1
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Levine AJ, Thadani C, Soontornniyomkij V, Lopez-Aranda MF, Mesa YG, Kitchen S, Rezek V, Silva A, Kolson DL. Behavioral and histological assessment of a novel treatment of neuroHIV in humanized mice. RESEARCH SQUARE 2023:rs.3.rs-3678629. [PMID: 38168407 PMCID: PMC10760308 DOI: 10.21203/rs.3.rs-3678629/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: 01/05/2024]
Abstract
Neurocognitive deficits are prevalent among people living with HIV, likely due to chronic inflammation and oxidative stress in the brain. To date, no pharmaceutical treatments beyond antiretroviral therapy (ARV) has been shown to reduce risk for, or severity of, HIV-associated neurocognitive disorder. Here we investigate a novel compound, CDDO-Me, with documented neuroprotective effects via activation of the nrf2 and inhibition of the NFkB pathways. Methods We conducted three studies to assess the efficacy of CDDO-Me alone or in combination with antiretroviral therapy in humanized mice infected with HIV; behavioral, histopathological, and immunohistochemical. Results CDDO-Me in combination with ARV rescued social interaction deficits; however, only ARV was associated with preserved functioning in other behaviors, and CDDO-Me may have attenuated those benefits. A modest neuroprotective effect was found for CDDO-Me when administered with ARV, via preservation of PSD-95 expression; however, ARV alone had a more consistent protective effect. No significant changes in antioxidant enzyme expression levels were observed in CDDO-Me-treated animals. Only ARV use seemed to affect some antioxidant levels, indicating that it is ARV rather than CDDO-Me that is the major factor providing neuroprotection in this animal model. Finally, immunohistochemical analysis found that several cellular markers in various brain regions varied due to ARV rather than CDDO-Me. Conclusion Limited benefit of CDDO-Me on behavior and neuroprotection were observed. Instead, ARV was shown to be the more beneficial treatment. These experiments support the future use of this chimeric mouse for behavioral experiments in neuroHIV research.
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Affiliation(s)
| | | | | | | | | | - Scott Kitchen
- UCLA Humanized Mouse Core Laboratory, University of California
| | - Valerie Rezek
- UCLA Humanized Mouse Core Laboratory, University of California
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2
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Lin J, Ehinger E, Hanna DB, Qi Q, Wang T, Ghosheh Y, Mueller K, Anastos K, Lazar JM, Mack WJ, Tien PC, Berman JW, Cohen MH, Ofotokun I, Gange S, Liu C, Heath SL, Tracy RP, Hodis HN, Landay AL, Ley K, Kaplan RC. HIV infection and cardiovascular disease have both shared and distinct monocyte gene expression features: Women's Interagency HIV study. PLoS One 2023; 18:e0285926. [PMID: 37205656 PMCID: PMC10198505 DOI: 10.1371/journal.pone.0285926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/04/2023] [Indexed: 05/21/2023] Open
Abstract
Persistent inflammation contributes to the development of cardiovascular disease (CVD) as an HIV-associated comorbidity. Innate immune cells such as monocytes are major drivers of inflammation in men and women with HIV. The study objectives are to examine the contribution of circulating non-classical monocytes (NCM, CD14dimCD16+) and intermediate monocytes (IM, CD14+CD16+) to the host response to long-term HIV infection and HIV-associated CVD. Women with and without chronic HIV infection (H) were studied. Subclinical CVD (C) was detected as plaques imaged by B-mode carotid artery ultrasound. The study included H-C-, H+C-, H-C+, and H+C+ participants (23 of each, matched on race/ethnicity, age and smoking status), selected from among enrollees in the Women's Interagency HIV Study. We assessed transcriptomic features associated with HIV or CVD alone or comorbid HIV/CVD comparing to healthy (H-C-) participants in IM and NCM isolated from peripheral blood mononuclear cells. IM gene expression was little affected by HIV alone or CVD alone. In IM, coexisting HIV and CVD produced a measurable gene transcription signature, which was abolished by lipid-lowering treatment. In NCM, versus non-HIV controls, women with HIV had altered gene expression, irrespective of whether or not they had comorbid CVD. The largest set of differentially expressed genes was found in NCM among women with both HIV and CVD. Genes upregulated in association with HIV included several potential targets of drug therapies, including LAG3 (CD223). In conclusion, circulating monocytes from patients with well controlled HIV infection demonstrate an extensive gene expression signature which may be consistent with the ability of these cells to serve as potential viral reservoirs. Gene transcriptional changes in HIV patients were further magnified in the presence of subclinical CVD.
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Affiliation(s)
- Juan Lin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Erik Ehinger
- Department of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States of America
| | - David B. Hanna
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Yanal Ghosheh
- Department of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States of America
| | - Karin Mueller
- Department of Cardiology, Eberhard Karls University, Tuebingen University Hospital, Tuebingen, Germany
| | - Kathryn Anastos
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Jason M. Lazar
- Department of Medicine, Downstate Medical Center, State University of New York, Brooklyn, NY, United States of America
| | - Wendy J. Mack
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Phyllis C. Tien
- Department of Medicine, and Department of Veterans Affairs, Medical Center, University of California, San Francisco, San Francisco, CA, United States of America
| | - Joan W. Berman
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Mardge H. Cohen
- Department of Medicine, John Stroger Hospital and Rush University, Chicago, IL, United States of America
| | - Igho Ofotokun
- Department of Medicine, Infectious Disease Division and Grady Health Care System, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Stephen Gange
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States of America
| | - Chenglong Liu
- Department of Medicine, Georgetown University Medical Center, Washington, DC, United States of America
| | - Sonya L. Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Russell P. Tracy
- Department of Pathology & Laboratory Medicine and Biochemistry, University of Vermont Larner College of Medicine, Colchester, VT, United States of America
| | - Howard N. Hodis
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Alan L. Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States of America
| | - Klaus Ley
- Department of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States of America
- Department of Bioengineering, University of California San Diego, San Diego, CA, United States of America
| | - Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States of America
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA, United States of America
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3
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Ehinger E, Ghosheh Y, Pramod AB, Lin J, Hanna DB, Mueller K, Durant CP, Baas L, Qi Q, Wang T, Buscher K, Anastos K, Lazar JM, Mack WJ, Tien PC, Cohen MH, Ofotokun I, Gange S, Heath SL, Hodis HN, Tracy RP, Landay AL, Kaplan RC, Ley K. Classical monocyte transcriptomes reveal significant anti-inflammatory statin effect in women with chronic HIV. Cardiovasc Res 2020; 117:1166-1177. [PMID: 32658258 DOI: 10.1093/cvr/cvaa188] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/04/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
AIMS During virally suppressed chronic HIV infection, persistent inflammation contributes to the development of cardiovascular disease (CVD), a major comorbidity in people living with HIV (LWH). Classical blood monocytes (CMs) remain activated during antiretroviral therapy and are a major source of pro-inflammatory and pro-thrombotic factors that contribute to atherosclerotic plaque development and instability. METHODS AND RESULTS Here, we identify transcriptomic changes in circulating CMs in peripheral blood mononuclear cell samples from participants of the Women's Interagency HIV Study, selected by HIV and subclinical CVD (sCVD) status. We flow-sorted CM from participants of the Women's Interagency HIV Study and deep-sequenced their mRNA (n = 92). CMs of HIV+ participants showed elevated interleukin (IL)-6, IL-1β, and IL-12β, overlapping with many transcripts identified in sCVD+ participants. In sCVD+ participants LWH, those reporting statin use showed reduced pro-inflammatory gene expression to a level comparable with healthy (HIV-sCVD-) participants. Statin non-users maintained an elevated inflammatory profile and increased cytokine production. CONCLUSION Statin therapy has been associated with a lower risk of cardiac events, such as myocardial infarction in the general population, but not in those LWH. Our data suggest that women LWH may benefit from statin therapy even in the absence of overt CVD.
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Affiliation(s)
- Erik Ehinger
- Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Yanal Ghosheh
- Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Akula Bala Pramod
- Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Juan Lin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - David B Hanna
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Karin Mueller
- Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Christopher P Durant
- Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Livia Baas
- Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Konrad Buscher
- Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jason M Lazar
- Department of Medicine, State University of New York, Downstate Medical Center, Bronx, NY, USA.,Department of Epidemiology & Population Health, State University of New York, Downstate Medical Center, Bronx, NY, USA
| | - Wendy J Mack
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Phyllis C Tien
- Department of Medicine and Medical Service, University of California, San Francisco, San Francisco, CA, USA.,Department of Veterans Affairs Medical Center, University of California, San Francisco, San Francisco, CA, USA
| | - Mardge H Cohen
- Department of Medicine, John Stroger Hospital and Rush University, Chicago, IL, USA
| | - Igho Ofotokun
- Department of Medicine, Infectious Disease Division and Grady Health Care System, Emory University School of Medicine, Atlanta, GA, USA
| | - Stephen Gange
- Division of Cardiovascular Medicine, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Sonya L Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Howard N Hodis
- Departments of Medicine and Preventative Medicine, Atherosclerosis Research Unit, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Russell P Tracy
- Department of Pathology & Laboratory Medicine and Biochemistry, University of Vermont Larner College of Medicine, Colchester, VT, USA
| | - Alan L Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA.,Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle WA 98109, USA
| | - Klaus Ley
- Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.,Department of Bioengineering, University of California San Diego, San Diego, CA, USA
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4
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Ivanov S, Lagunin A, Filimonov D, Tarasova O. Network-Based Analysis of OMICs Data to Understand the HIV-Host Interaction. Front Microbiol 2020; 11:1314. [PMID: 32625189 PMCID: PMC7311653 DOI: 10.3389/fmicb.2020.01314] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/25/2020] [Indexed: 12/22/2022] Open
Abstract
The interaction of human immunodeficiency virus with human cells is responsible for all stages of the viral life cycle, from the infection of CD4+ cells to reverse transcription, integration, and the assembly of new viral particles. To date, a large amount of OMICs data as well as information from functional genomics screenings regarding the HIV–host interaction has been accumulated in the literature and in public databases. We processed databases containing HIV–host interactions and found 2910 HIV-1-human protein-protein interactions, mostly related to viral group M subtype B, 137 interactions between human and HIV-1 coding and non-coding RNAs, essential for viral lifecycle and cell defense mechanisms, 232 transcriptomics, 27 proteomics, and 34 epigenomics HIV-related experiments. Numerous studies regarding network-based analysis of corresponding OMICs data have been published in recent years. We overview various types of molecular networks, which can be created using OMICs data, including HIV–human protein–protein interaction networks, co-expression networks, gene regulatory and signaling networks, and approaches for the analysis of their topology and dynamics. The network-based analysis can be used to determine the critical pathways and key proteins involved in the HIV life cycle, cellular and immune responses to infection, viral escape from host defense mechanisms, and mechanisms mediating different susceptibility of humans to infection. The proteins and pathways identified in these studies represent a basis for developing new anti-HIV therapeutic strategies such as new drugs preventing infection of CD4+ cells and viral replication, effective vaccines, “shock and kill” and “block and lock” approaches to cure latent infection.
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Affiliation(s)
- Sergey Ivanov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia.,Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexey Lagunin
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia.,Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry Filimonov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Olga Tarasova
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
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5
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Canchi S, Swinton MK, Rissman RA, Fields JA. Transcriptomic analysis of brain tissues identifies a role for CCAAT enhancer binding protein β in HIV-associated neurocognitive disorder. J Neuroinflammation 2020; 17:112. [PMID: 32276639 PMCID: PMC7149918 DOI: 10.1186/s12974-020-01781-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND HIV-associated neurocognitive disorders (HAND) persist in the era of combined antiretroviral therapy (ART) despite reductions in viral load (VL) and overall disease severity. The mechanisms underlying HAND in the ART era are not well understood but are likely multifactorial, involving alterations in common pathways such as inflammation, autophagy, neurogenesis, and mitochondrial function. Newly developed omics approaches hold potential to identify mechanisms driving neuropathogenesis of HIV in the ART era. METHODS In this study, using 33 postmortem frontal cortex (FC) tissues, neuropathological, molecular, and biochemical analyses were used to determine cellular localization and validate expression levels of the prolific transcription factor (TF), CCAAT enhancer binding protein (C/EBP) β, in brain tissues from HIV+ cognitively normal and HAND cases. RNA sequencing (seq) and transcriptomic analyses were performed on FC tissues including 24 specimens from well-characterized people with HIV that had undergone neurocognitive assessments. In vitro models for brain cells were used to investigate the role of C/EBPβ in mediating gene expression. RESULTS The most robust signal for TF dysregulation was observed in cases diagnosed with minor neurocognitive disorder (MND) compared to cognitive normal (CN) cases. Of particular interest, due to its role in inflammation, autophagy and neurogenesis, C/EBPβ was significantly upregulated in MND compared to CN brains. C/EBPβ was increased at the protein level in HAND brains. C/EBPβ levels were significantly reduced in neurons and increased in astroglia in HAND brains compared to CN. Transfection of human astroglial cells with a plasmid expressing C/EBPβ induced expression of multiple targets identified in the transcriptomic analysis of HAND brains, including dynamin-1-like protein (DNM1L) and interleukin-1 receptor-associated kinase 1. Recombinant HIV-Tat reduced and increased C/EBPβ levels in neuronal and astroglial cells, respectively. CONCLUSIONS These findings are the first to present RNAseq-based transcriptomic analyses of HIV+ brain tissues, providing further evidence of altered neuroinflammation, neurogenesis, mitochondrial function, and autophagy in HAND. Interestingly, these studies confirm a role for CEBPβ in regulating inflammation, metabolism, and autophagy in astroglia. Therapeutic strategies aimed at transcriptional regulation of astroglia or downstream pathways may provide relief to HIV+ patients at risk for HAND and other neurological disorders.
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Affiliation(s)
- Saranya Canchi
- Veterans Affairs San Diego Healthcare System, San Diego, CA USA
- Department of Neurosciences, University of California San Diego, San Diego, La Jolla, CA USA
| | - Mary K. Swinton
- Department of Psychiatry, School of Medicine, University of California San Diego, 9500 Gilman Dr., BSB 3009, San Diego, La Jolla, CA 92093-0603 USA
| | - Robert A. Rissman
- Veterans Affairs San Diego Healthcare System, San Diego, CA USA
- Department of Neurosciences, University of California San Diego, San Diego, La Jolla, CA USA
| | - Jerel Adam Fields
- Department of Psychiatry, School of Medicine, University of California San Diego, 9500 Gilman Dr., BSB 3009, San Diego, La Jolla, CA 92093-0603 USA
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6
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Levine A, Sacktor N, Becker JT. Studying the neuropsychological sequelae of SARS-CoV-2: lessons learned from 35 years of neuroHIV research. J Neurovirol 2020; 26:809-823. [PMID: 32880873 PMCID: PMC7471564 DOI: 10.1007/s13365-020-00897-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/11/2020] [Accepted: 08/18/2020] [Indexed: 01/14/2023]
Abstract
The virology of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and the human immune response to the virus are under vigorous investigation. There are now several reports describing neurological symptoms in individuals who develop coronavirus disease 2019 (COVID-19), the syndrome associated with SARS-CoV-2 infection. The prevalence, incidence, and clinical course of these symptoms will become clearer in the coming months and years through epidemiological studies. However, the long-term neurological and cognitive consequence of SARS-CoV-2 infection will remain conjectural for some time and will likely require the creation of cohort studies that include uninfected individuals. Considering the early evidence for neurological involvement in COVID-19 it may prove helpful to compare SARS-CoV-2 with another endemic and neurovirulent virus, human immunodeficiency virus-1 (HIV-1), when designing such cohort studies and when making predictions about neuropsychological outcomes. In this paper, similarities and differences between SARS-CoV-2 and HIV-1 are reviewed, including routes of neuroinvasion, putative mechanisms of neurovirulence, and factors involved in possible long-term neuropsychological sequelae. Application of the knowledge gained from over three decades of neuroHIV research is discussed, with a focus on alerting researchers and clinicians to the challenges in determining the cause of neurocognitive deficits among long-term survivors.
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Affiliation(s)
- Andrew Levine
- grid.19006.3e0000 0000 9632 6718Department of Neurology David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
| | - Ned Sacktor
- grid.21107.350000 0001 2171 9311Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - James T. Becker
- grid.21925.3d0000 0004 1936 9000Departments of Psychiatry, Neurology, and Psychology, University of Pittsburgh, Pittsburgh, PA 15260 USA
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7
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Lorenz DR, Misra V, Gabuzda D. Transcriptomic analysis of monocytes from HIV-positive men on antiretroviral therapy reveals effects of tobacco smoking on interferon and stress response systems associated with depressive symptoms. Hum Genomics 2019; 13:59. [PMID: 31779701 PMCID: PMC6883692 DOI: 10.1186/s40246-019-0247-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/17/2019] [Indexed: 02/08/2023] Open
Abstract
Background Tobacco smoking induces immunomodulatory and pro-inflammatory effects associated with transcriptome changes in monocytes and other immune cell types. While smoking is prevalent in HIV-infected (HIV+) individuals, few studies have investigated its effects on gene expression in this population. Here, we report whole-transcriptome analyses of 125 peripheral blood monocyte samples from ART-treated HIV+ and uninfected (HIV−) men enrolled in the Multicenter AIDS Cohort Study (MACS) (n = 25 HIV+ smokers, n = 60 HIV+ non-smokers, n = 40 HIV− non-smoking controls). Gene expression profiling was performed using Illumina HumanHT-12 Expression BeadChip microarrays. Differential expression analysis was performed with weighted linear regression models using the R limma package, followed by functional enrichment and Ingenuity Pathway analyses. Results A total of 286 genes were differentially expressed in monocytes from HIV+ smokers compared with HIV− non-smokers; upregulated genes (n = 180) were enriched for immune and interferon response, chemical/stress response, mitochondria, and extracellular vesicle gene ontology (GO) terms. Expression of genes related to immune/interferon responses (AIM2, FCGR1A-B, IFI16, SP100), stress/chemical responses (APAF1, HSPD1, KLF4), and mitochondrial function (CISD1, MTHFD2, SQOR) was upregulated in HIV+ non-smokers and further increased in HIV+ smokers. Gene expression changes associated with smoking in previous studies of human monocytes were also observed (SASH1, STAB1, PID1, MMP25). Depressive symptoms (CES-D scores ≥ 16) were more prevalent in HIV+ tobacco smokers compared with HIV+ and HIV− non-smokers (50% vs. 26% and 13%, respectively; p = 0.007), and upregulation of immune/interferon response genes, including IFI35, IFNAR1, OAS1-2, STAT1, and SP100, was associated with depressive symptoms in logistic regression models adjusted for HIV status and smoking (p < 0.05). Network models linked the Stat1-mediated interferon pathway to transcriptional regulator Klf4 and smoking-associated toll-like receptor scaffolding protein Sash1, suggesting inter-relationships between smoking-associated genes, control of monocyte differentiation, and interferon-mediated inflammatory responses. Conclusions This study characterizes immune, interferon, stress response, and mitochondrial-associated gene expression changes in monocytes from HIV+ tobacco smokers, and identifies augmented interferon and stress responses associated with depressive symptoms. These findings help to explain complex interrelationships between pro-inflammatory effects of HIV and smoking, and their combined impact on comorbidities prevalent in HIV+ individuals.
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Affiliation(s)
- David R Lorenz
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Center for Life Science 1010, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Vikas Misra
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Center for Life Science 1010, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Dana Gabuzda
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Center for Life Science 1010, 450 Brookline Avenue, Boston, MA, 02215, USA.
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8
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Mitchell HD, Eisfeld AJ, Stratton KG, Heller NC, Bramer LM, Wen J, McDermott JE, Gralinski LE, Sims AC, Le MQ, Baric RS, Kawaoka Y, Waters KM. The Role of EGFR in Influenza Pathogenicity: Multiple Network-Based Approaches to Identify a Key Regulator of Non-lethal Infections. Front Cell Dev Biol 2019; 7:200. [PMID: 31616667 PMCID: PMC6763731 DOI: 10.3389/fcell.2019.00200] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/05/2019] [Indexed: 12/14/2022] Open
Abstract
Despite high sequence similarity between pandemic and seasonal influenza viruses, there is extreme variation in host pathogenicity from one viral strain to the next. Identifying the underlying mechanisms of variability in pathogenicity is a critical task for understanding influenza virus infection and effective management of highly pathogenic influenza virus disease. We applied a network-based modeling approach to identify critical functions related to influenza virus pathogenicity using large transcriptomic and proteomic datasets from mice infected with six influenza virus strains or mutants. Our analysis revealed two pathogenicity-related gene expression clusters; these results were corroborated by matching proteomics data. We also identified parallel downstream processes that were altered during influenza pathogenesis. We found that network bottlenecks (nodes that bridge different network regions) were highly enriched in pathogenicity-related genes, while network hubs (highly connected network nodes) were significantly depleted in these genes. We confirmed that this trend persisted in a distinct virus: Severe Acute Respiratory Syndrome Coronavirus (SARS). The role of epidermal growth factor receptor (EGFR) in influenza pathogenesis, one of the bottleneck regulators with corroborating signals across transcript and protein expression data, was tested and validated in additional mouse infection experiments. We demonstrate that EGFR is important during influenza infection, but the role it plays changes for lethal versus non-lethal infections. Our results show that by using association networks, bottleneck genes that lack hub characteristics can be used to predict a gene's involvement in influenza virus pathogenicity. We also demonstrate the utility of employing multiple network approaches for analyzing host response data from viral infections.
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Affiliation(s)
- Hugh D Mitchell
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Amie J Eisfeld
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Kelly G Stratton
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Natalie C Heller
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Lisa M Bramer
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ji Wen
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Lisa E Gralinski
- Department of Microbiology and Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Amy C Sims
- Department of Microbiology and Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Mai Q Le
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Ralph S Baric
- Department of Microbiology and Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States.,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Sciences, The University of Tokyo, Tokyo, Japan.,International Research Center for Infectious Diseases, Institute of Medical Sciences, The University of Tokyo, Tokyo, Japan
| | - Katrina M Waters
- Pacific Northwest National Laboratory, Richland, WA, United States
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9
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Bandera A, Taramasso L, Bozzi G, Muscatello A, Robinson JA, Burdo TH, Gori A. HIV-Associated Neurocognitive Impairment in the Modern ART Era: Are We Close to Discovering Reliable Biomarkers in the Setting of Virological Suppression? Front Aging Neurosci 2019; 11:187. [PMID: 31427955 PMCID: PMC6687760 DOI: 10.3389/fnagi.2019.00187] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/10/2019] [Indexed: 11/24/2022] Open
Abstract
The prevalence of the most severe forms of HIV-associated neurocognitive disorders (HAND) is decreasing due to worldwide availability and high efficacy of antiretroviral treatment (ART). However, several grades of HIV-related cognitive impairment persist with effective ART and remain a clinical concern for people with HIV (PWH). The pathogenesis of these cognitive impairments has yet to be fully understood and probably multifactorial. In PWH with undetectable peripheral HIV-RNA, the presence of viral escapes in cerebrospinal fluid (CSF) might explain a proportion of cases, but not all. Many other mechanisms have been hypothesized to be involved in disease progression, in order to identify possible therapeutic targets. As potential indicators of disease staging and progression, numerous biomarkers have been used to characterize and implicate chronic inflammation in the pathogenesis of neuronal injuries, such as certain phenotypes of activated monocytes/macrophages, in the context of persistent immune activation. Despite none of them being disease-specific, the correlation of several CSF cellular biomarkers to HIV-induced neuronal damage has been investigated. Furthermore, recent studies have been evaluating specific microRNA (miRNA) profiles in the CSF of PWH with neurocognitive impairment (NCI). The aim of the present study is to review the body of evidence on different biomarkers use in research and clinical settings, focusing on PWH on ART with undetectable plasma HIV-RNA.
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Affiliation(s)
- Alessandra Bandera
- Infectious Disease Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milano, Milan, Italy
| | - Lucia Taramasso
- Infectious Disease Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Infectious Diseases Clinic, Department of Health Sciences, School of Medical and Pharmaceutical Sciences, Policlinico Hospital San Martino, University of Genova (DISSAL), Genova, Italy
| | - Giorgio Bozzi
- Infectious Disease Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Antonio Muscatello
- Infectious Disease Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Jake A Robinson
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Tricia H Burdo
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Andrea Gori
- Infectious Disease Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milano, Milan, Italy
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10
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No reliable gene expression biomarkers of current or impending neurocognitive impairment in peripheral blood monocytes of persons living with HIV. J Neurovirol 2018; 24:350-361. [PMID: 29582356 DOI: 10.1007/s13365-018-0625-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 02/20/2018] [Accepted: 02/22/2018] [Indexed: 10/17/2022]
Abstract
Events leading to and propagating neurocognitive impairment (NCI) in HIV-1-infected (HIV+) persons are largely mediated by peripheral blood monocytes. We previously identified expression levels of individual genes and gene networks in peripheral blood monocytes that correlated with neurocognitive functioning in HIV+ adults. Here, we expand upon those findings by examining if gene expression data at baseline is predictive of change in neurocognitive functioning 2 years later. We also attempt to validate the original findings in a new sample of HIV+ patients and determine if the findings are HIV specific by including HIV-uninfected (HIV-) participants as a comparison group. At two time points, messenger RNA (mRNA) was isolated from the monocytes of 123 HIV+ and 60 HIV- adults enrolled in the Multicenter AIDS Cohort Study and analyzed with the Illumina HT-12 v4 Expression BeadChip. All participants received baseline and follow-up neurocognitive testing 2 years after mRNA analysis. Data were analyzed using standard gene expression analysis and weighted gene co-expression network analysis with correction for multiple testing. Gene sets were analyzed for GO term enrichment. Only weak reproducibility of associations of single genes with neurocognitive functioning was observed, indicating that such measures are unreliable as biomarkers for HIV-related NCI; however, gene networks were generally preserved between time points and largely reproducible, suggesting that these may be more reliable. Several gene networks associated with variables related to HIV infection were found (e.g., MHC I antigen processing, TNF signaling, interferon gamma signaling, and antiviral defense); however, no significant associations were found for neurocognitive function. Furthermore, neither individual gene probes nor gene networks predicted later neurocognitive change. This study did not validate our previous findings and does not support the use of monocyte gene expression profiles as a biomarker for current or future HIV-associated neurocognitive impairment.
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11
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Venkatachari NJ, Jain S, Walker L, Bivalkar-Mehla S, Chattopadhyay A, Bar-Joseph Z, Rinaldo C, Ragin A, Seaberg E, Levine A, Becker J, Martin E, Sacktor N, Ayyavoo V. Transcriptome analyses identify key cellular factors associated with HIV-1-associated neuropathogenesis in infected men. AIDS 2017; 31:623-633. [PMID: 28005686 PMCID: PMC5389669 DOI: 10.1097/qad.0000000000001379] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
OBJECTIVE HIV-1 viral proteins and host inflammatory factors have a direct role in neuronal toxicity in vitro; however, the contribution of these factors in vivo in HIV-1-associated neurocognitive disorder (HAND) is not fully understood. We applied novel Systems Biology approaches to identify specific cellular and viral factors and their related pathways that are associated with different stages of HAND. DESIGN A cross-sectional study of individuals enrolled in the Multicenter AIDS Cohort Study including HIV-1-seronegative (N = 36) and HIV-1-seropositive individuals without neurocognitive symptoms (N = 16) or with mild neurocognitive disorder (MND) (N = 8) or HIV-associated dementia (HAD) (N = 16). METHODS A systematic evaluation of global transcriptome of peripheral blood mononuclear cells (PBMCs) obtained from HIV-1-seronegative individuals and from HIV-1-positive men without neurocognitive symptoms, or MND or HAD was performed. RESULTS MND and HAD were associated with specific changes in mRNA transcripts and microRNAs in PBMCs. Comparison of upstream regulators and TimePath analyses identified specific cellular factors associated with MND and HAD, whereas HIV-1 viral proteins played a greater role in HAD. In addition, expression of specific microRNAs - miR-let-7a, miR-124, miR-15a and others - were found to correlate with mRNA gene expression and may have a potential protective role in asymptomatic HIV-1-seropositive individuals by regulating cellular signal transduction pathways downstream of chemokines and cytokines. CONCLUSION These results identify signature transcriptome changes in PBMCs associated with stages of HAND and shed light on the potential contribution of host cellular factors and viral proteins in HAND development.
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Affiliation(s)
- Narasimhan J. Venkatachari
- Department of Infectious Diseases & Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
| | - Siddhartha Jain
- Computer Science Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15217, USA
| | - Leah Walker
- Department of Infectious Diseases & Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
| | - Shalmali Bivalkar-Mehla
- Department of Infectious Diseases & Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
| | - Ansuman Chattopadhyay
- Molecular Biology Information Service, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Computational Biology and Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA
| | - Ziv Bar-Joseph
- Computer Science Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15217, USA
| | - Charles Rinaldo
- Department of Infectious Diseases & Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
| | - Ann Ragin
- Department of Radiology, Feinberg School of Medicine, Northwestern University, Suite 1600, 737 N. Michigan Ave, Chicago, IL 60611, USA
| | - Eric Seaberg
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21209, USA
| | - Andrew Levine
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, CA 90095
| | - James Becker
- Department of Infectious Diseases & Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
| | - Eileen Martin
- Department of Psychiatry, Rush University Medical Center, 1645 W Jackson Blvd, Chicago, IL, 60612, USA
| | - Ned Sacktor
- Department of Neurology, Johns Hopkins Bayview Medical Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21209, USA
| | - Velpandi Ayyavoo
- Department of Infectious Diseases & Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
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12
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Corley MJ, Dye C, D'Antoni ML, Byron MM, Yo KLA, Lum-Jones A, Nakamoto B, Valcour V, SahBandar I, Shikuma CM, Ndhlovu LC, Maunakea AK. Comparative DNA Methylation Profiling Reveals an Immunoepigenetic Signature of HIV-related Cognitive Impairment. Sci Rep 2016; 6:33310. [PMID: 27629381 PMCID: PMC5024304 DOI: 10.1038/srep33310] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 08/24/2016] [Indexed: 11/20/2022] Open
Abstract
Monocytes/macrophages contribute to the neuropathogenesis of HIV-related cognitive impairment (CI); however, considerable gaps in our understanding of the precise mechanisms driving this relationship remain. Furthermore, whether a distinct biological profile associated with HIV-related CI resides in immune cell populations remains unknown. Here, we profiled DNA methylomes and transcriptomes of monocytes derived from HIV-infected individuals with and without CI using genome-wide DNA methylation and gene expression profiling. We identified 1,032 CI-associated differentially methylated loci in monocytes. These loci related to gene networks linked to the central nervous system (CNS) and interactions with HIV. Most (70.6%) of these loci exhibited higher DNA methylation states in the CI group and were preferentially distributed over gene bodies and intergenic regions of the genome. CI-associated DNA methylation states at 12 CpG sites associated with neuropsychological testing performance scores. CI-associated DNA methylation also associated with gene expression differences including CNS genes CSRNP1 (P = 0.017), DISC1 (P = 0.012), and NR4A2 (P = 0.005); and a gene known to relate to HIV viremia, THBS1 (P = 0.003). This discovery cohort data unveils cell type-specific DNA methylation patterns related to HIV-associated CI and provide an immunoepigenetic DNA methylation “signature” potentially useful for corroborating clinical assessments, informing pathogenic mechanisms, and revealing new therapeutic targets against CI.
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Affiliation(s)
- Michael J Corley
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Christian Dye
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Michelle L D'Antoni
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA
| | - Mary Margaret Byron
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA
| | - Kaahukane Leite-Ah Yo
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Annette Lum-Jones
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Beau Nakamoto
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB, Honolulu, HI 96815, USA
| | - Victor Valcour
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, USA
| | - Ivo SahBandar
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA
| | - Cecilia M Shikuma
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB, Honolulu, HI 96815, USA
| | - Lishomwa C Ndhlovu
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA.,Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB, Honolulu, HI 96815, USA
| | - Alika K Maunakea
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
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13
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Labrecque R, Fournier E, Sirard MA. Transcriptome analysis of bovine oocytes from distinct follicle sizes: Insights from correlation network analysis. Mol Reprod Dev 2016; 83:558-69. [DOI: 10.1002/mrd.22651] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/19/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Rémi Labrecque
- Faculté des sciences de l'Agriculture et de l'Alimentation; Département des Sciences Animales; Centre de Recherche en Biologie de la Reproduction; Pavillon INAF; Université Laval; Québec QC Canada
| | - Eric Fournier
- Faculté des sciences de l'Agriculture et de l'Alimentation; Département des Sciences Animales; Centre de Recherche en Biologie de la Reproduction; Pavillon INAF; Université Laval; Québec QC Canada
| | - Marc-André Sirard
- Faculté des sciences de l'Agriculture et de l'Alimentation; Département des Sciences Animales; Centre de Recherche en Biologie de la Reproduction; Pavillon INAF; Université Laval; Québec QC Canada
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14
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Rinchai D, Boughorbel S, Presnell S, Quinn C, Chaussabel D. A compendium of monocyte transcriptome datasets to foster biomedical knowledge discovery. F1000Res 2016; 5:291. [PMID: 27158451 DOI: 10.12688/f1000research.8182.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/25/2016] [Indexed: 12/24/2022] Open
Abstract
Systems-scale profiling approaches have become widely used in translational research settings. The resulting accumulation of large-scale datasets in public repositories represents a critical opportunity to promote insight and foster knowledge discovery. However, resources that can serve as an interface between biomedical researchers and such vast and heterogeneous dataset collections are needed in order to fulfill this potential. Recently, we have developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB). This tool can be used to overlay deep molecular phenotyping data with rich contextual information about analytes, samples and studies along with ancillary clinical or immunological profiling data. In this note, we describe a curated compendium of 93 public datasets generated in the context of human monocyte immunological studies, representing a total of 4,516 transcriptome profiles. Datasets were uploaded to an instance of GXB along with study description and sample annotations. Study samples were arranged in different groups. Ranked gene lists were generated based on relevant group comparisons. This resource is publicly available online at http://monocyte.gxbsidra.org/dm3/landing.gsp.
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Affiliation(s)
- Darawan Rinchai
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
| | - Sabri Boughorbel
- Biomedical informatics, Sidra Medical and Research Center, Doha, Qatar
| | - Scott Presnell
- Benaroya Research Institute at Virginia Mason, Seattle, USA
| | - Charlie Quinn
- Benaroya Research Institute at Virginia Mason, Seattle, USA
| | - Damien Chaussabel
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
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15
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Rinchai D, Boughorbel S, Presnell S, Quinn C, Chaussabel D. A curated compendium of monocyte transcriptome datasets of relevance to human monocyte immunobiology research. F1000Res 2016; 5:291. [PMID: 27158452 PMCID: PMC4856112 DOI: 10.12688/f1000research.8182.2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/12/2016] [Indexed: 12/19/2022] Open
Abstract
Systems-scale profiling approaches have become widely used in translational research settings. The resulting accumulation of large-scale datasets in public repositories represents a critical opportunity to promote insight and foster knowledge discovery. However, resources that can serve as an interface between biomedical researchers and such vast and heterogeneous dataset collections are needed in order to fulfill this potential. Recently, we have developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB). This tool can be used to overlay deep molecular phenotyping data with rich contextual information about analytes, samples and studies along with ancillary clinical or immunological profiling data. In this note, we describe a curated compendium of 93 public datasets generated in the context of human monocyte immunological studies, representing a total of 4,516 transcriptome profiles. Datasets were uploaded to an instance of GXB along with study description and sample annotations. Study samples were arranged in different groups. Ranked gene lists were generated based on relevant group comparisons. This resource is publicly available online at
http://monocyte.gxbsidra.org/dm3/landing.gsp.
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Affiliation(s)
- Darawan Rinchai
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
| | - Sabri Boughorbel
- Biomedical Informatics Division, Sidra Medical and Research Center, Doha, Qatar
| | - Scott Presnell
- Benaroya Research Institute at Virginia Mason, Seattle, USA
| | - Charlie Quinn
- Benaroya Research Institute at Virginia Mason, Seattle, USA
| | - Damien Chaussabel
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
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16
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Blazkova J, Boughorbel S, Presnell S, Quinn C, Chaussabel D. A curated transcriptome dataset collection to investigate the immunobiology of HIV infection. F1000Res 2016; 5:327. [PMID: 27134731 PMCID: PMC4838008 DOI: 10.12688/f1000research.8204.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/04/2016] [Indexed: 12/22/2022] Open
Abstract
Compendia of large-scale datasets available in public repositories provide an opportunity to identify and fill current gaps in biomedical knowledge. But first, these data need to be readily accessible to research investigators for interpretation. Here, we make available a collection of transcriptome datasets relevant to HIV infection. A total of 2717 unique transcriptional profiles distributed among 34 datasets were identified, retrieved from the NCBI Gene Expression Omnibus (GEO), and loaded in a custom web application, the Gene Expression Browser (GXB), designed for interactive query and visualization of integrated large-scale data. Multiple sample groupings and rank lists were created to facilitate dataset query and interpretation via this interface. Web links to customized graphical views can be generated by users and subsequently inserted in manuscripts reporting novel findings, such as discovery notes. The tool also enables browsing of a single gene across projects, which can provide new perspectives on the role of a given molecule across biological systems. This curated dataset collection is available at:
http://hiv.gxbsidra.org/dm3/geneBrowser/list.
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Affiliation(s)
| | | | - Scott Presnell
- Benaroya Research Institute, Research Technology, Seattle, WA, USA
| | - Charlie Quinn
- Benaroya Research Institute, Research Technology, Seattle, WA, USA
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17
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Accelerated epigenetic aging in brain is associated with pre-mortem HIV-associated neurocognitive disorders. J Neurovirol 2015; 22:366-75. [PMID: 26689571 DOI: 10.1007/s13365-015-0406-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/05/2015] [Accepted: 11/08/2015] [Indexed: 01/22/2023]
Abstract
HIV infection leads to age-related conditions in relatively young persons. HIV-associated neurocognitive disorders (HAND) are considered among the most prevalent of these conditions. To study the mechanisms underlying this disorder, researchers need an accurate method for measuring biological aging. Here, we apply a recently developed measure of biological aging, based on DNA methylation, to the study of biological aging in HIV+ brains. Retrospective analysis of tissue bank specimens and pre-mortem data was carried out. Fifty-eight HIV+ adults underwent a medical and neurocognitive evaluation within 1 year of death. DNA was obtained from occipital cortex and analyzed with the Illumina Infinium Human Methylation 450K platform. Biological age determined via the epigenetic clock was contrasted with chronological age to obtain a measure of age acceleration, which was then compared between those with HAND and neurocognitively normal individuals. The HAND and neurocognitively normal groups did not differ with regard to demographic, histologic, neuropathologic, or virologic variables. HAND was associated with accelerated aging relative to neurocognitively normal individuals, with average relative acceleration of 3.5 years. Age acceleration did not correlate with pre-mortem neurocognitive functioning or HAND severity. This is the first study to demonstrate that the epigenetic age of occipital cortex samples is associated with HAND status in HIV+ individuals pre-mortem. While these results suggest that the increased risk of a neurocognitive disorder due to HIV might be mediated by an epigenetic aging mechanism, future studies will be needed to validate the findings and dissect causal relationships and downstream effects.
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18
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Liu X, Xu Z, Zhu L, Liao S, Guo W. Transcriptome analysis of porcine thymus following porcine cytomegalovirus infection. PLoS One 2014; 9:e113921. [PMID: 25423176 PMCID: PMC4244220 DOI: 10.1371/journal.pone.0113921] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 10/31/2014] [Indexed: 11/19/2022] Open
Abstract
Porcine cytomegalovirus (PCMV) is a major immunosuppressive virus that mainly affects the immune function of T lymphocytes and macrophages. Despite being widely distributed around the world, no significantly different PCMV serotypes have been found. Moreover, the molecular immunosuppressive mechanisms of PCMV, along with the host antiviral mechanisms, are still not well characterized. To understand the potential impact of PCMV on the function of immune organs, we examined the transcriptome of PCMV-infected thymuses by microarray analysis. We identified 5,582 genes that were differentially expressed as a result of PCMV infection. Of these, 2,161 were upregulated and 3,421 were downregulated compared with the uninfected group. We confirmed the expression of 13 differentially expressed immune-related genes using quantitative real-time RT-PCR, and further confirmed the expression of six of those cytokines by western blot. Gene ontology, gene interaction networks, and KEGG pathway analysis of our results indicated that PCMV regulates multiple functional pathways, including the immune system, cellular and metabolic processes, networks of cytokine-cytokine receptor interactions, the TGF-β signaling pathway, the lymphocyte receptor signaling pathway, and the TNF-α signaling pathway. Our study is the first comprehensive attempt to explore the host transcriptional response to PCMV infection in the porcine immune system. It provides new insights into the immunosuppressive molecular mechanisms and pathogenesis of PCMV. This previously unrecognized endogenous antiviral mechanism has implications for the development of host-directed strategies for the prevention and treatment of immunosuppressive viral diseases.
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Affiliation(s)
- Xiao Liu
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Ya' an, China
| | - Zhiwen Xu
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Ya' an, China
- Key Laboratory of Animal Disease and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Ya' an, China
- * E-mail:
| | - Ling Zhu
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Ya' an, China
| | - Shan Liao
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Ya' an, China
| | - Wanzhu Guo
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Ya' an, China
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Genetic, transcriptomic, and epigenetic studies of HIV-associated neurocognitive disorder. J Acquir Immune Defic Syndr 2014; 65:481-503. [PMID: 24583618 DOI: 10.1097/qai.0000000000000069] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The Human Genome Project, coupled with rapidly evolving high-throughput technologies, has opened the possibility of identifying heretofore unknown biological processes underlying human disease. Because of the opaque nature of HIV-associated neurocognitive disorder (HAND) neuropathogenesis, the utility of such methods has gained notice among NeuroAIDS researchers. Furthermore, the merging of genetics with other research areas has also allowed for application of relatively nascent fields, such as neuroimaging genomics, and pharmacogenetics, to the context of HAND. In this review, we detail the development of genetic, transcriptomic, and epigenetic studies of HAND, beginning with early candidate gene association studies and culminating in current "omics" approaches that incorporate methods from systems biology to interpret data from multiple levels of biological functioning. Challenges with this line of investigation are discussed, including the difficulty of defining a valid phenotype for HAND. We propose that leveraging known associations between biology and pathology across multiple levels will lead to a more reliable and valid phenotype. We also discuss the difficulties of interpreting the massive and multitiered mountains of data produced by current high-throughput omics assays and explore the utility of systems biology approaches in this regard.
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