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Zheng X, Cai R, Gao C, Ponatshego P, Gao L, Montano MA, Hu K, Mosepele M, Li P. Poor sleep quality is linked to increased frailty in middle-aged people living with HIV in Botswana. RESEARCH SQUARE 2024:rs.3.rs-4462187. [PMID: 38883786 PMCID: PMC11177973 DOI: 10.21203/rs.3.rs-4462187/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
This work aims to evaluate associations between self-reported sleep health and frailty in Botswana, a sub-Saharan Africa setting. Fifty persons living with HIV (PLWH) on suppressive antiretroviral therapy (ART) and fifty HIV seronegative control participants are enrolled in Botswana. Sleep quality is scored subjectively as "good" or "poor" based on self-report. A frailty index (FI) is constructed based on thirty-three health deficits related to body mass index, waist circumference, physical activity, emotional status, and fatigue, and scored ranging between 0 (no deficit present) and 1 (all deficits present). Sleep quality between PLWH and controls is compared using logistic regression; linear regression is performed to compare the FI between them. Linear regressions are performed to examine the association between the FI and sleep quality stratified by HIV serostatus. Age, sex, and comorbidities are adjusted; when relevant, CD4 cell and ART duration are controlled. PLWH display 2.88 (95% CI: 1.22-6.79, p = 0.02) higher odds of having poor sleep than controls. Having poor sleep is associated with increased FI in PLWH but not in controls. Specifically, compared with PLWH who have good sleep, PLWH who report poor sleep have a > 1 standard deviation (p < 0.0001) increase in their FI score.
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Affiliation(s)
| | | | | | | | - Lei Gao
- Massachusetts General Hospital
| | | | - Kun Hu
- Massachusetts General Hospital
| | | | - Peng Li
- Massachusetts General Hospital
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2
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Kasamatsu T. Implications of Senescent T Cells for Cancer Immunotherapy. Cancers (Basel) 2023; 15:5835. [PMID: 38136380 PMCID: PMC10742305 DOI: 10.3390/cancers15245835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
T-cell senescence is thought to result from the age-related loss of the ability to mount effective responses to pathogens and tumor cells. In addition to aging, T-cell senescence is caused by repeated antigenic stimulation and chronic inflammation. Moreover, we demonstrated that T-cell senescence was induced by treatment with DNA-damaging chemotherapeutic agents. The characteristics of therapy-induced senescent T (TIS-T) cells and general senescent T cells are largely similar. Senescent T cells demonstrate an increase in the senescence-associated beta-galactosidase-positive population, cell cycle arrest, secretion of senescence-associated secretory phenotypic factors, and metabolic reprogramming. Furthermore, senescent T cells downregulate the expression of the co-stimulatory molecules CD27 and CD28 and upregulate natural killer cell-related molecules. Moreover, TIS-T cells showed increased PD-1 expression. However, the loss of proliferative capacity and decreased expression of co-stimulatory molecules associated with T-cell senescence cause a decrease in T-cell immunocompetence. In this review, we discuss the characteristics of senescent T-cells, including therapy-induced senescent T cells.
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Affiliation(s)
- Tetsuhiro Kasamatsu
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, 3-39-22 Showa-machi, Maebashi 371-8514, Gunma, Japan
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3
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Locatelli M, Faure-Dupuy S. Virus hijacking of host epigenetic machinery to impair immune response. J Virol 2023; 97:e0065823. [PMID: 37656959 PMCID: PMC10537592 DOI: 10.1128/jvi.00658-23] [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] [Indexed: 09/03/2023] Open
Abstract
Epigenetic modifications, such as DNA hypermethylation, histone acetylation/methylation, or nucleosome positioning, result in differential gene expression. These modifications can have an impact on various pathways, including host antiviral immune responses. In this review, we summarize the current understanding of epigenetic modifications induced by viruses to counteract host antiviral immune responses, which are crucial for establishing and maintaining infection of viruses. Finally, we provide insights into the potential use of epigenetic modulators in combating viral infections and virus-induced diseases.
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Affiliation(s)
- Maëlle Locatelli
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Suzanne Faure-Dupuy
- Université de Paris Cité, Institut Cochin, Inserm U1016-CNRS UMR8104, Paris, France
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4
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Anastasopoulou S, Georgakopoulos T, Mouzaki A. HIV-1 Transcriptional Activator Tat Inhibits IL2 Expression by Preventing the Presence of Pol II on the IL2 Promoter. Biomolecules 2023; 13:881. [PMID: 37371461 DOI: 10.3390/biom13060881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
HIV-1 infection leads to a gradual loss of T helper cells, chronic immune activation, and eventual immune system breakdown. HIV-1 causes deregulation of the expression of IL-2, a cytokine important for T helper cell growth and survival, which is downregulated in HIV-1 patients. The present study addresses the regulation of IL2 expression via HIV-1 Tat transcriptional activator. We used J-LAT cells, a T cell line that serves as a latency model for studies of HIV-1 expression in T cells, and as controls a T cell line lacking HIV-1 elements and a T cell line with a stably integrated copy of the HIV-1-LTR promoter. We show that endogenously expressed Tat inhibits IL2 transcription in J-Lat cells via its presence in the ARRE-1/2 elements of the IL2 promoter and that the inhibition of IL2 expression is mediated by Tat inhibiting Pol II activity at the IL2 promoter, which is mediated by preventing the presence of Pol II at the ARRE-1/2 elements. Overall, Tat is present at the IL2 promoter, apart from its cognate HIV-1 LTR target. This supports our current knowledge of how HIV-1 affects the host transcriptional machinery and reflects the potential of Tat to disrupt transcriptional regulation of host genes to manipulate cell responses.
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Affiliation(s)
- Spyridoula Anastasopoulou
- Laboratory of Immunohematology, Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, GR-26500 Patras, Greece
| | - Tassos Georgakopoulos
- Laboratory of Immunohematology, Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, GR-26500 Patras, Greece
| | - Athanasia Mouzaki
- Laboratory of Immunohematology, Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, GR-26500 Patras, Greece
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5
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Prinzing B, Zebley CC, Petersen CT, Fan Y, Anido AA, Yi Z, Nguyen P, Houke H, Bell M, Haydar D, Brown C, Boi SK, Alli S, Crawford JC, Riberdy JM, Park JJ, Zhou S, Velasquez MP, DeRenzo C, Lazzarotto CR, Tsai SQ, Vogel P, Pruett-Miller SM, Langfitt DM, Gottschalk S, Youngblood B, Krenciute G. Deleting DNMT3A in CAR T cells prevents exhaustion and enhances antitumor activity. Sci Transl Med 2021; 13:eabh0272. [PMID: 34788079 PMCID: PMC8733956 DOI: 10.1126/scitranslmed.abh0272] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chimeric antigen receptor (CAR) T cell therapy is revolutionizing cancer immunotherapy for patients with B cell malignancies and is now being developed for solid tumors and chronic viral infections. Although clinical trials have demonstrated the curative potential of CAR T cell therapy, a substantial and well-established limitation is the heightened contraction and transient persistence of CAR T cells during prolonged antigen exposure. The underlying mechanism(s) for this dysfunctional state, often termed CAR T cell exhaustion, remains poorly defined. Here, we report that exhaustion of human CAR T cells occurs through an epigenetic repression of the T cell’s multipotent developmental potential. Deletion of the de novo DNA methyltransferase 3 alpha (DNMT3A) in T cells expressing first- or second-generation CARs universally preserved the cells’ ability to proliferate and mount an antitumor response during prolonged tumor exposure. The increased functionality of the exhaustion-resistant DNMT3A knockout CAR T cells was coupled to an up-regulation of interleukin-10, and genome-wide DNA methylation profiling defined an atlas of genes targeted for epigenetic silencing. This atlas provides a molecular definition of CAR T cell exhaustion, which includes many transcriptional regulators that limit the “stemness” of immune cells, including CD28, CCR7, TCF7, and LEF1. Last, we demonstrate that this epigenetically regulated multipotency program is firmly coupled to the clinical outcome of prior CAR T cell therapies. These data document the critical role epigenetic mechanisms play in limiting the fate potential of human T cells and provide a road map for leveraging this information for improving CAR T cell efficacy.
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Affiliation(s)
- Brooke Prinzing
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Caitlin C. Zebley
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Christopher T. Petersen
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yiping Fan
- Department of Bioinformatics, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Alejandro Allo Anido
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zhongzhen Yi
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Phuong Nguyen
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Haley Houke
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Matthew Bell
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Dalia Haydar
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Charmaine Brown
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shannon K. Boi
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shanta Alli
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Janice M. Riberdy
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jeoungeun J. Park
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sheng Zhou
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Mireya Paulina Velasquez
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Chris DeRenzo
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Cicera R. Lazzarotto
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shengdar Q. Tsai
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Peter Vogel
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shondra M. Pruett-Miller
- Department of Cell and Molecular Biology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Deanna M. Langfitt
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ben Youngblood
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Giedre Krenciute
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
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6
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Mohan J, Ghazi T, Chuturgoon AA. A Critical Review of the Biochemical Mechanisms and Epigenetic Modifications in HIV- and Antiretroviral-Induced Metabolic Syndrome. Int J Mol Sci 2021; 22:ijms222112020. [PMID: 34769448 PMCID: PMC8584285 DOI: 10.3390/ijms222112020] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 02/07/2023] Open
Abstract
Metabolic syndrome (MetS) is a non-communicable disease characterised by a cluster of metabolic irregularities. Alarmingly, the prevalence of MetS in people living with Human Immunodeficiency Virus (HIV) and antiretroviral (ARV) usage is increasing rapidly. This study aimed to look at biochemical mechanisms and epigenetic modifications associated with HIV, ARVs, and MetS. More specifically, emphasis was placed on mitochondrial dysfunction, insulin resistance, inflammation, lipodystrophy, and dyslipidaemia. We found that mitochondrial dysfunction was the most common mechanism that induced metabolic complications. Our findings suggest that protease inhibitors (PIs) are more commonly implicated in MetS-related effects than other classes of ARVs. Furthermore, we highlight epigenetic studies linking HIV and ARV usage to MetS and stress the need for more studies, as the current literature remains limited despite the advancement in and popularity of epigenetics.
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7
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DNA Methylation and Immune Memory Response. Cells 2021; 10:cells10112943. [PMID: 34831166 PMCID: PMC8616503 DOI: 10.3390/cells10112943] [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: 08/26/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 12/16/2022] Open
Abstract
The generation of memory is a cardinal feature of the adaptive immune response, involving different factors in a complex process of cellular differentiation. This process is essential for protecting the second encounter with pathogens and is the mechanism by which vaccines work. Epigenetic changes play important roles in the regulation of cell differentiation events. There are three types of epigenetic regulation: DNA methylation, histone modification, and microRNA expression. One of these epigenetic changes, DNA methylation, occurs in cytosine residues, mainly in CpG dinucleotides. This brief review aimed to analyse the literature to verify the involvement of DNA methylation during memory T and B cell development. Several studies have highlighted the importance of the DNA methyltransferases, enzymes that catalyse the methylation of DNA, during memory differentiation, maintenance, and function. The methylation profile within different subsets of naïve activated and memory cells could be an interesting tool to help monitor immune memory response.
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8
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Rajeev R, Dwivedi AP, Sinha A, Agarwaal V, Dev RR, Kar A, Khosla S. Epigenetic interaction of microbes with their mammalian hosts. J Biosci 2021. [PMID: 34728591 PMCID: PMC8550911 DOI: 10.1007/s12038-021-00215-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The interaction of microbiota with its host has the ability to alter the cellular functions of both, through several mechanisms. Recent work, from many laboratories including our own, has shown that epigenetic mechanisms play an important role in the alteration of these cellular functions. Epigenetics broadly refers to change in the phenotype without a corresponding change in the DNA sequence. This change is usually brought by epigenetic modifications of the DNA itself, the histone proteins associated with the DNA in the chromatin, non-coding RNA or the modifications of the transcribed RNA. These modifications, also known as epigenetic code, do not change the DNA sequence but alter the expression level of specific genes. Microorganisms seem to have learned how to modify the host epigenetic code and modulate the host transcriptome in their favour. In this review, we explore the literature that describes the epigenetic interaction of bacteria, fungi and viruses, with their mammalian hosts.
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9
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Loucif H, Dagenais-Lussier X, Avizonis D, Choinière L, Beji C, Cassin L, Routy JP, Fritz JH, Olagnier D, van Grevenynghe J. Autophagy-dependent glutaminolysis drives superior IL21 production in HIV-1-specific CD4 T cells. Autophagy 2021; 18:1256-1273. [PMID: 34612140 DOI: 10.1080/15548627.2021.1972403] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The maintenance of a strong IL21 production in memory CD4 T cells, especially in HIV-1-specific cells, represents a major correlate of natural immune protection against the virus. However, the molecular mechanisms underlying IL21 production during HIV-1 infection, which is only elevated among the naturally protected elite controllers (EC), are still unknown. We recently found out that lipophagy is a critical immune mediator that control an antiviral metabolic state following CD8A T cell receptor engagement, playing an important role in the natural control of HIV-1 infection. This led us to investigate whether the beneficial role of a strong macroautophagy/autophagy, could also be used to ensure effective IL21 production as well. Herein, we confirm that after both polyclonal and HIV-1-specific activation, memory CD4 T cells (Mem) from EC display enhanced activity of the autophagy-mediated proteolysis compared to ART. Our results indicate that the enhanced autophagy activity in EC was controlled by the energy-sensing PRKAA1 (protein kinase AMP-activated catalytic subunit alpha 1). We further confirmed the critical role of the autophagy-mediated proteolysis in the strong IL21 production in EC by using BECN1 gene silencing as well as protease, PRKAA1, and lysosomal inhibitors. Finally, we established that high autophagy-mediated proteolysis in EC fuels their cellular rates of mitochondrial respiration due to glutaminolysis. Our data confirm the critical role of autophagy in dictating the metabolic input, which is required not only to ensure protective cytotoxic CD8A T cell responses, but also to provide strong IL21 production among antiviral CD4 T cells.Abbreviations: AKG: alpha-ketoglutarate; ART: patients under antiretroviral therapy; ATG7: autophagy related 7; BaF: bafilomycin A1; BECN1: beclin 1; Chloro.: chloroquine; EC: elite controllers; EIF4EBP1: eukaryotic translation initiation factor 4E binding protein 1; FOXO3: forkhead box O3; GLS: glutaminase; GLUD1: glutamate dehydrogenase 1; HIVneg: HIV-1-uninfected control donors; IFNG/IFN-γ: interferon gamma; IL21: interleukin 21; MTOR: mechanistic target of rapamycin kinase; PBMC: peripheral blood mononuclear cells; PRKAA1: protein kinase AMP-activated catalytic subunit alpha 1; SQSTM1: sequestosome 1; TCA: tricarboxylic acid cycle; ULK1: unc-51 like autophagy activating kinase.
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Affiliation(s)
- Hamza Loucif
- Institut National de la Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec, Canada
| | - Xavier Dagenais-Lussier
- Institut National de la Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec, Canada
| | - Daina Avizonis
- Metabolomics Innovation Resource, Rosalind and Morris Goodman Cancer Center, McGill University, Montreal, QC, Canada
| | - Luc Choinière
- Metabolomics Innovation Resource, Rosalind and Morris Goodman Cancer Center, McGill University, Montreal, QC, Canada
| | - Cherifa Beji
- Institut National de la Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec, Canada
| | - Léna Cassin
- Department of Biomedicine, Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Jean-Pierre Routy
- Chronic Viral Illness Service and Division of Hematology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Jörg H Fritz
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - David Olagnier
- Department of Biomedicine, Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Julien van Grevenynghe
- Institut National de la Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec, Canada
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10
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Kumar A, Mahajan A, Salazar EA, Pruitt K, Guzman CA, Clauss MA, Almodovar S, Dhillon NK. Impact of human immunodeficiency virus on pulmonary vascular disease. Glob Cardiol Sci Pract 2021; 2021:e202112. [PMID: 34285903 PMCID: PMC8272407 DOI: 10.21542/gcsp.2021.12] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/31/2021] [Indexed: 01/08/2023] Open
Abstract
With the advent of anti-retroviral therapy, non-AIDS-related comorbidities have increased in people living with HIV. Among these comorbidities, pulmonary hypertension (PH) is one of the most common causes of morbidity and mortality. Although chronic HIV-1 infection is independently associated with the development of pulmonary arterial hypertension, PH in people living with HIV may also be the outcome of various co-morbidities commonly observed in these individuals including chronic obstructive pulmonary disease, left heart disease and co-infections. In addition, the association of these co-morbidities and other risk factors, such as illicit drug use, can exacerbate the development of pulmonary vascular disease. This review will focus on these complex interactions contributing to PH development and exacerbation in HIV patients. We also examine the interactions of HIV proteins, including Nef, Tat, and gp120 in the pulmonary vasculature and how these proteins alter the endothelial and smooth muscle function by transforming them into susceptible PH phenotype. The review also discusses the available infectious and non-infectious animal models to study HIV-associated PAH, highlighting the advantages and disadvantages of each model, along with their ability to mimic the clinical manifestations of HIV-PAH.
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Affiliation(s)
- Ashok Kumar
- Pulmonary, Critical Care and Sleep Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Aatish Mahajan
- Pulmonary, Critical Care and Sleep Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Ethan A Salazar
- Department of Immunology & Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Kevin Pruitt
- Department of Immunology & Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Christian Arce Guzman
- Pulmonary, Critical Care, Sleep & Occupational Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Matthias A Clauss
- Pulmonary, Critical Care, Sleep & Occupational Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Sharilyn Almodovar
- Department of Immunology & Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Navneet K Dhillon
- Pulmonary, Critical Care and Sleep Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
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11
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Womersley JS, Nothling J, Toikumo S, Malan-Müller S, van den Heuvel LL, McGregor NW, Seedat S, Hemmings SMJ. Childhood trauma, the stress response and metabolic syndrome: A focus on DNA methylation. Eur J Neurosci 2021; 55:2253-2296. [PMID: 34169602 DOI: 10.1111/ejn.15370] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/13/2021] [Accepted: 06/12/2021] [Indexed: 12/12/2022]
Abstract
Childhood trauma (CT) is well established as a potent risk factor for the development of mental disorders. However, the potential of adverse early experiences to exert chronic and profound effects on physical health, including aberrant metabolic phenotypes, has only been more recently explored. Among these consequences is metabolic syndrome (MetS), which is characterised by at least three of five related cardiometabolic traits: hypertension, insulin resistance/hyperglycaemia, raised triglycerides, low high-density lipoprotein and central obesity. The deleterious effects of CT on health outcomes may be partially attributable to dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis, which coordinates the response to stress, and the consequent fostering of a pro-inflammatory environment. Epigenetic tags, such as DNA methylation, which are sensitive to environmental influences provide a means whereby the effects of CT can be biologically embedded and persist into adulthood to affect health and well-being. The methylome regulates the transcription of genes involved in the stress response, metabolism and inflammation. This narrative review examines the evidence for DNA methylation in CT and MetS in order to identify shared neuroendocrine and immune correlates that may mediate the increased risk of MetS following CT exposure. Our review specifically highlights differential methylation of FKBP5, the gene that encodes FK506-binding protein 51 and has pleiotropic effects on stress responding, inflammation and energy metabolism, as a central candidate to understand the molecular aetiology underlying CT-associated MetS risk.
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Affiliation(s)
- Jacqueline S Womersley
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jani Nothling
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Gender and Health Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Sylvanus Toikumo
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Stefanie Malan-Müller
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Leigh L van den Heuvel
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nathaniel W McGregor
- Systems Genetics Working Group, Department of Genetics, Faculty of Agriculture, Stellenbosch University, Stellenbosch, South Africa
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Sîan M J Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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12
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Abhimanyu, Ontiveros CO, Guerra-Resendez RS, Nishiguchi T, Ladki M, Hilton IB, Schlesinger LS, DiNardo AR. Reversing Post-Infectious Epigenetic-Mediated Immune Suppression. Front Immunol 2021; 12:688132. [PMID: 34163486 PMCID: PMC8215363 DOI: 10.3389/fimmu.2021.688132] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022] Open
Abstract
The immune response must balance the pro-inflammatory, cell-mediated cytotoxicity with the anti-inflammatory and wound repair response. Epigenetic mechanisms mediate this balance and limit host immunity from inducing exuberant collateral damage to host tissue after severe and chronic infections. However, following treatment for these infections, including sepsis, pneumonia, hepatitis B, hepatitis C, HIV, tuberculosis (TB) or schistosomiasis, detrimental epigenetic scars persist, and result in long-lasting immune suppression. This is hypothesized to be one of the contributing mechanisms explaining why survivors of infection have increased all-cause mortality and increased rates of unrelated secondary infections. The mechanisms that induce epigenetic-mediated immune suppression have been demonstrated in-vitro and in animal models. Modulation of the AMP-activated protein kinase (AMPK)-mammalian target of rapamycin (mTOR), nuclear factor of activated T cells (NFAT) or nuclear receptor (NR4A) pathways is able to block or reverse the development of detrimental epigenetic scars. Similarly, drugs that directly modify epigenetic enzymes, such as those that inhibit histone deacetylases (HDAC) inhibitors, DNA hypomethylating agents or modifiers of the Nucleosome Remodeling and DNA methylation (NuRD) complex or Polycomb Repressive Complex (PRC) have demonstrated capacity to restore host immunity in the setting of cancer-, LCMV- or murine sepsis-induced epigenetic-mediated immune suppression. A third clinically feasible strategy for reversing detrimental epigenetic scars includes bioengineering approaches to either directly reverse the detrimental epigenetic marks or to modify the epigenetic enzymes or transcription factors that induce detrimental epigenetic scars. Each of these approaches, alone or in combination, have ablated or reversed detrimental epigenetic marks in in-vitro or in animal models; translational studies are now required to evaluate clinical applicability.
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Affiliation(s)
- Abhimanyu
- The Global Tuberculosis Program, William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Immigrant and Global Health, Baylor College of Medicine, Houston, TX, United States
| | - Carlos O Ontiveros
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, United States.,UT Health San Antonio, San Antonio, TX, United States
| | - Rosa S Guerra-Resendez
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States
| | - Tomoki Nishiguchi
- The Global Tuberculosis Program, William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Immigrant and Global Health, Baylor College of Medicine, Houston, TX, United States
| | - Malik Ladki
- The Global Tuberculosis Program, William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Immigrant and Global Health, Baylor College of Medicine, Houston, TX, United States
| | - Isaac B Hilton
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States.,Department of Bioengineering, Rice University, Houston, TX, United States.,Department of BioSciences, Rice University, Houston, TX, United States
| | - Larry S Schlesinger
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Andrew R DiNardo
- The Global Tuberculosis Program, William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Immigrant and Global Health, Baylor College of Medicine, Houston, TX, United States
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13
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Singh R, Ramsuran V, Naranbhai V, Yende-Zuma N, Garrett N, Mlisana K, Dong KL, Walker BD, Abdool Karim SS, Carrington M, Ndung'u T. Epigenetic Regulation of BST-2 Expression Levels and the Effect on HIV-1 Pathogenesis. Front Immunol 2021; 12:669241. [PMID: 34025670 PMCID: PMC8131512 DOI: 10.3389/fimmu.2021.669241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/20/2021] [Indexed: 11/23/2022] Open
Abstract
HIV-1 must overcome host antiviral restriction factors for efficient replication. We hypothesized that elevated levels of bone marrow stromal cell antigen 2 (BST-2), a potent host restriction factor that interferes with HIV-1 particle release in some human cells and is antagonized by the viral protein Vpu, may associate with viral control. Using cryopreserved samples, from HIV-1 seronegative and seropositive Black women, we measured in vitro expression levels of BST-2 mRNA using a real-time PCR assay and protein levels were validated by Western blotting. The expression level of BST-2 showed an association with viral control within two independent cohorts of Black HIV infected females (r=-0.53, p=0.015, [n =21]; and r=-0.62, p=0.0006, [n=28]). DNA methylation was identified as a mechanism regulating BST-2 levels, where increased BST-2 methylation results in lower expression levels and associates with worse HIV disease outcome. We further demonstrate the ability to regulate BST-2 levels using a DNA hypomethylation drug. Our results suggest BST-2 as a factor for potential therapeutic intervention against HIV and other diseases known to involve BST-2.
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Affiliation(s)
- Ravesh Singh
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, MD, United States.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Vivek Naranbhai
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, MD, United States.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nonhlanhla Yende-Zuma
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Koleka Mlisana
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Krista L Dong
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Bruce D Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Mary Carrington
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, MD, United States
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Max Planck Institute for Infection Biology, Chariteplatz, Berlin, Germany.,Division of Infection and Immunity, University College London, London, United Kingdom
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14
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Rajeev R, Dwivedi AP, Sinha A, Agarwaal V, Dev RR, Kar A, Khosla S. Epigenetic interaction of microbes with their mammalian hosts. J Biosci 2021; 46:94. [PMID: 34728591 PMCID: PMC8550911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/20/2021] [Indexed: 02/11/2023]
Abstract
The interaction of microbiota with its host has the ability to alter the cellular functions of both, through several mechanisms. Recent work, from many laboratories including our own, has shown that epigenetic mechanisms play an important role in the alteration of these cellular functions. Epigenetics broadly refers to change in the phenotype without a corresponding change in the DNA sequence. This change is usually brought by epigenetic modifications of the DNA itself, the histone proteins associated with the DNA in the chromatin, non-coding RNA or the modifications of the transcribed RNA. These modifications, also known as epigenetic code, do not change the DNA sequence but alter the expression level of specific genes. Microorganisms seem to have learned how to modify the host epigenetic code and modulate the host transcriptome in their favour. In this review, we explore the literature that describes the epigenetic interaction of bacteria, fungi and viruses, with their mammalian hosts.
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Affiliation(s)
- Ramisetti Rajeev
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Ambey Prasad Dwivedi
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Anunay Sinha
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
- Graduate Studies, Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Viplove Agarwaal
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | | | - Anjana Kar
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Sanjeev Khosla
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
- Institute of Microbial Technology (IMTech), Chandigarh, India
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15
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Jochems SP, Jacquelin B, Tchitchek N, Busato F, Pichon F, Huot N, Liu Y, Ploquin MJ, Roché E, Cheynier R, Dereuddre-Bosquet N, Stahl-Henning C, Le Grand R, Tost J, Müller-Trutwin M. DNA methylation changes in metabolic and immune-regulatory pathways in blood and lymph node CD4 + T cells in response to SIV infections. Clin Epigenetics 2020; 12:188. [PMID: 33298174 PMCID: PMC7724887 DOI: 10.1186/s13148-020-00971-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
The molecular mechanisms underlying HIV-induced inflammation, which persists even during effective long-term treatment, remain incompletely defined. Here, we studied pathogenic and nonpathogenic simian immunodeficiency virus (SIV) infections in macaques and African green monkeys, respectively. We longitudinally analyzed genome-wide DNA methylation changes in CD4 + T cells from lymph node and blood, using arrays. DNA methylation changes after SIV infection were more pronounced in lymph nodes than blood and already detected in primary infection. Differentially methylated genes in pathogenic SIV infection were enriched for Th1-signaling (e.g., RUNX3, STAT4, NFKB1) and metabolic pathways (e.g., PRKCZ). In contrast, nonpathogenic SIVagm infection induced DNA methylation in genes coding for regulatory proteins such as LAG-3, arginase-2, interleukin-21 and interleukin-31. Between 15 and 18% of genes with DNA methylation changes were differentially expressed in CD4 + T cells in vivo. Selected identified sites were validated using bisulfite pyrosequencing in an independent cohort of uninfected, viremic and SIV controller macaques. Altered DNA methylation was confirmed in blood and lymph node CD4 + T cells in viremic macaques but was notably absent from SIV controller macaques. Our study identified key genes differentially methylated already in primary infection and in tissues that could contribute to the persisting metabolic disorders and inflammation in HIV-infected individuals despite effective treatment.
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Affiliation(s)
- Simon P Jochems
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
- Sorbonne Paris Cité, Université Paris Diderot, Paris, France
- Leiden University Medical Center, Leiden, The Netherlands
| | - Beatrice Jacquelin
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
| | - Nicolas Tchitchek
- IDMIT Department/IBFJ, Immunology of Viral Infections and Autoimmune Diseases (IMVA), INSERM U1184, CEA, Université Paris Sud, Fontenay-aux-Roses, France
| | - Florence Busato
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Fabien Pichon
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Nicolas Huot
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
| | - Yi Liu
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Mickaël J Ploquin
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
| | - Elodie Roché
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Rémi Cheynier
- UMR8104, CNRS, U1016, INSERM, Institut Cochin, Université de Paris, 75014, Paris, France
| | - Nathalie Dereuddre-Bosquet
- IDMIT Department/IBFJ, Immunology of Viral Infections and Autoimmune Diseases (IMVA), INSERM U1184, CEA, Université Paris Sud, Fontenay-aux-Roses, France
| | | | - Roger Le Grand
- IDMIT Department/IBFJ, Immunology of Viral Infections and Autoimmune Diseases (IMVA), INSERM U1184, CEA, Université Paris Sud, Fontenay-aux-Roses, France
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Michaela Müller-Trutwin
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France.
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16
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Zebley CC, Gottschalk S, Youngblood B. Rewriting History: Epigenetic Reprogramming of CD8 + T Cell Differentiation to Enhance Immunotherapy. Trends Immunol 2020; 41:665-675. [PMID: 32624330 PMCID: PMC7395868 DOI: 10.1016/j.it.2020.06.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 12/31/2022]
Abstract
The full potential of T cell-based immunotherapies remains limited by a variety of T cell extrinsic and intrinsic immunosuppressive mechanisms that can become imprinted to stably reduce the antitumor ability of T cells. Here, we discuss recent insights into memory CD8+ T cell differentiation and exhaustion and the association of these differentiation states with clinical outcomes during immune checkpoint blockade and chimeric antigen receptor (CAR) T cell therapeutic modalities. We consider the barriers limiting immunotherapy with a focus on epigenetic regulation impeding efficacy of adoptively transferred T cells and other approaches that augment T cell responses such as immune checkpoint blockade. Furthermore, we outline conceptual and technical breakthroughs that can be applied to existing therapeutic approaches and to the development of novel cutting-edge strategies.
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Affiliation(s)
- Caitlin C Zebley
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ben Youngblood
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN 38105, USA.
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17
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DiNardo AR, Rajapakshe K, Nishiguchi T, Grimm SL, Mtetwa G, Dlamini Q, Kahari J, Mahapatra S, Kay A, Maphalala G, Mace EM, Makedonas G, Cirillo JD, Netea MG, van Crevel R, Coarfa C, Mandalakas AM. DNA hypermethylation during tuberculosis dampens host immune responsiveness. J Clin Invest 2020; 130:3113-3123. [PMID: 32125282 PMCID: PMC7260034 DOI: 10.1172/jci134622] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/27/2020] [Indexed: 12/21/2022] Open
Abstract
Mycobacterium tuberculosis (M. tuberculosis) has coevolved with humans for millennia and developed multiple mechanisms to evade host immunity. Restoring host immunity in order to improve outcomes and potentially shorten existing therapy will require identification of the full complement by which host immunity is inhibited. Perturbation of host DNA methylation is a mechanism induced by chronic infections such as HIV, HPV, lymphocytic choriomeningitis virus (LCMV), and schistosomiasis to evade host immunity. Here, we evaluated the DNA methylation status of patients with tuberculosis (TB) and their asymptomatic household contacts and found that the patients with TB have DNA hypermethylation of the IL-2/STAT5, TNF/NF-κB, and IFN-γ signaling pathways. We performed methylation-sensitive restriction enzyme-quantitative PCR (MSRE-qPCR) and observed that multiple genes of the IL-12/IFN-γ signaling pathway (IL12B, IL12RB2, TYK2, IFNGR1, JAK1, and JAK2) were hypermethylated in patients with TB. The DNA hypermethylation of these pathways was associated with decreased immune responsiveness with decreased mitogen-induced upregulation of IFN-γ, TNF, IL-6, CXCL9, CXCL10, and IL-1β production. The DNA hypermethylation of the IL-12/IFN-γ pathway was associated with decreased IFN-γ-induced gene expression and decreased IL-12-inducible upregulation of IFN-γ. This study demonstrates that immune cells from patients with TB are characterized by DNA hypermethylation of genes critical to mycobacterial immunity resulting in decreased mycobacteria-specific and nonspecific immune responsiveness.
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Affiliation(s)
- Andrew R. DiNardo
- Global Tuberculosis Program, Texas Children’s Hospital, Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Kimal Rajapakshe
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Tomoki Nishiguchi
- Global Tuberculosis Program, Texas Children’s Hospital, Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Sandra L. Grimm
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Godwin Mtetwa
- Baylor-Swaziland Children’s Foundation, Mbabane, Swaziland
| | - Qiniso Dlamini
- Baylor-Swaziland Children’s Foundation, Mbabane, Swaziland
| | | | - Sanjana Mahapatra
- Global Tuberculosis Program, Texas Children’s Hospital, Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Alexander Kay
- Baylor-Swaziland Children’s Foundation, Mbabane, Swaziland
| | | | - Emily M. Mace
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | | | - Jeffrey D. Cirillo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, Texas, USA
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Reinout van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Cristian Coarfa
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Anna M. Mandalakas
- Global Tuberculosis Program, Texas Children’s Hospital, Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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18
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Huang H, Wu P, Zhang S, Shang Q, Yin H, Hou Q, Zhong J, Guo X. DNA methylomes and transcriptomes analysis reveal implication of host DNA methylation machinery in BmNPV proliferation in Bombyx mori. BMC Genomics 2019; 20:736. [PMID: 31615392 PMCID: PMC6792228 DOI: 10.1186/s12864-019-6146-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 09/29/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bombyx mori nucleopolyhedrosis virus (BmNPV) is a major pathogen that threatens the sustainability of the sericultural industry. DNA methylation is a widespread gene regulation mode in epigenetics, which plays an important role in host immune response. Until now, little has been known about epigenetic regulation on virus diseases in insects. This study aims to explore the role of DNA methylation in BmNPV proliferation. RESULTS Inhibiting DNA methyltransferase (DNMT) activity of silkworm can suppress BmNPV replication. The integrated analysis of transcriptomes and DNA methylomes in silkworm midguts infected with or without BmNPV showed that both the expression pattern of transcriptome and DNA methylation pattern are changed significantly upon BmNPV infection. A total of 241 differentially methylated regions (DMRs) were observed in BmNPV infected midguts, among which, 126 DMRs were hyper-methylated and 115 DMRs were hypo-methylated. Significant differences in both mRNA transcript level and DNA methylated levels were found in 26 genes. BS-PCR validated the hypermethylation of BGIBMGA014008, a structural maintenance of chromosomes protein gene in the BmNPV-infected midgut. In addition, DNMT inhibition reduced the expression of inhibitor of apoptosis family genes, iap1 from BmNPV, Bmiap2, BmSurvivin1 and BmSurvivin2. CONCLUSION Our results indicate that DNA methylation plays positive roles in BmNPV proliferation and loss of DNMT activity could induce the apoptosis of infected cells to suppress BmNPV proliferation. Our results may provide a new idea and research direction for the molecular mechanism on insect-virus interaction.
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Affiliation(s)
- Haoling Huang
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China
| | - Ping Wu
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China. .,The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018, China. .,Quality inspection center for sericultural products, Ministry of Agriculture and Rural Affairs, Zhenjiang, 212018, China.
| | - Shaolun Zhang
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China
| | - Qi Shang
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China
| | - Haotong Yin
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China
| | - Qirui Hou
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China.,The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018, China.,Quality inspection center for sericultural products, Ministry of Agriculture and Rural Affairs, Zhenjiang, 212018, China
| | - Jinbo Zhong
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China
| | - Xijie Guo
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China. .,The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018, China.
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19
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Li CW, Chen BS. Investigating HIV-Human Interaction Networks to Unravel Pathogenic Mechanism for Drug Discovery: A Systems Biology Approach. Curr HIV Res 2019; 16:77-95. [PMID: 29468972 DOI: 10.2174/1570162x16666180219155324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 01/18/2018] [Accepted: 02/14/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND Two big issues in the study of pathogens are determining how pathogens infect hosts and how the host defends itself against infection. Therefore, investigating host-pathogen interactions is important for understanding pathogenicity and host defensive mechanisms and treating infections. METHODS In this study, we used omics data, including time-course data from high-throughput sequencing, real-time polymerase chain reaction, and human microRNA (miRNA) and protein-protein interaction to construct an interspecies protein-protein and miRNA interaction (PPMI) network of human CD4+ T cells during HIV-1 infection through system modeling and identification. RESULTS By applying a functional annotation tool to the identified PPMI network at each stage of HIV infection, we found that repressions of three miRNAs, miR-140-5p, miR-320a, and miR-941, are involved in the development of autoimmune disorders, tumor proliferation, and the pathogenesis of T cells at the reverse transcription stage. Repressions of miR-331-3p and miR-320a are involved in HIV-1 replication, replicative spread, anti-apoptosis, cell proliferation, and dysregulation of cell cycle control at the integration/replication stage. Repression of miR-341-5p is involved in carcinogenesis at the late stage of HIV-1 infection. CONCLUSION By investigating the common core proteins and changes in specific proteins in the PPMI network between the stages of HIV-1 infection, we obtained pathogenic insights into the functional core modules and identified potential drug combinations for treating patients with HIV-1 infection, including thalidomide, oxaprozin, and metformin, at the reverse transcription stage; quercetin, nifedipine, and fenbendazole, at the integration/replication stage; and staurosporine, quercetin, prednisolone, and flufenamic acid, at the late stage.
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Affiliation(s)
- Cheng-Wei Li
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Bor-Sen Chen
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
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20
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Nag M, Wang Y, De Paris K, E Fogle J. Histone Modulation Blocks Treg-Induced Foxp3 Binding to the IL-2 Promoter of Virus-Specific CD8⁺ T Cells from Feline Immunodeficiency Virus-Infected Cats. Viruses 2018; 10:v10060287. [PMID: 29861472 PMCID: PMC6024775 DOI: 10.3390/v10060287] [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: 03/27/2018] [Revised: 05/25/2018] [Accepted: 05/25/2018] [Indexed: 12/05/2022] Open
Abstract
CD8+ T cells are critical for controlling HIV infection. During the chronic phase of lentiviral infection, CD8+ T cells lose their proliferative capacity and exhibit impaired antiviral function. This loss of CD8+ T cell function is due, in part, to CD4+CD25+ T regulatory (Treg) cell-mediated suppression. Our research group has demonstrated that lentivirus-activated CD4+CD25+ Treg cells induce the repressive transcription factor forkhead box P3 (Foxp3) in autologous CD8+ T cells following co-culture. We have recently reported that Treg-induced Foxp3 binds the interleukin-2 (IL-2), interferon-γ (IFN- γ), and tumor necrosis factor-α (TNF-α) promoters in virus-specific CD8+ T cells. These data suggest an important role of Foxp3-mediated CD8+ T cell dysfunction in lentiviral infection. To elucidate the mechanism of this suppression, we previously reported that decreased methylation facilitates Foxp3 binding in mitogen-activated CD8+ T cells from feline immunodeficiency virus (FIV)-infected cats. We demonstrated the reduced binding of Foxp3 to the IL-2 promoter by increasing methylation of CD8+ T cells. In the studies presented here, we ask if another form of epigenetic modulation might alleviate Foxp3-mediated suppression in CD8+ T cells. We hypothesized that decreasing histone acetylation in virus-specific CD8+ T cells would decrease Treg-induced Foxp3 binding to the IL-2 promoter. Indeed, using anacardic acid (AA), a known histone acetyl transferase (HAT) inhibitor, we demonstrate a reduction in Foxp3 binding to the IL-2 promoter in virus-specific CD8+ T cells co-cultured with autologous Treg cells. These data identify a novel mechanism of Foxp3-mediated CD8+ T cell dysfunction during lentiviral infection.
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Affiliation(s)
- Mukta Nag
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Yan Wang
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Kristina De Paris
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Jonathan E Fogle
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA.
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21
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DiNardo AR, Nishiguchi T, Mace EM, Rajapakshe K, Mtetwa G, Kay A, Maphalala G, Secor WE, Mejia R, Orange JS, Coarfa C, Bhalla KN, Graviss EA, Mandalakas AM, Makedonas G. Schistosomiasis Induces Persistent DNA Methylation and Tuberculosis-Specific Immune Changes. THE JOURNAL OF IMMUNOLOGY 2018; 201:124-133. [PMID: 29752313 DOI: 10.4049/jimmunol.1800101] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/09/2018] [Indexed: 12/29/2022]
Abstract
Epigenetic mechanisms, such as DNA methylation, determine immune cell phenotype. To understand the epigenetic alterations induced by helminth coinfections, we evaluated the longitudinal effect of ascariasis and schistosomiasis infection on CD4+ T cell DNA methylation and the downstream tuberculosis (TB)-specific and bacillus Calmette-Guérin-induced immune phenotype. All experiments were performed on human primary immune cells from a longitudinal cohort of recently TB-exposed children. Compared with age-matched uninfected controls, children with active Schistosoma haematobium and Ascaris lumbricoides infection had 751 differentially DNA-methylated genes, with 72% hypermethylated. Gene ontology pathway analysis identified inhibition of IFN-γ signaling, cellular proliferation, and the Th1 pathway. Targeted real-time quantitative PCR after methyl-specific endonuclease digestion confirmed DNA hypermethylation of the transcription factors BATF3, ID2, STAT5A, IRF5, PPARg, RUNX2, IRF4, and NFATC1 and cytokines or cytokine receptors IFNGR1, TNFS11, RELT (TNF receptor), IL12RB2, and IL12B (p < 0.001; Sidak-Bonferroni). Functional blockage of the IFN-γ signaling pathway was confirmed, with helminth-infected individuals having decreased upregulation of IFN-γ-inducible genes (Mann-Whitney p < 0.05). Hypomethylation of the IL-4 pathway and DNA hypermethylation of the Th1 pathway was confirmed by Ag-specific multidimensional flow cytometry demonstrating decreased TB-specific IFN-γ and TNF and increased IL-4 production by CD4+ T cells (Wilcoxon signed-rank p < 0.05). In S. haematobium-infected individuals, these DNA methylation and immune phenotypic changes persisted at least 6 mo after successful deworming. This work demonstrates that helminth infection induces DNA methylation and immune perturbations that inhibit TB-specific immune control and that the duration of these changes are helminth specific.
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Affiliation(s)
- Andrew R DiNardo
- The Global Tuberculosis Program, Immigrant and Global Health, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030;
| | - Tomoki Nishiguchi
- The Global Tuberculosis Program, Immigrant and Global Health, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030
| | - Emily M Mace
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030.,Texas Children's Hospital Center for Human Immunobiology, Department of Pediatrics, Texas Children's Hospital Center for Human Immunobiology, Baylor College of Medicine, Houston, TX 77030
| | - Kimal Rajapakshe
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Godwin Mtetwa
- Baylor-Swaziland Children's Foundation, Mbabane H100, Swaziland
| | - Alexander Kay
- Baylor-Swaziland Children's Foundation, Mbabane H100, Swaziland
| | | | - W Evan Secor
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA 30333
| | - Rojelio Mejia
- Department of Pediatrics, National School of Tropical Medicine, Texas Children's Hospital Center for Human Immunobiology, Houston, TX 77030
| | - Jordan S Orange
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030.,Texas Children's Hospital Center for Human Immunobiology, Department of Pediatrics, Texas Children's Hospital Center for Human Immunobiology, Baylor College of Medicine, Houston, TX 77030
| | - Cristian Coarfa
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Kapil N Bhalla
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX 77030; and
| | - Edward A Graviss
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, TX 77030
| | - Anna M Mandalakas
- The Global Tuberculosis Program, Immigrant and Global Health, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030
| | - George Makedonas
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030.,Texas Children's Hospital Center for Human Immunobiology, Department of Pediatrics, Texas Children's Hospital Center for Human Immunobiology, Baylor College of Medicine, Houston, TX 77030
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22
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Nag M, De Paris K, E Fogle J. Epigenetic Modulation of CD8⁺ T Cell Function in Lentivirus Infections: A Review. Viruses 2018; 10:v10050227. [PMID: 29710792 PMCID: PMC5977220 DOI: 10.3390/v10050227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 01/16/2023] Open
Abstract
CD8+ T cells are critical for controlling viremia during human immunodeficiency virus (HIV) infection. These cells produce cytolytic factors and antiviral cytokines that eliminate virally- infected cells. During the chronic phase of HIV infection, CD8+ T cells progressively lose their proliferative capacity and antiviral functions. These dysfunctional cells are unable to clear the productively infected and reactivated cells, representing a roadblock in HIV cure. Therefore, mechanisms to understand CD8+ T cell dysfunction and strategies to boost CD8+ T cell function need to be investigated. Using the feline immunodeficiency virus (FIV) model for lentiviral persistence, we have demonstrated that CD8+ T cells exhibit epigenetic changes such as DNA demethylation during the course of infection as compared to uninfected cats. We have also demonstrated that lentivirus-activated CD4+CD25+ T regulatory cells induce forkhead box P3 (Foxp3) expression in virus-specific CD8+ T cell targets, which binds the interleukin (IL)-2, tumor necrosis factor (TNF)-α, and interferon (IFN)-γ promoters in these CD8+ T cells. Finally, we have reported that epigenetic modulation reduces Foxp3 binding to these promoter regions. This review compares and contrasts our current understanding of CD8+ T cell epigenetics and mechanisms of lymphocyte suppression during the course of lentiviral infection for two animal models, FIV and simian immunodeficiency virus (SIV).
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Affiliation(s)
- Mukta Nag
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA.
| | - Kristina De Paris
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Jonathan E Fogle
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA.
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23
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DNA Tumor Virus Regulation of Host DNA Methylation and Its Implications for Immune Evasion and Oncogenesis. Viruses 2018; 10:v10020082. [PMID: 29438328 PMCID: PMC5850389 DOI: 10.3390/v10020082] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/07/2018] [Accepted: 02/07/2018] [Indexed: 12/11/2022] Open
Abstract
Viruses have evolved various mechanisms to evade host immunity and ensure efficient viral replication and persistence. Several DNA tumor viruses modulate host DNA methyltransferases for epigenetic dysregulation of immune-related gene expression in host cells. The host immune responses suppressed by virus-induced aberrant DNA methylation are also frequently involved in antitumor immune responses. Here, we describe viral mechanisms and virus–host interactions by which DNA tumor viruses regulate host DNA methylation to evade antiviral immunity, which may contribute to the generation of an immunosuppressive microenvironment during cancer development. Recent trials of immunotherapies have shown promising results to treat multiple cancers; however, a significant number of non-responders necessitate identifying additional targets for cancer immunotherapies. Thus, understanding immune evasion mechanisms of cancer-causing viruses may provide great insights for reversing immune suppression to prevent and treat associated cancers.
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Expression profiling of chromatin-modifying enzymes and global DNA methylation in CD4+ T cells from patients with chronic HIV infection at different HIV control and progression states. Clin Epigenetics 2018; 10:20. [PMID: 29449904 PMCID: PMC5812196 DOI: 10.1186/s13148-018-0448-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/24/2018] [Indexed: 12/19/2022] Open
Abstract
Background Integration of human immunodeficiency virus type 1 (HIV-1) into the host genome causes global disruption of the chromatin environment. The abundance level of various chromatin-modifying enzymes produces these alterations and affects both the provirus and cellular gene expression. Here, we investigated potential changes in enzyme expression and global DNA methylation in chronically infected individuals with HIV-1 and compared these changes with non-HIV infected individuals. We also evaluated the effect of viral replication and degree of disease progression over these changes. Results Individuals with HIV-1 had a significant surge in the expression of DNA and histone methyltransferases (DNMT3A and DNMT3B, SETDB1, SUV39H1) compared with non-infected individuals, with the exception of PRMT6, which was downregulated. Some histone deacetylases (HDAC2 and HDAC3) were also upregulated in patients with HIV. Among individuals with HIV-1 with various degrees of progression and HIV control, the group of treated patients with undetectable viremia showed greater differences with the other two groups (untreated HIV-1 controllers and non-controllers). These latter two groups exhibited a similar behavior between them. Of interest, the overexpression of genes that associate with viral protein Tat (such as SETDB1 along with DNMT3A and HDAC1, and SIRT-1) was more prevalent in treated patients. We also observed elevated levels of global DNA methylation in individuals with HIV-1 in an inverse correlation with the CD4/CD8 ratio. Conclusions The current study shows an increase in chromatin-modifying enzymes and remodelers and in global DNA methylation in patients with chronic HIV-1 infection, modulated by various levels of viral control and progression.
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Panagoulias I, Karagiannis F, Aggeletopoulou I, Georgakopoulos T, Argyropoulos CP, Akinosoglou K, Gogos C, Skoutelis A, Mouzaki A. Ets-2 Acts As a Transcriptional Repressor of the Human Immunodeficiency Virus Type 1 through Binding to a Repressor-Activator Target Sequence of 5'-LTR. Front Immunol 2018; 8:1924. [PMID: 29354130 PMCID: PMC5758550 DOI: 10.3389/fimmu.2017.01924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/15/2017] [Indexed: 01/02/2023] Open
Abstract
HIV-1 is transcriptionally active in activated T helper (Th)-cells and inactive in naive or resting memory Th-cells. Ets-2 is a preinduction transcriptional repressor of the IL-2 gene in naive Th-cells and a candidate transcriptional repressor of HIV-1 in the same cells, because the −279 to −250 upstream region of HIV-1-LTR [repressor–activator target sequence (RATS)], that participates in HIV-1-LTR transcriptional silencing, encompasses the AAGGAG Ets-2 binding site. In this proof of concept study, we investigated whether Ets-2 represses the expression of HIV-1. To assess whether Ets-2 can repress HIV-1 transcriptional activation acting through RATS, we transfected Jurkat cells with an Ets-2 overexpression plasmid (pCDNA3-ets-2) or Ets-2 silencing plasmids (ets-2-shRNA) and, as target genes, plasmids carrying the whole HIV-1-LTR sequence (HIV-1-LTR-CAT) or two copies of the RATS sequence (2× RATS-CAT) or a point mutation in the Ets-2 binding site (2× mutantRATS-CAT) or CMV-CAT (control). Ets-2 overexpression resulted in a significant reduction of HIV-1-LTR-CAT and 2× RATS-CAT activities in stimulated cells, but not of the 2× mutantRATS-CAT or CMV-CAT. Ets-2 silencing led to increased activities of HIV-1-LTR-CAT and 2× RATS-CAT in unstimulated cells, but had no effect on the activities of 2× mutantRATS-CAT and CMV-CAT. To assess Ets-2 binding to HIV-1-LTR–RATS in naive Th-cells, we isolated naive Th-cell nuclear proteins and passed them through an Ets-2 antibody column; electrophoretic mobility shift assays were performed using an RATS probe mixed with consecutive protein eluates. Ets-2 bound to the HIV-1-LTR–RATS in a dose-dependent manner. To assess Ets-2 binding to RATS in vivo, Jurkat cells were transfected with 2× RATS-CAT and stained for the Ets-2 protein and the RATS sequence by combining immunofluorescence and fluorescence in situ hybridization techniques. In unstimulated cells, Ets-2 bound to RATS, whereas no binding was observed in stimulated cells. To test for RATS specificity, the same experiments were performed with 2× mutantRATS-CAT, and no binding of Ets-2 was observed. The results were corroborated by chromatin immunoprecipitation assays performed with the same cells. Our results show that Ets-2 is a transcriptional repressor of HIV-1. Repression of HIV-LTR-RATS mediated by Ets-2 may account for the low-level transcription and replication of HIV-1 in naive Th-cells, and contribute to the viral latency and maintenance of viral reservoirs in patients, despite long-term therapy.
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Affiliation(s)
- Ioannis Panagoulias
- Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Fotios Karagiannis
- Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Ioanna Aggeletopoulou
- Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Tassos Georgakopoulos
- Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Christos P Argyropoulos
- Division of Nephrology, Department of Internal Medicine, Medical School, University of New Mexico, Albuquerque, NM, United States
| | - Karolina Akinosoglou
- Infectious Diseases Unit, Department of Internal Medicine, University Hospital of Patras, Patras, Greece
| | - Charalambos Gogos
- Infectious Diseases Unit, Department of Internal Medicine, University Hospital of Patras, Patras, Greece
| | - Athanasios Skoutelis
- Department of Internal Medicine and Infectious Diseases Unit, Evangelismos General Hospital, Athens, Greece
| | - Athanasia Mouzaki
- Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
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26
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Peters FS, Peeters AMA, Hofland LJ, Betjes MGH, Boer K, Baan CC. Interferon-Gamma DNA Methylation Is Affected by Mycophenolic Acid but Not by Tacrolimus after T-Cell Activation. Front Immunol 2017; 8:822. [PMID: 28747916 PMCID: PMC5506181 DOI: 10.3389/fimmu.2017.00822] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/29/2017] [Indexed: 12/20/2022] Open
Abstract
Immunosuppressive drug therapy is required to treat patients with autoimmune disease and patients who have undergone organ transplantation. The main targets of the immunosuppressive drugs tacrolimus and mycophenolic acid (MPA; the active metabolite of mycophenolate mofetil) are T cells. It is currently unknown whether these immunosuppressive drugs have an effect on DNA methylation—an epigenetic regulator of cellular function. Here, we determined the effect of tacrolimus and MPA on DNA methylation of the gene promoter region of interferon gamma (IFNγ), a pro-inflammatory cytokine. Total T cells, naive T cells (CCR7+CD45RO−), and memory T cells (CD45RO+ and CCR7−CD45RO−) were isolated from CMV seropositive healthy controls and stimulated with α-CD3/CD28 in the presence or absence of tacrolimus or MPA. DNA methylation of the IFNγ promoter region was quantified by pyrosequencing at 4 h, days 1, 3, and 4 after stimulation. In parallel, T-cell differentiation, and IFNγ protein production were analyzed by flow cytometry at days 1 and 3 after stimulation. Our results show that MPA induced changes in IFNγ DNA methylation of naive T cells; MPA counteracted the decrease in methylation after stimulation. Tacrolimus did not affect IFNγ DNA methylation of naive T cells. In the memory T cells, both immunosuppressive drugs did not affect IFNγ DNA methylation. Differentiation of naive T cells into a central-memory-like phenotype (CD45RO+) was inhibited by both immunosuppressive drugs, while differentiation of memory T cells remained unaffected by both MPA and tacrolimus. IFNγ protein production was suppressed by tacrolimus. Our results demonstrate that MPA influenced IFNγ DNA methylation of naive T cells after stimulation of T cells, while tacrolimus had no effect. Both tacrolimus and MPA did not affect IFNγ DNA methylation of memory T cells.
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Affiliation(s)
- Fleur S Peters
- Nephrology and Transplantation, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Erasmus MC, Rotterdam, Netherlands
| | - Annemiek M A Peeters
- Nephrology and Transplantation, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Erasmus MC, Rotterdam, Netherlands
| | - Leo J Hofland
- Endocrinology, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Erasmus MC, Rotterdam, Netherlands
| | - Michiel G H Betjes
- Nephrology and Transplantation, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Erasmus MC, Rotterdam, Netherlands
| | - Karin Boer
- Nephrology and Transplantation, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Erasmus MC, Rotterdam, Netherlands
| | - Carla C Baan
- Nephrology and Transplantation, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Erasmus MC, Rotterdam, Netherlands
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Identification of HIV infection-related DNA methylation sites and advanced epigenetic aging in HIV-positive, treatment-naive U.S. veterans. AIDS 2017; 31:571-575. [PMID: 27922854 DOI: 10.1097/qad.0000000000001360] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
OBJECTIVE HIV-positive individuals are at higher risk than healthy persons for aging-related diseases, including myocardial infarction and non-AIDS defining cancers. Recent evidence suggests that HIV infection may modulate changes in the host cell epigenome, and these changes represent a potential mechanism through which HIV infection accelerates aging. We assessed the difference in DNA methylation (DNAm) age, an aging marker involving multiple age-related cytosine-guanine dinucleotide (CpG) sites, among antiretroviral treatment (ART)-naive HIV-positive and HIV-negative individuals in a cohort of veterans from the Veterans Aging Cohort Study. DESIGN Peripheral blood samples were collected from 19 ART-naive, HIV-positive, and 19 HIV-negative male participants, matched by age and race. Blood samples were collected from HIV-positive participants 7-11 years after ART initiation. METHODS We compared DNAm age between HIV-positive and HIV-negative groups at baseline and between HIV-positive patients at baseline and follow-up. We also performed an epigenome-wide analysis to identify CpG methylation sites associated with HIV infection. RESULTS DNAm age in HIV-positive individuals is, on average, 11.2 years higher than HIV study participants at baseline, and two of 10 HIV-positive individuals showed an increase in DNAm age after ART initiation. Epigenome-wide association studies showed an association of HIV infection with one site, in gene VPS37B, which approached statistical significance in our cohort (P = 3.30 × 10, Bonferroni-corrected threshold = 1.22 × 10) and was replicated in a second, larger cohort. CONCLUSION ART treatment-naive HIV-positive individuals have significantly older DNAm age compared to HIV-negative individuals in the Veterans Aging Cohort Study cohort. Longitudinal changes in DNAm age are highly variable across individuals after initiation of antiretroviral therapy.
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Zhang X, Justice AC, Hu Y, Wang Z, Zhao H, Wang G, Johnson EO, Emu B, Sutton RE, Krystal JH, Xu K. Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals. Epigenetics 2016; 11:750-760. [PMID: 27672717 PMCID: PMC5094631 DOI: 10.1080/15592294.2016.1221569] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Epigenetic control of human immunodeficiency virus-1 (HIV-1) genes is critical for viral integration and latency. However, epigenetic changes in the HIV-1-infected host genome have not been well characterized. Here, we report the first large-scale epigenome-wide association study of DNA methylation for HIV-1 infection. We recruited HIV-infected (n = 261) and uninfected (n = 117) patients from the Veteran Aging Cohort Study (VACS) and all samples were profiled for 485,521 CpG sites in DNA extracted from the blood. After adjusting for cell type and clinical confounders, we identified 20 epigenome-wide significant CpGs for HIV-1 infection. Importantly, 2 CpGs in the promoter of the NLR family, CARD domain containing gene 5 (NLRC5), a key regulator of major histocompatibility complex class I gene expression, showed significantly lower methylation in HIV-infected subjects than in uninfected subjects (cg07839457: t = −6.03, Pnominal = 4.96 × 10−9; cg16411857: t = −7.63, Pnominal = 3.07 × 10−13). Hypomethylation of these 2 CpGs was replicated in an independent sample (GSE67705: cg07839457: t = −4.44, Pnominal = 1.61 × 10−5; cg16411857: t = −5.90; P = 1.99 × 10−8). Methylation of these 2 CpGs in NLRC5 was negatively correlated with viral load in the 2 HIV-infected samples (cg07839457: P = 1.8 × 10−4; cg16411857: P = 0.03 in the VACS; and cg07839457: P = 0.04; cg164111857: P = 0.01 in GSE53840). Our findings demonstrate that differential DNA methylation is associated with HIV infection and suggest the involvement of a novel host gene, NLRC5, in HIV pathogenesis.
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Affiliation(s)
- Xinyu Zhang
- a Department of Psychiatry , Yale School of Medicine , New Haven , CT , USA.,b Connecticut Veteran Health System , West Haven , CT , USA
| | - Amy C Justice
- c Yale University School of Medicine, New Haven Veterans Affairs Connecticut Healthcare System , West Haven , CT , USA
| | - Ying Hu
- d Center for Biomedical Informatics & Information Technology, National Cancer Institute , Bethesda , MD , USA
| | - Zuoheng Wang
- e Department of Internal Medicine , Division of Infectious Disease, Yale University School of Medicine , New Haven , CT , USA
| | - Hongyu Zhao
- f Department of Biostatistics , Yale School of Public Health , New Haven , CT , USA
| | - Guilin Wang
- g Yale Center of Genomic Analysis, West Campus , Orange , CT , USA
| | - Eric O Johnson
- h Fellow Program and Behavioral Health and Criminal Justice Division, RTI International , Research Triangle Park, NC , USA
| | - Brinda Emu
- e Department of Internal Medicine , Division of Infectious Disease, Yale University School of Medicine , New Haven , CT , USA
| | - Richard E Sutton
- e Department of Internal Medicine , Division of Infectious Disease, Yale University School of Medicine , New Haven , CT , USA
| | - John H Krystal
- a Department of Psychiatry , Yale School of Medicine , New Haven , CT , USA.,b Connecticut Veteran Health System , West Haven , CT , USA
| | - Ke Xu
- a Department of Psychiatry , Yale School of Medicine , New Haven , CT , USA.,b Connecticut Veteran Health System , West Haven , CT , USA
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29
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Clinical potential of DNA methylation in organ transplantation. J Heart Lung Transplant 2016; 35:843-50. [DOI: 10.1016/j.healun.2016.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/18/2016] [Accepted: 02/26/2016] [Indexed: 01/17/2023] Open
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López-Abente J, Correa-Rocha R, Pion M. Functional Mechanisms of Treg in the Context of HIV Infection and the Janus Face of Immune Suppression. Front Immunol 2016; 7:192. [PMID: 27242797 PMCID: PMC4871867 DOI: 10.3389/fimmu.2016.00192] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/02/2016] [Indexed: 12/20/2022] Open
Abstract
Regulatory T cells (Tregs) play an important role in infections, by modulating host immune responses and avoiding the overreactive immunity that in the case of human immunodeficiency virus (HIV) infection leads to a marked erosion and deregulation of the entire immune system. Therefore, the suppressive function of Treg in HIV-infected patients is critical because of their implication on preventing the immune hyperactivation, even though it could also have a detrimental effect by suppressing HIV-specific immune responses. In recent years, several studies have shown that HIV-1 can directly infect Treg, disturbing their phenotype and suppressive capacity via different mechanisms. These effects include Foxp3 and CD25 downregulation, and the impairment of suppressive capacity. This review describes the functional mechanisms of Treg to modulate immune activation during HIV infection, and how such control is no longer fine-tune orchestrated once Treg itself get infected. We will review the current knowledge about the HIV effects on the Treg cytokine expression, on pathways implying the participation of different ectoenzymes (i.e., CD39/CD73 axis), transcription factors (ICER), and lastly on cyclic adenosine monophosphate (cAMP), one of the keystones in Treg-suppressive function. To define which are the HIV effects upon these regulatory mechanisms is crucial not only for the comprehension of immune deregulation in HIV-infected patients but also for the correct understanding of the role of Tregs in HIV infection.
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Affiliation(s)
- Jacobo López-Abente
- Laboratory of Immunoregulation, "Gregorio Marañón" Health Research Institute (IISGM) , Madrid , Spain
| | - Rafael Correa-Rocha
- Laboratory of Immunoregulation, "Gregorio Marañón" Health Research Institute (IISGM) , Madrid , Spain
| | - Marjorie Pion
- Laboratory of Immunoregulation, "Gregorio Marañón" Health Research Institute (IISGM) , Madrid , Spain
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31
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Charles TP, Shellito JE. Human Immunodeficiency Virus Infection and Host Defense in the Lungs. Semin Respir Crit Care Med 2016; 37:147-56. [PMID: 26974294 DOI: 10.1055/s-0036-1572553] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Immunosuppression associated with human immunodeficiency virus (HIV) infection impacts all components of host defense against pulmonary infection. Cells within the lung have altered immune function and are important reservoirs for HIV infection. The host immune response to infected lung cells further compromises responses to a secondary pathogenic insult. In the upper respiratory tract, mucociliary function is impaired and there are decreased levels of salivary immunoglobulin A. Host defenses in the lower respiratory tract are controlled by alveolar macrophages, lymphocytes, and polymorphonuclear leukocytes. As HIV infection progresses, lung CD4 T cells are reduced in number causing a lack of activation signals from CD4 T cells and impaired defense by macrophages. CD8 T cells, on the other hand, are increased in number and cause lymphocytic alveolitis. Specific antibody responses by B-lymphocytes are decreased and opsonization of microorganisms is impaired. These observed defects in host defense of the respiratory tract explain the susceptibility of HIV-infected persons for oropharyngeal candidiasis, bacterial pneumonia, Pneumocystis pneumonia, and other opportunistic infections.
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Affiliation(s)
- Tysheena P Charles
- Section of Pulmonary/Critical Care & Allergy/Immunology, Department of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Judd E Shellito
- Section of Pulmonary/Critical Care & Allergy/Immunology, Department of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana
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Gomes AVBT, de Souza Morais SM, Menezes-Filho SL, de Almeida LGN, Rocha RP, Ferreira JMS, Dos Santos LL, Malaquias LCC, Coelho LFL. Demethylation profile of the TNF-α promoter gene is associated with high expression of this cytokine in Dengue virus patients. J Med Virol 2016; 88:1297-302. [PMID: 26792115 DOI: 10.1002/jmv.24478] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2016] [Indexed: 11/09/2022]
Abstract
Dengue is the most prevalent arthropod-borne viral illness in humans. The overexpression of cytokines by Dengue virus (DENV) infected cells is associated with the most severe forms of the disease. Unmethylated CpG islands are related to a transcriptionally active structure, whereas methylated DNA recruits methyl-binding proteins that inhibit gene expression. Several studies have described the importance of epigenetic events in the regulation and expression of many cytokines. The purpose of the present study was to evaluate the methylation status of the IFN-γ and TNF-α promoters in DNA extracted from dengue infected patients using methylation-specific polymerase chain reaction. A high frequency of demethylation was observed in the TNF-α promoter of DENV infected patients when compared to non-infected controls. The patients with an unmethylated profile showed higher expression of TNF-α mRNA than patients with the methylated status. No difference was found in the methylation frequency between the two analyzed groups regarding the IFN-γ promoter or in the expression of IFN-γ transcripts. The present study provides the first association of TNF-α promoter demethylation in DENV infected individuals and demonstrates a correlation between the methylation status of the region analyzed and the expression of TNF-α transcripts in DENV infected patients. J. Med. Virol. 88:1297-1302, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Stella Maria de Souza Morais
- Laboratório de Vacinas, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, Minas Gerais, Brazil
| | - Sergio Luiz Menezes-Filho
- Laboratório de Vacinas, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, Minas Gerais, Brazil
| | | | - Raissa Prado Rocha
- Laboratório de Vacinas, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, Minas Gerais, Brazil
| | | | - Luciana Lara Dos Santos
- Campus Centro-Oeste Dona Lindu, Universidade Federal de São João Del-Rei, Divinópolis, Brazil
| | - Luiz Cosme Cotta Malaquias
- Laboratório de Vacinas, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, Minas Gerais, Brazil
| | - Luiz Felipe Leomil Coelho
- Laboratório de Vacinas, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, Minas Gerais, Brazil
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Miller MM, Akaronu N, Thompson EM, Hood SF, Fogle JE. Modulating DNA methylation in activated CD8+ T cells inhibits regulatory T cell-induced binding of Foxp3 to the CD8+ T Cell IL-2 promoter. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2015; 194:990-8. [PMID: 25548225 PMCID: PMC4297683 DOI: 10.4049/jimmunol.1401762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have previously demonstrated that CD4(+)CD25(+) regulatory T cells (Tregs) activated during the course of feline immunodeficiency virus (FIV) infection suppress CD8(+) CTL function in a TGF-β-dependent fashion, inhibiting IFN-γ and IL-2 production and inducing G1 cell-cycle arrest. In this article, we describe the molecular events occurring at the IL-2 promoter leading to suppression of IL-2 production. These experiments demonstrate that Foxp3 induced by lentivirus-activated Tregs in the CD8(+) target cells binds to the IL-2 promoter, actively repressing IL-2 transcription. We further demonstrate that the chronic activation of CD8(+) T cells during FIV infection results in chromatin remodeling at the IL-2 promoter, specifically, demethylation of CpG residues. These DNA modifications occur during active transcription and translation of IL-2; however, these changes render the IL-2 promoter permissive to Foxp3-induced transcriptional repression. These data help explain, in part, the seemingly paradoxical observations that CD8(+) T cells displaying an activation phenotype exhibit altered antiviral function. Further, we demonstrate that blocking demethylation of CpG residues at the IL-2 promoter inhibits Foxp3 binding, suggesting a potential mechanism for rescue and/or reactivation of CD8(+) T cells. Using the FIV model for lentiviral persistence, these studies provide a framework for understanding how immune activation combined with Treg-mediated suppression may affect CD8(+) T cell IL-2 transcription, maturation, and antiviral function.
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Affiliation(s)
- Michelle M Miller
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607
| | - Nnenna Akaronu
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607
| | - Elizabeth M Thompson
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607
| | - Sylvia F Hood
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607
| | - Jonathan E Fogle
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607
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