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Murray DD, Grund B, MacPherson CR, Ekenberg C, Zucco AG, Reekie J, Dominguez-Dominguez L, Leung P, Fusco D, Gras J, Gerstoft J, Helleberg M, Borges ÁH, Polizzotto MN, Lundgren JD. Association between ten-eleven methylcytosine dioxygenase 2 genetic variation and viral load in people with HIV. AIDS 2023; 37:379-387. [PMID: 36473831 PMCID: PMC9894145 DOI: 10.1097/qad.0000000000003427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/29/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Identifying genetic factors that influence HIV-pathogenesis is critical for understanding disease pathways. Previous studies have suggested a role for the human gene ten-eleven methylcytosine dioxygenase 2 (TET2) in modulating HIV-pathogenesis. METHODS We assessed whether genetic variation in TET2 was associated with markers of HIV-pathogenesis using both gene level and single nucleotide polymorphism (SNP) level association in 8512 HIV-positive persons across five clinical trial cohorts. RESULTS Variation at both the gene and SNP-level of TET2 was found to be associated with levels of HIV viral load (HIV-VL) consistently in the two cohorts that recruited antiretroviral-naïve participants. The SNPs occurred in two clusters of high linkage disequilibrium (LD), one associated with high HIV-VL and the other low HIV-VL, and were predominantly found in Black participants. CONCLUSION Genetic variation in TET2 was associated with HIV-VL in two large antiretroviral therapy (ART)-naive clinical trial cohorts. The role of TET2 in HIV-pathogenesis warrants further investigation.
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Affiliation(s)
- Daniel D. Murray
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Birgit Grund
- School of Statistics, University of Minnesota, Minneapolis, MN, USA
| | - Cameron R. MacPherson
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Christina Ekenberg
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Adrian G. Zucco
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Joanne Reekie
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lourdes Dominguez-Dominguez
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Preston Leung
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Dahlene Fusco
- Tulane University Medical Center, Tulane University, New Orleans, LA, USA
| | - Julien Gras
- Service de Maladies infectieuses et tropicales, APHP-Hôpital Saint Louis, Paris, France
| | - Jan Gerstoft
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet
| | - Marie Helleberg
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet
| | - Álvaro H. Borges
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Mark N. Polizzotto
- Clinical Hub for Interventional Research, College of Health and Medicine, The Australian National University, Canberra, Australia
| | - Jens D. Lundgren
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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Pupo A, Fernández A, Low SH, François A, Suárez-Amarán L, Samulski RJ. AAV vectors: The Rubik's cube of human gene therapy. Mol Ther 2022; 30:3515-3541. [PMID: 36203359 PMCID: PMC9734031 DOI: 10.1016/j.ymthe.2022.09.015] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 12/12/2022] Open
Abstract
Defective genes account for ∼80% of the total of more than 7,000 diseases known to date. Gene therapy brings the promise of a one-time treatment option that will fix the errors in patient genetic coding. Recombinant viruses are highly efficient vehicles for in vivo gene delivery. Adeno-associated virus (AAV) vectors offer unique advantages, such as tissue tropism, specificity in transduction, eliciting of a relatively low immune responses, no incorporation into the host chromosome, and long-lasting delivered gene expression, making them the most popular viral gene delivery system in clinical trials, with three AAV-based gene therapy drugs already approved by the US Food and Drug Administration (FDA) or European Medicines Agency (EMA). Despite the success of AAV vectors, their usage in particular scenarios is still limited due to remaining challenges, such as poor transduction efficiency in certain tissues, low organ specificity, pre-existing humoral immunity to AAV capsids, and vector dose-dependent toxicity in patients. In the present review, we address the different approaches to improve AAV vectors for gene therapy with a focus on AAV capsid selection and engineering, strategies to overcome anti-AAV immune response, and vector genome design, ending with a glimpse at vector production methods and the current state of recombinant AAV (rAAV) at the clinical level.
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Affiliation(s)
- Amaury Pupo
- R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, Durham, NC 27709, USA
| | - Audry Fernández
- R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, Durham, NC 27709, USA
| | - Siew Hui Low
- R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, Durham, NC 27709, USA
| | - Achille François
- Viralgen. Parque Tecnológico de Guipuzkoa, Edificio Kuatro, Paseo Mikeletegui, 83, 20009 San Sebastián, Spain
| | - Lester Suárez-Amarán
- R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, Durham, NC 27709, USA
| | - Richard Jude Samulski
- R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, Durham, NC 27709, USA,Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Corresponding author: Richard Jude Samulski, R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, NC 27709, USA.
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3
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Faia C, Plaisance-Bonstaff K, Vittori C, Wyczechowska D, Lassak A, Meyaski-Schluter M, Reiss K, Peruzzi F. Attenuated Negative Feedback in Monocyte-Derived Macrophages From Persons Living With HIV: A Role for IKAROS. Front Immunol 2021; 12:785905. [PMID: 34917094 PMCID: PMC8668949 DOI: 10.3389/fimmu.2021.785905] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/11/2021] [Indexed: 11/21/2022] Open
Abstract
Persons living with HIV (PLWH) are at higher risk of developing secondary illnesses than their uninfected counterparts, suggestive of a dysfunctional immune system in these individuals. Upon exposure to pathogens, monocytes undergo epigenetic remodeling that results in either a trained or a tolerant phenotype, characterized by hyper-responsiveness or hypo-responsiveness to secondary stimuli, respectively. We utilized CD14+ monocytes from virally suppressed PLWH and healthy controls for in vitro analysis following polarization of these cells toward a pro-inflammatory monocyte-derived macrophage (MDM) phenotype. We found that in PLWH-derived MDMs, pro-inflammatory signals (TNFA, IL6, IL1B, miR-155-5p, and IDO1) dominate over negative feedback signals (NCOR2, GSN, MSC, BIN1, and miR-146a-5p), favoring an abnormally trained phenotype. The mechanism of this reduction in negative feedback involves the attenuated expression of IKZF1, a transcription factor required for de novo synthesis of RELA during LPS-induced inflammatory responses. Furthermore, restoring IKZF1 expression in PLWH-MDMs partially reinstated expression of negative regulators of inflammation and lowered the expression of pro-inflammatory cytokines. Overall, this mechanism may provide a link between dysfunctional immune responses and susceptibility to co-morbidities in PLWH with low or undetectable viral load.
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Affiliation(s)
- Celeste Faia
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Karlie Plaisance-Bonstaff
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Cecilia Vittori
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Dorota Wyczechowska
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Adam Lassak
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Mary Meyaski-Schluter
- Clinical and Translational Research Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Krzysztof Reiss
- Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Francesca Peruzzi
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Medicine and Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
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4
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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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5
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Omar M, Marchionni L, Häcker G, Badr MT. Host Blood Gene Signatures Can Detect the Progression to Severe and Cerebral Malaria. Front Cell Infect Microbiol 2021; 11:743616. [PMID: 34746025 PMCID: PMC8569259 DOI: 10.3389/fcimb.2021.743616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
Malaria is a major international public health problem that affects millions of patients worldwide especially in sub-Saharan Africa. Although many tests have been developed to diagnose malaria infections, we still lack reliable diagnostic biomarkers for the identification of disease severity, especially in endemic areas where the diagnosis of cerebral malaria is very difficult and requires the exclusion of all other possible causes. Previous host and pathogen transcriptomic studies have not yielded homogenous results that can be harnessed into a reliable diagnostic tool. Here we utilized a multi-cohort analysis approach using machine-learning algorithms to identify blood gene signatures that can distinguish severe and cerebral malaria from moderate and non-cerebral cases. Using a Regularized Random Forest model, we identified 28-gene and 32-gene signatures that can reliably distinguish severe and cerebral malaria, respectively. We tested the specificity of both signatures against other common infectious diseases to ensure the signatures reliability and suitability as diagnostic markers. The severe and cerebral malaria gene-signatures were further integrated through k-top scoring pairs classifiers into ten and nine gene pairs that could distinguish severe and cerebral malaria, respectively. These signatures have various implications that can be utilized as blood diagnostic tools for malaria severity in endemic countries.
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Affiliation(s)
- Mohamed Omar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Luigi Marchionni
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Georg Häcker
- Institute of Medical Microbiology and Hygiene, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Mohamed Tarek Badr
- Institute of Medical Microbiology and Hygiene, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany.,IMM-PACT-Program, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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6
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Svensson JP. Targeting Epigenetics to Cure HIV-1: Lessons From (and for) Cancer Treatment. Front Cell Infect Microbiol 2021; 11:668637. [PMID: 34026665 PMCID: PMC8137950 DOI: 10.3389/fcimb.2021.668637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/21/2021] [Indexed: 11/17/2022] Open
Abstract
The Human Immunodeficiency Virus type 1 (HIV-1) integrates in the host genome as a provirus resulting in a long-lived reservoir of infected CD4 cells. As a provirus, HIV-1 has several aspects in common with an oncogene. Both the HIV-1 provirus and oncogenes only cause disease when expressed. A successful cure of both cancer and HIV-1 includes elimination of all cells with potential to regenerate the disease. For over two decades, epigenetic drugs developed against cancer have been used in the HIV-1 field to modulate the state of the proviral chromatin. Cells with an intact HIV-1 provirus exist in three states of infection: productive, inducible latent, and non-inducible latent. Here focus is on HIV-1, transcription control and chromatin structure; how the inducible proviruses are maintained in a chromatin structure that allows reactivation of transcription; and how transcription switches between different stages to allow for an abundance of different transcripts from a single promoter. Recently it was shown that a functional cure of HIV can be achieved by encapsulating all intact HIV-1 proviruses in heterochromatin, giving hope that epigenetic interventions may be used to end the HIV-1 epidemic.
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Affiliation(s)
- J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet (KI), Huddinge, Sweden
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7
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Meisen WH, Nejad ZB, Hardy M, Zhao H, Oliverio O, Wang S, Hale C, Ollmann MM, Collins PJ. Pooled Screens Identify GPR108 and TM9SF2 as Host Cell Factors Critical for AAV Transduction. Mol Ther Methods Clin Dev 2020; 17:601-611. [PMID: 32280726 PMCID: PMC7139131 DOI: 10.1016/j.omtm.2020.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/12/2020] [Indexed: 12/19/2022]
Abstract
Adeno-associated virus (AAV) has been used extensively as a vector for gene therapy. Despite its widespread use, the mechanisms by which AAV enters the cell and is trafficked to the nucleus are poorly understood. In this study, we performed two pooled, genome-wide screens to identify positive and negative factors modulating AAV2 transduction. Genome-wide libraries directed against all human genes with four designs per gene or eight designs per gene were transduced into U-2 OS cells. These pools were transduced with AAV2 encoding EGFP and sorted based on the intensity of EGFP expression. Analysis of enriched and depleted barcodes in the sorted samples identified several genes that putatively decreased AAV2 transduction. A subset of screen hits was validated in flow cytometry and imaging studies. In addition to KIAA0319L (AAVR), we confirmed the role of two genes, GPR108 and TM9SF2, in mediating viral transduction in eight different AAV serotypes. Interestingly, GPR108 displayed serotype selectivity and was not required for AAV5 transduction. Follow-up studies suggested that GPR108 localized primarily to the Golgi, where it may interact with AAV and play a critical role in mediating virus escape or trafficking. Cumulatively, these results expand our understanding of the process of AAV transduction in different cell types and serotypes.
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Affiliation(s)
- W. Hans Meisen
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
| | | | - Miki Hardy
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
| | - Huiren Zhao
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
| | - Oliver Oliverio
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
| | - Songli Wang
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
| | - Christopher Hale
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
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8
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Luteijn RD, van Diemen F, Blomen VA, Boer IGJ, Manikam Sadasivam S, van Kuppevelt TH, Drexler I, Brummelkamp TR, Lebbink RJ, Wiertz EJ. A Genome-Wide Haploid Genetic Screen Identifies Heparan Sulfate-Associated Genes and the Macropinocytosis Modulator TMED10 as Factors Supporting Vaccinia Virus Infection. J Virol 2019; 93:e02160-18. [PMID: 30996093 PMCID: PMC6580964 DOI: 10.1128/jvi.02160-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/11/2019] [Indexed: 12/15/2022] Open
Abstract
Vaccinia virus is a promising viral vaccine and gene delivery candidate and has historically been used as a model to study poxvirus-host cell interactions. We employed a genome-wide insertional mutagenesis approach in human haploid cells to identify host factors crucial for vaccinia virus infection. A library of mutagenized HAP1 cells was exposed to modified vaccinia virus Ankara (MVA). Deep-sequencing analysis of virus-resistant cells identified host factors involved in heparan sulfate synthesis, Golgi organization, and vesicular protein trafficking. We validated EXT1, TM9SF2, and TMED10 (TMP21/p23/p24δ) as important host factors for vaccinia virus infection. The critical roles of EXT1 in heparan sulfate synthesis and vaccinia virus infection were confirmed. TM9SF2 was validated as a player mediating heparan sulfate expression, explaining its contribution to vaccinia virus infection. In addition, TMED10 was found to be crucial for virus-induced plasma membrane blebbing and phosphatidylserine-induced macropinocytosis, presumably by regulating the cell surface expression of the TAM receptor Axl.IMPORTANCE Poxviruses are large DNA viruses that can infect a wide range of host species. A number of these viruses are clinically important to humans, including variola virus (smallpox) and vaccinia virus. Since the eradication of smallpox, zoonotic infections with monkeypox virus and cowpox virus are emerging. Additionally, poxviruses can be engineered to specifically target cancer cells and are used as a vaccine vector against tuberculosis, influenza, and coronaviruses. Poxviruses rely on host factors for most stages of their life cycle, including attachment to the cell and entry. These host factors are crucial for virus infectivity and host cell tropism. We used a genome-wide knockout library of host cells to identify host factors necessary for vaccinia virus infection. We confirm a dominant role for heparin sulfate in mediating virus attachment. Additionally, we show that TMED10, previously not implicated in virus infections, facilitates virus uptake by modulating the cellular response to phosphatidylserine.
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Affiliation(s)
- Rutger D Luteijn
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ferdy van Diemen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Ingrid G J Boer
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Toin H van Kuppevelt
- Department of Biochemistry, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ingo Drexler
- Institute for Virology, Universitätsklinikum Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | | | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Emmanuel J Wiertz
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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9
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Chang SJ, Jin SC, Jiao X, Galán JE. Unique features in the intracellular transport of typhoid toxin revealed by a genome-wide screen. PLoS Pathog 2019; 15:e1007704. [PMID: 30951565 PMCID: PMC6469816 DOI: 10.1371/journal.ppat.1007704] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/17/2019] [Accepted: 03/13/2019] [Indexed: 12/29/2022] Open
Abstract
Typhoid toxin is a virulence factor for Salmonella Typhi and Paratyphi, the cause of typhoid fever in humans. This toxin has a unique architecture in that its pentameric B subunit, made of PltB, is linked to two enzymatic A subunits, the ADP ribosyl transferase PltA and the deoxyribonuclease CdtB. Typhoid toxin is uniquely adapted to humans, recognizing surface glycoprotein sialoglycans terminated in acetyl neuraminic acid, which are preferentially expressed by human cells. The transport pathway to its cellular targets followed by typhoid toxin after receptor binding is currently unknown. Through a genome-wide CRISPR/Cas9-mediated screen we have characterized the mechanisms by which typhoid toxin is transported within human cells. We found that typhoid toxin hijacks specific elements of the retrograde transport and endoplasmic reticulum-associated degradation machineries to reach its subcellular destination within target cells. Our study reveals unique and common features in the transport mechanisms of bacterial toxins that could serve as the bases for the development of novel anti-toxin therapeutic strategies.
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Affiliation(s)
- Shu-Jung Chang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Xuyao Jiao
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Jorge E Galán
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
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Cellular Determinants of HIV Persistence on Antiretroviral Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1075:213-239. [PMID: 30030795 DOI: 10.1007/978-981-13-0484-2_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The era of antiretroviral therapy has made HIV-1 infection a manageable chronic disease for those with access to treatment. Despite treatment, virus persists in tissue reservoirs seeded with long-lived infected cells that are resistant to cell death and immune recognition. Which cells contribute to this reservoir and which factors determine their persistence are central questions that need to be answered to achieve viral eradication. In this chapter, we describe how cell susceptibility to infection, resistance to cell death, and immune-mediated killing as well as natural cell life span and turnover potential are central components that allow persistence of different lymphoid and myeloid cell subsets that were recently identified as key players in harboring latent and actively replicating virus. The relative contribution of these subsets to persistence of viral reservoir is described, and the open questions are highlighted.
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11
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Association of a 3' untranslated region polymorphism in proprotein convertase subtilisin/kexin type 9 with HIV viral load and CD4+ levels in HIV/hepatitis C virus coinfected women. AIDS 2017; 31:2483-2492. [PMID: 29120899 DOI: 10.1097/qad.0000000000001648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVE To assess variation in genes that regulate cholesterol metabolism in relation to the natural history of HIV infection. DESIGN Cross-sectional and longitudinal analysis of the Women's Interagency HIV Study. METHODS We examined 2050 single nucleotide polymorphisms (SNPs) in 19 genes known to regulate cholesterol metabolism in relation to HIV viral load and CD4 T-cell levels in a multiracial cohort of 1066 antiretroviral therapy-naive women. RESULTS Six SNPs were associated with both HIV viral load and CD4 T-cell levels at a false discovery rate of 0.01. Bioinformatics tools did not predict functional activity for five SNPs, located in introns of nuclear receptor corepressor 2, retinoid X receptor alpha (RXRA), and tetratricopeptide repeat domain 39B. Rs17111557 located in the 3' untranslated region of proprotein convertase subtilisin/kexin type 9 (PCSK9) putatively affects binding of hsa-miR-548t-5p and hsa-miR-4796-3p, which could regulate PCSK9 expression levels. Interrogation of rs17111557 revealed stronger associations in the subset of women with HIV/hepatitis C virus (HCV) coinfection (n = 408, 38% of women). Rs17111557 was also associated with low-density lipoprotein cholesterol levels in HIV/HCV coinfected (β: -10.4; 95% confidence interval: -17.9, -2.9; P = 0.007), but not in HIV monoinfected (β:1.2; 95% confidence interval: -6.3, 8.6; P = 0.76) women in adjusted analysis. CONCLUSION PCSK9 polymorphism may affect HIV pathogenesis, particularly in HIV/HCV coinfected women. A likely mechanism for this effect is PCSK9-mediated regulation of cholesterol metabolism. Replication in independent cohorts is needed to clarify the generalizability of the observed associations.
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12
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McLaren PJ, Pulit SL, Gurdasani D, Bartha I, Shea PR, Pomilla C, Gupta N, Gkrania-Klotsas E, Young EH, Bannert N, Del Amo J, Gill MJ, Gilmour J, Kellam P, Kelleher AD, Sönnerborg A, Wolinsky SM, Zangerle R, Post FA, Fisher M, Haas DW, Walker BD, Porter K, Goldstein DB, Sandhu MS, de Bakker PIW, Fellay J. Evaluating the Impact of Functional Genetic Variation on HIV-1 Control. J Infect Dis 2017; 216:1063-1069. [PMID: 28968755 PMCID: PMC5853944 DOI: 10.1093/infdis/jix470] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/06/2017] [Indexed: 12/21/2022] Open
Abstract
Background Previous genetic association studies of human immunodeficiency virus-1 (HIV-1) progression have focused on common human genetic variation ascertained through genome-wide genotyping. Methods We sought to systematically assess the full spectrum of functional variation in protein coding gene regions on HIV-1 progression through exome sequencing of 1327 individuals. Genetic variants were tested individually and in aggregate across genes and gene sets for an influence on HIV-1 viral load. Results Multiple single variants within the major histocompatibility complex (MHC) region were observed to be strongly associated with HIV-1 outcome, consistent with the known impact of classical HLA alleles. However, no single variant or gene located outside of the MHC region was significantly associated with HIV progression. Set-based association testing focusing on genes identified as being essential for HIV replication in genome-wide small interfering RNA (siRNA) and clustered regularly interspaced short palindromic repeats (CRISPR) studies did not reveal any novel associations. Conclusions These results suggest that exonic variants with large effect sizes are unlikely to have a major contribution to host control of HIV infection.
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Affiliation(s)
- Paul J McLaren
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Laboratory, Public Health Agency of Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Sara L Pulit
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
| | - Deepti Gurdasani
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Istvan Bartha
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University, New York
| | - Cristina Pomilla
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA
| | | | - Elizabeth H Young
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Norbert Bannert
- Division of HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Julia Del Amo
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III, Madrid, Spain
| | - M John Gill
- Department of Medicine, University of Calgary, Canada
| | - Jill Gilmour
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College, London, United Kingdom
| | - Paul Kellam
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Research Department of Infection, Division of Infection and Immunity, University College London, United Kingdom
| | - Anthony D Kelleher
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Sydney, Australia
| | - Anders Sönnerborg
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Steven M Wolinsky
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago
| | - Robert Zangerle
- Department of Dermatology and Venereology, Medical University Innsbruck, Austria
| | | | - Martin Fisher
- Royal Sussex County Hospital, Brighton, United Kingdom
| | - David W Haas
- Department of Medicine, Vanderbilt University School of Medicine, Nashville
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Boston
- Howard Hughes Medical Institute, Chevy Chase
| | | | | | - Manjinder S Sandhu
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Paul I W de Bakker
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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13
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Thaler J, Sigel C, Beasley MB, Wisnivesky J, Crothers K, Bauml J, Hysell K, Emu B, Borsu L, Sigel K. Clinically significant mutations in HIV-infected patients with lung adenocarcinoma. Br J Cancer 2017; 117:1392-1395. [PMID: 28934759 PMCID: PMC5672933 DOI: 10.1038/bjc.2017.333] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 08/06/2017] [Accepted: 08/30/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Lung cancer is a major cause of death in HIV-infected (HIV+) persons. In this study, we compared the prevalence of tumour EGFR and KRAS mutations in a cohort of lung adenocarcinoma patients by HIV status. METHODS We collected data from 55 HIV+ patients with lung adenocarcinoma matched to 136 uninfected comparators. We compared the prevalence of EGFR and KRAS mutations by HIV status. We then compared survival by HIV status and by cancer mutation status among HIV+ subjects. RESULTS Presence of KRAS and EGFR genetic alterations did not vary by HIV status (all P>0.1). There was no difference in overall survival by HIV status or by mutation status among HIV+ subjects. CONCLUSIONS We found no major differences in the prevalence of EGFR or KRAS lung adenocarcinoma mutations by HIV status, suggesting that mutational testing should be conducted similarly regardless of the HIV status.
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Affiliation(s)
- Jonathan Thaler
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carlie Sigel
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mary Beth Beasley
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juan Wisnivesky
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristina Crothers
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Joshua Bauml
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen Hysell
- Department of Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Brinda Emu
- Department of Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Laetitia Borsu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Keith Sigel
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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14
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Rogers GL, Cannon PM. Gene Therapy Approaches to Human Immunodeficiency Virus and Other Infectious Diseases. Hematol Oncol Clin North Am 2017; 31:883-895. [PMID: 28895854 DOI: 10.1016/j.hoc.2017.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Advances in gene therapy technologies, particularly in gene editing, are suggesting new avenues for the treatment of human immunodeficiency virus and other infectious diseases. This article outlines recent developments in antiviral gene therapies, including those based on the disruption of entry receptors or that target viral genomes using targeted nucleases, such as the CRISPR/Cas9 system. In addition, new ways to express circulating antiviral factors, such as antibodies, and approaches to harness and engineer the immune system to provide an antiviral effect that is not naturally achieved are described.
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Affiliation(s)
- Geoffrey L Rogers
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, HMR 413A, Los Angeles, CA 90033, USA
| | - Paula M Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, HMR 413A, Los Angeles, CA 90033, USA.
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15
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The clinical applications of genome editing in HIV. Blood 2016; 127:2546-52. [PMID: 27053530 DOI: 10.1182/blood-2016-01-678144] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 02/09/2016] [Indexed: 12/13/2022] Open
Abstract
HIV/AIDS has long been at the forefront of the development of gene- and cell-based therapies. Although conventional gene therapy approaches typically involve the addition of anti-HIV genes to cells using semirandomly integrating viral vectors, newer genome editing technologies based on engineered nucleases are now allowing more precise genetic manipulations. The possible outcomes of genome editing include gene disruption, which has been most notably applied to the CCR5 coreceptor gene, or the introduction of small mutations or larger whole gene cassette insertions at a targeted locus. Disruption of CCR5 using zinc finger nucleases was the first-in-human application of genome editing and remains the most clinically advanced platform, with 7 completed or ongoing clinical trials in T cells and hematopoietic stem/progenitor cells (HSPCs). Here we review the laboratory and clinical findings of CCR5 editing in T cells and HSPCs for HIV therapy and summarize other promising genome editing approaches for future clinical development. In particular, recent advances in the delivery of genome editing reagents and the demonstration of highly efficient homology-directed editing in both T cells and HSPCs are expected to spur the development of even more sophisticated applications of this technology for HIV therapy.
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16
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Naruse TK, Sakurai D, Ohtani H, Sharma G, Sharma SK, Vajpayee M, Mehra NK, Kaur G, Kimura A. APOBEC3H polymorphisms and susceptibility to HIV-1 infection in an Indian population. J Hum Genet 2015; 61:263-5. [PMID: 26559750 DOI: 10.1038/jhg.2015.136] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 10/06/2015] [Accepted: 10/21/2015] [Indexed: 11/09/2022]
Abstract
Human APOBEC3H (A3H) is a member of APOBEC cytidine deaminase family intensively constraining the HIV-1 replication. A3H is known to be polymorphic with different protein stability and anti-HIV-1 activity in vitro. We recently reported that A3H haplotypes composed of two functional polymorphisms, rs139292 (N15del) and rs139297 (G105R), were associated with the susceptibility to HIV-1 infection in Japanese. To confirm the association of A3H and HIV-1 infection in another ethnic group, a total of 241 HIV-1-infected Indian individuals and ethnic-matched 286 healthy controls were analyzed for the A3H polymorphisms. The frequency of 15del allele was high in the HIV-1-infected subjects as compared with the controls (0.477 vs 0.402, odds ratio (OR)=1.36, P=0.014). Haplotype analysis showed that the frequencies of 15del-105R was high (0.475 vs 0.400, OR=1.36, permutation P=0.037) in the HIV-1-infected subjects, confirming the association of A3H polymorphisms with the susceptibility to HIV-1 infection.
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Affiliation(s)
- Taeko K Naruse
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Daisuke Sakurai
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hitoshi Ohtani
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Gaurav Sharma
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Surendra K Sharma
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Madhu Vajpayee
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Narinder K Mehra
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Gurvinder Kaur
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Akinori Kimura
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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17
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Ross CT, Roodgar M, Smith DG. Evolutionary distance of amino acid sequence orthologs across macaque subspecies: identifying candidate genes for SIV resistance in Chinese rhesus macaques. PLoS One 2015; 10:e0123624. [PMID: 25884674 PMCID: PMC4401517 DOI: 10.1371/journal.pone.0123624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 02/20/2015] [Indexed: 11/18/2022] Open
Abstract
We use the Reciprocal Smallest Distance (RSD) algorithm to identify amino acid sequence orthologs in the Chinese and Indian rhesus macaque draft sequences and estimate the evolutionary distance between such orthologs. We then use GOanna to map gene function annotations and human gene identifiers to the rhesus macaque amino acid sequences. We conclude methodologically by cross-tabulating a list of amino acid orthologs with large divergence scores with a list of genes known to be involved in SIV or HIV pathogenesis. We find that many of the amino acid sequences with large evolutionary divergence scores, as calculated by the RSD algorithm, have been shown to be related to HIV pathogenesis in previous laboratory studies. Four of the strongest candidate genes for SIVmac resistance in Chinese rhesus macaques identified in this study are CDK9, CXCL12, TRIM21, and TRIM32. Additionally, ANKRD30A, CTSZ, GORASP2, GTF2H1, IL13RA1, MUC16, NMDAR1, Notch1, NT5M, PDCD5, RAD50, and TM9SF2 were identified as possible candidates, among others. We failed to find many laboratory experiments contrasting the effects of Indian and Chinese orthologs at these sites on SIVmac pathogenesis, but future comparative studies might hold fertile ground for research into the biological mechanisms underlying innate resistance to SIVmac in Chinese rhesus macaques.
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Affiliation(s)
- Cody T. Ross
- Department of Anthropology, University of California, Davis. Davis, United States of America
- Molecular Anthropology Laboratory, University of California, Davis. Davis, United States of America
| | - Morteza Roodgar
- Molecular Anthropology Laboratory, University of California, Davis. Davis, United States of America
- California National Primate Research Center, University of California, Davis. Davis, United States of America
- Graduate Group of Comparative Pathology, University of California, Davis. Davis, United States of America
| | - David Glenn Smith
- Department of Anthropology, University of California, Davis. Davis, United States of America
- Molecular Anthropology Laboratory, University of California, Davis. Davis, United States of America
- California National Primate Research Center, University of California, Davis. Davis, United States of America
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18
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Sakurai D, Iwatani Y, Ohtani H, Naruse TK, Terunuma H, Sugiura W, Kimura A. APOBEC3H polymorphisms associated with the susceptibility to HIV-1 infection and AIDS progression in Japanese. Immunogenetics 2015; 67:253-7. [PMID: 25721876 DOI: 10.1007/s00251-015-0829-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 02/12/2015] [Indexed: 10/23/2022]
Abstract
Human APOBEC3H (A3H) is a member of APOBEC3 cytidine deaminase family that potently restricts HIV-1 replication. Because A3H is genetically divergent with different intracellular stability and anti-HIV-1 activity in vitro, we investigated a possible association of A3H with susceptibility to HIV-1 infection and disease progression in Japanese populations. A total of 191 HIV-1-infected individuals (HIV group), 93 long-term non-progressors to AIDS (LTNP group) and 421 healthy controls were genotyped for two functional APOBEC3H polymorphisms, rs139292 and rs139297. As compared with the controls, minor allele frequency (MAF) for rs139292 was high in the HIV group (MAF in cases vs. controls; 0.322 vs. 0.263, odds ratio (OR) = 1.33, 95% confidence interval (95% CI) = 1.02-1.74, p = 0.035) and low in the LTNP group (0.161 vs. 0.263, OR = 0.54, 95% CI = 0.36-0.82, p = 0.004, pc = 0.007), whereas the MAF for rs139297 was high in the HIV group (0.367 vs. 0.298, OR = 1.36, 95% CI = 1.07-1.76, p = 0.017, pc = 0.035). In addition, haplotype analyses revealed that the frequencies of A3H-hapC and -hapA were high (0.322 vs. 0.262, OR = 1.33, 95% CI = 1.02-1.74, p = 0.003) and low (0.634 vs. 0.697, OR = 0.75, 95 % CI = 0.58-0.97, p = 0.002), respectively, in the HIV group, whereas the frequencies of A3H-hapC and -hapB were low (0.161 vs. 0.262, OR = 0.54, 95% CI = 0.36-0.82, p = 0.00003) and high (0.097 vs. 0.040, OR = 2.55, 95% CI = 1.40-4.62, p = 0.000008), respectively, in the LTNP group, as compared with those in the controls. These observations suggest that the A3H with low anti-HIV-1 activity, A3H-hapC, is associated with the susceptibility to HIV-1 infection, whereas the A3H producing a stable protein, A3H-hapB, may confer a low risk of disease progression to AIDS.
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Affiliation(s)
- Daisuke Sakurai
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
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Ako-Adjei D, Fu W, Wallin C, Katz KS, Song G, Darji D, Brister JR, Ptak RG, Pruitt KD. HIV-1, human interaction database: current status and new features. Nucleic Acids Res 2014; 43:D566-70. [PMID: 25378338 DOI: 10.1093/nar/gku1126] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The 'Human Immunodeficiency Virus Type 1 (HIV-1), Human Interaction Database', available through the National Library of Medicine at http://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses/hiv-1/interactions, serves the scientific community exploring the discovery of novel HIV vaccine candidates and therapeutic targets. Each HIV-1 human protein interaction can be retrieved without restriction by web-based downloads and ftp protocols and includes: Reference Sequence (RefSeq) protein accession numbers, National Center for Biotechnology Information Gene identification numbers, brief descriptions of the interactions, searchable keywords for interactions and PubMed identification numbers (PMIDs) of journal articles describing the interactions. In addition to specific HIV-1 protein-human protein interactions, included are interaction effects upon HIV-1 replication resulting when individual human gene expression is blocked using siRNA. A total of 3142 human genes are described participating in 12,786 protein-protein interactions, along with 1316 replication interactions described for each of 1250 human genes identified using small interfering RNA (siRNA). Together the data identifies 4006 human genes involved in 14,102 interactions. With the inclusion of siRNA interactions we introduce a redesigned web interface to enhance viewing, filtering and downloading of the combined data set.
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Affiliation(s)
- Danso Ako-Adjei
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - William Fu
- Department of Infectious Disease Research, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701, USA
| | - Craig Wallin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kenneth S Katz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Guangfeng Song
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Dakshesh Darji
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Roger G Ptak
- Department of Infectious Disease Research, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
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20
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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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21
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Common polymorphic effectors of immunity against hepatitis B and C modulate susceptibility to infection and spontaneous clearance in a Moroccan population. INFECTION GENETICS AND EVOLUTION 2014; 26:1-7. [DOI: 10.1016/j.meegid.2014.04.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/14/2014] [Accepted: 04/25/2014] [Indexed: 12/30/2022]
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22
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Haverland NA, Fox HS, Ciborowski P. Quantitative proteomics by SWATH-MS reveals altered expression of nucleic acid binding and regulatory proteins in HIV-1-infected macrophages. J Proteome Res 2014; 13:2109-19. [PMID: 24564501 PMCID: PMC3993959 DOI: 10.1021/pr4012602] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection remains a worldwide epidemic, and innovative therapies to combat the virus are needed. Developing a host-oriented antiviral strategy capable of targeting the biomolecules that are directly or indirectly required for viral replication may provide advantages over traditional virus-centric approaches. We used quantitative proteomics by SWATH-MS in conjunction with bioinformatic analyses to identify host proteins, with an emphasis on nucleic acid binding and regulatory proteins, which could serve as candidates in the development of host-oriented antiretroviral strategies. Using SWATH-MS, we identified and quantified the expression of 3608 proteins in uninfected and HIV-1-infected monocyte-derived macrophages. Of these 3608 proteins, 420 were significantly altered upon HIV-1 infection. Bioinformatic analyses revealed functional enrichment for RNA binding and processing as well as transcription regulation. Our findings highlight a novel subset of proteins and processes that are involved in the host response to HIV-1 infection. In addition, we provide an original and transparent methodology for the analysis of label-free quantitative proteomics data generated by SWATH-MS that can be readily adapted to other biological systems.
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Affiliation(s)
- Nicole A Haverland
- Department of Pharmacology and Experimental Neuroscience University of Nebraska Medical Center , Durham Research Center I, 985800 Nebraska Medical Center Omaha, Nebraska 68198-5800, United States
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23
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Zhao J, Jiang D, Liu R, Li X. [A report of lung adenocarcinoma with HIV carrier and the literature review]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2013; 16:114-6. [PMID: 23425905 PMCID: PMC6000392 DOI: 10.3779/j.issn.1009-3419.2013.02.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jing Zhao
- Department of Oncology, the Fourth Hospital of Hebei Medical University, Shijiazhuang 050000, China
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24
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Abstract
The AIDS era has seen multiple advances in the power of genetics research; scores of host genetic protective factors have been nominated and several have translated to the bedside. We discuss how genomics may inform HIV/AIDS prevention, treatment and eradication.
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25
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Louvain de Souza T, de Souza Campos Fernandes RC, Medina-Acosta E. HIV-1 control in battlegrounds: important host genetic variations for HIV-1 mother-to-child transmission and progression to clinical pediatric AIDS. Future Virol 2012. [DOI: 10.2217/fvl.12.49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HIV-1 mother-to-child transmission (MTCT) is the passing of maternal HIV-1 to the offspring during pregnancy, labor and delivery, and/or breastfeeding. HIV-1 MTCT and the evolution to pediatric AIDS are multifactorial, dynamic and variable phenotypic conditions. Both genetic and nongenetic variables can influence susceptibility to HIV-1 MTCT or the rate of progression to clinical pediatric AIDS. In this review, we summarize the current state of knowledge about the roles of genetic variations seen in host immune response genes, and those that have been independently associated, mostly through population genetics of candidate genes, with interindividual susceptibility to HIV-1 MTCT, and progression to pediatric AIDS. We examine common and rare host genetic variations at coding and noncoding polymorphisms, whether functional or not, in agonists and antagonists of the immune response, which have been implicated in HIV-1 control in battlegrounds of cell entry, replication and evolution to AIDS. Further, we point to over 380 single-nucleotide polymorphisms, mostly within the HLA super region, recently identified in unbiased genome-wide association studies of HIV replication and evolution in adults, still unexplored in the context of HIV-1 MTCT, and which are likely to also influence susceptibility to pediatric HIV-1/AIDS.
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Affiliation(s)
- Thais Louvain de Souza
- Molecular Identification & Diagnosis Unit, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Brazil
| | - Regina Célia de Souza Campos Fernandes
- Municipal Program for the Surveillance of Sexually Transmitted Diseases & Acquired Immunodeficiency Syndrome of Campos dos Goytacazes, Brazil
- Faculty of Medicine of Campos, Campos dos Goytacazes, Brazil
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Nuclear receptor signaling inhibits HIV-1 replication in macrophages through multiple trans-repression mechanisms. J Virol 2011; 85:10834-50. [PMID: 21849441 DOI: 10.1128/jvi.00789-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Sexually transmitted pathogens activate HIV-1 replication and inflammatory gene expression in macrophages through engagement of Toll-like receptors (TLRs). Ligand-activated nuclear receptor (NR) transcription factors, including glucocorticoid receptor (GR), peroxisome proliferator-activated receptor gamma (PPARγ), and liver X receptor (LXR), are potent inhibitors of TLR-induced inflammatory gene expression. We therefore hypothesized that ligand-activated NRs repress both basal and pathogen-enhanced HIV-1 replication in macrophages by directly repressing HIV-1 transcription and by ameliorating the local proinflammatory response to pathogens. We show that the TLR2 ligand PAM3CSK4 activated virus transcription in macrophages and that NR signaling repressed both basal and TLR-induced HIV-1 transcription. NR ligand treatment repressed HIV-1 expression when added concurrently with TLR ligands and in the presence of cycloheximide, demonstrating that they act independently of new cellular gene expression. We found that treatment with NR ligands inhibited the association of AP-1 and NF-κB subunits, as well as the coactivator CBP, with the long terminal repeat (LTR). We show for the first time that the nuclear corepressor NCoR is bound to HIV-1 LTR in unstimulated macrophages and is released from the LTR after TLR engagement. Treatment with PPARγ and LXR ligands, but not GR ligands, prevented this TLR-induced clearance of NCoR from the LTR. Our data demonstrate that both classical and nonclassical trans-repression mechanisms account for NR-mediated HIV-1 repression. Finally, NR ligand treatment inhibited the potent proinflammatory response induced by PAM3CSK4 that would otherwise activate HIV-1 expression in infected cells. Our findings provide a rationale for studying ligand-activated NRs as modulators of basal and inflammation-induced HIV-1 replication.
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