, USA
| | - Myron Essex
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, Massachusetts 02115, USA
| | - Tianxi Cai
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, Massachusetts 02115, USA
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8
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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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9
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Xie W, Agniel D, Shevchenko A, Malov SV, Svitin A, Cherkasov N, Baum MK, Campa A, Gaseitsiwe S, Bussmann H, Makhema J, Marlink R, Novitsky V, Lee TH, Cai T, O'Brien SJ, Essex M. Genome-Wide Analyses Reveal Gene Influence on HIV Disease Progression and HIV-1C Acquisition in Southern Africa. AIDS Res Hum Retroviruses 2017; 33:597-609. [PMID: 28132517 DOI: 10.1089/aid.2016.0017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sub-Saharan Africans infected with HIV-1C make up the largest AIDS patient population in the world and exhibit large heterogeneity in disease progression before initiating antiretroviral therapy. To identify host variants associated with HIV disease progression, we performed genome-wide association studies on a total of 556 treatment-naive HIV-infected individuals in Botswana. We characterized the pattern of HIV disease progression using a novel functional principal component analysis, which can better capture longitudinal CD4 and viral load (VL) trajectories. Two single-nucleotide polymorphisms (SNPs) near HCG22 (chr6, peak variant rs2535307, combined p = 3.72 × 10-7, minor allele as risky allele) and CCNG1 (chr5, peak variant kgp22385164, combined p = 1.88 × 10-6, minor allele as risky allele) were significantly associated with CD4 and VL dynamics. Inspection of SNPs in these gene regions in a third Botswana cohort (using GWATCH) also revealed a strong association of HCG22 with HIV-1C acquisition, suggesting that this region is associated with infection as well as disease progression. Our study uncovered two genetic regions that are significant and have specific effects on HIV-1C acquisition or progression in sub-Saharan Africans, and the result suggested new potential targets for AIDS prevention and treatment. In addition, our results also indicate the possibility of using genetic markers as HIV disease progression indicators in sub-Saharan Africans to prioritize fast progressors for antiretroviral treatment.
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Affiliation(s)
- Wen Xie
- Harvard T.H. Chan School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
| | - Denis Agniel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Andrey Shevchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Sergey V. Malov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
- Department of Mathematics, St. Petersburg Electrotechnical University, St Petersburg, Russia
| | - Anton Svitin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Nikolay Cherkasov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Marianna K. Baum
- Department of Dietetics and Nutrition, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, Florida
| | - Adriana Campa
- Department of Dietetics and Nutrition, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, Florida
| | - Simani Gaseitsiwe
- Harvard T.H. Chan School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
| | - Hermann Bussmann
- Harvard T.H. Chan School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
| | - Joseph Makhema
- Harvard T.H. Chan School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
| | - Richard Marlink
- Harvard T.H. Chan School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
| | - Vladimir Novitsky
- Harvard T.H. Chan School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
| | - Tun-Hou Lee
- Harvard T.H. Chan School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Tianxi Cai
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Stephen J. O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
- Oceanographic Center, Nova Southeastern University, Ft. Lauderdale, Florida
| | - M. Essex
- Harvard T.H. Chan School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
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10
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Medrano LM, Rallón N, Berenguer J, Jiménez-Sousa MA, Soriano V, Aldámiz-Echevarria T, Fernández-Rodríguez A, García M, Tejerina F, Martínez I, Benito JM, Resino S. Relationship of TRIM5 and TRIM22 polymorphisms with liver disease and HCV clearance after antiviral therapy in HIV/HCV coinfected patients. J Transl Med 2016; 14:257. [PMID: 27590274 PMCID: PMC5010694 DOI: 10.1186/s12967-016-1005-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 08/16/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND AND AIMS TRIM5 and TRIM22 are restriction factors involved in innate immune response and exhibit anti-viral activity. Single nucleotide polymorphisms (SNPs) at TRIM5 and TRIM22 genes have shown to influence several viral infections such as human immunodeficiency virus (HIV), hepatitis B, as well as measles and rubella vaccination. The aim of this study is to analyze whether TRIM5 and TRIM22 polymorphisms are associated with liver fibrosis inflammation-related biomarkers and response to pegylated-interferon-alpha plus ribavirin (pegIFNα/RBV) therapy in HIV/hepatitis C virus (HCV) coinfected patients. METHODS A retrospective study was performed in 319 patients who started pegIFNα/RBV therapy. Liver fibrosis stage was characterized in 288 patients. TRIM5 rs3824949 and TRIM22 polymorphisms (rs1063303, rs7935564, and rs7113258) were genotyped using the GoldenGate assay. The primary outcomes were: a) significant liver fibrosis (≥F2) evaluated by liver biopsy or transient elastography (liver stiffness values ≥7.1 Kpa); b) sustained virological response (SVR) defined as no detectable HCV viral load (<10 IU/mL) at week 24 after the end of the treatment. The secondary outcome variable was plasma chemokine levels. RESULTS Patients with TRIM5 rs3824949 GG genotype had higher SVR rate than patients with TRIM5 rs3824949 CC/CG genotypes (p = 0.013), and they had increased odds of achieving SVR (adjusted odds ratio (aOR = 2.58; p = 0.012). Patients with TRIM22 rs1063303 GG genotype had higher proportion of significant liver fibrosis than patients with rs1063303 CC/CG genotypes (p = 0.021), and they had increased odds of having significant hepatic fibrosis (aOR = 2.19; p = 0.034). Patients with TRIM22 rs7113258 AT/AA genotype had higher SVR rate than patients with rs7113258 TT genotypes (p = 0.013), and they had increased odds of achieving SVR (aOR = 1.88; p = 0.041). The TRIM22 haplotype conformed by rs1063303_C and rs7113258_A was more frequent in patients with SVR (p = 0.018) and was significantly associated with achieving SVR (aOR = 2.80; p = 0.013). The TRIM5 rs3824949 GG genotype was significantly associated with higher levels of GRO-α (adjusted arithmetic mean ratio ((aAMR) = 1.40; p = 0.011) and MCP-1 (aAMR = 1.61; p = 0.003). CONCLUSIONS TRIM5 and TRIM22 SNPs are associated to increased odds of significant liver fibrosis and SVR after pegIFNα/RBV therapy in HIV/HCV coinfected patients. Besides, TRIM5 SNP was associated to higher baseline levels of circulating biomarkers GRO and MCP-1.
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Affiliation(s)
- Luz M. Medrano
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III (Campus Majadahonda), Carretera Majadahonda- Pozuelo, Km 2.2, 28220 Majadahonda Madrid, Spain
| | - Norma Rallón
- Instituto de Investigación Sanitaria de La Fundación Jiménez Díaz (IIS-FJD), Universidad Autónoma de Madrid, Madrid, Spain
- Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - Juan Berenguer
- Unidad de Enfermedades Infecciosas/VIH, Hospital General Universitario “Gregorio Marañón”, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - María A. Jiménez-Sousa
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III (Campus Majadahonda), Carretera Majadahonda- Pozuelo, Km 2.2, 28220 Majadahonda Madrid, Spain
| | - Vicente Soriano
- Unidad de Enfermedades Infecciosas, Hospital Universitario La Paz, Madrid, Spain
| | - Teresa Aldámiz-Echevarria
- Unidad de Enfermedades Infecciosas/VIH, Hospital General Universitario “Gregorio Marañón”, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Amanda Fernández-Rodríguez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III (Campus Majadahonda), Carretera Majadahonda- Pozuelo, Km 2.2, 28220 Majadahonda Madrid, Spain
| | - Marcial García
- Instituto de Investigación Sanitaria de La Fundación Jiménez Díaz (IIS-FJD), Universidad Autónoma de Madrid, Madrid, Spain
- Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - Francisco Tejerina
- Unidad de Enfermedades Infecciosas/VIH, Hospital General Universitario “Gregorio Marañón”, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Isidoro Martínez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III (Campus Majadahonda), Carretera Majadahonda- Pozuelo, Km 2.2, 28220 Majadahonda Madrid, Spain
| | - José M. Benito
- Instituto de Investigación Sanitaria de La Fundación Jiménez Díaz (IIS-FJD), Universidad Autónoma de Madrid, Madrid, Spain
- Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - Salvador Resino
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III (Campus Majadahonda), Carretera Majadahonda- Pozuelo, Km 2.2, 28220 Majadahonda Madrid, Spain
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A Canonical Correlation Analysis of AIDS Restriction Genes and Metabolic Pathways Identifies Purine Metabolism as a Key Cooperator. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2016; 2016:2460184. [PMID: 27462363 PMCID: PMC4947641 DOI: 10.1155/2016/2460184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/08/2016] [Indexed: 02/07/2023]
Abstract
Human immunodeficiency virus causes a severe disease in humans, referred to as immune deficiency syndrome. Studies on the interaction between host genetic factors and the virus have revealed dozens of genes that impact diverse processes in the AIDS disease. To resolve more genetic factors related to AIDS, a canonical correlation analysis was used to determine the correlation between AIDS restriction and metabolic pathway gene expression. The results show that HIV-1 postentry cellular viral cofactors from AIDS restriction genes are coexpressed in human transcriptome microarray datasets. Further, the purine metabolism pathway comprises novel host factors that are coexpressed with AIDS restriction genes. Using a canonical correlation analysis for expression is a reliable approach to exploring the mechanism underlying AIDS.
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Burman CJ, Aphane M, Delobelle P. Reducing the overall HIV-burden in South Africa: is 'reviving ABC' an appropriate fit for a complex, adaptive epidemiological HIV landscape? AJAR-AFRICAN JOURNAL OF AIDS RESEARCH 2016; 14:13-28. [PMID: 25920980 DOI: 10.2989/16085906.2015.1016988] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This article questions the recommendations to 'revive ABC (abstain, be faithful, condomise)' as a mechanism to 'educate' people in South Africa about HIV prevention as the South African National HIV Prevalence, Incidence and Behaviour Survey, 2012, suggests. We argue that ABC was designed as a response to a particular context which has now radically changed. In South Africa the contemporary context reflects the mass roll-out of antiretroviral treatment; significant bio-medical knowledge gains; a generalised population affected by HIV that has made sense of and embodied those diverse experiences; and a government committed to confronting the epidemic. We suggest that the situation can now be plausibly conceptualised as a complex, adaptive epidemiological landscape that could benefit from an expansion of the existing, 'descriptive' prevention paradigm towards strategies that focus on the dynamics of transmission. We argue for this shift by proposing a theoretical framework based on complexity theory and pattern management. We interrogate one educational prevention heuristic that emphasises the importance of risk-reduction through the lens of transmission, called A-3B-4C-T. We argue that this type of approach provides expansive opportunities for people to engage with the epidemic in contextualised, innovative ways that supersede the opportunities afforded by ABC. We then suggest that framing the prevention imperative through the lens of 'dynamic prevention' at scale opens more immediate opportunities, as well as developing a future-oriented mind-set, than the 'descriptive prevention' parameters can facilitate. The parameters of the 'descriptive prevention' paradigm, that maintain - and partially reinforce - the presence of ABC, do not have the flexibility required to develop the armamentarium of tools required to contribute to the management of a complex epidemiological landscape. Uncritically adhering to both the 'descriptive paradigm', and ABC, represents an historically dislocated form of prevention - with restrictive options for reducing the overall burden of HIV-related challenges in South Africa.
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Affiliation(s)
- Christopher J Burman
- a The Rural Development and Innovation Hub , University of Limpopo , Turfloop Campus, Polokwane , South Africa
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Maestri A, dos Santos MC, Ribeiro-Rodrigues EM, de Mello WA, Sousa RCM, dos Santos SE, Sortica VA. The CCR5Δ32 (rs333) polymorphism is not a predisposing factor for severe pandemic influenza in the Brazilian admixed population. BMC Res Notes 2015. [PMID: 26223981 PMCID: PMC4520097 DOI: 10.1186/s13104-015-1299-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background Recent studies have tried to identify host genetic variants that could explain severe cases and deaths in infection with Influenza A(H1N1)pdm09, especially among children and young adults. CCR5 is a chemokine receptor expressed on T cells, macrophages and dendritic cells, which is an important mediator of leukocyte chemotaxis during the immune response. A deletion mutation (Δ32) in this gene interferes with the response of immune cells, impairing viral clearance. We evaluated the CCR5Δ32 polymorphism (rs333) in individuals of the Brazilian admixed population with a diagnosis of Influenza A(H1N1)pdm09 infection. Methods A total of 330 subjects with a diagnosis of Influenza A(H1N1)pdm09, evaluated at health services in the northern and northeastern regions of Brazil between June 2009 and August 2010, were genotyped for the Δ32 deletion (rs333). The cases were classified according to the progression of infection into a group of hospitalized patients (n = 156) and a group of non-hospitalized patients (n = 174). Results No significant differences in the allele or genotype frequencies of the CCR5Δ32 polymorphism were observed between non-hospitalized and hospitalized patients (p = 0.289 and p = 0.431, respectively). Conclusion The Δ32 deletion in the CCR5 gene is not associated with an unfavorable outcome in patients infected with Influenza A(H1N1)pdm09 in the Brazilian admixed population. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1299-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alvino Maestri
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Cidade Universitária Prof. José da Silveira Neto, Rua Augusto Corrêa, 01, BOX: 8615, Belém, Pará, CEP: 66.075-970, Brazil.
| | | | - Elzemar M Ribeiro-Rodrigues
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Cidade Universitária Prof. José da Silveira Neto, Rua Augusto Corrêa, 01, BOX: 8615, Belém, Pará, CEP: 66.075-970, Brazil.
| | | | | | - Sidney Emanuel dos Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Cidade Universitária Prof. José da Silveira Neto, Rua Augusto Corrêa, 01, BOX: 8615, Belém, Pará, CEP: 66.075-970, Brazil.
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Focosi D, Maggi F, Ceccherini-Nelli L, Pistello M. Cell therapies for treatment of human immunodeficiency virus infection. Rev Med Virol 2015; 25:156-74. [PMID: 25727480 DOI: 10.1002/rmv.1831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/30/2015] [Accepted: 02/05/2015] [Indexed: 12/15/2022]
Abstract
After the serendipitous discovery of HIV eradication in the "Berlin patient", interest has grown in curing HIV infection by replacing the patient's replication-competent blood cells with infection-resistant ones. At the same time, induced pluripotent stem cell technologies and genetic engineering have boosted cell therapy transfer into the clinic. Currently available cell therapy approaches to attempt to cure HIV infection include the following: (1) Transplantation of autologous or allogeneic cells spontaneously resistant or edited to resist HIV infection; (2) Transplantation of autologous T-lymphocytes spontaneously targeting or redirected against HIV; and (3) Transplantation of autologous cells engineered to work as anti-HIV antibody factories. We review here the preliminary results and potential for future applications of these approaches.
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Affiliation(s)
- Daniele Focosi
- Retrovirus Center and Virology Section, Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
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GWATCH: a web platform for automated gene association discovery analysis. Gigascience 2014; 3:18. [PMID: 25374661 PMCID: PMC4220276 DOI: 10.1186/2047-217x-3-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 09/30/2014] [Indexed: 01/08/2023] Open
Abstract
Background As genome-wide sequence analyses for complex human disease determinants are expanding, it is increasingly necessary to develop strategies to promote discovery and validation of potential disease-gene associations. Findings Here we present a dynamic web-based platform – GWATCH – that automates and facilitates four steps in genetic epidemiological discovery: 1) Rapid gene association search and discovery analysis of large genome-wide datasets; 2) Expanded visual display of gene associations for genome-wide variants (SNPs, indels, CNVs), including Manhattan plots, 2D and 3D snapshots of any gene region, and a dynamic genome browser illustrating gene association chromosomal regions; 3) Real-time validation/replication of candidate or putative genes suggested from other sources, limiting Bonferroni genome-wide association study (GWAS) penalties; 4) Open data release and sharing by eliminating privacy constraints (The National Human Genome Research Institute (NHGRI) Institutional Review Board (IRB), informed consent, The Health Insurance Portability and Accountability Act (HIPAA) of 1996 etc.) on unabridged results, which allows for open access comparative and meta-analysis. Conclusions GWATCH is suitable for both GWAS and whole genome sequence association datasets. We illustrate the utility of GWATCH with three large genome-wide association studies for HIV-AIDS resistance genes screened in large multicenter cohorts; however, association datasets from any study can be uploaded and analyzed by GWATCH.
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