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Wu X, Liu YK, Iliuk AB, Tao WA. Mass spectrometry-based phosphoproteomics in clinical applications. Trends Analyt Chem 2023; 163:117066. [PMID: 37215489 PMCID: PMC10195102 DOI: 10.1016/j.trac.2023.117066] [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] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is an essential post-translational modification that regulates many aspects of cellular physiology, and dysregulation of pivotal phosphorylation events is often responsible for disease onset and progression. Clinical analysis on disease-relevant phosphoproteins, while quite challenging, provides unique information for precision medicine and targeted therapy. Among various approaches, mass spectrometry (MS)-centered characterization features discovery-driven, high-throughput and in-depth identification of phosphorylation events. This review highlights advances in sample preparation and instrument in MS-based phosphoproteomics and recent clinical applications. We emphasize the preeminent data-independent acquisition method in MS as one of the most promising future directions and biofluid-derived extracellular vesicles as an intriguing source of the phosphoproteome for liquid biopsy.
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Affiliation(s)
- Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Yi-Kai Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Tymora Analytical Operations, West Lafayette, IN, USA
| | - W. Andy Tao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Tymora Analytical Operations, West Lafayette, IN, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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Huang Y, Abdelgawad A, Turchinovich A, Queen S, Abreu CM, Zhu X, Batish M, Zheng L, Witwer KW. RNA landscapes of brain tissue and brain tissue-derived extracellular vesicles in simian immunodeficiency virus (SIV) infection and SIV-related central nervous system pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.01.535193. [PMID: 37034720 PMCID: PMC10081316 DOI: 10.1101/2023.04.01.535193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Introduction Antiretroviral treatment regimens can effectively control HIV replication and some aspects of disease progression. However, molecular events in end-organ diseases such as central nervous system (CNS) disease are not yet fully understood, and routine eradication of latent reservoirs is not yet in reach. Brain tissue-derived extracellular vesicles (bdEVs) act locally in the source tissue and may indicate molecular mechanisms in HIV CNS pathology. Regulatory RNAs from EVs have emerged as important participants in HIV disease pathogenesis. Using brain tissue and bdEVs from the simian immunodeficiency virus (SIV) model of HIV disease, we profiled messenger RNAs (mRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), seeking to identify possible networks of RNA interaction in SIV infection and neuroinflammation. Methods Postmortem occipital cortex tissue were collected from pigtailed macaques: uninfected controls and SIV-infected subjects (acute phase and chronic phase with or without CNS pathology). bdEVs were separated and characterized in accordance with international consensus standards. RNAs from bdEVs and source tissue were used for sequencing and qPCR to detect mRNA, miRNA, and circRNA levels. Results Multiple dysregulated bdEV RNAs, including mRNAs, miRNAs, and circRNAs, were identified in acute infection and chronic infection with pathology. Most dysregulated mRNAs in bdEVs reflected dysregulation in their source tissues. These mRNAs are disproportionately involved in inflammation and immune responses, especially interferon pathways. For miRNAs, qPCR assays confirmed differential abundance of miR-19a-3p, let-7a-5p, and miR-29a-3p (acute SIV infection), and miR-146a-5p and miR-449a-5p (chronic with pathology) in bdEVs. In addition, target prediction suggested that several circRNAs that were differentially abundant in source tissue might be responsible for specific differences in small RNA levels in bdEVs during SIV infection. Conclusions RNA profiling of bdEVs and source tissues reveals potential regulatory networks in SIV infection and SIV-related CNS pathology.
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Affiliation(s)
- Yiyao Huang
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ahmed Abdelgawad
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE, USA
| | - Andrey Turchinovich
- Division of Cancer Genome Research, German Cancer Research Center DKFZ, Heidelberg, Germany
- Heidelberg Biolabs GmbH, Mannheim, Germany
| | - Suzanne Queen
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Celina Monteiro Abreu
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xianming Zhu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mona Batish
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE, USA
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Huang Y, Liao Z, Dang P, Queen S, Abreu CM, Gololobova O, Zheng L, Witwer KW. Longitudinal characterization of circulating extracellular vesicles and small RNA during simian immunodeficiency virus infection and antiretroviral therapy. AIDS 2023; 37:733-744. [PMID: 36779477 PMCID: PMC9994802 DOI: 10.1097/qad.0000000000003487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/11/2023] [Indexed: 02/14/2023]
Abstract
OBJECTIVES Latent infection by HIV hinders viral eradication despite effective antiretroviral treatment (ART). Among proposed contributors to viral latency are cellular small RNAs that have also been proposed to shuttle between cells in extracellular vesicles. Thus, we profiled extracellular vesicle small RNAs during different infection phases to understand the potential relationship between these extracellular vesicle associated small RNAs and viral infection. DESIGN A well characterized simian immunodeficiency virus (SIV)/macaque model of HIV was used to profile extracellular vesicle enriched blood plasma fractions harvested during preinfection, acute infection, latent infection/ART treatment, and rebound after ART interruption. METHODS Measurement of extracellular vesicle concentration, size distribution, and morphology was complemented with qPCR array for small RNA expression, followed by individual qPCR validations. Iodixanol density gradients were used to separate extracellular vesicle subtypes and virions. RESULTS Plasma extracellular vesicle particle counts correlated with viral load and peaked during acute infection. However, SIV gag RNA detection showed that virions did not fully explain this peak. Extracellular vesicle microRNAs miR-181a, miR-342-3p, and miR-29a decreased with SIV infection and remained downregulated in latency. Interestingly, small nuclear RNA U6 had a tight association with viral load peak. CONCLUSION This study is the first to monitor how extracellular vesicle concentration and extracellular vesicle small RNA expression change dynamically in acute viral infection, latency, and rebound in a carefully controlled animal model. These changes may also reveal regulatory roles in retroviral infection and latency.
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Affiliation(s)
- Yiyao Huang
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zhaohao Liao
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Phuong Dang
- College of Pharmacy, University of Texas, Houston, Texas, USA
| | - Suzanne Queen
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Celina Monteiro Abreu
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Olesia Gololobova
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Kenneth W. Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Neurology
- Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Boucher J, Rousseau A, Boucher C, Subra C, Bazié WW, Hubert A, Bourgeault E, Benmoussa A, Goyer B, Tessier PA, Gilbert C. Immune Cells Release MicroRNA-155 Enriched Extracellular Vesicles That Promote HIV-1 Infection. Cells 2023; 12:cells12030466. [PMID: 36766808 PMCID: PMC9914104 DOI: 10.3390/cells12030466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
The hallmark of HIV-1 infection is the rapid dysregulation of immune functions. Recent investigations for biomarkers of such dysregulation in people living with HIV (PLWH) reveal a strong correlation between viral rebound and immune activation with an increased abundance of extracellular vesicles (EVs) enriched with microRNA-155. We propose that the activation of peripheral blood mononuclear cells (PBMCs) leads to an increased miR-155 expression and production of miR-155-rich extracellular vesicles (miR-155-rich EVs), which can exacerbate HIV-1 infection by promoting viral replication. PBMCs were incubated with either HIV-1 (NL4.3Balenv), a TLR-7/8 agonist, or TNF. EVs were harvested from the cell culture supernatant by differential centrifugation, and RT-qPCR quantified miR-155 in cells and derived EVs. The effect of miR-155-rich EVs on replication of HIV-1 in incubated PBMCs was then measured by viral RNA and DNA quantification. HIV-1, TLR7/8 agonist, and TNF each induced the release of miR-155-rich EVs by PBMCs. These miR-155-rich EVs increased viral replication in PBMCs infected in vitro. Infection with HIV-1 and inflammation promote the production of miR-155-rich EVs, enhancing viral replication. Such autocrine loops, therefore, could influence the course of HIV-1 infection by promoting viral replication.
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Affiliation(s)
- Julien Boucher
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Alyssa Rousseau
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Catherine Boucher
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Caroline Subra
- U.S. Military HIV Research Program, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Wilfried W. Bazié
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso 01 BP 390, Burkina Faso
| | - Audrey Hubert
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Emma Bourgeault
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Abderrahim Benmoussa
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Benjamin Goyer
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Philippe A. Tessier
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
- Département de Microbiologie-Infectiologie et d’Immunologie, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Caroline Gilbert
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
- Département de Microbiologie-Infectiologie et d’Immunologie, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
- Correspondence: ; Tel.: +1-418-525-4444 (ext. 46107); Fax: +1-418-654-2765
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HIV Replication Increases the Mitochondrial DNA Content of Plasma Extracellular Vesicles. Int J Mol Sci 2023; 24:ijms24031924. [PMID: 36768245 PMCID: PMC9916095 DOI: 10.3390/ijms24031924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/05/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Extracellular vesicles (EVs) and their cargo have been studied intensively as potential sources of biomarkers in HIV infection; however, their DNA content, particularly the mitochondrial portion (mtDNA), remains largely unexplored. It is well known that human immunodeficiency virus (HIV) infection and prolonged antiretroviral therapy (ART) lead to mitochondrial dysfunction and reduced mtDNA copy in cells and tissues. Moreover, mtDNA is a well-known damage-associated molecular pattern molecule that could potentially contribute to increased immune activation, oxidative stress, and inflammatory response. We investigated the mtDNA content of large and small plasma EVs in persons living with HIV (PLWH) and its implications for viral replication, ART use, and immune status. Venous blood was collected from 196 PLWH, ART-treated or ART-naïve (66 with ongoing viral replication, ≥20 copies/mL), and from 53 HIV-negative persons, all recruited at five HIV testing or treatment centers in Burkina Faso. Large and small plasma EVs were purified and counted, and mtDNA level was measured by RT-qPCR. Regardless of HIV status, mtDNA was more abundant in large than small EVs. It was more abundant in EVs of viremic than aviremic and control participants and tended to be more abundant in participants treated with Tenofovir compared with Zidovudine. When ART treatment was longer than six months and viremia was undetectable, no variation in EV mtDNA content versus CD4 and CD8 count or CD4/CD8 ratio was observed. However, mtDNA in large and small EVs decreased with years of HIV infection and ART. Our results highlight the impact of viral replication and ART on large and small EVs' mtDNA content. The mechanisms underlying the differential incorporation of mtDNA into EVs and their effects on the surrounding cells warrant further investigation.
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Translational proteomics and phosphoproteomics: Tissue to extracellular vesicles. Adv Clin Chem 2022; 112:119-153. [PMID: 36642482 DOI: 10.1016/bs.acc.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We are currently experiencing a rapidly developing era in terms of translational and clinical medical sciences. The relatively mature state of nucleic acid examination has significantly improved our understanding of disease mechanism and therapeutic potential of personalized treatment, but misses a large portion of phenotypic disease information. Proteins, in particular phosphorylation events that regulates many cellular functions, could provide real-time information for disease onset, progression and treatment efficacy. The technical advances in liquid chromatography and mass spectrometry have realized large-scale and unbiased proteome and phosphoproteome analyses with disease relevant samples such as tissues. However, tissue biopsy still has multiple shortcomings, such as invasiveness of sample collection, potential health risk for patients, difficulty in protein preservation and extreme heterogeneity. Recently, extracellular vesicles (EVs) have offered a great promise as a unique source of protein biomarkers for non-invasive liquid biopsy. Membranous EVs provide stable preservation of internal proteins and especially labile phosphoproteins, which is essential for effective routine biomarker detection. To aid efficient EV proteomic and phosphoproteomic analyses, recent developments showcase clinically-friendly EV techniques, facilitating diagnostic and therapeutic applications. Ultimately, we envision that with streamlined sample preparation from tissues and EVs proteomics and phosphoproteomics analysis will become routine in clinical settings.
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Bazié WW, Boucher J, Goyer B, Traoré IT, Kania D, Somé DY, Alary M, Gilbert C. Plasma vesicular miR-155 as a biomarker of immune activation in antiretroviral treated people living with HIV. Front Immunol 2022; 13:916599. [PMID: 36105810 PMCID: PMC9464867 DOI: 10.3389/fimmu.2022.916599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
People living with HIV (PLWH), despite suppression of viral replication with antiretroviral therapy (ART), have high morbidity and mortality due to immune activation and chronic inflammation. Discovering new biomarkers of immune activation status under ART will be pertinent to improve PLWH quality of life when the majority will be treated. We stipulate that plasma large and small extracellular vesicle (EVs) and their microRNA content could be easily measured biomarkers to monitor immune activation in PLWH. Venous blood samples from n = 128 ART-treated PLWH with suppressed viral load (≤ 20 copies/mL) and n = 60 HIV-uninfected participants were collected at five testing or treatment centers of PLWH in Burkina Faso. Large and small plasma EVs were purified, counted, and the mature miRNAs miR-29a, miR-146a, and miR-155 were quantified by RT-qPCR. Diagnostic performances of large and small EVs miRNAs level were evaluated by receiver operating characteristic (ROC) curve analysis and principal component analysis (PCA). Among the EVs microRNA measured, only large EVs miR-155 copies distinguished PLWH with immune activation, with AUC of 0.75 for CD4/CD8 < 1 (95% CI: 0.58–0.91, P = 0.0212), and 0.77 for CD8 T cells ≥ 500/µL (95% CI: 0.63–0.92, P = 0.0096). In addition, PCA results suggest that large EVs miR-155 copies may be a biomarker of immune activation. Since miR-155 may influence immune cell function, its enrichment in large EV subpopulations could be a functional biomarker of immune activation in PLWH on ART. This measure could help to monitor and diagnose the immune activation with more accuracy.
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Affiliation(s)
- Wilfried Wenceslas Bazié
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso, Burkina Faso
- *Correspondence: Caroline Gilbert, ; Wilfried Wenceslas Bazié,
| | - Julien Boucher
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Benjamin Goyer
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Isidore Tiandiogo Traoré
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso, Burkina Faso
- Institut Supérieur des Sciences de la Santé, Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | - Dramane Kania
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso, Burkina Faso
| | - Diane Yirgnur Somé
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso, Burkina Faso
| | - Michel Alary
- Axe de Recherche Santé des Populations et Pratiques Optimales en Santé, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Québec, QC, Canada
- Institut National de Santé Publique du Québec, Québec, QC, Canada
| | - Caroline Gilbert
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Département de Microbiologie-Infectiologie et d’Immunologie, Faculté de Médecine, Université Laval, Québec, QC, Canada
- *Correspondence: Caroline Gilbert, ; Wilfried Wenceslas Bazié,
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Bazié WW, Boucher J, Traoré IT, Kania D, Somé DY, Alary M, Gilbert C. Vesicular MicroRNA as Potential Biomarkers of Viral Rebound. Cells 2022; 11:cells11050859. [PMID: 35269481 PMCID: PMC8909274 DOI: 10.3390/cells11050859] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023] Open
Abstract
Changes in the cellular microRNA (miRNA) expression profile in response to HIV infection, replication or latency have been reported. Nevertheless, little is known concerning the abundance of miRNA in extracellular vesicles (EVs). In the search for a reliable predictor of viral rebound, we quantified the amount of miR-29a, miR-146a, and miR-155 in two types of plasma extracellular vesicles. Venous blood was collected from 235 ART-treated and ART-naive persons living with HIV (85 with ongoing viral replication, ≥20 copies/mL) and 60 HIV-negative participants at five HIV testing or treatment centers in Burkina Faso. Large and small plasma EVs were purified and counted, and mature miRNA miR-29a, miR-146a, and miR-155 were measured by RT-qPCR. Diagnostic performance of miRNA levels in large and small EVs was evaluated by a receiver operating characteristic curve analysis. The median duration of HIV infection was 36 months (IQR 14-117). The median duration of ART was 34 months (IQR 13-85). The virus was undetectable in 63.8% of these persons. In the others, viral load ranged from 108 to 33,978 copies/mL (median = 30,032). Large EVs were more abundant in viremic participants than aviremic. All three miRNAs were significantly more abundant in small EVs in persons with detectable HIV RNA, and their expression levels in copies per vesicle were a more reliable indicator of viral replication in ART-treated patients with low viremia (20-1000 copies/mL). HIV replication increased the production of large EVs more than small EVs. Combined with viral load measurement, quantifying EV-associated miRNA abundance relative to the number of vesicles provides a more reliable marker of the viral status. The expression level as copies per small vesicle could predict the viral rebound in ART-treated patients with undetectable viral loads.
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Affiliation(s)
- Wilfried Wenceslas Bazié
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada;
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso 01 BP 390, Burkina Faso; (I.T.T.); (D.K.); (D.Y.S.)
- Correspondence: (W.W.B.); (C.G.); Tel.: +1-(418)-525-4444 (ext. 44104) (W.W.B.); +1-(418)-525-4444 (ext. 46107) (C.G.); Fax: +1-(418)-654-2765 (C.G.)
| | - Julien Boucher
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada;
| | - Isidore Tiandiogo Traoré
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso 01 BP 390, Burkina Faso; (I.T.T.); (D.K.); (D.Y.S.)
- Département de Santé Publique, Institut Supérieur des Sciences de la Santé, Université Nazi Boni, Bobo-Dioulasso 01 BP 1091, Burkina Faso
| | - Dramane Kania
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso 01 BP 390, Burkina Faso; (I.T.T.); (D.K.); (D.Y.S.)
| | - Diane Yirgnur Somé
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso 01 BP 390, Burkina Faso; (I.T.T.); (D.K.); (D.Y.S.)
| | - Michel Alary
- Axe de Recherche Santé des Populations et Pratiques Optimales en Santé, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC G1S 4L8, Canada;
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut National de Santé Publique du Québec, Quebec City, QC G1V 5B3, Canada
| | - Caroline Gilbert
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada;
- Département de Microbiologie-Infectiologie et d’Immunologie, Faculté de Médecine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Correspondence: (W.W.B.); (C.G.); Tel.: +1-(418)-525-4444 (ext. 44104) (W.W.B.); +1-(418)-525-4444 (ext. 46107) (C.G.); Fax: +1-(418)-654-2765 (C.G.)
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Ostermeier B, Soriano-Sarabia N, Maggirwar SB. Platelet-Released Factors: Their Role in Viral Disease and Applications for Extracellular Vesicle (EV) Therapy. Int J Mol Sci 2022; 23:2321. [PMID: 35216433 PMCID: PMC8876984 DOI: 10.3390/ijms23042321] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/13/2022] [Accepted: 02/17/2022] [Indexed: 02/04/2023] Open
Abstract
Platelets, which are small anuclear cell fragments, play important roles in thrombosis and hemostasis, but also actively release factors that can both suppress and induce viral infections. Platelet-released factors include sCD40L, microvesicles (MVs), and alpha granules that have the capacity to exert either pro-inflammatory or anti-inflammatory effects depending on the virus. These factors are prime targets for use in extracellular vesicle (EV)-based therapy due to their ability to reduce viral infections and exert anti-inflammatory effects. While there are some studies regarding platelet microvesicle-based (PMV-based) therapy, there is still much to learn about PMVs before such therapy can be used. This review provides the background necessary to understand the roles of platelet-released factors, how these factors might be useful in PMV-based therapy, and a critical discussion of current knowledge of platelets and their role in viral diseases.
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Affiliation(s)
| | | | - Sanjay B. Maggirwar
- Department of Microbiology Immunology and Tropical Medicine, The George Washington University, 2300 I Street NW, Washington, DC 20037, USA; (B.O.); (N.S.-S.)
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Ramirez SH, Buzhdygan TP, Hale JF, Cheng L, Li G, Hoover-Hankerson B, Razmpour R, Sriram U, Su L, Potula R, Andrews AM. Extracellular Microvesicles Released From Brain Endothelial Cells are Detected in Animal Models Of HIV-1 Signifying Unresolved Inflammation. J Neuroimmune Pharmacol 2021; 16:785-795. [PMID: 34435263 PMCID: PMC8714626 DOI: 10.1007/s11481-021-10008-5] [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: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 11/28/2022]
Abstract
Treatment of HIV-infected patients with antiretroviral therapy (ART) has effectively suppressed viral replication; however, the central nervous system is still a major target and reservoir of the virus leading to the possible development of HIV-associated neurocognitive disorders (HAND). Furthermore, a hallmark feature of HAND is the disruption of the blood–brain barrier that leads to loss of tight junction protein (TJP) complexes. Extracellular vesicles (EVs), released by every cell type in the body, occur in greater quantities in response to cellular activation or injury. We have found that inflammatory insults activate brain endothelial cells (EC) and induce the release of EVs containing TJPs such as Occludin. We thus hypothesized that HIV infection and unresolved neuroinflammation will result in the release of brain-EC derived EVs. Herein, our results show elevated levels of brain-EC EVs in a humanized mouse model of HIV infection. Furthermore, while ART reduced brain-EC EVs, it was unable to completely resolve increased vesicles detectable in the blood. In addition to inflammatory insults, HIV-1 viral proteins (Tat and gp120) increased the release of Occludin + vesicles from human brain microvasculature ECs. This increase in vesicle release could be prevented by knock-down of the small GTPase ARF6. ARF6 has been shown to regulate EV biogenesis in other cell types, and we provide further evidence for the involvement of ARF6 in brain EC derived EVs. Overall, this study offers insight into the process of brain vascular remodeling (via EVs) in the setting of neuroinflammation and thus provides possibilities for biomarker monitoring and targeting of ARF6.
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Affiliation(s)
- Servio H Ramirez
- Department of Pathology &, Laboratory Medicine Lewis Katz School of Medicine at Temple University, 3500 N Broad St, PA, 19140, Philadelphia, USA.,The Center for Substance Abuse Research Lewis Katz School of Medicine at Temple University, 3500 N Broad St, PA, 19140, Philadelphia, USA.,The Shriners Hospitals Pediatric Research Center, Philadelphia, PA, 19140, USA
| | - Tetyana P Buzhdygan
- Department of Pathology &, Laboratory Medicine Lewis Katz School of Medicine at Temple University, 3500 N Broad St, PA, 19140, Philadelphia, USA.,The Center for Substance Abuse Research Lewis Katz School of Medicine at Temple University, 3500 N Broad St, PA, 19140, Philadelphia, USA
| | - Jonathan F Hale
- Department of Pathology &, Laboratory Medicine Lewis Katz School of Medicine at Temple University, 3500 N Broad St, PA, 19140, Philadelphia, USA
| | - Liang Cheng
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, The University of North Carolina At Chapel Hill, Chapel Hill, NC, 27599, USA.,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Guangming Li
- Division of Virology, Pathogenesis and Cancer, Institute of Human Virology, Departments of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, The University of North Carolina At Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bryson Hoover-Hankerson
- Department of Pathology &, Laboratory Medicine Lewis Katz School of Medicine at Temple University, 3500 N Broad St, PA, 19140, Philadelphia, USA
| | - Roshanak Razmpour
- Department of Pathology &, Laboratory Medicine Lewis Katz School of Medicine at Temple University, 3500 N Broad St, PA, 19140, Philadelphia, USA
| | - Uma Sriram
- Department of Pathology &, Laboratory Medicine Lewis Katz School of Medicine at Temple University, 3500 N Broad St, PA, 19140, Philadelphia, USA
| | - Lishan Su
- Division of Virology, Pathogenesis and Cancer, Institute of Human Virology, Departments of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, The University of North Carolina At Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Raghava Potula
- Department of Pathology &, Laboratory Medicine Lewis Katz School of Medicine at Temple University, 3500 N Broad St, PA, 19140, Philadelphia, USA.,The Center for Substance Abuse Research Lewis Katz School of Medicine at Temple University, 3500 N Broad St, PA, 19140, Philadelphia, USA
| | - Allison M Andrews
- Department of Pathology &, Laboratory Medicine Lewis Katz School of Medicine at Temple University, 3500 N Broad St, PA, 19140, Philadelphia, USA. .,The Center for Substance Abuse Research Lewis Katz School of Medicine at Temple University, 3500 N Broad St, PA, 19140, Philadelphia, USA.
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Vaillancourt M, Hubert A, Subra C, Boucher J, Bazié WW, Vitry J, Berrazouane S, Routy JP, Trottier S, Tremblay C, Jenabian MA, Benmoussa A, Provost P, Tessier PA, Gilbert C. Velocity Gradient Separation Reveals a New Extracellular Vesicle Population Enriched in miR-155 and Mitochondrial DNA. Pathogens 2021; 10:526. [PMID: 33925397 PMCID: PMC8146806 DOI: 10.3390/pathogens10050526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/10/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022] Open
Abstract
Extracellular vesicles (EVs) and their contents (proteins, lipids, messenger RNA, microRNA, and DNA) are viewed as intercellular signals, cell-transforming agents, and shelters for viruses that allow both diagnostic and therapeutic interventions. EVs circulating in the blood of individuals infected with human immunodeficiency virus (HIV-1) may provide insights into pathogenesis, inflammation, and disease progression. However, distinguishing plasma membrane EVs from exosomes, exomeres, apoptotic bodies, virions, and contaminating proteins remains challenging. We aimed at comparing sucrose and iodixanol density and velocity gradients along with commercial kits as a means of separating EVs from HIV particles and contaminating protein like calprotectin; and thereby evaluating the suitability of current plasma EVs analysis techniques for identifying new biomarkers of HIV-1 immune activation. Multiple analysis have been performed on HIV-1 infected cell lines, plasma from HIV-1 patients, or plasma from HIV-negative individuals spiked with HIV-1. Commercial kits, the differential centrifugation and density or velocity gradients to precipitate and separate HIV, EVs, and proteins such as calprotectin, have been used. EVs, virions, and contaminating proteins were characterized using Western blot, ELISA, RT-PCR, hydrodynamic size measurement, and enzymatic assay. Conversely to iodixanol density or velocity gradient, protein and virions co-sedimented in the same fractions of the sucrose density gradient than AChE-positive EVs. Iodixanol velocity gradient provided the optimal separation of EVs from viruses and free proteins in culture supernatants and plasma samples from a person living with HIV (PLWH) or a control and revealed a new population of large EVs enriched in microRNA miR-155 and mitochondrial DNA. Although EVs and their contents provide helpful information about several key events in HIV-1 pathogenesis, their purification and extensive characterization by velocity gradient must be investigated thoroughly before further use as biomarkers. By revealing a new population of EVs enriched in miR-155 and mitochondrial DNA, this study paves a way to increase our understanding of HIV-1 pathogenesis.
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Affiliation(s)
- Myriam Vaillancourt
- Centre de Recherche du CHU de Québec-Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada; (M.V.); (A.H.); (C.S.); (J.B.); (W.W.B.); (J.V.); (S.B.); (S.T.); (A.B.); (P.P.); (P.A.T.)
| | - Audrey Hubert
- Centre de Recherche du CHU de Québec-Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada; (M.V.); (A.H.); (C.S.); (J.B.); (W.W.B.); (J.V.); (S.B.); (S.T.); (A.B.); (P.P.); (P.A.T.)
| | - Caroline Subra
- Centre de Recherche du CHU de Québec-Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada; (M.V.); (A.H.); (C.S.); (J.B.); (W.W.B.); (J.V.); (S.B.); (S.T.); (A.B.); (P.P.); (P.A.T.)
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Julien Boucher
- Centre de Recherche du CHU de Québec-Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada; (M.V.); (A.H.); (C.S.); (J.B.); (W.W.B.); (J.V.); (S.B.); (S.T.); (A.B.); (P.P.); (P.A.T.)
| | - Wilfried Wenceslas Bazié
- Centre de Recherche du CHU de Québec-Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada; (M.V.); (A.H.); (C.S.); (J.B.); (W.W.B.); (J.V.); (S.B.); (S.T.); (A.B.); (P.P.); (P.A.T.)
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso 01 BP 390, Burkina Faso
| | - Julien Vitry
- Centre de Recherche du CHU de Québec-Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada; (M.V.); (A.H.); (C.S.); (J.B.); (W.W.B.); (J.V.); (S.B.); (S.T.); (A.B.); (P.P.); (P.A.T.)
| | - Sofiane Berrazouane
- Centre de Recherche du CHU de Québec-Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada; (M.V.); (A.H.); (C.S.); (J.B.); (W.W.B.); (J.V.); (S.B.); (S.T.); (A.B.); (P.P.); (P.A.T.)
| | - Jean-Pierre Routy
- Chronic Viral Illness Service and Division of Hematology, McGill University Health Centre, Montréal, QC H4A 3J1, Canada;
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Sylvie Trottier
- Centre de Recherche du CHU de Québec-Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada; (M.V.); (A.H.); (C.S.); (J.B.); (W.W.B.); (J.V.); (S.B.); (S.T.); (A.B.); (P.P.); (P.A.T.)
- Centre de Recherche du CHU de Québec, Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada
| | - Cécile Tremblay
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, QC H3C 3J7, Canada;
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Mohammad-Ali Jenabian
- Département des Sciences Biologiques et Centre de Recherche CERMO-FC, Université du Québec à Montréal (UQAM), Montréal, QC H2L 2C4, Canada;
| | - Abderrahim Benmoussa
- Centre de Recherche du CHU de Québec-Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada; (M.V.); (A.H.); (C.S.); (J.B.); (W.W.B.); (J.V.); (S.B.); (S.T.); (A.B.); (P.P.); (P.A.T.)
- Department of Nutrition, CHU Sainte-Justine—Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Patrick Provost
- Centre de Recherche du CHU de Québec-Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada; (M.V.); (A.H.); (C.S.); (J.B.); (W.W.B.); (J.V.); (S.B.); (S.T.); (A.B.); (P.P.); (P.A.T.)
- Centre de Recherche du CHU de Québec, Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada
| | - Philippe A. Tessier
- Centre de Recherche du CHU de Québec-Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada; (M.V.); (A.H.); (C.S.); (J.B.); (W.W.B.); (J.V.); (S.B.); (S.T.); (A.B.); (P.P.); (P.A.T.)
- Centre de Recherche du CHU de Québec, Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada
| | - Caroline Gilbert
- Centre de Recherche du CHU de Québec-Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada; (M.V.); (A.H.); (C.S.); (J.B.); (W.W.B.); (J.V.); (S.B.); (S.T.); (A.B.); (P.P.); (P.A.T.)
- Centre de Recherche du CHU de Québec, Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université Laval, T1-49, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada
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Diurnal Variation of Plasma Extracellular Vesicle Is Disrupted in People Living with HIV. Pathogens 2021; 10:pathogens10050518. [PMID: 33923310 PMCID: PMC8145918 DOI: 10.3390/pathogens10050518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/10/2021] [Accepted: 04/19/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Several types of extracellular vesicles (EVs) secreted by various immune and non-immune cells are present in the human plasma. We previously demonstrated that EV abundance and microRNA content change in pathological conditions, such as HIV infection. Here, we investigated daily variations of large and small EVs, in terms of abundance and microRNA contents in people living with HIV (PLWH) receiving antiretroviral therapy (HIV+ART) and uninfected controls (HIV-). METHODS Venous blood samples from n = 10 HIV+ART and n = 10 HIV- participants were collected at 10:00 and 22:00 the same day. Large and small plasma EVs were purified, counted, and the mature miRNAs miR-29a, miR-29b, miR-92, miR-155, and miR-223 copies were measured by RT-PCR. RESULTS Large EVs were significantly bigger in the plasma collected at 10:00 versus 22:00 in both groups. There was a significant day-night increase in the quantity of 5 miRNAs in HIV- large EVs. In HIV+ART, only miR-155 daily variation has been observed in large EVs. Finally, EV-miRNA content permits to distinguish HIV- to HIV+ART in multivariate analysis. CONCLUSION These results point that plasma EV amount and microRNA contents are under daily variation in HIV- people. This new dynamic measure is disrupted in PLWH despite viral-suppressive ART. This study highlights a significant difference concerning EV abundance and their content measured at 22:00 between both groups. Therefore, the time of blood collection must be considered in the future for the EV as biomarkers.
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