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Di Carlo D, Falasca F, Mazzuti L, Guerrizio G, Migliara G, Santori M, Lazzaro A, Mezzaroma I, D'Ettorre G, Fimiani C, Iaiani G, Antonelli G, Turriziani O. MicroRNA Expression Levels in Peripheral Blood Mononuclear Cells from Human Immunodeficiency Virus Type 1 Positive Individuals and Relationship with Different Levels of Viral Suppression. AIDS Res Hum Retroviruses 2024; 40:321-329. [PMID: 37523231 DOI: 10.1089/aid.2022.0165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023] Open
Abstract
The persistence of low human immunodeficiency virus type 1 (HIV-1) replication in individuals undergoing antiretroviral therapy (ART) still threatens their health. Previous findings have shown that microRNAs (miRNAs) could interfere with several steps of the viral life cycle. Herein, we set out to investigate the expression of miR-150, miR-223, miR-382, miR-324-5p, miR-33a-5p, miR-34a, and miR-132 in the whole peripheral blood mononuclear cell (PBMC) population from people living with HIV-1 showing different levels of viral suppression. Levels of PBMC-associated miRNAs were analyzed in 30 individuals with undetectable viremia (target not detected) and 30 individuals with detectable low-level viremia (1-200 copies/mL). In addition, 30 samples from treatment-naive (NAIVE) individuals were investigated. Results were compared to a control group of 28 HIV-negative donors. All miRNAs analyzed were strongly downregulated in the NAIVE population, either compared to the treated group or to controls. Stratification of ART-treated donors according to the therapeutic regimen showed the downregulation of miR-33a-5p in subjects treated with non-nucleoside reverse transcriptase inhibitors compared with those treated with protease inhibitors. Collectively, the present study shows that uncontrolled viral replication leads to profound miRNA deregulation while treated individuals, irrespective of the degree of viral suppression, and even the types of antiviral drugs seem to be specifically associated with miRNA expression profiles. These evidences suggest that virological suppression could be favored by miRNA modulation.
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Affiliation(s)
- Daniele Di Carlo
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
- Pasteur Laboratories, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Francesca Falasca
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
- Transfusion Medicine Unit, "F. Veneziale" Hospital, Isernia, Italy
| | - Laura Mazzuti
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
- Department of Clinical and Molecular Medicine, Sapienza University, Sant'Andrea Hospital, Rome, Italy
| | - Giuliana Guerrizio
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Giuseppe Migliara
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Marta Santori
- Department Internal Medicine, Endocrine-Metabolic Sciences and Infectious Diseases, Policlinico Umberto I, Rome, Italy
| | - Alessandro Lazzaro
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Ivano Mezzaroma
- Department of Translational and Precision Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Gabriella D'Ettorre
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Caterina Fimiani
- Department Internal Medicine, Endocrine-Metabolic Sciences and Infectious Diseases, Policlinico Umberto I, Rome, Italy
| | - Giancarlo Iaiani
- Department Internal Medicine, Endocrine-Metabolic Sciences and Infectious Diseases, Policlinico Umberto I, Rome, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Ombretta Turriziani
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
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2
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Morando N, Rosenzvit MC, Pando MA, Allmer J. The Role of MicroRNAs in HIV Infection. Genes (Basel) 2024; 15:574. [PMID: 38790203 PMCID: PMC11120859 DOI: 10.3390/genes15050574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
MicroRNAs (miRNAs), a class of small, non-coding RNAs, play a pivotal role in regulating gene expression at the post-transcriptional level. These regulatory molecules are integral to many biological processes and have been implicated in the pathogenesis of various diseases, including Human Immunodeficiency Virus (HIV) infection. This review aims to cover the current understanding of the multifaceted roles miRNAs assume in the context of HIV infection and pathogenesis. The discourse is structured around three primary focal points: (i) elucidation of the mechanisms through which miRNAs regulate HIV replication, encompassing both direct targeting of viral transcripts and indirect modulation of host factors critical for viral replication; (ii) examination of the modulation of miRNA expression by HIV, mediated through either viral proteins or the activation of cellular pathways consequent to viral infection; and (iii) assessment of the impact of miRNAs on the immune response and the progression of disease in HIV-infected individuals. Further, this review delves into the potential utility of miRNAs as biomarkers and therapeutic agents in HIV infection, underscoring the challenges and prospects inherent to this line of inquiry. The synthesis of current evidence positions miRNAs as significant modulators of the host-virus interplay, offering promising avenues for enhancing the diagnosis, treatment, and prevention of HIV infection.
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Affiliation(s)
- Nicolas Morando
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires, Buenos Aires 1121, Argentina; (N.M.); (M.A.P.)
| | - Mara Cecilia Rosenzvit
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires 1121, Argentina;
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Buenos Aires 1121, Argentina
| | - Maria A. Pando
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires, Buenos Aires 1121, Argentina; (N.M.); (M.A.P.)
| | - Jens Allmer
- Medical Informatics and Bioinformatics, Institute for Measurement Engineering and Sensor Technology, Hochschule Ruhr West, University of Applied Sciences, 45479 Mülheim an der Ruhr, Germany
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3
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Cuesta-Sancho S, Márquez-Ruiz D, Illanes-Álvarez F, Campaña-Gómez I, Martín-Aspas A, Trujillo-Soto MT, Romero A, Galán F, Rodríguez-Iglesias M, Márquez-Coello M, Girón-González JA. Expression profile of microRNAs related with viral infectivity, inflammatory response, and immune activation in people living with HIV. Front Microbiol 2023; 14:1136718. [PMID: 36937285 PMCID: PMC10017538 DOI: 10.3389/fmicb.2023.1136718] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
Objective To evaluate the serum expression of microRNAs (miRNAs) with ability to modulate the human immunodeficiency (HIV) replication or inflammatory status in people living with HIV (PLWH). Methods Forty healthy controls and two groups of PLWH were evaluated: (a) Group 1 (n = 30), patients with detectable viral load at inclusion, analyzed before receiving antiretroviral therapy (ART) and 12 months after initiating it; (b) Group 2 (n = 55), PLWH with prolonged undetectable viral load. Intestinal barrier disruption (I-FABP) and bacterial translocation (16S rDNA) markers, inflammatory markers such as interleukin (IL)-6 and sCD163, immune activation and expression of specific miRNAs were evaluated. Results Serum concentrations of I-FABP, 16S rDNA, IL-6, sCD163 and activated T lymphocytes were increased in PLWH. Serum miR-34a was overexpressed at inclusion and remained elevated after ART. The expression of the remaining miRNAs that modulate HIV infectivity (miR-7, mir-29a, miR-150, and miR-223) was similar in PLWH and controls. Related to miRNAs implicated in inflammation (miR-21, miR-155, and miR-210), significant overexpression were observed in miR-21 and miR-210 levels in untreated PLWH, but levels were restored in those patients treated for a long period. Conclusion A sustained overexpression of miR-34a was detected even after prolonged HIV controlled replication. miR-21 and miR-210 can be considered new markers of inflammation with high sensitivity to its modifications.
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Affiliation(s)
- Sara Cuesta-Sancho
- Unidad de Enfermedades Infecciosas, Servicio de Medicina Interna, Facultad de Medicina, Hospital Universitario Puerta del Mar, Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Universidad de Cádiz, Cádiz, Spain
| | - Denisse Márquez-Ruiz
- Unidad de Enfermedades Infecciosas, Servicio de Medicina Interna, Facultad de Medicina, Hospital Universitario Puerta del Mar, Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Universidad de Cádiz, Cádiz, Spain
| | - Francisco Illanes-Álvarez
- Unidad de Enfermedades Infecciosas, Servicio de Medicina Interna, Facultad de Medicina, Hospital Universitario Puerta del Mar, Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Universidad de Cádiz, Cádiz, Spain
| | - Irene Campaña-Gómez
- Unidad de Enfermedades Infecciosas, Servicio de Medicina Interna, Facultad de Medicina, Hospital Universitario Puerta del Mar, Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Universidad de Cádiz, Cádiz, Spain
| | - Andrés Martín-Aspas
- Unidad de Enfermedades Infecciosas, Servicio de Medicina Interna, Facultad de Medicina, Hospital Universitario Puerta del Mar, Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Universidad de Cádiz, Cádiz, Spain
| | - María Teresa Trujillo-Soto
- Servicio de Microbiología, Facultad de Medicina, Hospital Universitario Puerta del Mar, Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Universidad de Cádiz, Cádiz, Spain
| | - Alberto Romero
- Unidad de Enfermedades Infecciosas, Facultad de Medicina, Hospital Universitario Puerto Real, Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Universidad de Cádiz, Cádiz, Spain
| | - Fátima Galán
- Servicio de Microbiología, Facultad de Medicina, Hospital Universitario Puerta del Mar, Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Universidad de Cádiz, Cádiz, Spain
| | - Manuel Rodríguez-Iglesias
- Servicio de Microbiología, Facultad de Medicina, Hospital Universitario Puerta del Mar, Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Universidad de Cádiz, Cádiz, Spain
| | - Mercedes Márquez-Coello
- Unidad de Enfermedades Infecciosas, Servicio de Medicina Interna, Facultad de Medicina, Hospital Universitario Puerta del Mar, Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Universidad de Cádiz, Cádiz, Spain
| | - José-Antonio Girón-González
- Unidad de Enfermedades Infecciosas, Servicio de Medicina Interna, Facultad de Medicina, Hospital Universitario Puerta del Mar, Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Universidad de Cádiz, Cádiz, Spain
- *Correspondence: José-Antonio Girón-González,
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4
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Xiao Q, Yu F, Yan L, Zhao H, Zhang F. Alterations in circulating markers in HIV/AIDS patients with poor immune reconstitution: Novel insights from microbial translocation and innate immunity. Front Immunol 2022; 13:1026070. [PMID: 36325329 PMCID: PMC9618587 DOI: 10.3389/fimmu.2022.1026070] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
After long-term anti-retroviral therapy (ART) treatment, most human immunodeficiency virus (HIV)/Acquired Immure Deficiency Syndrome (AIDS) patients can achieve virological suppression and gradual recovery of CD4+ T-lymphocyte (CD4+ T cell) counts. However, some patients still fail to attain normal CD4+ T cell counts; this group of patients are called immune non-responders (INRs), and these patients show severe immune dysfunction. The potential mechanism of poor immune reconstitution (PIR) remains unclear and the identification of uniform biomarkers to predict the occurrence of PIR is particularly vital. But limited information is available on the relationship between circulating markers of INRs and immune recovery. Hence, this review summarises alterations in the intestine microbiota and associated markers in the setting of PIR to better understand host-microbiota-metabolite interactions in HIV immune reconstitution and to identify biomarkers that can predict recovery of CD4+ T cell counts in INRs.
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Affiliation(s)
- Qing Xiao
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Fengting Yu
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Liting Yan
- Infectious Disease Department, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Hongxin Zhao
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Fujie Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
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5
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Zeng Q, Qi X, Ma J, Hu F, Wang X, Qin H, Li M, Huang S, Yang Y, Li Y, Bai H, Jiang M, Ren D, Kang Y, Zhao Y, Chen X, Ding X, Ye D, Wang Y, Jiang J, Li D, Chen X, Hu K, Zhang B, Shi B, Zhang C. Distinct miRNAs associated with various clinical presentations of SARS-CoV-2 infection. iScience 2022; 25:104309. [PMID: 35502319 PMCID: PMC9044631 DOI: 10.1016/j.isci.2022.104309] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/04/2022] [Accepted: 04/22/2022] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) have been shown to play important roles in viral infections, but their associations with SARS-CoV-2 infection remain poorly understood. Here, we detected 85 differentially expressed miRNAs (DE-miRNAs) from 2,336 known and 361 novel miRNAs that were identified in 233 plasma samples from 61 healthy controls and 116 patients with COVID-19 using the high-throughput sequencing and computational analysis. These DE-miRNAs were associated with SASR-CoV-2 infection, disease severity, and viral persistence in the patients with COVID-19, respectively. Gene ontology and KEGG pathway analyses of the DE-miRNAs revealed their connections to viral infections, immune responses, and lung diseases. Finally, we established a machine learning model using the DE-miRNAs between various groups for classification of COVID-19 cases with different clinical presentations. Our findings may help understand the contribution of miRNAs to the pathogenesis of COVID-19 and identify potential biomarkers and molecular targets for diagnosis and treatment of SARS-CoV-2 infection. 2,336 known and 361 novel miRNAs identified in this study 85 miRNAs associated with COVID-19 A panel of miRNAs targeting the viral or cellular genes Machine learning using miRNAs for classification of COVID-19
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Affiliation(s)
- Qiqi Zeng
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Xin Qi
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Junpeng Ma
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Fang Hu
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Xiaorui Wang
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Hongyu Qin
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Mengyang Li
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Shaoxin Huang
- SpecAlly Life Technology Co, Ltd, Wuhan East Lake High-tech Development Zone, 666 Gaoxin Road, Wuhan 430075, China
| | - Yong Yang
- SpecAlly Life Technology Co, Ltd, Wuhan East Lake High-tech Development Zone, 666 Gaoxin Road, Wuhan 430075, China
| | - Yixin Li
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Han Bai
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Meng Jiang
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Doudou Ren
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Ye Kang
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Yang Zhao
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, 99 Zhangzhidong Road, Wuhan 430060, China
| | - Xiaobei Chen
- Department of Infectious Diseases, The Renmin Hospital of Wuhan University, East Campus, East Lake New Technology Development Zone, Gaoxin 6th Road, Wuhan 430040, China
| | - Xi Ding
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China
| | - Di Ye
- Department of Rehabilitation, The Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan 430060, China
| | - Yankui Wang
- Dialysis Center, The Renmin Hospital of Wuhan University, East Campus, East Lake New Technology Development Zone, Gaoxin 6th Road, Wuhan 430040, China
| | - Jianguo Jiang
- LC-Bio Technologies (Hangzhou) Co., Ltd., Hanghzhou 310000, China
| | - Dong Li
- Department of Clinical Laboratory, The Renmin Hospital of Wuhan University, East Campus, East Lake New Technology Development Zone, Gaoxin 6th Road, Wuhan 430040, China
| | - Xi Chen
- SpecAlly Life Technology Co, Ltd, Wuhan East Lake High-tech Development Zone, 666 Gaoxin Road, Wuhan 430075, China.,Wuhan Institute of Biotechnology, Wuhan East Lake High-tech Development Zone, 666 Gaoxin Road, Wuhan 430040, China
| | - Ke Hu
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, 99 Zhangzhidong Road, Wuhan 430060, China
| | - Binghong Zhang
- The Renmin Hospital of Wuhan University, East Campus, East Lake New Technology Development Zone, Gaoxin 6th Road, Wuhan 430040, China
| | - Bingyin Shi
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China
| | - Chengsheng Zhang
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China.,Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
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6
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Letafati A, Najafi S, Mottahedi M, Karimzadeh M, Shahini A, Garousi S, Abbasi-Kolli M, Sadri Nahand J, Tamehri Zadeh SS, Hamblin MR, Rahimian N, Taghizadieh M, Mirzaei H. MicroRNA let-7 and viral infections: focus on mechanisms of action. Cell Mol Biol Lett 2022; 27:14. [PMID: 35164678 PMCID: PMC8853298 DOI: 10.1186/s11658-022-00317-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/26/2022] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are fundamental post-transcriptional modulators of several critical cellular processes, a number of which are involved in host defense mechanisms. In particular, miRNA let-7 functions as an essential regulator of the function and differentiation of both innate and adaptive immune cells. Let-7 is involved in several human diseases, including cancer and viral infections. Several viral infections have found ways to dysregulate the expression of miRNAs. Extracellular vesicles (EV) are membrane-bound lipid structures released from many types of human cells that can transport proteins, lipids, mRNAs, and miRNAs, including let-7. After their release, EVs are taken up by the recipient cells and their contents released into the cytoplasm. Let-7-loaded EVs have been suggested to affect cellular pathways and biological targets in the recipient cells, and can modulate viral replication, the host antiviral response, and the action of cancer-related viruses. In the present review, we summarize the available knowledge concerning the expression of let-7 family members, functions, target genes, and mechanistic involvement in viral pathogenesis and host defense. This may provide insight into the development of new therapeutic strategies to manage viral infections.
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Affiliation(s)
- Arash Letafati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Sajad Najafi
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehran Mottahedi
- Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Karimzadeh
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Shahini
- Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Setareh Garousi
- Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Abbasi-Kolli
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, 2028 South Africa
| | - Neda Rahimian
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Department of Internal Medicine, School of Medicine, Firoozgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Taghizadieh
- Department of Pathology, School of Medicine, Center for Women’s Health Research Zahra, Tabriz University of Medical Sciences, Tabriz, Islamic Republic of Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
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7
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Lv JN, Li JQ, Cui YB, Ren YY, Fu YJ, Jiang YJ, Shang H, Zhang ZN. Plasma MicroRNA Signature Panel Predicts the Immune Response After Antiretroviral Therapy in HIV-Infected Patients. Front Immunol 2021; 12:753044. [PMID: 34887859 PMCID: PMC8650117 DOI: 10.3389/fimmu.2021.753044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022] Open
Abstract
Background Approximately 10–40% of people with human immunodeficiency virus (HIV) infection are unable to obtain successful improvements in immune function after antiretroviral therapy (ART). These patients are at greater risk of developing non-acquired immunodeficiency syndrome (AIDS)-related conditions, with the accompanying increased morbidity and mortality. Discovering predictive biomarkers can help to identify patients with a poor immune response earlier and provide new insights into the mechanisms of this condition. Methods A total of 307 people with HIV were enrolled, including 110 immune non-responders (INRs) and 197 immune responders (IRs). Plasma samples were taken before ART, and quantities of plasma microRNAs (miRNAs) were determined using reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR). Candidate biomarkers were established through four phases: discovery, training, validation, and blinded test. Binary logistic regression was used to analyze the combined predictive capacity of the identified miRNAs. The effect of one miRNA, miR-16-5p, on T cell function was assessed in vitro. Results Expression of five miRNAs (miR-580, miR-627, miR-138-5p, miR-16-5p, and miR-323-3p) was upregulated in the plasma of INRs compared with that in IRs. Expression of these miRNAs was negatively correlated with both CD4+ T cell counts and the increase in the proportion of CD4+ T cells after one year of ART. These five miRNAs were combined in a predictive model, which could effectively identify INRs or IRs. Furthermore, we found that miR-16-5p inhibits CD4+ T cell proliferation by regulating calcium flux. Conclusion We established a five-miRNA panel in plasma that accurately predicts poor immune response after ART, which could inform strategies to reduce the incidence of this phenomenon and improve the clinical management of these patients.
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Affiliation(s)
- Jun-Nan Lv
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China
| | - Jia-Qi Li
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China
| | - Ying-Bin Cui
- R&D Department, Beijing Quantobio Star Biotechnology Co., Ltd., Beijing, China
| | - Yuan-Yuan Ren
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China
| | - Ya-Jing Fu
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China
| | - Yong-Jun Jiang
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China
| | - Hong Shang
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China
| | - Zi-Ning Zhang
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China
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8
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Leo CG, Mincarone P, Tumolo MR, Panico A, Guido M, Zizza A, Guarino R, De Santis G, Sedile R, Sabina S. MiRNA expression profiling in HIV pathogenesis, disease progression and response to treatment: a systematic review. Epigenomics 2021; 13:1653-1671. [PMID: 34693727 DOI: 10.2217/epi-2021-0237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: A systematic review was conducted to identify the association of miRNA expression with HIV pathogenesis, progression and treatment. Methods: A search of articles was conducted in MEDLINE®, Cochrane Central Register of Controlled Trials and Global Health. Results: 35 articles were included. Due to the heterogeneity of HIV phenotypes, a harmonization based on key progression parameters was proposed. The hsa-miR-29 family, hsa-miR-146b-5p and hsa-miR-150-5p, are the most frequently differentially expressed in HIV. Direct comparison of studies was not possible due to heterogeneity in biological samples and miRNA analysis techniques. Conclusion: This is the first attempt to systematically identify miRNA's different expression in well-defined patient phenotypes and could represent a helpful way to increase general knowledge in this field.
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Affiliation(s)
- Carlo Giacomo Leo
- Institute of Clinical Physiology National Research Council, Branch of Lecce, 73100, Italy
| | - Pierpaolo Mincarone
- Institute for Research on Population & Social Policies National Research Council, Research Unit of Brindisi, 72100, Italy
| | - Maria Rosaria Tumolo
- Institute for Research on Population & Social Policies National Research Council, Research Unit of Brindisi, 72100, Italy
| | - Alessandra Panico
- University of Salento, Department of Biological & Environmental Sciences & Technologies, Lecce, 73039, Italy
| | - Marcello Guido
- University of Salento, Department of Biological & Environmental Sciences & Technologies, Lecce, 73039, Italy
| | - Antonella Zizza
- Institute of Clinical Physiology National Research Council, Branch of Lecce, 73100, Italy
| | - Roberto Guarino
- Institute of Clinical Physiology National Research Council, Branch of Lecce, 73100, Italy
| | - Giuseppe De Santis
- Department of Neurology, Card. G. Panico Hospital, Tricase, 73039, Italy
| | - Raffaella Sedile
- Institute of Clinical Physiology National Research Council, Branch of Lecce, 73100, Italy
| | - Saverio Sabina
- Institute of Clinical Physiology National Research Council, Branch of Lecce, 73100, Italy
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9
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Krishnan S, Queiroz ATL, Gupta A, Gupte N, Bisson GP, Kumwenda J, Naidoo K, Mohapi L, Mave V, Mngqibisa R, Lama JR, Hosseinipour MC, Andrade BB, Karakousis PC. Integrative Multi-Omics Reveals Serum Markers of Tuberculosis in Advanced HIV. Front Immunol 2021; 12:676980. [PMID: 34168648 PMCID: PMC8217878 DOI: 10.3389/fimmu.2021.676980] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/13/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) accounts for disproportionate morbidity and mortality among persons living with HIV (PLWH). Conventional methods of TB diagnosis, including smear microscopy and Xpert MTB/RIF, have lower sensitivity in PLWH. Novel high-throughput approaches, such as miRNAomics and metabolomics, may advance our ability to recognize subclinical and difficult-to-diagnose TB, especially in very advanced HIV. We conducted a case-control study leveraging REMEMBER, a multi-country, open-label randomized controlled trial comparing 4-drug empiric standard TB treatment with isoniazid preventive therapy in PLWH initiating antiretroviral therapy (ART) with CD4 cell counts <50 cells/μL. Twenty-three cases of incident TB were site-matched with 32 controls to identify microRNAs (miRNAs), metabolites, and cytokines/chemokines, associated with the development of newly diagnosed TB in PLWH. Differentially expressed miRNA analysis revealed 11 altered miRNAs with a fold change higher than 1.4 or lower than -1.4 in cases relative to controls (p<0.05). Our analysis revealed no differentially abundant metabolites between cases and controls. We found higher TNFα and IP-10/CXCL10 in cases (p=0.011, p=0.0005), and higher MDC/CCL22 in controls (p=0.0072). A decision-tree algorithm identified gamma-glutamylthreonine and hsa-miR-215-5p as the optimal variables to classify incident TB cases (AUC 0.965; 95% CI 0.925-1.000). hsa-miR-215-5p, which targets genes in the TGF-β signaling pathway, was downregulated in cases. Gamma-glutamylthreonine, a breakdown product of protein catabolism, was less abundant in cases. To our knowledge, this is one of the first uses of a multi-omics approach to identify incident TB in severely immunosuppressed PLWH.
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Affiliation(s)
- Sonya Krishnan
- Center for Clinical Global Health Education and Center for Tuberculosis Research, Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Artur T. L. Queiroz
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
| | - Amita Gupta
- Center for Clinical Global Health Education and Center for Tuberculosis Research, Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Nikhil Gupte
- Center for Clinical Global Health Education and Center for Tuberculosis Research, Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
| | - Gregory P. Bisson
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | | | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Lerato Mohapi
- Soweto ACTG CRS, Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Vidya Mave
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
| | - Rosie Mngqibisa
- Durban International Clinical Research Site, Enhancing Care Foundation, Durban, South Africa
| | | | - Mina C. Hosseinipour
- University of North Carolina Project-Malawi, Lilongwe, Malawi
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
| | - Bruno B. Andrade
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
- Curso de Medicina, Faculdade de Tecnologia e Ciências (FTC), Salvador, Brazil
- Curso de Medicina, Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador, Brazil
| | - Petros C. Karakousis
- Center for Clinical Global Health Education and Center for Tuberculosis Research, Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
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10
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Comparison of miRNA Expression Profiles between HIV-1 and HIV-2 Infected Monocyte-Derived Macrophages (MDMs) and Peripheral Blood Mononuclear Cells (PBMCs). Int J Mol Sci 2020; 21:ijms21186970. [PMID: 32971935 PMCID: PMC7556008 DOI: 10.3390/ijms21186970] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/17/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
During the progression of HIV-1 infection, macrophage tropic HIV-1 that use the CCR5 co-receptor undergoes a change in co-receptor use to CXCR4 that is predominately T cell tropic. This change in co-receptor preference makes the virus able to infect T cells. HIV-2 is known to infect MDMs and T cells and is dual tropic. The aim of this study was to elucidate the differential expression profiles of host miRNAs and their role in cells infected with HIV-1/HIV-2. To achieve this goal, a comparative global miRNA expression profile was determined in human PBMCs and MDMs infected with HIV-1/HIV-2. Differentially expressed miRNAs were identified in HIV-1/HIV-2 infected PBMCs and MDMs using the next-generation sequencing (NGS) technique. A comparative global miRNA expression profile in infected MDMs and PBMCs with HIV-1 and HIV-2 identified differential expression of several host miRNAs. These differentially expressed miRNAs are likely to be involved in many signaling pathways, like the p53 signaling pathway, PI3K-Akt signaling pathways, MAPK signaling pathways, FoxO signaling pathway, and viral carcinogenesis. Thus, a comparative study of the differential expression of host miRNAs in MDMs and T cell in response to HIV-1 and HIV-2 infection will help us to identify unique biomarkers that can differentiate HIV-1 and HIV-2 infection.
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11
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León-Rivera R, Morsey B, Niu M, Fox HS, Berman JW. Interactions of Monocytes, HIV, and ART Identified by an Innovative scRNAseq Pipeline: Pathways to Reservoirs and HIV-Associated Comorbidities. mBio 2020; 11:e01037-20. [PMID: 32723919 PMCID: PMC7387797 DOI: 10.1128/mbio.01037-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/22/2020] [Indexed: 12/31/2022] Open
Abstract
HIV reservoirs persist despite successful antiretroviral therapy (ART) and are a major obstacle to the eradication and cure of HIV. The mature monocyte subset, CD14+CD16+, contributes to viral reservoirs and HIV-associated comorbidities. Only a subset of monocytes harbors HIV (HIV+), while the rest remain uninfected, exposed cells (HIVexp). We developed an innovative single cell RNA sequencing (scRNAseq) pipeline that detects HIV and host transcripts simultaneously, enabling us to examine differences between HIV+ and HIVexp mature monocytes. Using this, we characterized uninfected, HIV+, and HIVexp primary human mature monocytes with and without ART. We showed that HIV+ mature monocytes do not form their own cluster separately from HIVexp but can be distinguished by significant differential gene expression. We found that ART decreased levels of unspliced HIV transcripts potentially by modulating host transcriptional regulators shown to decrease viral infection and replication. We also identified and characterized mature monocyte subpopulations differentially impacted by HIV and ART. We identified genes dysregulated by ART in HIVexp monocytes compared to their uninfected counterpart and, of interest, the junctional protein ALCAM, suggesting that ART impacts monocyte functions. Our data provide a novel method for simultaneous detection of HIV and host transcripts. We identify potential targets, such as those genes whose expression is increased in HIV+ mature monocytes compared to HIVexp, to block their entry into tissues, preventing establishment/replenishment of HIV reservoirs even with ART, thereby reducing and/or eliminating viral burden and HIV-associated comorbidities. Our data also highlight the heterogeneity of mature monocyte subsets and their potential contributions to HIV pathogenesis in the ART era.IMPORTANCE HIV enters tissues early after infection, leading to establishment and persistence of HIV reservoirs despite antiretroviral therapy (ART). Viral reservoirs are a major obstacle to the eradication and cure of HIV. CD14+CD16+ (mature) monocytes may contribute to establishment and reseeding of reservoirs. A subset of monocytes, consisting mainly of CD14+CD16+ cells, harbors HIV (HIV+), while the rest remain uninfected, exposed cells (HIVexp). It is important to identify cells harboring virus to eliminate reservoirs. Using an innovative single-cell RNA sequencing (scRNAseq) pipeline to detect HIV and host transcripts simultaneously, we characterized HIV+ and HIVexp primary human mature monocytes with and without ART. HIV+ mature monocytes are not a unique subpopulation but rather can be distinguished from HIVexp by differential gene expression. We characterized mature monocyte subpopulations differently impacted by HIV and ART, highlighting their potential contributions to HIV-associated comorbidities. Our data propose therapeutic targets to block HIV+ monocyte entry into tissues, preventing establishment and replenishment of reservoirs even with ART.
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Affiliation(s)
- Rosiris León-Rivera
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Brenda Morsey
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Meng Niu
- Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Howard S Fox
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Joan W Berman
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
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12
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Veziroglu EM, Mias GI. Characterizing Extracellular Vesicles and Their Diverse RNA Contents. Front Genet 2020; 11:700. [PMID: 32765582 PMCID: PMC7379748 DOI: 10.3389/fgene.2020.00700] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/09/2020] [Indexed: 12/15/2022] Open
Abstract
Cells release nanometer-scale, lipid bilayer-enclosed biomolecular packages (extracellular vesicles; EVs) into their surrounding environment. EVs are hypothesized to be intercellular communication agents that regulate physiological states by transporting biomolecules between near and distant cells. The research community has consistently advocated for the importance of RNA contents in EVs by demonstrating that: (1) EV-related RNA contents can be detected in a liquid biopsy, (2) disease states significantly alter EV-related RNA contents, and (3) sensitive and specific liquid biopsies can be implemented in precision medicine settings by measuring EV-derived RNA contents. Furthermore, EVs have medical potential beyond diagnostics. Both natural and engineered EVs are being investigated for therapeutic applications such as regenerative medicine and as drug delivery agents. This review focuses specifically on EV characterization, analysis of their RNA content, and their functional implications. The NIH extracellular RNA communication (ERC) program has catapulted human EV research from an RNA profiling standpoint by standardizing the pipeline for working with EV transcriptomics data, and creating a centralized database for the scientific community. There are currently thousands of RNA-sequencing profiles hosted on the Extracellular RNA Atlas alone (Murillo et al., 2019), encompassing a variety of human biofluid types and health conditions. While a number of significant discoveries have been made through these studies individually, integrative analyses of these data have thus far been limited. A primary focus of the ERC program over the next five years is to bring higher resolution tools to the EV research community so that investigators can isolate and analyze EV sub-populations, and ultimately single EVs sourced from discrete cell types, tissues, and complex biofluids. Higher resolution techniques will be essential for evaluating the roles of circulating EVs at a level which impacts clinical decision making. We expect that advances in microfluidic technologies will drive near-term innovation and discoveries about the diverse RNA contents of EVs. Long-term translation of EV-based RNA profiling into a mainstay medical diagnostic tool will depend upon identifying robust patterns of circulating genetic material that correlate with a change in health status.
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Affiliation(s)
- Eren M. Veziroglu
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States
| | - George I. Mias
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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13
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Hernández-Walias FJ, Vázquez E, Pacheco Y, Rodríguez-Fernández JM, Pérez-Elías MJ, Dronda F, Casado JL, Moreno A, Hermida JM, Quereda C, Hernando A, Tejerina-Picado F, Asensi V, Galindo MJ, Leal M, Moreno S, Vallejo A. Risk, Diagnostic and Predictor Factors for Classical Hodgkin Lymphoma in HIV-1-Infected Individuals: Role of Plasma Exosome-Derived miR-20a and miR-21. J Clin Med 2020; 9:jcm9030760. [PMID: 32168859 PMCID: PMC7141191 DOI: 10.3390/jcm9030760] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/27/2020] [Accepted: 03/08/2020] [Indexed: 02/07/2023] Open
Abstract
The incidence of classical Hodgkin lymphoma (cHL) in the HIV-1 setting has increased 5–25-fold compared to that observed in the general population. This study aimed to determine whether selected micro RNAs (miRs) and other soluble biomarkers and cellular subsets are dysregulated in cHL and could be used as biomarkers. This was a retrospective and longitudinal matched case-control study of 111 Caucasian, HIV-1-infected adult individuals, including 37 individuals with cHL and 74 with no type of cancer. Immunovirological data, plasma exosome-derived miR-16, miR-20a, miR-21, miR-221, miR-223, miR-106a, miR-185, miR-23, miR-30d, miR-222, miR-146a and miR-324, plasma IL-6, sCD14, sCD27, sCD30, sIL-2R, TNFR1, and cell phenotyping of T and B lymphocytes and natural killer (NK) cells were analyzed. Before cHL diagnosis, miR-20a, miR-21, and sCD30 were higher in cHL (p = 0.008, p = 0.009 and p = 0.042, respectively), while miR-16 was down-regulated (p = 0.040). miR-20a and miR-21 were independently associated with cHL (p = 0.049 and p = 0.035, respectively). The combination of miR-20a and miR-21 showed a good AUC value of 0.832 with a moderate likelihood ratio positive (LR+) value of 5.6 and a slight likelihood ratio negative (LR−) value of 0.23. At cHL diagnosis, miR-20a, miR-21 and miR-324 were overexpressed in cHL (p = 0.005, p = 0.024, and p = 0.001, respectively), while miR-223, miR-16, miR-185 and miR-106a were down regulated (p = 0.042, p = 0.007, p = 0.006, and p = 0.002, respectively). In addition, sCD14, sCD27, sCD30 and IL2R levels were higher in these individuals (p = 0.038, p = 0.010, p = 0.030, p = 0.006, respectively). miR-20a was independently associated with cHL (p = 0.011). The diagnostic value of miR-20a showed good AUC value of 0.754 (p = 0.074) with a slight LR+ value of 2 and a slight LR− of 0.25. After chemotherapy, miR-20a was higher in those individuals who had an adverse outcome (p < 0.001), while sCD14 and sCD30 were higher (p < 0.001). A specific signature of miRs and cytokines associated with a subsequent cHL diagnosis was found in this study, especially miR-20a and miR-21. Also, another biomarker signature was found at cHL diagnosis, with a relevant discriminant disease value for miR-20a. Of note, miR-20a expression was higher in those individuals who had an adverse clinical outcome after chemotherapy.
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Affiliation(s)
- Francisco J. Hernández-Walias
- Laboratory of Immunovirology, Infectious Diseases Department, Health Research Institute Ramon y Cajal (IRyCIS), Ramon y Cajal University Hospital, 28034 Madrid, Spain; (F.J.H.-W.); (E.V.); (M.J.P.-E.); (F.D.); (J.L.C.); (A.M.); (J.M.H.); (C.Q.); (S.M.)
| | - Esther Vázquez
- Laboratory of Immunovirology, Infectious Diseases Department, Health Research Institute Ramon y Cajal (IRyCIS), Ramon y Cajal University Hospital, 28034 Madrid, Spain; (F.J.H.-W.); (E.V.); (M.J.P.-E.); (F.D.); (J.L.C.); (A.M.); (J.M.H.); (C.Q.); (S.M.)
| | - Yolanda Pacheco
- Biomedicine Institute of Seville (IBiS), University Hospital Virgen del Rocío, 41013 Seville, Spain; (Y.P.); (M.L.)
| | | | - María J. Pérez-Elías
- Laboratory of Immunovirology, Infectious Diseases Department, Health Research Institute Ramon y Cajal (IRyCIS), Ramon y Cajal University Hospital, 28034 Madrid, Spain; (F.J.H.-W.); (E.V.); (M.J.P.-E.); (F.D.); (J.L.C.); (A.M.); (J.M.H.); (C.Q.); (S.M.)
| | - Fernando Dronda
- Laboratory of Immunovirology, Infectious Diseases Department, Health Research Institute Ramon y Cajal (IRyCIS), Ramon y Cajal University Hospital, 28034 Madrid, Spain; (F.J.H.-W.); (E.V.); (M.J.P.-E.); (F.D.); (J.L.C.); (A.M.); (J.M.H.); (C.Q.); (S.M.)
| | - José L. Casado
- Laboratory of Immunovirology, Infectious Diseases Department, Health Research Institute Ramon y Cajal (IRyCIS), Ramon y Cajal University Hospital, 28034 Madrid, Spain; (F.J.H.-W.); (E.V.); (M.J.P.-E.); (F.D.); (J.L.C.); (A.M.); (J.M.H.); (C.Q.); (S.M.)
| | - Ana Moreno
- Laboratory of Immunovirology, Infectious Diseases Department, Health Research Institute Ramon y Cajal (IRyCIS), Ramon y Cajal University Hospital, 28034 Madrid, Spain; (F.J.H.-W.); (E.V.); (M.J.P.-E.); (F.D.); (J.L.C.); (A.M.); (J.M.H.); (C.Q.); (S.M.)
| | - José M. Hermida
- Laboratory of Immunovirology, Infectious Diseases Department, Health Research Institute Ramon y Cajal (IRyCIS), Ramon y Cajal University Hospital, 28034 Madrid, Spain; (F.J.H.-W.); (E.V.); (M.J.P.-E.); (F.D.); (J.L.C.); (A.M.); (J.M.H.); (C.Q.); (S.M.)
| | - Carmen Quereda
- Laboratory of Immunovirology, Infectious Diseases Department, Health Research Institute Ramon y Cajal (IRyCIS), Ramon y Cajal University Hospital, 28034 Madrid, Spain; (F.J.H.-W.); (E.V.); (M.J.P.-E.); (F.D.); (J.L.C.); (A.M.); (J.M.H.); (C.Q.); (S.M.)
| | - Asunción Hernando
- Department of Medicine, 12 de Octubre University Hospital, Universidad European University of Madrid, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain;
| | | | - Víctor Asensi
- Infectious Diseases Department, Central University Hospital of Asturias, University Medical School, 33011 Oviedo, Spain;
- Group of Translational Research in Infectious Diseases, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | | | - Manuel Leal
- Biomedicine Institute of Seville (IBiS), University Hospital Virgen del Rocío, 41013 Seville, Spain; (Y.P.); (M.L.)
- Department of Internal Medicine and Infectious Diseases, Viamed Hospital, Santa Ángela de la Cruz, 41014 Seville, Spain
| | - Santiago Moreno
- Laboratory of Immunovirology, Infectious Diseases Department, Health Research Institute Ramon y Cajal (IRyCIS), Ramon y Cajal University Hospital, 28034 Madrid, Spain; (F.J.H.-W.); (E.V.); (M.J.P.-E.); (F.D.); (J.L.C.); (A.M.); (J.M.H.); (C.Q.); (S.M.)
| | - Alejandro Vallejo
- Laboratory of Immunovirology, Infectious Diseases Department, Health Research Institute Ramon y Cajal (IRyCIS), Ramon y Cajal University Hospital, 28034 Madrid, Spain; (F.J.H.-W.); (E.V.); (M.J.P.-E.); (F.D.); (J.L.C.); (A.M.); (J.M.H.); (C.Q.); (S.M.)
- Correspondence:
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14
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New signatures of poor CD4 cell recovery after suppressive antiretroviral therapy in HIV-1-infected individuals: involvement of miR-192, IL-6, sCD14 and miR-144. Sci Rep 2020; 10:2937. [PMID: 32076107 PMCID: PMC7031287 DOI: 10.1038/s41598-020-60073-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 02/05/2020] [Indexed: 02/08/2023] Open
Abstract
Up to 40% of newly diagnosed cases of HIV-1 infection are late diagnoses, with a profound decrease in CD4 cell counts in many cases. One-third of these individuals do not achieve optimal CD4 cell recovery (OR) after suppressive antiretroviral treatment (ART). This retrospective/longitudinal study of poor recovery (PR) included 79 HIV-1-infected individuals with CD4 count <200 cells/mm3 (25 PR and 54 OR) before ART. After suppressive ART, 21 PR and 24 OR individuals were further analysed, including paired samples. Selected miRs and plasma inflammatory markers were determined to investigate their potential predictive/diagnostic value for poor recovery. miR-192, IL-6 and sCD14 were independently associated with CD4 recovery before ART (p = 0.031, p = 0.007, and p = 0.008, respectively). The combination of these three factors returned a good discrimination (predictive value for PR) value of 0.841 (AUC, p < 0.001). After suppressive ART, miR-144 was independently associated with CD4 recovery (p = 0.017), showing a moderate discrimination value of 0.730 (AUC, p = 0.008) for PR. Our study provides new evidence on the relationship between miRs and HIV-1 infection that could help improve the management of individuals at HIV-1 diagnosis. These miRs and cytokines signature sets provide novel tools to predict CD4 cell recovery and its progression after ART.
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15
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Parikh VN. Circulating microRNAs as Biomarkers for Sudden Cardiac Death. JACC Clin Electrophysiol 2020; 6:80-82. [DOI: 10.1016/j.jacep.2019.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 09/12/2019] [Indexed: 11/25/2022]
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Abstract
OBJECTIVE Individuals with HIV suffer a higher burden of cardiovascular diseases. Traditional cardiovascular risk scores consistently underestimate cardiovascular risk in this population. Subsets of microRNAs (miRNAs) are differentially expressed among individuals with cardiovascular disease and individuals infected with HIV. However, no study has clarified whether specific miRNAs may be biomarkers for cardiovascular disease in individuals with HIV. DESIGN/METHODS We compared the miRNA expression profiles of 34 HIV-positive individuals who had experienced clinically adjudicated type I myocardial infarctions (MI) with the profiles of 76 HIV-positive controls matched by traditional cardiovascular risk factors and HIV-specific measures. Using the elastic net algorithm, we selected miRNAs most strongly associated with incident MI and then used conditional Cox proportional hazards regression and cross-validation to evaluate miRNAs and their association with incident MI. We evaluated whether miRNA markers would improve risk classification relative to the Framingham Risk Score. RESULTS Higher miR-125a-5p and miR-139-5p expression levels were each associated with increased risk of developing MI after adjustment for Framingham Risk Score and HIV-related factors (hazard ratio 2.43, P = 0.018; hazard ratio 2.13, P = 0.048, respectively). Compared with the Framingham Risk Score alone, adding expression levels of miR-125a-5p or miR-139-5p resulted in an integrated discrimination improvement of 10.1 or 5.8%, respectively. CONCLUSION MiR-125a-5p and miR-139-5p, transcripts known to be differentially expressed in HIV-positive individuals, may serve as unique biomarkers predictive of cardiovascular disease in these patients and may help clarify processes because of HIV infection that contribute to cardiovascular disorders in this population.
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Beck R, Bommarito P, Douillet C, Kanke M, Del Razo LM, García-Vargas G, Fry RC, Sethupathy P, Stýblo M. Circulating miRNAs Associated with Arsenic Exposure. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:14487-14495. [PMID: 30457847 PMCID: PMC7036137 DOI: 10.1021/acs.est.8b06457] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Arsenic (As) is a toxic metalloid. Inorganic arsenic (iAs) is a form of As commonly found in drinking water and in some foods. Overwhelming evidence suggests that people chronically exposed to iAs are at risk of developing cancer or cardiovascular, neurological, and metabolic diseases. Although the mechanisms underlying iAs-associated illness remain poorly characterized, a growing body of literature raises the possibility that microRNAs (miRNAs), post-transcriptional gene suppressors, may serve as mediators and/or early indicators of the pathologies associated with iAs exposure. To characterize the circulating miRNA profiles of individuals chronically exposed to iAs, samples of plasma were collected from 109 healthy residents of the city of Zimapán and the Lagunera area in Mexico, the regions with historically high exposures to iAs in drinking water. These plasma samples were analyzed for small RNAs using high-throughput sequencing and for iAs and its methylated metabolites. Associations between plasma levels of arsenic species and miRNAs were evaluated. Six circulating miRNAs (miRs-423-5p, -142-5p -2, -423-5p +1, -320c-1, -320c-2, and -454-5p), two of which have been previously linked to cardiovascular disease and diabetes (miRs-423-5p, -454-5p), were found to be significantly correlated with plasma MAs. No miRNAs were associated with plasma iAs or DMAs after correction for multiple testing. These miRNAs may represent mechanistic links between iAs exposure and disease or serve as markers of disease risks associated with this exposure.
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Affiliation(s)
- Rowan Beck
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Paige Bommarito
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Christelle Douillet
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Luz M Del Razo
- Department of Toxicology, Center of Investigation and of Advanced Studies of the National Polytechnic Institute (Cinvestav-IPN), México City, Mexico
| | | | - Rebecca C. Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
- Corresponding Authors: Praveen Sethupathy, ; Miroslav Styblo,
| | - Miroslav Stýblo
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Corresponding Authors: Praveen Sethupathy, ; Miroslav Styblo,
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