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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 and Brain-Derived Extracellular Vesicles in Simian Immunodeficiency Virus Infection and Central Nervous System Pathology. J Infect Dis 2024; 229:1295-1305. [PMID: 38079216 PMCID: PMC11095537 DOI: 10.1093/infdis/jiad563] [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: 07/24/2023] [Revised: 11/20/2023] [Accepted: 12/07/2023] [Indexed: 12/26/2023] Open
Abstract
BACKGROUND Brain tissue-derived extracellular vesicles (bdEVs) act locally in the central nervous system (CNS) and may indicate molecular mechanisms in human immunodeficiency virus (HIV) CNS pathology. Using brain homogenate (BH) and bdEVs from a simian immunodeficiency virus (SIV) model of HIV disease, we identified RNA networks in SIV infection and neuroinflammation. METHODS Postmortem occipital cortex samples were obtained from uninfected controls and SIV-infected subjects (acute and chronic phases with or without CNS pathology [SIV encephalitis]). bdEVs were separated and characterized per international consensus guidelines. RNAs from bdEVs and BH were sequenced and quantitative polymerase chain reaction (qPCR)-amplified to detect levels of small RNAs (sRNAs, including microRNAs [miRNAs]) and longer RNAs including messenger RNAs (mRNAs) and circular RNAs (circRNAs). RESULTS Dysregulated RNAs in BH and bdEVs were identified in acute and chronic infection with pathology groups, including mRNAs, miRNAs, and circRNAs. Most dysregulated mRNAs in bdEVs reflected dysregulation in source BH. These mRNAs are disproportionately involved in inflammation and immune responses. Based on target prediction, several circRNAs that were differentially abundant in source tissue might be responsible for specific differences in sRNA 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, Maryland, 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, Delaware, USA
| | - Andrey Turchinovich
- Division of Cancer Genome Research, German Cancer Research Center, Heidelberg, Germany
- Heidelberg Biolabs, GmbH, Heidelberg, Germany
| | - Suzanne Queen
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Celina Monteiro Abreu
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Xianming Zhu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mona Batish
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, 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, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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2
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Huang Y, Driedonks TAP, Cheng L, Turchinovich A, Pletnikova O, Redding-Ochoa J, Troncoso JC, Hill AF, Mahairaki V, Zheng L, Witwer KW. Small RNA Profiles of Brain Tissue-Derived Extracellular Vesicles in Alzheimer's Disease. J Alzheimers Dis 2024; 99:S235-S248. [PMID: 37781809 DOI: 10.3233/jad-230872] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Background Extracellular vesicles (EVs) and non-coding RNAs (ncRNAs) are emerging contributors to Alzheimer's disease (AD) pathophysiology. Differential abundance of ncRNAs carried by EVs may provide valuable insights into underlying disease mechanisms. Brain tissue-derived EVs (bdEVs) are particularly relevant, as they may offer valuable insights about the tissue of origin. However, there is limited research on diverse ncRNA species in bdEVs in AD. Objective This study explored whether the non-coding RNA composition of EVs isolated from post-mortem brain tissue is related to AD pathogenesis. Methods bdEVs from age-matched late-stage AD patients (n = 23) and controls (n = 10) that had been separated and characterized in our previous study were used for RNA extraction, small RNA sequencing, and qPCR verification. Results Significant differences of non-coding RNAs between AD and controls were found, especially for miRNAs and tRNAs. AD pathology-related miRNA and tRNA differences of bdEVs partially matched expression differences in source brain tissues. AD pathology had a more prominent association than biological sex with bdEV miRNA and tRNA components in late-stage AD brains. Conclusions Our study provides further evidence that EV non-coding RNAs from human brain tissue, including but not limited to miRNAs, may be altered and contribute to AD pathogenesis.
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Affiliation(s)
- Yiyao Huang
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tom A P Driedonks
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lesley Cheng
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Andrey Turchinovich
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Biolabs GmbH, Heidelberg, Germany
| | - Olga Pletnikova
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Javier Redding-Ochoa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew F Hill
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
- Institute of Health and Sport, Victoria University, Melbourne, Australia
| | - Vasiliki Mahairaki
- Department of Genetic Medicine, 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
| | - 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 Genetic Medicine, 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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3
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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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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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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Pinapati KK, Tandon R, Tripathi P, Srivastava N. Recent advances to overcome the burden of Japanese encephalitis: A zoonotic infection with problematic early detection. Rev Med Virol 2023; 33:e2383. [PMID: 35983697 DOI: 10.1002/rmv.2383] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/21/2022] [Accepted: 07/29/2022] [Indexed: 01/28/2023]
Abstract
Japanese encephalitis (JE) is a vector-borne neurotropic disease caused by Japanese encephalitis virus (JEV) associated with high mortality rate distributed from Eastern and Southern Asia to Northern Queensland (Australia). The challenges in early detection and lack of point-of-care biomarkers make it the most important Flavivirus causing encephalitis. There is no specific treatment for the disease, although vaccines are licenced. In this review, we focussed on point-of-care biomarkers as early detection tools and developing the effective therapeutic agents that could halt JE. We have also provided molecular details of JEV, disease progression, and its pathogenesis with recent findings which might bring insights to overcome the disease burden.
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Affiliation(s)
- Kishore Kumar Pinapati
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Raebareli (NIPER-R), Lucknow, Uttra Pradesh, India
| | - Reetika Tandon
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Raebareli (NIPER-R), Lucknow, Uttra Pradesh, India
| | - Pratima Tripathi
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Raebareli (NIPER-R), Lucknow, Uttra Pradesh, India
| | - Nidhi Srivastava
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Raebareli (NIPER-R), Lucknow, Uttra Pradesh, India
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6
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Zhu X, Hollinger KR, Huang Y, Borjabad A, Kim BH, Arab T, Thomas AG, Moniruzzaman M, Lovell L, Turchinovich A, Witwer KW, Volsky DJ, Haughey NJ, Slusher BS. Neutral sphingomyelinase 2 inhibition attenuates extracellular vesicle release and improves neurobehavioral deficits in murine HIV. Neurobiol Dis 2022; 169:105734. [PMID: 35462006 PMCID: PMC9202342 DOI: 10.1016/j.nbd.2022.105734] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/22/2022] [Accepted: 04/13/2022] [Indexed: 01/11/2023] Open
Abstract
People living with HIV (PLH) have significantly higher rates of cognitive impairment (CI) and major depressive disorder (MDD) versus the general population. The enzyme neutral sphingomyelinase 2 (nSMase2) is involved in the biogenesis of ceramide and extracellular vesicles (EVs), both of which are dysregulated in PLH, CI, and MDD. Here we evaluated EcoHIV-infected mice for behavioral abnormalities relevant to depression and cognition deficits, and assessed the behavioral and biochemical effects of nSMase2 inhibition. Mice were infected with EcoHIV and daily treatment with either vehicle or the nSMase2 inhibitor (R)-(1-(3-(3,4-dimethoxyphenyl)-2,6-dimethylimidazo[1,2-b]pyridazin-8-yl)pyrrolidin-3-yl)-carbamate (PDDC) began 3 weeks post-infection. After 2 weeks of treatment, mice were subjected to behavior tests. EcoHIV-infected mice exhibited behavioral abnormalities relevant to MDD and CI that were reversed by PDDC treatment. EcoHIV infection significantly increased cortical brain nSMase2 activity, resulting in trend changes in sphingomyelin and ceramide levels that were normalized by PDDC treatment. EcoHIV-infected mice also exhibited increased levels of brain-derived EVs and altered microRNA cargo, including miR-183-5p, miR-200c-3p, miR-200b-3p, and miR-429-3p, known to be associated with MDD and CI; all were normalized by PDDC. In conclusion, inhibition of nSMase2 represents a possible new therapeutic strategy for the treatment of HIV-associated CI and MDD.
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Affiliation(s)
- Xiaolei Zhu
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kristen R Hollinger
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yiyao Huang
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alejandra Borjabad
- Department of Medicine, Infectious Diseases Division, Icahn School of Medicine at Mount Sinai, NY, New York, USA
| | - Boe-Hyun Kim
- Department of Medicine, Infectious Diseases Division, Icahn School of Medicine at Mount Sinai, NY, New York, USA
| | - Tanina Arab
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ajit G Thomas
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mohammed Moniruzzaman
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lyndah Lovell
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrey Turchinovich
- Heidelberg Biolabs GmbH, Heidelberg, Germany; Division of Cancer Genome Research, German Cancer Research Center, Heidelberg, Germany
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David J Volsky
- Department of Medicine, Infectious Diseases Division, Icahn School of Medicine at Mount Sinai, NY, New York, USA
| | - Norman J Haughey
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Barbara S Slusher
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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7
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Wang Z, Lu T, Li X, Jiang M, Jia M, Liu J, Zhang D, Li J, Wang L. Altered Expression of Brain-specific Autism-Associated miRNAs in the Han Chinese Population. Front Genet 2022; 13:865881. [PMID: 35342389 PMCID: PMC8942769 DOI: 10.3389/fgene.2022.865881] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 02/14/2022] [Indexed: 11/16/2022] Open
Abstract
Autism is a complex neurodevelopmental disorder. However, its etiology is still unknown. MicroRNAs (miRNAs) are key post-transcriptional regulators. They play an important role in neurodevelopment and brain functions and may be involved in the pathogenesis of autism. Previous studies indicated altered expression of miRNAs in patients with autism. However, the findings were not consistent, and further explorations were needed. This study aimed to investigate whether miRNAs were dysregulated in autism. We examined the expression of 30 brain-specific autism-associated miRNAs in 110 patients with autism and 113 controls in the Han Chinese population using quantitative reverse transcription–polymerase chain reaction. The results demonstrated that 10 miRNAs (hsa-miR-191-5p, hsa-miR-151a-3p, hsa-miR-139-5p, hsa-miR-181a-5p, hsa-miR-432-5p, hsa-miR-181b-5p, hsa-miR-195-5p, hsa-miR-328-3p, hsa-miR-106a-5p, and hsa-miR-484) were significantly differentially expressed (false discovery rate <0.05). All of them were up-regulated in patients with autism compared with controls. The targets of these miRNAs were enriched for genes and pathways related to neurodevelopment, brain functions and autism. These findings suggested the participation of these 10 miRNAs in the pathogenesis of autism in the Han Chinese population.
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Affiliation(s)
- Ziqi Wang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Tianlan Lu
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Xianjing Li
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Miaomiao Jiang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Meixiang Jia
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Jing Liu
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Dai Zhang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China.,Chinese Institute for Brain Research, Beijing, China.,Guangdong Key Laboratory of Mental Health and Cognitive Science, Institute for Brain Research and Rehabilitation (IBRR), South China Normal University, Guangzhou, China
| | - Jun Li
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Lifang Wang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
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8
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Valacchi G, Pambianchi E, Coco S, Pulliero A, Izzotti A. MicroRNA Alterations Induced in Human Skin by Diesel Fumes, Ozone, and UV Radiation. J Pers Med 2022; 12:176. [PMID: 35207665 PMCID: PMC8880698 DOI: 10.3390/jpm12020176] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022] Open
Abstract
Epigenetic alterations are a driving force of the carcinogenesis process. MicroRNAs play a role in silencing mutated oncogenes, thus defending the cell against the adverse consequences of genotoxic damages induced by environmental pollutants. These processes have been well investigated in lungs; however, although skin is directly exposed to a great variety of environmental pollutants, more research is needed to better understand the effect on cutaneous tissue. Therefore, we investigated microRNA alteration in human skin biopsies exposed to diesel fumes, ozone, and UV light for over 24 h of exposure. UV and ozone-induced microRNA alteration right after exposure, while the peak of their deregulations induced by diesel fumes was reached only at the end of the 24 h. Diesel fumes mainly altered microRNAs involved in the carcinogenesis process, ozone in apoptosis, and UV in DNA repair. Accordingly, each tested pollutant induced a specific pattern of microRNA alteration in skin related to the intrinsic mechanisms activated by the specific pollutant. These alterations, over a short time basis, reflect adaptive events aimed at defending the tissue against damages. Conversely, whenever environmental exposure lasts for a long time, the irreversible alteration of the microRNA machinery results in epigenetic damage contributing to the pathogenesis of inflammation, dysplasia, and cancer induced by environmental pollutants.
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Affiliation(s)
- Giuseppe Valacchi
- Animal Science Department, Plants for Human Health Institute, North Carolina State University, Research Campus Kannapolis, Kannapolis, NC 28081, USA; (G.V.); (E.P.)
- Department of Environmental Sciences and Prevention, University of Ferrara, 44121 Ferrara, Italy
- Department of Food and Nutrition, Kyung Hee University, Seoul 130-701, Korea
| | - Erika Pambianchi
- Animal Science Department, Plants for Human Health Institute, North Carolina State University, Research Campus Kannapolis, Kannapolis, NC 28081, USA; (G.V.); (E.P.)
| | - Simona Coco
- Lung Cancer Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy;
| | | | - Alberto Izzotti
- Department of Experimental Medicine, University of Genova, 16132 Genova, Italy
- UOC Mutagenesis and Cancer Prevention, IRCCS San Martino Hospital, 16132 Genova, Italy
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9
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Consuegra I, Gasco S, Serramía MJ, Jiménez JL, Mellado MJ, Muñoz-Fernández MÁ. Establishment of a miRNA profile in paediatric HIV-1 patients and its potential as a biomarker for effectiveness of the combined antiretroviral therapy. Sci Rep 2021; 11:23477. [PMID: 34873266 PMCID: PMC8648729 DOI: 10.1038/s41598-021-03020-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 11/12/2021] [Indexed: 11/18/2022] Open
Abstract
miRNAs have been extensively studied in pathological conditions, including viral infections, such as those provoked by HIV-1. Several cellular and circulating miRNAs are altered during HIV-1 infection, with either beneficial effects on host defenses or enhanced virus infectivity. Blood samples were collected in sterile EDTA tubes and plasma was separated and stored, as were PBMCs. RNA was isolated and reverse-transcribed. Finally, the miRNA gene expression profile was assessed using TaqMan Array Human microRNA Card A v2.0. A comprehensive statistical analysis was performed on the results obtained. This is the first study on miRNAs in HIV-1 paediatric patients, and a miRNA profile differentiating patients starting combination antiretroviral therapy (cART) at different times after HIV-1 diagnosis was established. Thirty-four miRNAs were observed to have different expression levels between the control group and the cART group. The data indicates the need to start cART as soon as possible after the establishment of HIV-1 infection to assure the best outcome possible. Finally, the selected 34 miRNAs may be used as biomarkers for prognosis and assessing therapy effectiveness. However, more research must be conducted to establish adequate quantitative correlations.
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Affiliation(s)
- Irene Consuegra
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.,Spanish HIV HGM BioBank, Madrid, Spain
| | - Samanta Gasco
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - María Jesús Serramía
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.,Laboratorio InmunoBiología Molecular, Head Immunology Section, (Hospital General Universitario Gregorio Marañón), C/Dr. Esquerdo 46, 28007, Madrid, Spain
| | - José Luis Jiménez
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.,Spanish HIV HGM BioBank, Madrid, Spain.,Plataforma-Laboratorio (IiSGM), Madrid, Spain
| | - Maria Jose Mellado
- General Pediatrics, Infectious and Tropical Diseases Department Hospital, Universitario La Paz, Madrid, Spain.,IdiPAZ, Madrid, Spain.,Translational Research Network in Pediatric Infectious Diseases (RITIP), Madrid, Spain
| | - María Ángeles Muñoz-Fernández
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain. .,Spanish HIV HGM BioBank, Madrid, Spain. .,Laboratorio InmunoBiología Molecular, Head Immunology Section, (Hospital General Universitario Gregorio Marañón), C/Dr. Esquerdo 46, 28007, Madrid, Spain. .,Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain.
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10
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Zhu L, Qiu C, Dai L, Zhang L, Feng M, Yang Y, Qiu C, Zhang A, Huang J, Wang Y, Wan Y, Zhao C, Wu H, Lyu J, Zhang X, Xu J. Hsa-miR-31 Governs T-Cell Homeostasis in HIV Protection via IFN-γ-Stat1-T-Bet Axis. Front Immunol 2021; 12:771279. [PMID: 34804062 PMCID: PMC8602903 DOI: 10.3389/fimmu.2021.771279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/21/2021] [Indexed: 11/20/2022] Open
Abstract
It remains poorly defined whether any human miRNAs play protective roles during HIV infection. Here, focusing on a unique cohort of HIV-infected former blood donors, we identified miR-31 (hsa-miR-31) by comparative miRNA profiling as the only miRNA inversely correlating with disease progression. We further validated this association in two prospective cohort studies. Despite conservation during evolution, hsa-miR-31, unlike its mouse counterpart (mmu-miR-31), was downregulated in human T cell upon activation. Our ex vivo studies showed that inhibiting miR-31 in naïve CD4+ T cells promoted a transcriptional profile with activation signature. Consistent with this skewing effect, miR-31 inhibition led to remarkably increased susceptibility to HIV infection. The suppressive nature of miR-31 in CD4+ T cell activation was pinpointed to its ability to decrease T-bet, the key molecule governing IFN-γ production and activation of CD4+ T cells, by directly targeting the upstream STAT1 transcriptional factor for downregulation, thus blunting Th1 response. Our results implicated miR-31 as a useful biomarker for tracking HIV disease progression and, by demonstrating its importance in tuning the activation of CD4+ T cells, suggested that miR-31 may play critical roles in other physiological contexts where the CD4+ T cell homeostasis needs to be deliberately controlled.
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Affiliation(s)
- Lingyan Zhu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Chao Qiu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lili Dai
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Linxia Zhang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Meiqi Feng
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yu Yang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Chenli Qiu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Anli Zhang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jun Huang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ying Wang
- Department of AIDS/STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Ying Wan
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Chen Zhao
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hao Wu
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Jianxin Lyu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jianqing Xu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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11
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Zhao Z, Muth DC, Mulka K, Liao Z, Powell BH, Hancock GV, Metcalf Pate KA, Witwer KW. miRNA profiling of primate cervicovaginal lavage and extracellular vesicles reveals miR-186-5p as a potential antiretroviral factor in macrophages. FEBS Open Bio 2020; 10:2021-2039. [PMID: 33017084 PMCID: PMC7530394 DOI: 10.1002/2211-5463.12952] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 06/03/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022] Open
Abstract
Cervicovaginal secretions, or their components collected, are referred to as cervicovaginal lavage (CVL). CVL constituents have utility as biomarkers and play protective roles in wound healing and against HIV-1 infection. However, several components of cervicovaginal fluids are less well understood, such as extracellular RNAs and their carriers, for example, extracellular vesicles (EVs). EVs comprise a wide array of double-leaflet membrane extracellular particles and range in diameter from 30 nm to over one micron. The aim of this study was to determine whether differentially regulated CVL microRNAs (miRNAs) might influence retrovirus replication. To this end, we characterized EVs and miRNAs of primate CVL during the menstrual cycle and simian immunodeficiency virus (SIV) infection of macaques. EVs were enriched by stepped ultracentrifugation, and miRNA profiles were assessed with a medium-throughput stem-loop/hydrolysis probe qPCR platform. Whereas hormone cycling was abnormal in infected subjects, EV concentration correlated with progesterone concentration in uninfected subjects. miRNAs were present predominantly in the EV-depleted CVL supernatant. Only a small number of CVL miRNAs changed during the menstrual cycle or SIV infection, for example, miR-186-5p, which was depleted in retroviral infection. This miRNA inhibited HIV replication in infected macrophages in vitro. In silico target prediction and pathway enrichment analyses shed light on the probable functions of miR-186-5p in hindering HIV infections via immunoregulation, T-cell regulation, disruption of viral pathways, etc. These results provide further evidence for the potential of EVs and small RNAs as biomarkers or effectors of disease processes in the reproductive tract.
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Affiliation(s)
- Zezhou Zhao
- Department of Molecular and Comparative PathobiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | - Dillon C. Muth
- Department of Molecular and Comparative PathobiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | - Kathleen Mulka
- Department of Molecular and Comparative PathobiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | - Zhaohao Liao
- Department of Molecular and Comparative PathobiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | - Bonita H. Powell
- Department of Molecular and Comparative PathobiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | | | - Kelly A. Metcalf Pate
- Department of Molecular and Comparative PathobiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | - Kenneth W. Witwer
- Department of Molecular and Comparative PathobiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
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12
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Lv Y, Jing G, Zhu G, Luo H, Li B, Xie Y, Li C, Wang X. Effects and mechanism of the etanercept on pancreatic encephalopathy. Mol Med Rep 2020; 21:2615-2623. [PMID: 32323789 DOI: 10.3892/mmr.2020.11062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 02/25/2020] [Indexed: 11/05/2022] Open
Abstract
Pancreatic encephalopathy (PE) is a common fatal complication of acute pancreatitis (AP). Proinflammatory cytokines such as tumor necrosis factor (TNF)‑α and interleukin (IL)‑6 are generated during AP, and act synergistically to promote PE and multisystem failure. Caerulein‑induced AP provides a convenient model to explore the role of proinflammatory cytokines in PE. The aim of the present study was to examine the effect of the TNF‑α inhibitor etanercept in PE models and elucidate the regulatory mechanisms. To model PE in vitro, rat hippocampal H19‑7/IGF‑IR neuronal cells were treated with 10 nmol/ml caerulein alone or in combination with etanercept (1, 10 or 100 µmol/ml). To model PE in vivo, rats were injected with 50 µg/kg caerulein alone or combined with 10 mg/kg etanercept. At 6 h after administration, it was noted that etanercept downregulated expression of TNF‑α, IL‑1β and IL‑6 by negatively regulating NF‑κB (a master regulator of cytokine expression) signaling, and prevented the accumulation of reactive oxygen species. Conversely, etanercept promoted the expression of the neurotrophic and anti‑inflammatory hypoxia‑inducible factor 1 α (HIF‑1α). In rat hippocampus, etanercept also reduced the levels of TNF‑α, IL‑1β and IL‑6, upregulated HIF‑1α expression and inhibited the inflammatory response to reduce edema and neural necrosis. Together, these data suggested that etanercept could attenuate caerulein‑induced PE, at least in part via suppression of NF‑κB signaling and alleviation of oxidative stress.
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Affiliation(s)
- Yifan Lv
- Department of Neurosurgery, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Guojie Jing
- Department of Neurosurgery, Huizhou First People's Hospital, Huizhou, Guangdong 516000, P.R. China
| | - Gang Zhu
- Department of Neurosurgery, Huizhou Central People's Hospital, Huizhou, Guangdong 516000, P.R. China
| | - Honghai Luo
- Department of Neurosurgery, Huizhou Central People's Hospital, Huizhou, Guangdong 516000, P.R. China
| | - Baisheng Li
- Department of Neurosurgery, Huizhou Central People's Hospital, Huizhou, Guangdong 516000, P.R. China
| | - Yituan Xie
- Department of Neurosurgery, Huizhou First People's Hospital, Huizhou, Guangdong 516000, P.R. China
| | - Caiming Li
- Department of Neurosurgery, Huizhou First People's Hospital, Huizhou, Guangdong 516000, P.R. China
| | - Xiangyu Wang
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510220, P.R. China
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13
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Wang X, Sun L, Zhou Y, Su QJ, Li JL, Ye L, Liu MQ, Zhou W, Ho WZ. Heroin Abuse and/or HIV Infection Dysregulate Plasma Exosomal miRNAs. J Neuroimmune Pharmacol 2019; 15:400-408. [PMID: 31828734 DOI: 10.1007/s11481-019-09892-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 10/29/2019] [Indexed: 12/13/2022]
Abstract
Exosomes play an important role in cell-to-cell communication as they can transfer functional molecules such as microRNAs (miRNAs) from one cell to another, exerting biological and immunological functions. Here, we investigated the impact of HIV infection and/or heroin use on the expression of the miRNAs in plasma exosomes. We found that HIV infection or heroin use upregulated the majority (98%) of a panel of plasma exosomal miRNAs associated with immune regulation and inflammation. We also observed the enhanced effect of HIV infection and heroin use on some of these upregulated miRNAs. Our further investigation showed that the levels of four of neuro-inflammation-related miRNAs (146a, 126, 21, and let-7a) were higher in HIV-infected heroin users as compared with the control subjects. These findings indicate that the dysregulations of the plasma exosomal miRNAs support further studies to determine the role of the miRNAs in HIV and/or heroin use-mediated immune modulation and neuro-inflammation. Graphical abstract.
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Affiliation(s)
- Xu Wang
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Li Sun
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA.,Xinjiang Uygur Pharmaceutical Co., Ltd, Wulumuqi, 830000, China
| | - Yu Zhou
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA.,Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, NJ, 08512, USA
| | - Qi-Jian Su
- Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, 530021, China
| | - Jie-Liang Li
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, 530021, China
| | - Man-Qing Liu
- Wuhan Centers for Disease Prevention & Control, Wuhan, 430024, China
| | - Wang Zhou
- Wuhan Centers for Disease Prevention & Control, Wuhan, 430024, China
| | - Wen-Zhe Ho
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA.
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14
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Abstract
OBJECTIVE MicroRNAs (miRNAs) are noncoding RNAs that regulate gene expression. We aimed to determine the association between extracellular miRNAs and HIV infection. DESIGN Single-center, cross-sectional study. METHODS We analyzed the expression of 192 plasma-derived miRNAs in 69 HIV-infected individuals and 24 uninfected controls using TaqMan miRNA assays and a high-throughput Real-Time PCR instrument (Fluidigm). False discovery rate (FDR) was applied. RESULTS HIV-infected individuals and controls were similar in age, sex, and traditional risk factors. Among those with HIV, 72.5% were on antiretroviral therapy (ARVs) and 64% had an undetectable viral load. Twenty-nine miRNAs were differentially expressed in the plasma of HIV-infected individuals compared with controls (P < 0.05, FDR < 0.15). Nineteen miRNAs were differentially expressed among HIV+ subjects on ARVs, HIV+ subjects not on ARVs, and HIV- subjects (P < 0.05 and FDR < 0.15). Thirty-four miRNAs were differentially expressed between HIV- subjects and elite controllers (ie, suppressed viral loads despite the absence of ARVs; P < 0.05 and FDR < 0.15). These 34 miRNAs included miRs-29c, 146b, 223, and 382, which were previously reported to have intracellular roles in HIV latency, as well as miRs-126, 145, and let-7, which were previously shown to be differentially expressed in coronary artery disease among uninfected individuals. CONCLUSIONS We demonstrate a unique expression profile of 29 miRNAs in HIV+ subjects and 34 miRNAs in elite controllers as compared to HIV- subjects. These miRNA signatures may be useful in further elucidating mechanisms of viral and immunological control and may have diagnostic or prognostic value in HIV-associated coronary artery disease.
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15
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Molina PE, Simon L, Amedee AM, Welsh DA, Ferguson TF. Impact of Alcohol on HIV Disease Pathogenesis, Comorbidities and Aging: Integrating Preclinical and Clinical Findings. Alcohol Alcohol 2018; 53:439-447. [PMID: 29546271 DOI: 10.1093/alcalc/agy016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/01/2018] [Indexed: 12/12/2022] Open
Abstract
Short Summary : Effective combined antiretroviral therapy regimens have extended survival of persons living with HIV (PLWH). Heavy alcohol consumption is common in PLWH. This overview integrates evidence from clinical and preclinical research to identify salient alcohol-related mechanisms and comorbidities contributing to disease pathogenesis and accelerated aging and senescence in PLWH.
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Affiliation(s)
- Patricia E Molina
- Comprehensive Alcohol-HIV/AIDS Research Center and Alcohol and Drug Abuse Center of Excellence, LSUHSC, 1901 Perdido St., New Orleans, LA, USA
| | - Liz Simon
- Comprehensive Alcohol-HIV/AIDS Research Center and Alcohol and Drug Abuse Center of Excellence, LSUHSC, 1901 Perdido St., New Orleans, LA, USA
| | - Angela M Amedee
- Comprehensive Alcohol-HIV/AIDS Research Center and Alcohol and Drug Abuse Center of Excellence, LSUHSC, 1901 Perdido St., New Orleans, LA, USA
| | - David A Welsh
- Comprehensive Alcohol-HIV/AIDS Research Center and Alcohol and Drug Abuse Center of Excellence, LSUHSC, 1901 Perdido St., New Orleans, LA, USA
| | - Tekeda F Ferguson
- Comprehensive Alcohol-HIV/AIDS Research Center and Alcohol and Drug Abuse Center of Excellence, LSUHSC, 1901 Perdido St., New Orleans, LA, USA
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16
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Qin X, Li L, Lv Q, Shu Q, Zhang Y, Wang Y. Expression profile of plasma microRNAs and their roles in diagnosis of mild to severe traumatic brain injury. PLoS One 2018; 13:e0204051. [PMID: 30226895 PMCID: PMC6143266 DOI: 10.1371/journal.pone.0204051] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/31/2018] [Indexed: 02/07/2023] Open
Abstract
Traumatic brain injury (TBI) is associated with trauma-related death. In this study, we evaluated differences in the expression of plasma microRNAs (miRNAs) in patients with different degrees of TBI, and explored the potential of miRNAs for use as diagnostic TBI biomarkers. The miRNA microarray results showed upregulation of 65, 33, and 16 miRNAs and downregulation of 29, 27, and 6 miRNAs in patients with mild, moderate, and severe TBI, respectively, compared with healthy controls. Thirteen miRNAs (seven upregulated and six downregulated) were found to be present in all TBI groups. Seven upregulated miRNAs were selected for validation in an enlarged cohort of samples and showed good diagnostic accuracy. The expression levels of miR-3195 and miR-328-5p were higher in the severe TBI group than in the mild and moderate TBI groups. In summary, our study demonstrates different expression profiles in plasma miRNAs among patients with mild to severe TBI. A subset of seven miRNAs can be used for diagnosis of TBI. Moreover, miR-3195 and miR-328-5p may be utilized during diagnosis to distinguish mild and moderate TBI from severe TBI.
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Affiliation(s)
- Xiaojing Qin
- Department of Histology and Embryology, Chongqing Medical University, Chongqing, China
- Department of Pathology, Affiliated Hospital of Logistic University of PAP, Tianjin, China
| | - Lingzhi Li
- Tianjin Key Laboratory for Prevention and Control of Occupational and Environmental Hazard, Tianjin, China
| | - Qi Lv
- Institute of Disaster Medicine, Tianjin University, Tianjin, China
| | | | - Yongliang Zhang
- Tianjin Key Laboratory for Prevention and Control of Occupational and Environmental Hazard, Tianjin, China
- * E-mail: (YW); (YZ)
| | - Yaping Wang
- Department of Histology and Embryology, Chongqing Medical University, Chongqing, China
- * E-mail: (YW); (YZ)
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17
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Baluni M, Ghildiyal S, Singh D, Himanshu Reddy D, Kumar R, Dhole TN. Increased serum microRNA-29b expression and bad recovery in Japanese encephalitis virus infected patients; A new component to improve the disease recovery. J Neuroimmunol 2018; 323:56-61. [PMID: 30196835 DOI: 10.1016/j.jneuroim.2018.07.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/25/2018] [Accepted: 07/25/2018] [Indexed: 12/25/2022]
Abstract
BACKGROUND Japanese encephalitis virus (JEV) is a neurotropic mosquito-borne Flavivirus, mainly prevalent in Asia. It is the most important causative agent of acute viral encephalitis in humans. Recently, micro RNAs are discovered as a key regulator of inflammatory and immune responses in various diseases including neurological and viral infections. Thus, this study was proposed to check whether changes in cellular miRNA expression due to JE virus infection, can be detected in circulation which would be helpful in diagnosis and treatment. METHODS miRNAs (miR-29b and miR-146a) were analyzed in the serum of JEV infected patients using quantitative reverse transcription polymerase chain reaction (RT-qPCR). RESULTS miR-146a was found significantly decreased (p = 0.0008) in JEV infected patients as compared to healthy controls whereas miR-29b was significantly increased (p = 0.001) in JEV patients recovered with neurological sequelae when compared to those recovered without sequelae. CONCLUSION In conclusion, miRNA can be measured in serum. Studying microRNAs will provide novel information and help us to identify the components that can serve as biomarkers and can lead to new discovery in controlling disease recovery.
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Affiliation(s)
- Manjari Baluni
- Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow 226014, Uttar Pradesh, India
| | - Sneha Ghildiyal
- Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow 226014, Uttar Pradesh, India
| | - Dharamveer Singh
- Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow 226014, Uttar Pradesh, India
| | - D Himanshu Reddy
- King George Medical University, Lucknow 226003, Uttar Pradesh, India
| | - Rashmi Kumar
- King George Medical University, Lucknow 226003, Uttar Pradesh, India
| | - Tapan N Dhole
- Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow 226014, Uttar Pradesh, India.
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18
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Yan F, Tu Z, Duan L, Wang D, Lin F. MicroRNA-383 suppresses cell proliferation and invasion in colorectal cancer by directly targeting paired box 6. Mol Med Rep 2018; 17:6893-6901. [PMID: 29512711 DOI: 10.3892/mmr.2018.8682] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/09/2017] [Indexed: 12/16/2022] Open
Abstract
Colorectal cancer (CRC) is the third-most prevalent cancer and the fourth‑most common cause of cancer-associated fatality worldwide. The expression and biological roles of microRNAs (miRNAs/miRs) in tumourigenesis, and their regulatory function in a number of biological processes correlated with cancer have been investigated. miR‑383 has been reported to be deregulated in several human cancer types. However, the involvement and effects of miR‑383 on CRC progression and its underlying mechanism remain unknown. Therefore, the present study aimed to examine miR‑383 expression, investigate the biological functions of miR‑383 and identify its mechanism of action in CRC cells. In the present study, miR‑383 was significantly downregulated in CRC tissues and cell lines. Low miR‑383 expression was negatively associated with tumour size, lymph node metastasis and TNM stage. Function experiments demonstrated that miR‑383 upregulation inhibited the proliferation and invasion of CRC cells. Paired box 6 (PAX6) was confirmed as a direct target of miR‑383. PAX6 was upregulated in CRC tissues and was negatively correlated with miR‑383 expression. Induced PAX6 overexpression effectively rescued the tumour‑suppressing roles of miR‑383 on CRC cell proliferation and invasion. These findings suggested that miR‑383 may act as a tumour suppressor in CRC by directly targeting PAX6 and may serve as a promising therapeutic target for CRC treatment.
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Affiliation(s)
- Fei Yan
- Department of Oncology, The Eighth People's Hospital of Shanghai, Shanghai 200233, P.R. China
| | - Zhiquan Tu
- Department of Oncology, The Eighth People's Hospital of Shanghai, Shanghai 200233, P.R. China
| | - Li Duan
- Department of Oncology, The Eighth People's Hospital of Shanghai, Shanghai 200233, P.R. China
| | - Dexing Wang
- Department of Oncology, The Eighth People's Hospital of Shanghai, Shanghai 200233, P.R. China
| | - Feng Lin
- Department of Oncology, The Eighth People's Hospital of Shanghai, Shanghai 200233, P.R. China
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19
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Oda H, Ikeguchi R, Aoyama T, Ohta S, Noguchi T, Kaizawa Y, Yurie H, Takeuchi H, Yamamoto K, Matsuda S. MicroRNAs are potential objective and early biomarkers for acute rejection of transplanted limbs in a rat model. Microsurgery 2017; 37:930-936. [DOI: 10.1002/micr.30236] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 06/29/2017] [Accepted: 08/25/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Hiroki Oda
- Department of Orthopaedic SurgeryGraduate School of Medicine, Kyoto UniversityKyoto Japan
| | - Ryosuke Ikeguchi
- Department of Orthopaedic SurgeryGraduate School of Medicine, Kyoto UniversityKyoto Japan
| | - Tomoki Aoyama
- Department of Physical TherapyHuman Health Sciences, Graduate School of Medicine, Kyoto UniversityKyoto Japan
| | - Souichi Ohta
- Department of Orthopaedic SurgeryGraduate School of Medicine, Kyoto UniversityKyoto Japan
| | - Takashi Noguchi
- Department of Orthopaedic SurgeryGraduate School of Medicine, Kyoto UniversityKyoto Japan
| | - Yukitoshi Kaizawa
- Department of Orthopaedic SurgeryGraduate School of Medicine, Kyoto UniversityKyoto Japan
| | - Hirofumi Yurie
- Department of Orthopaedic SurgeryGraduate School of Medicine, Kyoto UniversityKyoto Japan
| | - Hisataka Takeuchi
- Department of Orthopaedic SurgeryGraduate School of Medicine, Kyoto UniversityKyoto Japan
| | - Koji Yamamoto
- Department of Biomedical Engineering, Faculty of Life and Medical SciencesDoshisha UniversityKyotanabe, Kyoto Japan
| | - Shuichi Matsuda
- Department of Orthopaedic SurgeryGraduate School of Medicine, Kyoto UniversityKyoto Japan
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20
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Hu G, Liao K, Yang L, Pendyala G, Kook Y, Fox HS, Buch S. Tat-Mediated Induction of miRs-34a & -138 Promotes Astrocytic Activation via Downregulation of SIRT1: Implications for Aging in HAND. J Neuroimmune Pharmacol 2017; 12:420-432. [PMID: 28236278 PMCID: PMC5546000 DOI: 10.1007/s11481-017-9730-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 02/15/2017] [Indexed: 12/13/2022]
Abstract
Astrocyte activation is a hallmark of HIV infection and aging in the CNS. In chronically infected HIV patients, prolonged activation of astrocytes has been linked to accelerated aging including but not limited to neurocognitive impairment and frailty. The current study addresses the role of HIV protein Tat in inducing a set of small noncoding microRNAs (miRNA) that play critical role in astrogliosis. In our efforts to link astrocyte activation as an indicator of aging, we assessed the brains of both wild type and HIV transgenic rats for the expression of glial fibrillary acidic protein (GFAP). As expected, in the WT animals we observed age-dependent increase in astrogliosis in the older animals compared to the younger group. Interestingly, compared to the young WT group, young HIV Tg rats exhibited higher levels of GFAP in this trend was also observed in the older HIV Tg rats compared to the older WT group. Based on the role of SIRT1 in aging and the regulation of SIRT1 by miRNAs-34a and -138, we next assessed the expression levels of these miRs in the brains of both the young an old WT and HIV Tg rats. While there were no significant differences in the young WT versus the HIV Tg rats, in the older HIV Tg rats there was a significant upregulation in the expression of miRs-34a & -138 in the brains. Furthermore, increased expression of miRs-34a & -138 in the older Tg rats, correlated with a concomitant decrease in their common anti-aging target protein SIRT1, in the brains of these animals. To delineate the mechanism of action we assessed the role of HIV-Tat (present in the Tg rats) in inducing miRs-34a & -138 in both the primary astrocytes and the astrocytoma cell line A172, thereby leading to posttranscriptional suppression of SIRT1 with a concomitant up regulation of NF-kB driven expression of GFAP.
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Affiliation(s)
- Guoku Hu
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ke Liao
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lu Yang
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Gurudutt Pendyala
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yeonhee Kook
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Howard S Fox
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shilpa Buch
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA.
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21
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Pavani KC, Alminana C, Wydooghe E, Catteeuw M, Ramírez MA, Mermillod P, Rizos D, Van Soom A. Emerging role of extracellular vesicles in communication of preimplantation embryos in vitro. Reprod Fertil Dev 2017; 29:66-83. [PMID: 28278795 DOI: 10.1071/rd16318] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In vitro, efficient communication between mammalian embryos in groups or between embryos and cocultured somatic cells implies that there is a sender, a message and a receiver that is able to decode the message. Embryos secrete a variety of autocrine and paracrine factors and, of these, extracellular vesicles have recently been implicated as putative messengers in embryo-embryo communication, as well as in communication of the embryo with the maternal tract. Extracellular vesicles (EVs) are membrane-bound vesicles that are found in biofluids and in culture media conditioned by the presence of embryos or cells. EVs carry and transfer regulatory molecules, such as microRNAs, mRNAs, lipids and proteins. We conducted a systematic search of the literature to review and present the currently available evidence regarding the possible roles of EVs in in vitro embryo communication and embryo development. It is important to note that there is limited information available on the molecular mechanisms and many of the biologically plausible functions of EVs in embryo communication have not yet been substantiated by conclusive experimental evidence. However, indirect evidence, such as the use of media conditioned by embryos or by somatic cells with improved embryo development as a result, may indicate that EVs can be an important asset for the development of tailor-made media, allowing better embryo development in vitro, even for single embryo culture.
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Affiliation(s)
- Krishna C Pavani
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, University of Ghent, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - Carmen Alminana
- INRA, Reproductive Physiology and Behavior, UMR085, INRA, CNRS, Université de Tours, IFCE, 37380 Nouzilly, France
| | - Eline Wydooghe
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, University of Ghent, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - Maaike Catteeuw
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, University of Ghent, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - Miguel A Ramírez
- Departamento de Reproduccion Animal, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Madrid 28040, Spain
| | - Pascal Mermillod
- INRA, Reproductive Physiology and Behavior, UMR085, INRA, CNRS, Université de Tours, IFCE, 37380 Nouzilly, France
| | - Dimitrios Rizos
- Departamento de Reproduccion Animal, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Madrid 28040, Spain
| | - Ann Van Soom
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, University of Ghent, Salisburylaan 133, B-9820 Merelbeke, Belgium
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MicroRNA-210, MicroRNA-331, and MicroRNA-7 Are Differentially Regulated in Treated HIV-1-Infected Individuals and Are Associated With Markers of Systemic Inflammation. J Acquir Immune Defic Syndr 2017; 74:e104-e113. [PMID: 27749601 DOI: 10.1097/qai.0000000000001191] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Inflammation may contribute to an increased risk of cardiovascular disease (CVD) in HIV-1 infection. MicroRNAs (miRNAs) are involved in the regulation of inflammation. In treated HIV-1-infected individuals, we aimed to identify differentially expressed miRNAs with known roles in inflammation and CVD risk and to investigate associations between these and systemic inflammation. METHODS In a screening cohort including 14 HIV-1-infected individuals and 9 uninfected controls, microarray profiling was performed using peripheral blood mononuclear cells (PBMCs). Differentially regulated miRNAs previously related to inflammation and CVD were validated using real-time quantitative reverse-transcription polymerase chain reaction in 26 HIV-1-infected individuals and 20 uninfected controls. Validated miRNAs were measured in PBMCs, CD4 and CD8 T cells. Interleukin-6, tumor necrosis factor-alpha, high-sensitivity C-reactive protein, lipopolysaccharide (LPS), cytomegalovirus immunoglobulin G, lipids, and fasting glucose were measured, and associations with validated miRNAs were assessed with multiple linear regression analysis. RESULTS Upregulation of miR-210, miR-7, and miR-331 was found in PBMCs from HIV-1-infected individuals when compared with those from uninfected controls (P < 0.005). In contrast, miR-210 and miR-331 were downregulated in CD8 T cells. In multivariate analysis, miR-210 in CD8 T cells was negatively associated with LPS (P = 0.023) and triglycerides (P = 0.003) but positively associated with tumor necrosis factor-alpha (P = 0.004). MiR-7 in PBMC was positively associated with interleukin-6 (P = 0.025) and fasting glucose (P = 0.005), whereas miR-331 was negatively associated with LPS (P = 0.006). In PBMCs from HIV-1-infected individuals with low cytomegalovirus immunoglobulin G, miR-7, miR-29a, miR-221, and miR-222 were downregulated. CONCLUSION In 2 independent cohorts, miR-210, miR-7, and miR-331 were differentially regulated in treated HIV-1-infected individuals and associated with markers of systemic inflammation.
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Liao Z, Muth DC, Eitan E, Travers M, Learman LN, Lehrmann E, Witwer KW. Serum extracellular vesicle depletion processes affect release and infectivity of HIV-1 in culture. Sci Rep 2017; 7:2558. [PMID: 28566772 PMCID: PMC5451420 DOI: 10.1038/s41598-017-02908-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/20/2017] [Indexed: 01/07/2023] Open
Abstract
Extracellular vesicles (EVs) are involved in intercellular communication and affect processes including immune and antiviral responses. Blood serum, a common cell culture medium component, is replete with EVs and must be depleted prior to EV-related experiments. The extent to which depletion processes deplete non-EV particles is incompletely understood, but depleted serum is associated with reduced viability and growth in cell culture. Here, we examined whether serum depleted by two methods affected HIV-1 replication. In cell lines, including HIV-1 latency models, increased HIV-1 production was observed, along with changes in cell behavior and viability. Add-back of ultracentrifuge pellets (enriched in EVs but possibly other particles) rescued baseline HIV-1 production. Primary cells were less sensitive to serum depletion processes. Virus produced under processed serum conditions was more infectious. Finally, changes in cellular metabolism, surface markers, and gene expression, but not miRNA profiles, were associated with depleted serum culture. In conclusion, depleted serum conditions have a substantial effect on HIV-1 production and infectivity. Dependence of cell cultures on “whole serum” must be examined carefully along with other experimental variables, keeping in mind that the effects of EVs may be accompanied by or confused with those of closely associated or physically similar particles.
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Affiliation(s)
- Zhaohao Liao
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Dillon C Muth
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Cellular and Molecular Medicine Program, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Erez Eitan
- Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, 21224, United States
| | - Meghan Travers
- Cellular and Molecular Medicine Program, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lisa N Learman
- Cellular and Molecular Medicine Program, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Elin Lehrmann
- Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, 21224, United States
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States. .,Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States. .,Cellular and Molecular Medicine Program, The Johns Hopkins University School of Medicine, Baltimore, MD, United States.
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Identification of a Specific miRNA Profile in HIV-Exposed Seronegative Individuals. J Acquir Immune Defic Syndr 2017; 73:11-9. [PMID: 27171739 DOI: 10.1097/qai.0000000000001070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE MicroRNAs (miRNAs) are small noncoding RNAs involved in the posttranscriptional regulation of gene expression that play important roles in viral infections. Alterations of specific miRNAs are described in HIV infection, suggesting a role for miRNAs in pathogenesis of this disease. We verified whether a particular miRNA signature could be identified in natural resistance to HIV-1. METHODS Expression level of 84 miRNAs was analyzed by RT-qPCR in plasma and unstimulated peripheral blood mononuclear cell (PBMC) of 30 seronegative individuals repeatedly exposed to HIV-1 (HESN), 30 HIV seropositive subjects (HIV+), and 30 healthy controls (HC). Results were confirmed by individual RT-qPCR in in vitro HIV-1-infected PBMC and in their cell culture medium. Dicer and Drosha expression was analyzed in basal PBMC. RESULTS Whereas Dicer and Drosha expression was comparable in HESN, HIV+ and HC, several miRNAs were upregulated both in HESN and HIV+ compared with HC. Furthermore, miRNA-29a and miR-223 were upregulated in both unstimulated PBMC and plasma of HESN alone; their expression was reduced upon in vitro HIV-1 infection of HESN PBMC indicating that, upon infection, they are secreted in the extracellular milieu. These results were confirmed by individual qPCR. CONCLUSIONS Our studies demonstrate that HIV-1 exposure modifies miRNAs expression even in the absence of productive infection. Because those miRNAs that are specifically increased only in HESN have been known to reduce HIV-1 replication, their modulation could represent an important mechanism in resistance to HIV-1 infection.
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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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Correia CN, Nalpas NC, McLoughlin KE, Browne JA, Gordon SV, MacHugh DE, Shaughnessy RG. Circulating microRNAs as Potential Biomarkers of Infectious Disease. Front Immunol 2017; 8:118. [PMID: 28261201 PMCID: PMC5311051 DOI: 10.3389/fimmu.2017.00118] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 01/25/2017] [Indexed: 12/12/2022] Open
Abstract
microRNAs (miRNAs) are a class of small non-coding endogenous RNA molecules that regulate a wide range of biological processes by post-transcriptionally regulating gene expression. Thousands of these molecules have been discovered to date, and multiple miRNAs have been shown to coordinately fine-tune cellular processes key to organismal development, homeostasis, neurobiology, immunobiology, and control of infection. The fundamental regulatory role of miRNAs in a variety of biological processes suggests that differential expression of these transcripts may be exploited as a novel source of molecular biomarkers for many different disease pathologies or abnormalities. This has been emphasized by the recent discovery of remarkably stable miRNAs in mammalian biofluids, which may originate from intracellular processes elsewhere in the body. The potential of circulating miRNAs as biomarkers of disease has mainly been demonstrated for various types of cancer. More recently, however, attention has focused on the use of circulating miRNAs as diagnostic/prognostic biomarkers of infectious disease; for example, human tuberculosis caused by infection with Mycobacterium tuberculosis, sepsis caused by multiple infectious agents, and viral hepatitis. Here, we review these developments and discuss prospects and challenges for translating circulating miRNA into novel diagnostics for infectious disease.
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Affiliation(s)
- Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Nicolas C Nalpas
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Kirsten E McLoughlin
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - John A Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland; University College Dublin, UCD Conway Institute of Biomolecular and Biomedical Research, Dublin, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland; University College Dublin, UCD Conway Institute of Biomolecular and Biomedical Research, Dublin, Ireland
| | - Ronan G Shaughnessy
- UCD School of Veterinary Medicine, University College Dublin , Dublin , Ireland
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Abstract
OBJECTIVE HIV-associated neurocognitive disorder (HAND) is a common neurological disorder among HIV-infected patients despite the availability of combination antiretroviral therapy. Host-encoded microRNAs (miRNA) regulate both host and viral gene expression contributing to HAND pathogenesis and can also serve as disease biomarkers. Herein, plasma miRNA profiles were investigated in HIV/AIDS patients with HAND. METHODS Discovery and Validation Cohorts comprising HIV/AIDS patients were studied that included patients with and without HAND (non-HAND). Plasma miRNA levels were measured by array hybridization and verified by quantitative real-time reverse transcriptase PCR (qRT-PCR). Multiple bioinformatic and biostatistical analyses were applied to the data from each cohort. RESULTS Expression analyses identified nine miRNAs in the Discovery Cohort (HAND, n = 22; non-HAND, n = 25) with increased levels (≥two-fold) in the HAND group compared with the non-HAND group (P < 0.05). In the Validation Cohort (HAND, n = 12; non-HAND, n = 12) upregulation (≥two-fold) of three miRNAs (miR-3665, miR-4516 and miR-4707-5p) was observed in the HAND group that were also increased in the Discovery Cohort's HAND patients, which were verified subsequently by qRT-PCR. Receiver-operating characteristic curve analyses for the three miRNAs also pointed to the diagnosis of HAND (area under curve, 0.87, P < 0.005). Bioinformatics tools predicted that all three miRNAs targeted sequences of genes implicated in neural development, cell death, inflammation, cell signalling and cytokine functions. CONCLUSION Differentially expressed plasma-derived miRNAs were detected in HIV/AIDS patients with HAND that were conserved across different patient cohorts and laboratory methods. Plasma-derived miRNAs might represent biomarkers for HAND and also provide insights into disease mechanisms.
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Kadri F, LaPlante A, De Luca M, Doyle L, Velasco-Gonzalez C, Patterson JR, Molina PE, Nelson S, Zea A, Parsons CH, Peruzzi F. Defining Plasma MicroRNAs Associated With Cognitive Impairment In HIV-Infected Patients. J Cell Physiol 2016; 231:829-36. [PMID: 26284581 PMCID: PMC4758906 DOI: 10.1002/jcp.25131] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 08/11/2015] [Indexed: 01/05/2023]
Abstract
Human Immunodeficiency Virus (HIV)-infected individuals are at increased risk for developing neurocognitive disorders and depression. These conditions collectively affect more than 50% of people living with HIV/AIDS and adversely impact adherence to HIV therapy. Thus, identification of early markers of neurocognitive impairment could lead to interventions that improve psychosocial functioning and slow or reverse disease progression through improved treatment adherence. Evidence has accumulated for the role and function of microRNAs in normal and pathological conditions. We have optimized a protocol to profile microRNAs in body fluids. Using this methodology, we have profiled plasma microRNA expression for 30 age-matched, HIV-infected (HIV(+) ) patients and identified highly sensitive and specific microRNA signatures distinguishing HIV(+) patients with cognitive impairment from those without cognitive impairment. These results justify follow-on studies to determine whether plasma microRNA signatures can be used as a screening or prognostic tool for HIV(+) patients with neurocognitive impairment. J. Cell. Physiol. 231: 829-836, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Ferdous Kadri
- LSU Health Sciences Center, Medical School, Stanley S. Scott Cancer Center, New Orleans, LA 70112, USA
- Department of Microbiology, Immunology and Parasitology, New Orleans, LA 70112, USA
| | - Andrea LaPlante
- LSU Health Sciences Center, Medical School, Stanley S. Scott Cancer Center, New Orleans, LA 70112, USA
| | - Mariacristina De Luca
- LSU Health Sciences Center, Medical School, Stanley S. Scott Cancer Center, New Orleans, LA 70112, USA
| | - Lisa Doyle
- LSU Health Sciences Center, Medical School, Stanley S. Scott Cancer Center, New Orleans, LA 70112, USA
| | - Cruz Velasco-Gonzalez
- LSU Health Sciences Center, Medical School, Stanley S. Scott Cancer Center, New Orleans, LA 70112, USA
| | - Jonathan R. Patterson
- LSU Health Sciences Center, Medical School, Stanley S. Scott Cancer Center, New Orleans, LA 70112, USA
| | | | - Steve Nelson
- LSU Health Sciences Center, Medical School, Stanley S. Scott Cancer Center, New Orleans, LA 70112, USA
| | - Arnold Zea
- LSU Health Sciences Center, Medical School, Stanley S. Scott Cancer Center, New Orleans, LA 70112, USA
| | - Christopher H. Parsons
- LSU Health Sciences Center, Medical School, Stanley S. Scott Cancer Center, New Orleans, LA 70112, USA
| | - Francesca Peruzzi
- LSU Health Sciences Center, Medical School, Stanley S. Scott Cancer Center, New Orleans, LA 70112, USA
- Correspondence: Francesca Peruzzi, LSU Health Sciences Center, 1700 Tulane Avenue, New Orleans, LA 70112, , Tel: (504) 210-2978, Fax: (504) 210-2970
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Simon L, Song K, Vande Stouwe C, Hollenbach A, Amedee A, Mohan M, Winsauer P, Molina P. Δ9-Tetrahydrocannabinol (Δ9-THC) Promotes Neuroimmune-Modulatory MicroRNA Profile in Striatum of Simian Immunodeficiency Virus (SIV)-Infected Macaques. J Neuroimmune Pharmacol 2016; 11:192-213. [PMID: 26607731 PMCID: PMC4773048 DOI: 10.1007/s11481-015-9645-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 11/12/2015] [Indexed: 12/22/2022]
Abstract
Cannabinoid administration before and after simian immunodeficiency virus (SIV)-inoculation ameliorated disease progression and decreased inflammation in male rhesus macaques. Δ9-tetrahydrocannabinol (Δ9-THC) did not increase viral load in brain tissue or produce additive neuropsychological impairment in SIV-infected macaques. To determine if the neuroimmunomodulation of Δ9-THC involved differential microRNA (miR) expression, miR expression in the striatum of uninfected macaques receiving vehicle (VEH) or Δ9-THC (THC) and SIV-infected macaques administered either vehicle (VEH/SIV) or Δ9-THC (THC/SIV) was profiled using next generation deep sequencing. Among the 24 miRs that were differentially expressed among the four groups, 16 miRs were modulated by THC in the presence of SIV. These 16 miRs were classified into four categories and the biological processes enriched by the target genes determined. Our results indicate that Δ9-THC modulates miRs that regulate mRNAs of proteins involved in 1) neurotrophin signaling, 2) MAPK signaling, and 3) cell cycle and immune response thus promoting an overall neuroprotective environment in the striatum of SIV-infected macaques. This is also reflected by increased Brain Derived Neurotrophic Factor (BDNF) and decreased proinflammatory cytokine expression compared to the VEH/SIV group. Whether Δ9-THC-mediated modulation of epigenetic mechanisms provides neuroprotection in other regions of the brain and during chronic SIV-infection remains to be determined.
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Affiliation(s)
- Liz Simon
- Department of Physiology, Alcohol and Drug Abuse Center of Excellence, Louisiana State University Health Sciences, 1901 Perdido Street, Medical Education Building 7205, P7-3, New Orleans, LA, 70112, USA
| | - Keijing Song
- Department of Physiology, Louisiana State University Health Sciences Center, 1901 Perdido Street, New Orleans, LA, 70112, USA
| | - Curtis Vande Stouwe
- Department of Physiology, Louisiana State University Health Sciences Center, 1901 Perdido Street, New Orleans, LA, 70112, USA
| | - Andrew Hollenbach
- Department of Genetics, Louisiana State University Health Sciences Center, 1901 Perdido Street, New Orleans, LA, 70112, USA
| | - Angela Amedee
- Department of Microbiology, Immunology, & Parasitology; Alcohol and Drug Abuse Center of Excellence, Louisiana State University Health Sciences Center, 1901 Perdido Street, New Orleans, LA, 70112, USA
| | - Mahesh Mohan
- Department of Comparative Pathology, Tulane National Primate Research Center, 18703 3 Rivers Rd, Covington, LA, 70433, USA
| | - Peter Winsauer
- Department of Pharmacology; Alcohol and Drug Abuse Center of Excellence, Louisiana State University Health Sciences Center, 1901 Perdido Street, New Orleans, LA, 70112, USA
| | - Patricia Molina
- Department of Physiology, Alcohol and Drug Abuse Center of Excellence, Louisiana State University Health Sciences, 1901 Perdido Street, Medical Education Building 7205, P7-3, New Orleans, LA, 70112, USA.
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Brief Report: Coordinated Modulation of Circulating miR-21 in HIV, HIV-Associated Pulmonary Arterial Hypertension, and HIV/Hepatitis C Virus Coinfection. J Acquir Immune Defic Syndr 2016; 70:236-41. [PMID: 26473639 DOI: 10.1097/qai.0000000000000741] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dysregulation of microRNA-21 (miR-21) is independently associated with HIV infection, pulmonary arterial hypertension (PAH), and hepatitis C virus (HCV) infection. To assess the expression of miR-21 in these overlapping comorbidities, we measured plasma miR-21 in HIV with and without PAH and then stratified by concomitant HCV infection. MiR-21 was increased in HIV and HIV-PAH versus uninfected subjects, but it did not differ between these groups. HIV/HCV coinfection correlated with even higher miR-21 levels within the HIV-infected population. These data reveal specific regulation of plasma miR-21 in HIV, HIV/HCV coinfection, and PAH and suggest that miR-21 may integrate complex disease-specific signaling in the setting of HIV infection.
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Hou W, Li H, Jiang W, Zhang C, McNutt MA, Li G. Simian Immunodeficiency Virus Impacts MicroRNA-16 Mediated Post-Transcriptional Regulation of mu Opioid Receptor in CEM ×174 Cells. J Cell Biochem 2015; 117:84-93. [DOI: 10.1002/jcb.25251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/04/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Wenting Hou
- Department of Biochemistry and Molecular Biology; Peking University Health Science Center; Peking University; Beijing 100191 China
| | - Hui Li
- Department of Biochemistry and Molecular Biology; Peking University Health Science Center; Peking University; Beijing 100191 China
| | - Wei Jiang
- Department of Biochemistry and Molecular Biology; Peking University Health Science Center; Peking University; Beijing 100191 China
| | - Chao Zhang
- Department of Biochemistry and Molecular Biology; Peking University Health Science Center; Peking University; Beijing 100191 China
| | - Michael A McNutt
- Department of Pathology; Peking University Health Science Center; Peking University; Beijing 100191 China
| | - Gang Li
- Department of Biochemistry and Molecular Biology; Peking University Health Science Center; Peking University; Beijing 100191 China
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Murray DD, Suzuki K, Law M, Trebicka J, Neuhaus J, Wentworth D, Johnson M, Vjecha MJ, Kelleher AD, Emery S. Circulating microRNAs in Sera Correlate with Soluble Biomarkers of Immune Activation but Do Not Predict Mortality in ART Treated Individuals with HIV-1 Infection: A Case Control Study. PLoS One 2015; 10:e0139981. [PMID: 26465293 PMCID: PMC4605674 DOI: 10.1371/journal.pone.0139981] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 09/18/2015] [Indexed: 01/10/2023] Open
Abstract
Introduction The use of anti-retroviral therapy (ART) has dramatically reduced HIV-1 associated morbidity and mortality. However, HIV-1 infected individuals have increased rates of morbidity and mortality compared to the non-HIV-1 infected population and this appears to be related to end-organ diseases collectively referred to as Serious Non-AIDS Events (SNAEs). Circulating miRNAs are reported as promising biomarkers for a number of human disease conditions including those that constitute SNAEs. Our study sought to investigate the potential of selected miRNAs in predicting mortality in HIV-1 infected ART treated individuals. Materials and Methods A set of miRNAs was chosen based on published associations with human disease conditions that constitute SNAEs. This case: control study compared 126 cases (individuals who died whilst on therapy), and 247 matched controls (individuals who remained alive). Cases and controls were ART treated participants of two pivotal HIV-1 trials. The relative abundance of each miRNA in serum was measured, by RTqPCR. Associations with mortality (all-cause, cardiovascular and malignancy) were assessed by logistic regression analysis. Correlations between miRNAs and CD4+ T cell count, hs-CRP, IL-6 and D-dimer were also assessed. Results None of the selected miRNAs was associated with all-cause, cardiovascular or malignancy mortality. The levels of three miRNAs (miRs -21, -122 and -200a) correlated with IL-6 while miR-21 also correlated with D-dimer. Additionally, the abundance of miRs -31, -150 and -223, correlated with baseline CD4+ T cell count while the same three miRNAs plus miR-145 correlated with nadir CD4+ T cell count. Discussion No associations with mortality were found with any circulating miRNA studied. These results cast doubt onto the effectiveness of circulating miRNA as early predictors of mortality or the major underlying diseases that contribute to mortality in participants treated for HIV-1 infection.
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Affiliation(s)
- Daniel D. Murray
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Sydney, Australia
- * E-mail:
| | - Kazuo Suzuki
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Sydney, Australia
| | - Matthew Law
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Sydney, Australia
| | - Jonel Trebicka
- Department of Internal Medicine, University of Bonn, Bonn, Germany
| | - Jacquie Neuhaus
- University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Deborah Wentworth
- University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Margaret Johnson
- Ian Charleson Day Centre, Royal Free Hampstead NHS Trust, London, United Kingdom
| | - Michael J. Vjecha
- Institute for Clinical Research, Veterans Affairs Medical Center, Washington D.C., United States of America
| | - Anthony D. Kelleher
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Sydney, Australia
| | - Sean Emery
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Sydney, Australia
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Application of “Omics” Technologies for Diagnosis and Pathogenesis of Neurological Infections. Curr Neurol Neurosci Rep 2015. [DOI: 10.1007/s11910-015-0580-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Acute Hepatitis C Virus Infection Induces Consistent Changes in Circulating MicroRNAs That Are Associated with Nonlytic Hepatocyte Release. J Virol 2015; 89:9454-64. [PMID: 26157120 DOI: 10.1128/jvi.00955-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/22/2015] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Plasma microRNAs (miRNAs) change in abundance in response to disease and have been associated with liver fibrosis severity in chronic hepatitis C virus (HCV) infection. However, the early dynamics of miRNA release during acute HCV infection are poorly understood. In addition, circulating miRNA signatures have been difficult to reproduce among separate populations. We studied plasma miRNA abundance during acute HCV infection to identify an miRNA signature of early infection. We measured 754 plasma miRNAs by quantitative PCR array in a discovery cohort of 22 individuals before and during acute HCV infection and after spontaneous resolution (n = 11) or persistence (n = 11) to identify a plasma miRNA signature. The discovery cohort derived from the Baltimore Before and After Acute Study of Hepatitis. During acute HCV infection, increases in miR-122 (P < 0.01) and miR-885-5p (Pcorrected < 0.05) and a decrease in miR-494 (Pcorrected < 0.05) were observed at the earliest time points after virus detection. Changes in miR-122 and miR-885-5p were sustained in persistent (P < 0.001) but not resolved HCV infection. The circulating miRNA signature of acute HCV infection was confirmed in a separate validation cohort that was derived from the San Francisco-based You Find Out (UFO) Study (n = 28). As further confirmation, cellular changes of signature miRNAs were examined in a tissue culture model of HCV in hepatoma cells: HCV infection induced extracellular release of miR-122 and miR-885-5p despite unperturbed intracellular levels. In contrast, miR-494 accumulated intracellularly (P < 0.05). Collectively, these data are inconsistent with necrolytic release of hepatocyte miRNAs into the plasma during acute HCV infection of humans. IMPORTANCE MicroRNAs are small noncoding RNA molecules that emerging research shows can transmit regulatory signals between cells in health and disease. HCV infects 2% of humans worldwide, and chronic HCV infection is a major cause of severe liver disease. We profiled plasma miRNAs in injection drug users before, during, and (in the people with resolution) after HCV infection. We discovered miRNA signatures of acute and persistent viremia and confirmed these findings two ways: (i) in a separate cohort of people with newly acquired HCV infection and (ii) in an HCV cell culture system. Our results demonstrate that acute HCV infection induces early changes in the abundance of specific plasma miRNAs that may affect the host response to HCV infection.
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Dufresne A, Paturel M, Alberti L, Philippon H, Duc A, Decouvelaere AV, Cassier P, Blay JY. Prediction of desmoid tumor progression using miRNA expression profiling. Cancer Sci 2015; 106:650-5. [PMID: 25707497 PMCID: PMC4452168 DOI: 10.1111/cas.12640] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/04/2015] [Accepted: 02/15/2015] [Indexed: 12/15/2022] Open
Abstract
Desmoid tumor is a rare connective tissue tumor with locoregional aggressiveness but unpredictable behavior. The miRNA profile was ascertained for 26 patients included in the Desminib phase II trial and an independent validation cohort of 15 patients. Predictive and prognostic supervised analysis on the Desminib cohort failed to identify miRNAs differentially expressed between progressive and non-progressive patients under imatinib treatment or between progressive and non-progressive patients after discontinuation of imatinib. However, an unsupervised hierarchical clustering of the Desminib cohort identified two groups (A and B) of 13 patients each, where only the number of previous lines of treatment before inclusion in the study differed significantly between the two groups. Time to progression after discontinuation of imatinib was longer in group B than in group A. Fifteen miRNAs were highly statistically differentially expressed between groups A and B, targeting more than 3000 genes, including AGO1, BCL2, CDK6, SMAD4, PTEN, CCND1, VEGFA, and RB1. These results were confirmed in the independent validation cohort: hierarchical clustering of these 15 miRNAs identified two groups, in which time to recurrence was statistically different (28.8 months vs 68.8 months). These results provide the first indication of the prognostic value of miRNA expression profiling with a possible direct impact on patient management. A more precise miRNA signature must now be determined to select patients who would not benefit from surgical resection of their tumor and who ought to be monitored without treatment.
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Affiliation(s)
- Armelle Dufresne
- Team 11 of the Cancer Research Center of Lyon, Institute of Health and Medical Research (INSERM U1052-CNRS 5286), Lyon, France
| | - Marie Paturel
- Team 11 of the Cancer Research Center of Lyon, Institute of Health and Medical Research (INSERM U1052-CNRS 5286), Lyon, France
| | - Laurent Alberti
- Team 11 of the Cancer Research Center of Lyon, Institute of Health and Medical Research (INSERM U1052-CNRS 5286), Lyon, France
| | - Heloise Philippon
- Team 11 of the Cancer Research Center of Lyon, Institute of Health and Medical Research (INSERM U1052-CNRS 5286), Lyon, France
| | - Adeline Duc
- Team 11 of the Cancer Research Center of Lyon, Institute of Health and Medical Research (INSERM U1052-CNRS 5286), Lyon, France
| | | | - Philippe Cassier
- Department of Medical Oncology, Leon Berard Cancer Center, Lyon, France
| | - Jean-Yves Blay
- Team 11 of the Cancer Research Center of Lyon, Institute of Health and Medical Research (INSERM U1052-CNRS 5286), Lyon, France.,Department of Medical Oncology, Leon Berard Cancer Center, Lyon, France
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Beck SE, Queen SE, Witwer KW, Metcalf Pate KA, Mangus LM, Gama L, Adams RJ, Clements JE, Christine Zink M, Mankowski JL. Paving the path to HIV neurotherapy: Predicting SIV CNS disease. Eur J Pharmacol 2015; 759:303-12. [PMID: 25818747 DOI: 10.1016/j.ejphar.2015.03.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 01/23/2015] [Accepted: 03/12/2015] [Indexed: 12/31/2022]
Abstract
HIV-induced damage to the CNS remains a major challenge for over 30 million people in the world despite the successes of combined antiretroviral therapy in limiting viral replication. Predicting development and progression of HIV-associated CNS disease is crucial because prevention and early intervention could be more effective than attempts to promote repair. The SIV/macaque model is the premier platform to study HIV neuropathogenesis, including discovery of predictive factors such as neuroprotective host genes and both blood and CSF biomarkers that precede and predict development of SIV CNS disease. This report details the role of macaque MHC class I genes, longitudinal alterations in biomarkers in the circulation, and expression of inflammatory and neuronal damage markers in CSF using samples from SIV-inoculated pigtailed macaques collected during acute, asymptomatic, and terminal stages of infection.
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Affiliation(s)
- Sarah E Beck
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Suzanne E Queen
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Kelly A Metcalf Pate
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Lisa M Mangus
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Lucio Gama
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Robert J Adams
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Janice E Clements
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - M Christine Zink
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Joseph L Mankowski
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States.
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Chandra LC, Kumar V, Torben W, Vande Stouwe C, Winsauer P, Amedee A, Molina PE, Mohan M. Chronic administration of Δ9-tetrahydrocannabinol induces intestinal anti-inflammatory microRNA expression during acute simian immunodeficiency virus infection of rhesus macaques. J Virol 2015; 89:1168-81. [PMID: 25378491 PMCID: PMC4300675 DOI: 10.1128/jvi.01754-14] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 10/30/2014] [Indexed: 01/16/2023] Open
Abstract
UNLABELLED Recreational and medical use of cannabis among human immunodeficiency virus (HIV)-infected individuals has increased in recent years. In simian immunodeficiency virus (SIV)-infected macaques, chronic administration of Δ9-tetrahydrocannabinol (Δ9-THC) inhibited viral replication and intestinal inflammation and slowed disease progression. Persistent gastrointestinal disease/inflammation has been proposed to facilitate microbial translocation and systemic immune activation and promote disease progression. Cannabinoids including Δ9-THC attenuated intestinal inflammation in mouse colitis models and SIV-infected rhesus macaques. To determine if the anti-inflammatory effects of Δ9-THC involved differential microRNA (miRNA) modulation, we profiled miRNA expression at 14, 30, and 60 days postinfection (days p.i.) in the intestine of uninfected macaques receiving Δ9-THC (n=3) and SIV-infected macaques administered either vehicle (VEH/SIV; n=4) or THC (THC/SIV; n=4). Chronic Δ9-THC administration to uninfected macaques significantly and positively modulated intestinal miRNA expression by increasing the total number of differentially expressed miRNAs from 14 to 60 days p.i. At 60 days p.i., ∼28% of miRNAs showed decreased expression in the VEH/SIV group compared to none showing decrease in the THC/SIV group. Furthermore, compared to the VEH/SIV group, THC selectively upregulated the expression of miR-10a, miR-24, miR-99b, miR-145, miR-149, and miR-187, previously been shown to target proinflammatory molecules. NOX4, a potent reactive oxygen species generator, was confirmed as a direct miR-99b target. A significant increase in NOX4+ crypt epithelial cells was detected in VEH/SIV macaques compared to the THC/SIV group. We speculate that miR-99b-mediated NOX4 downregulation may protect the intestinal epithelium from oxidative stress-induced damage. These results support a role for differential miRNA induction in THC-mediated suppression of intestinal inflammation. Whether similar miRNA modulation occurs in other tissues requires further investigation. IMPORTANCE Gastrointestinal (GI) tract disease/inflammation is a hallmark of HIV/SIV infection. Previously, we showed that chronic treatment of SIV-infected macaques with Δ9-tetrahydrocannabinol (Δ9-THC) increased survival and decreased viral replication and infection-induced gastrointestinal inflammation. Here, we show that chronic THC administration to SIV-infected macaques induced an anti-inflammatory microRNA expression profile in the intestine at 60 days p.i. These included several miRNAs bioinformatically predicted to directly target CXCL12, a chemokine known to regulate lymphocyte and macrophage trafficking into the intestine. Specifically, miR-99b was significantly upregulated in THC-treated SIV-infected macaques and confirmed to directly target NADPH oxidase 4 (NOX4), a reactive oxygen species generator known to damage intestinal epithelial cells. Elevated miR-99b expression was associated with a significantly decreased number of NOX4+ epithelial cells in the intestines of THC-treated SIV-infected macaques. Overall, our results show that selective upregulation of anti-inflammatory miRNA expression contributes to THC-mediated suppression of gastrointestinal inflammation and maintenance of intestinal homeostasis.
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Affiliation(s)
- Lawrance C Chandra
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana, USA
| | - Vinay Kumar
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana, USA
| | - Workineh Torben
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana, USA
| | - Curtis Vande Stouwe
- Department of Physiology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Peter Winsauer
- LSUHSC Alcohol and Drug Abuse Center, New Orleans, Louisiana, USA Department of Pharmacology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Angela Amedee
- LSUHSC Alcohol and Drug Abuse Center, New Orleans, Louisiana, USA Department of Microbiology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Patricia E Molina
- LSUHSC Alcohol and Drug Abuse Center, New Orleans, Louisiana, USA Department of Physiology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Mahesh Mohan
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana, USA
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Abstract
Autism is a complex neurodevelopmental disorder characterized by deficiencies in social interaction and communication, and by repetitive and stereotyped behaviors. According to a recent report, the prevalence of this pervasive developmental disorder has risen to 1 in 88. This will have enormous public health implications in the future, and has necessitated the need to discover predictive biomarkers that could index for autism before the onset of symptoms. microRNAs (miRNAs) are small, noncoding RNAs that regulate gene expression at the posttranscriptional level. They have recently emerged as prominent epigenetic regulators of various cellular processes including neurodevelopment. They are abundantly present in the brain, and their dysfunction has been implicated in an array of neuropathological conditions including autism. miRNAs, previously known to be expressed only in cells and tissues, have also been detected in extracellular body fluids such as serum, plasma, saliva, and urine. Altered expression of cellular and circulating miRNAs have been observed in autistic individuals compared to healthy controls. miRNAs are now being considered as potential targets for the development of novel therapeutic strategies for autism.
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Mohan M, Kumar V, Lackner AA, Alvarez X. Dysregulated miR-34a-SIRT1-acetyl p65 axis is a potential mediator of immune activation in the colon during chronic simian immunodeficiency virus infection of rhesus macaques. THE JOURNAL OF IMMUNOLOGY 2014; 194:291-306. [PMID: 25452565 DOI: 10.4049/jimmunol.1401447] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Persistent gastrointestinal inflammation, a hallmark of progressive HIV/SIV infection, causes disruption of the gastrointestinal epithelial barrier, microbial translocation, and generalized immune activation/inflammation driving AIDS progression. Apart from protein regulators, recent studies strongly suggest critical roles for microRNAs (miRNAs) in regulating and managing certain aspects of the inflammatory process. To examine their immunoregulatory role, we profiled miRNA expression in the colon from 12 chronic SIV-infected and 4 control macaques. After applying multiple comparisons correction, 10 (3 upregulated and 7 downregulated) miRNAs showed differential expression. Most notably, miR-34a showed significant upregulation in both epithelial and lamina propria leukocyte (LPL) compartments. Intense γH2A.X expression in colonic epithelium and LPLs confirmed the contribution of DNA damage response in driving miR-34a upregulation. SIRT1 mRNA and protein decreased significantly in both colonic epithelium and LPLs. Luciferase reporter assays validated rhesus macaque SIRT1 as a direct miR-34a target. Decreased SIRT1 expression was associated with constitutively enhanced expression of the transcriptionally active form of the p65 (acetylated on lysine 310) subunit of NF-κB exclusively in the LPL compartment. The intensity and number of acetylated p65(+) cells was markedly elevated in LPLs of chronically SIV-infected macaques compared with uninfected controls and localized to increased numbers of IgA(+) and IgG(+) plasma cells. These findings provide new insights into the potential role of the miR-34a-SIRT1-p65 axis in causing hyperactivation of the intestinal B cell system. Our results point to a possible mechanism where the normal immunosuppressive function of SIRT1 is inhibited by elevated miR-34a expression resulting in constitutive activation of acetylated p65 (lysine 310).
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Affiliation(s)
- Mahesh Mohan
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433
| | - Vinay Kumar
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433
| | - Andrew A Lackner
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433
| | - Xavier Alvarez
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433
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Mohan M, Chandra LC, Torben W, Aye PP, Alvarez X, Lackner AA. miR-190b is markedly upregulated in the intestine in response to simian immunodeficiency virus replication and partly regulates myotubularin-related protein-6 expression. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2014; 193:1301-13. [PMID: 24981450 PMCID: PMC4108538 DOI: 10.4049/jimmunol.1303479] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
HIV replication and the cellular micro-RNA (miRNA) machinery interconnect at several posttranscriptional levels. To understand their regulatory role in the intestine, a major site of HIV/SIV replication, dissemination, and CD4(+) T cell depletion, we profiled miRNA expression in colon following SIV infection (10 acute SIV, 5 uninfected). Nine (four up and five down) miRNAs showed statistically significant differential expression. Most notably, miR-190b expression showed high statistical significance (adjusted p = 0.0032), the greatest fold change, and was markedly elevated in colon and jejunum throughout SIV infection. In addition, miR-190b upregulation was detected before peak viral replication and the nadir of CD4(+) T cell depletion predominantly in lamina propria leukocytes. Interestingly non-SIV-infected macaques with diarrhea and colitis failed to upregulate miR-190b, suggesting that its upregulation was neither inflammation nor immune-activation driven. SIV infection of in vitro-cultured CD4(+) T cells and primary intestinal macrophages conclusively identified miR-190b upregulation to be driven in response to viral replication. Further miR-190b expression levels in colon and jejunum positively correlated with tissue viral loads. In contrast, mRNA expression of myotubularin-related protein 6 (MTMR6), a negative regulator of CD4(+) T cell activation/proliferation, significantly decreased in SIV-infected macrophages. Luciferase reporter assays confirmed MTMR6 as a direct miR-190b target. To our knowledge, this is the first report, which describes dysregulated miRNA expression in the intestine, that identifies a potentially significant role for miR-190b in HIV/SIV pathogenesis. More importantly, miR-190b-mediated MTMR6 downregulation suggests an important mechanism that could keep infected cells in an activated state, thereby promoting viral replication. In the future, the mechanisms driving miR-190b upregulation including other cellular processes it regulates in SIV-infected cells need determination.
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Affiliation(s)
- Mahesh Mohan
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433
| | - Lawrance C Chandra
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433
| | - Workineh Torben
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433
| | - Pyone P Aye
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433
| | - Xavier Alvarez
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433
| | - Andrew A Lackner
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433
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Serum microRNAs in HIV-infected individuals as pre-diagnosis biomarkers for AIDS-NHL. J Acquir Immune Defic Syndr 2014; 66:229-37. [PMID: 24675587 DOI: 10.1097/qai.0000000000000146] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To determine if changes in levels of serum microRNAs (miRNAs) were seen preceding the diagnosis of AIDS-related non-Hodgkin lymphoma (AIDS-NHL). DESIGN Serum miRNA levels were compared in 3 subject groups from the Multicenter AIDS Cohort Study: HIV-negative men (n = 43), HIV-positive men who did not develop NHL (n = 45), and HIV-positive men before AIDS-NHL diagnosis (n = 62, median time before diagnosis, 8.8 months). METHODS A total of 175 serum-enriched miRNAs were initially screened to identify differentially expressed miRNAs among these groups and the results validated by quantitative polymerase chain reaction. Receiver-operating characteristic analysis was then performed to assess biomarker utility. RESULTS Higher levels of miR-21 and miR-122, and a lower level of miR-223, were able to discriminate HIV-infected from the HIV-uninfected groups, suggesting that these miRNAs are biomarkers for HIV infection but are not AIDS-NHL specific. Among the HIV-infected groups, a higher level of miR-222 was able to discriminate diffuse large B-cell lymphoma (DLBCL) and primary central nervous system lymphoma (PCNSL) subjects from HIV-infected subjects who did not develop NHL, with area under the receiver-operating characteristic curve of 0.777 and 0.792, respectively. At miR-222 cutoff values of 0.105 for DLBCL and 0.109 for PCNSL, the sensitivity and specificity were 75% and 77%, and 80% and 82%, respectively. CONCLUSIONS Altered serum levels of miR-21, miR-122, and miR-223 are seen in HIV-infected individuals. Higher serum level of miR-222 has clear potential as a serum biomarker for earlier detection of DLBCL and PCNSL among HIV-infected individuals.
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Christofidou-Solomidou M, Pietrofesa R, Arguiri E, McAlexander MA, Witwer KW. Dietary flaxseed modulates the miRNA profile in irradiated and non-irradiated murine lungs: a novel mechanism of tissue radioprotection by flaxseed. Cancer Biol Ther 2014; 15:930-7. [PMID: 24755684 DOI: 10.4161/cbt.28905] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
INTRODUCTION Dietary flaxseed (FS) displays antioxidant and anti-inflammatory properties in preclinical models of lung disease including radiation-induced pneumonopathy, however the mechanisms of lung radioprotection are incompletely understood. MicroRNAs (miRNAs) are short oligonucleotides that act as important posttranscriptional regulators of diverse networks including inflammatory response networks. Responses of miRNA profiles to diet and radiation exposure have been reported, but the potential contribution of miRNAs to diet-related radioprotection has never been tested. METHODS In this exploratory pilot study, mice were fed 10% FS or a 0% FS isocaloric control diet and exposed to a single-fraction 13.5 Gy thoracic X-ray radiation treatment (XRT). Lung RNA was extracted 48 h post-XRT and small RNAs profiled by OpenArray. RESULTS FS significantly modulated expression of multiple miRNAs, including 7 with P<0.001. miR-150 was downregulated approximately 2.9-fold in the FS groups and is disproportionately integrated into immune response-related networks. Although few miRNAs were significantly changed by radiation, interaction between diet and radiation was observed. For example, miR-29c was greatly downregulated in the FS/Control group (10- to 50-fold) but slightly upregulated in the FS/radiation group. Compared with FS/control, the FS/radiation group experienced a 50% decrease of the p53-responsive miR-34a, which regulates senescence- and apoptosis-related factors. CONCLUSIONS FS induced significant changes in lung miRNA profile suggesting that modulation of small RNA by dietary supplements may represent a novel strategy to prevent adverse side-effects of thoracic radiotherapy. This pilot study provides insight into a potential mechanism of flaxseed's radioprotection and provides a useful model-system to further explore and optimize such small RNA-based therapies.
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Affiliation(s)
- Melpo Christofidou-Solomidou
- Department of Medicine, Pulmonary Allergy and Critical Care Division; Perelman School of Medicine; University of Pennsylvania; Philadelphia, PA USA
| | - Ralph Pietrofesa
- Department of Medicine, Pulmonary Allergy and Critical Care Division; Perelman School of Medicine; University of Pennsylvania; Philadelphia, PA USA
| | - Evguenia Arguiri
- Department of Medicine, Pulmonary Allergy and Critical Care Division; Perelman School of Medicine; University of Pennsylvania; Philadelphia, PA USA
| | - Melissa A McAlexander
- Department of Molecular and Comparative Pathobiology; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology; Johns Hopkins University School of Medicine; Baltimore, MD USA
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Intestinal epithelial barrier disruption through altered mucosal microRNA expression in human immunodeficiency virus and simian immunodeficiency virus infections. J Virol 2014; 88:6268-80. [PMID: 24672033 DOI: 10.1128/jvi.00097-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED Epithelial barrier dysfunction during human immunodeficiency virus (HIV) infection has largely been attributed to the rapid and severe depletion of CD4(+) T cells in the gastrointestinal (GI) tract. Although it is known that changes in mucosal gene expression contribute to intestinal enteropathy, the role of small noncoding RNAs, specifically microRNA (miRNA), has not been investigated. Using the simian immunodeficiency virus (SIV)-infected nonhuman primate model of HIV pathogenesis, we investigated the effect of viral infection on miRNA expression in intestinal mucosa. SIV infection led to a striking decrease in the expression of mucosal miRNA compared to that in uninfected controls. This decrease coincided with an increase in 5'-3'-exoribonuclease 2 protein and alterations in DICER1 and Argonaute 2 expression. Targets of depleted miRNA belonged to molecular pathways involved in epithelial proliferation, differentiation, and immune response. Decreased expression of several miRNA involved in maintaining epithelial homeostasis in the gut was localized to the proliferative crypt region of the intestinal epithelium. Our findings suggest that SIV-induced decreased expression of miRNA involved in epithelial homeostasis, disrupted expression of miRNA biogenesis machinery, and increased expression of XRN2 are involved in the development of epithelial barrier dysfunction and gastroenteropathy. IMPORTANCE MicroRNA (miRNA) regulate the development and function of intestinal epithelial cells, and many viruses disrupt normal host miRNA expression. In this study, we demonstrate that SIV and HIV disrupt expression of miRNA in the small intestine during infection. The depletion of several key miRNA is localized to the proliferative crypt region of the gut epithelium. These miRNA are known to control expression of genes involved in inflammation, cell death, and epithelial maturation. Our data indicate that this disruption might be caused by altered expression of miRNA biogenesis machinery during infection. These findings suggest that the disruption of miRNA in the small intestine likely plays a role in intestinal enteropathy during HIV infection.
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Swaminathan S, Murray DD, Kelleher AD. miRNAs and HIV: unforeseen determinants of host-pathogen interaction. Immunol Rev 2014; 254:265-80. [PMID: 23772625 DOI: 10.1111/imr.12077] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Our understanding of the complexity of gene regulation has significantly improved in the last decade as the role of small non-coding RNAs, called microRNAs (miRNAs), has been appreciated. These 19-22 nucleotide RNA molecules are critical regulators of mRNA translation and turnover. The miRNAs bind via a protein complex to the 3' untranslated region (3' UTR) of mRNA, ultimately leading to mRNA translational inhibition, degradation, or repression. Although many mechanisms by which human immunodeficiency virus-1 (HIV-1) infection eventually induces catastrophic immune destruction have been elucidated, the important role that miRNAs play in HIV-1 pathogenesis is only now emerging. Accumulating evidence demonstrates that changes to endogenous miRNA levels following infection is important: in maintaining HIV-1 latency in resting CD4(+) T cells, potentially affect immune function via changes to cytokines such as interleukin-2 (IL-2) and IL-10 and may predict disease progression. We review the roles that both viral and host miRNAs play in different cell types and disease conditions that are important in HIV-1 infection and discuss how miRNAs affect key immunomodulatory molecules contributing to immune dysfunction. Further, we discuss whether miRNAs may be used as novel biomarkers in serum and the potential to modulate miRNA levels as a unique approach to combating this pathogen.
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Affiliation(s)
- Sanjay Swaminathan
- Laboratory of Human Retrovirology, Applied and Developmental Research Directorate (ADD), Science Application International Corporation (SAIC)-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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Liu J, Sisk JM, Gama L, Clements JE, Witwer KW. Tristetraprolin expression and microRNA-mediated regulation during simian immunodeficiency virus infection of the central nervous system. Mol Brain 2013; 6:40. [PMID: 24103357 PMCID: PMC3766027 DOI: 10.1186/1756-6606-6-40] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 08/28/2013] [Indexed: 03/13/2023] Open
Abstract
BACKGROUND The RNA-binding protein tristetraprolin (TTP) participates in normal post-transcriptional control of cytokine and chemokine gene expression, dysregulation of which contributes to the HIV-associated neurocognitive disorders. Transcriptional and post-transcriptional regulation of TTP has been described, including regulation by microRNA-29a. In the simian immunodeficiency virus (SIV) model of HIV CNS disease, control of cytokine/chemokine expression coincides with the end of acute phase infection. This control is lost during progression to disease. In this study, we assessed TTP regulation and association with cytokine regulation in the brain during SIV infection. RESULTS Quantitation of TTP expression over the course of SIV infection revealed downregulation of TTP during acute infection, maintenance of relatively low levels during asymptomatic phase, and increased expression only during late-stage CNS disease, particularly in association with severe disease. The ability of miR-29a to regulate TTP was confirmed, and evidence for additional miRNA targeters of TTP was found. However, increased miR-29a expression in brain was not found to be significantly negatively correlated with TTP. Similarly, increased TTP during late-stage disease was not associated with lower cytokine expression. CONCLUSIONS TTP expression is regulated during SIV infection of the CNS. The lack of significant negative correlation of miR-29a and TTP expression levels suggests that while miR-29a may contribute to TTP regulation, additional factors are involved. Reduced TTP expression during acute infection is consistent with increased cytokine production during this phase of infection, but the increases in TTP observed during late-stage infection were insufficient to halt runaway cytokine levels. While antisense inhibitors of the post-transcriptional targeters of TTP identified here could conceivably be used further to augment TTP regulation of cytokines, it is possible that high levels of TTP are undesirable. Additional research is needed to characterize members of the miRNA/TTP/cytokine regulatory network and identify nodes that may be best targeted therapeutically to ameliorate the effects of chronic inflammation in retrovirus-associated CNS disease.
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Affiliation(s)
- Jonathan Liu
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, 733 N, Broadway, Miller Research Building Rm, 829, Baltimore, MD 21205, USA.
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Sisk JM, Witwer KW, Tarwater PM, Clements JE. SIV replication is directly downregulated by four antiviral miRNAs. Retrovirology 2013; 10:95. [PMID: 23988154 PMCID: PMC3766675 DOI: 10.1186/1742-4690-10-95] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/21/2013] [Indexed: 12/30/2022] Open
Abstract
Background Host cell microRNAs (miRNAs) have been shown to regulate the expression of both cellular and viral RNAs, in particular impacting both Hepatitis C Virus (HCV) and Human Immunodeficiency Virus (HIV). To investigate the role of miRNAs in regulating replication of the simian immunodeficiency virus (SIV) in macrophage lineage cells, we used primary macrophages to study targeting of SIV RNA by miRNAs. We examined whether specific host miRNAs directly target SIV RNA early in infection and might be induced via type I interferon pathways. Results miRNA target prediction programs identified miRNA binding sites within SIV RNA. Predicted binding sites for miRs-29a, -29b, -9 and -146a were identified in the SIV Nef/U3 and R regions, and all four miRNAs decreased virus production and viral RNA expression in primary macrophages. To determine whether levels of these miRNAs were affected by SIV infection, IFNβ or TNFα treatments, miRNA RT-qPCR assays measured miRNA levels after infection or treatment of macrophages. SIV RNA levels as well as virus production was downregulated by direct targeting of the SIV Nef/U3 and R regions by four miRNAs. miRs-29a, -29b, -9 and -146a were induced in primary macrophages after SIV infection. Each of these miRNAs was regulated by innate immune signaling through TNFα and/or the type I IFN, IFNβ. Conclusions The effects on miRNAs caused by HIV/SIV infection are illustrated by changes in their cellular expression throughout the course of disease, and in different patient populations. Our data demonstrate that levels of primary transcripts and mature miRs-29a, -29b, -9 and -146a are modulated by SIV infection. We show that the SIV 3′ UTR contains functional miRNA response elements (MREs) for all four miRNAs. Notably, these miRNAs regulate virus production and viral RNA levels in macrophages, the primary cells infected in the CNS that drive inflammation leading to HIV-associated neurocognitive disorders. This report may aid in identification miRNAs that target viral RNAs and HIV/SIV specifically, as well as in identification of miRNAs that may be targets of new therapies to treat HIV.
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Affiliation(s)
- Jeanne M Sisk
- Department of Molecular and Comparative Pathobiology, Edward D, Miller Research Building, The Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA.
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Tang YW. Transcriptomic approach predicts tempo of disease progression in HIV-1 infections. Clin Chem 2013; 59:1143-4. [PMID: 23748854 DOI: 10.1373/clinchem.2013.206912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Witwer KW, McAlexander MA, Queen SE, Adams RJ. Real-time quantitative PCR and droplet digital PCR for plant miRNAs in mammalian blood provide little evidence for general uptake of dietary miRNAs: limited evidence for general uptake of dietary plant xenomiRs. RNA Biol 2013; 10:1080-6. [PMID: 23770773 PMCID: PMC3849155 DOI: 10.4161/rna.25246] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Evidence that exogenous dietary miRNAs enter the bloodstream and tissues of ingesting animals has been accompanied by an indication that at least one plant miRNA, miR168, participates in “cross-kingdom” regulation of a mammalian transcript. If confirmed, these findings would support investigation of miRNA-based dietary interventions in disease. Here, blood was obtained pre- and post-prandially (1, 4, 12 h) from pigtailed macaques that received a miRNA-rich plant-based substance. Plant and endogenous miRNAs were measured by RT-qPCR. Although low-level amplification was observed for some plant miRNA assays, amplification was variable and possibly non-specific, as suggested by droplet digital PCR. A consistent response to dietary intake was not observed. While our results do not support general and consistent uptake of dietary plant miRNAs, additional studies are needed to establish whether or not plant or animal xenomiRs are transferred across the gut in sufficient quantity to regulate endogenous genes.
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Affiliation(s)
- Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology; The Johns Hopkins University School of Medicine; Baltimore, ME USA
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Witwer KW, Buzás EI, Bemis LT, Bora A, Lässer C, Lötvall J, Nolte-'t Hoen EN, Piper MG, Sivaraman S, Skog J, Théry C, Wauben MH, Hochberg F. Standardization of sample collection, isolation and analysis methods in extracellular vesicle research. J Extracell Vesicles 2013; 2:20360. [PMID: 24009894 PMCID: PMC3760646 DOI: 10.3402/jev.v2i0.20360] [Citation(s) in RCA: 1628] [Impact Index Per Article: 148.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 04/05/2013] [Accepted: 04/11/2013] [Indexed: 12/13/2022] Open
Abstract
The emergence of publications on extracellular RNA (exRNA) and extracellular vesicles (EV) has highlighted the potential of these molecules and vehicles as biomarkers of disease and therapeutic targets. These findings have created a paradigm shift, most prominently in the field of oncology, prompting expanded interest in the field and dedication of funds for EV research. At the same time, understanding of EV subtypes, biogenesis, cargo and mechanisms of shuttling remains incomplete. The techniques that can be harnessed to address the many gaps in our current knowledge were the subject of a special workshop of the International Society for Extracellular Vesicles (ISEV) in New York City in October 2012. As part of the “ISEV Research Seminar: Analysis and Function of RNA in Extracellular Vesicles (evRNA)”, 6 round-table discussions were held to provide an evidence-based framework for isolation and analysis of EV, purification and analysis of associated RNA molecules, and molecular engineering of EV for therapeutic intervention. This article arises from the discussion of EV isolation and analysis at that meeting. The conclusions of the round table are supplemented with a review of published materials and our experience. Controversies and outstanding questions are identified that may inform future research and funding priorities. While we emphasize the need for standardization of specimen handling, appropriate normative controls, and isolation and analysis techniques to facilitate comparison of results, we also recognize that continual development and evaluation of techniques will be necessary as new knowledge is amassed. On many points, consensus has not yet been achieved and must be built through the reporting of well-controlled experiments.
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Affiliation(s)
- Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, MD, USA
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McAlexander MA, Phillips MJ, Witwer KW. Comparison of Methods for miRNA Extraction from Plasma and Quantitative Recovery of RNA from Cerebrospinal Fluid. Front Genet 2013; 4:83. [PMID: 23720669 PMCID: PMC3655275 DOI: 10.3389/fgene.2013.00083] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 04/24/2013] [Indexed: 11/30/2022] Open
Abstract
Interest in extracellular RNA (exRNA) has intensified as evidence accumulates that these molecules may be useful as indicators of a wide variety of biological conditions. To establish specific exRNA molecules as clinically relevant biomarkers, reproducible recovery from biological samples and reliable measurements of the isolated RNA are paramount. Toward these ends, careful and rigorous comparisons of technical procedures are needed at all steps from sample handling to RNA isolation to RNA measurement protocols. In the investigations described in this methods paper, RT-qPCR was used to examine the apparent recovery of specific endogenous miRNAs and a spiked-in synthetic RNA from blood plasma samples. RNA was isolated using several widely used RNA isolation kits, with or without the addition of glycogen as a carrier. Kits examined included total RNA isolation systems that have been commercially available for several years and commonly adapted for extraction of biofluid RNA, as well as more recently introduced biofluids-specific RNA methods. Our conclusions include the following: some RNA isolation methods appear to be superior to others for the recovery of RNA from biological fluids; addition of a carrier molecule seems to be beneficial for some but not all isolation methods; and quantitative recovery of RNA is observed from increasing volumes of cerebrospinal fluid.
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Affiliation(s)
- Melissa A McAlexander
- Retrovirus Laboratory, Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine Baltimore, MD, USA
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