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Ilia K, Shakiba N, Bingham T, Jones RD, Kaminski MM, Aravera E, Bruno S, Palacios S, Weiss R, Collins JJ, Del Vecchio D, Schlaeger TM. Synthetic genetic circuits to uncover the OCT4 trajectories of successful reprogramming of human fibroblasts. SCIENCE ADVANCES 2023; 9:eadg8495. [PMID: 38019912 PMCID: PMC10686568 DOI: 10.1126/sciadv.adg8495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023]
Abstract
Reprogramming human fibroblasts to induced pluripotent stem cells (iPSCs) is inefficient, with heterogeneity among transcription factor (TF) trajectories driving divergent cell states. Nevertheless, the impact of TF dynamics on reprogramming efficiency remains uncharted. We develop a system that accurately reports OCT4 protein levels in live cells and use it to reveal the trajectories of OCT4 in successful reprogramming. Our system comprises a synthetic genetic circuit that leverages noise to generate a wide range of OCT4 trajectories and a microRNA targeting endogenous OCT4 to set total cellular OCT4 protein levels. By fusing OCT4 to a fluorescent protein, we are able to track OCT4 trajectories with clonal resolution via live-cell imaging. We discover that a supraphysiological, stable OCT4 level is required, but not sufficient, for efficient iPSC colony formation. Our synthetic genetic circuit design and high-throughput live-imaging pipeline are generalizable for investigating TF dynamics for other cell fate programming applications.
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Affiliation(s)
- Katherine Ilia
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nika Shakiba
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3 Canada
| | - Trevor Bingham
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard University, Boston, MA 02115, USA
| | - Ross D. Jones
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3 Canada
| | - Michael M. Kaminski
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz-Association, Berlin 10115, Germany
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Medizinische Klinik m.S. Nephrologie und Intensivmedizin, Berlin 10117, Germany
- Berlin Institute of Health, Berlin 13125, Germany
| | - Eliezer Aravera
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Simone Bruno
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
| | - Sebastian Palacios
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - James J. Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Domitilla Del Vecchio
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
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Tumolo MR, Scoditti E, Guarino R, Grassi T, Bagordo F, Sabina S. MIR-29A-3P, MIR-29C-3P, MIR-146B-5P AND MIR-150-5P, Their Target Genes and lncrnas in HIV Infection: A Bioinformatic Study. Curr HIV Res 2023; 21:128-139. [PMID: 37226785 DOI: 10.2174/1570162x21666230524151328] [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: 12/22/2022] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 05/26/2023]
Abstract
INTRODUCTION Increasing evidence suggests that microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) have emerged as attractive targets in viral infections, including Human immunodeficiency virus (HIV). OBJECTIVE To deepen the understanding of the molecular mechanisms that lead to HIV and provide potential targets for the future development of molecular therapies for its treatment. METHODS Four miRNAs were selected as candidates based on a previous systematic review. A combination of bioinformatic analyses was performed to identify their target genes, lncRNAs and biological processes that regulate them. RESULTS In the constructed miRNA-mRNA network, 193 gene targets are identified. These miRNAs potentially control genes from several important processes, including signal transduction and cancer. LncRNA-XIST, lncRNA-NEAT1 and lncRNA-HCG18 interact with all four miRNAs. CONCLUSION This preliminary result forms the basis for improving reliability in future studies to fully understand the role these molecules and their interactions play in HIV.
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Affiliation(s)
- Maria Rosaria Tumolo
- Department of Biological and Environmental Sciences and Technology, University of Salento, Lecce, Italy
| | - Egeria Scoditti
- Institute of Clinical Physiology, National Research Council, Branch of Lecce, Lecce, Italy
| | - Roberto Guarino
- Institute of Clinical Physiology, National Research Council, Branch of Lecce, Lecce, Italy
| | - Tiziana Grassi
- Department of Biological and Environmental Sciences and Technology, University of Salento, Lecce, Italy
| | - Francesco Bagordo
- Department of Pharmacy- Pharmaceutical Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Saverio Sabina
- Institute of Clinical Physiology, National Research Council, Branch of Lecce, Lecce, Italy
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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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Liu Y, Meng FZ, Wang X, Wang P, Liu JB, Hu WH, Young WB, Ho WZ. Methamphetamine facilitates HIV infection of primary human monocytes through inhibiting cellular viral restriction factors. Cell Biosci 2021; 11:194. [PMID: 34758885 PMCID: PMC8579418 DOI: 10.1186/s13578-021-00703-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
Background Methamphetamine (METH), a potent addictive psychostimulant, is highly prevalent in HIV-infected individuals. Clinically, METH use is implicated in alteration of immune system and increase of HIV spread/replication. Therefore, it is of importance to examine whether METH has direct effect on HIV infection of monocytes, the major target and reservoir cells for the virus. Results METH-treated monocytes were more susceptible to HIV infection as evidenced by increased levels of viral proteins (p24 and Pr55Gag) and expression of viral GAG gene. In addition, using HIV Bal with luciferase reporter gene (HIV Bal-eLuc), we showed that METH-treated cells expressed higher luciferase activities than untreated monocytes. Mechanistically, METH inhibited the expression of IFN-λ1, IRF7, STAT1, and the antiviral IFN-stimulated genes (ISGs: OAS2, GBP5, ISG56, Viperin and ISG15). In addition, METH down-regulated the expression of the HIV restriction microRNAs (miR-28, miR-29a, miR-125b, miR-146a, miR-155, miR-223, and miR-382). Conclusions METH compromises the intracellular anti-HIV immunity and facilitates HIV replication in primary human monocytes. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00703-4.
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Affiliation(s)
- Yu Liu
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA
| | - Feng-Zhen Meng
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA
| | - Xu Wang
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA.,Center for Substance Abuse Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140 USA
| | - Peng Wang
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA.,Center for Substance Abuse Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140 USA
| | - Jin-Biao Liu
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA
| | - Wen-Hui Hu
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA
| | - Won-Bin Young
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA
| | - Wen-Zhe Ho
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA.,Center for Substance Abuse Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140 USA
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Valle-Millares D, Brochado-Kith Ó, Martín-Carbonero L, Domínguez-Domínguez L, Ryan P, De los Santos I, De la Fuente S, Castro JM, Lagarde M, Cuevas G, Mayoral-Muñoz M, Matarranz M, Díez V, Gómez-Sanz A, Martínez-Román P, Crespo-Bermejo C, Palladino C, Muñoz-Muñoz M, Jiménez-Sousa MA, Resino S, Briz V, Fernández-Rodríguez A, (COVIHEP) OBOMGOVCHIV. Different HCV Exposure Drives Specific miRNA Profile in PBMCs of HIV Patients. Biomedicines 2021; 9:biomedicines9111627. [PMID: 34829855 PMCID: PMC8615810 DOI: 10.3390/biomedicines9111627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 12/11/2022] Open
Abstract
Micro RNAs (miRNAs) are essential players in HIV and HCV infections, as both viruses modulate cellular miRNAs and interact with the miRNA-mediated host response. We aim to analyze the miRNA profile of HIV patients with different exposure to HCV to explore specific signatures in the miRNA profile of PBMCs for each type of infection. We massively sequenced small RNAs of PBMCs from 117 HIV+ infected patients: 45 HIV+ patients chronically infected with HCV (HIV/HCV+), 36 HIV+ that spontaneously clarified HCV after acute infection (HIV/HCV-) and 36 HIV+ patients without previous HCV infection (HIV). Thirty-two healthy patients were used as healthy controls (HC). Differential expression analysis showed significantly differentially expressed (SDE) miRNAs in HIV/HCV+ (n = 153), HIV/HCV- (n = 169) and HIV (n = 153) patients. We found putative dysregulated pathways, such as infectious-related and PI3K signaling pathways, common in all contrasts. Specifically, putatively targeted genes involved in antifolate resistance (HIV/HV+), cancer-related pathways (HIV/HCV-) and HIF-signaling (HIV) were identified, among others. Our findings revealed that HCV strongly influences the expression profile of PBMCs from HIV patients through the disruption of its miRNome. Thus, different HCV exposure can be identified by specific miRNA signatures in PBMCs.
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Affiliation(s)
- Daniel Valle-Millares
- Unit of Viral Infection and Immunity, National Center for Microbiology, Institute of Health Carlos III, 28220 Majadahonda, Madrid, Spain; (D.V.-M.); (Ó.B.-K.); (A.G.-S.); (P.M.-R.); (M.A.J.-S.); (S.R.)
| | - Óscar Brochado-Kith
- Unit of Viral Infection and Immunity, National Center for Microbiology, Institute of Health Carlos III, 28220 Majadahonda, Madrid, Spain; (D.V.-M.); (Ó.B.-K.); (A.G.-S.); (P.M.-R.); (M.A.J.-S.); (S.R.)
| | - Luz Martín-Carbonero
- Hospital La Paz Institute for Health Research (IdiPAZ), 28046 Madrid, Spain; (L.M.-C.); (J.M.C.); (M.M.-M.)
| | - Lourdes Domínguez-Domínguez
- VIH Servicio de Medicina Interna Research Institute Hospital 12 de Octubre (i+12), 28041 Madrid, Spain; (L.D.-D.); (M.L.); (M.M.)
| | - Pablo Ryan
- Department of Infectious Diseases, Infanta Leonor Teaching Hospital, 28031 Madrid, Spain; (P.R.); (G.C.); (V.D.)
| | - Ignacio De los Santos
- Internal Medicine Servicie Hospital Universitario de La Princesa, 28006 Madrid, Spain;
| | - Sara De la Fuente
- Internal Medicine Service Hospital Puerta de Hierro, 28222 Madrid, Spain;
| | - Juan M. Castro
- Hospital La Paz Institute for Health Research (IdiPAZ), 28046 Madrid, Spain; (L.M.-C.); (J.M.C.); (M.M.-M.)
| | - María Lagarde
- VIH Servicio de Medicina Interna Research Institute Hospital 12 de Octubre (i+12), 28041 Madrid, Spain; (L.D.-D.); (M.L.); (M.M.)
| | - Guillermo Cuevas
- Department of Infectious Diseases, Infanta Leonor Teaching Hospital, 28031 Madrid, Spain; (P.R.); (G.C.); (V.D.)
| | - Mario Mayoral-Muñoz
- Hospital La Paz Institute for Health Research (IdiPAZ), 28046 Madrid, Spain; (L.M.-C.); (J.M.C.); (M.M.-M.)
| | - Mariano Matarranz
- VIH Servicio de Medicina Interna Research Institute Hospital 12 de Octubre (i+12), 28041 Madrid, Spain; (L.D.-D.); (M.L.); (M.M.)
| | - Victorino Díez
- Department of Infectious Diseases, Infanta Leonor Teaching Hospital, 28031 Madrid, Spain; (P.R.); (G.C.); (V.D.)
| | - Alicia Gómez-Sanz
- Unit of Viral Infection and Immunity, National Center for Microbiology, Institute of Health Carlos III, 28220 Majadahonda, Madrid, Spain; (D.V.-M.); (Ó.B.-K.); (A.G.-S.); (P.M.-R.); (M.A.J.-S.); (S.R.)
| | - Paula Martínez-Román
- Unit of Viral Infection and Immunity, National Center for Microbiology, Institute of Health Carlos III, 28220 Majadahonda, Madrid, Spain; (D.V.-M.); (Ó.B.-K.); (A.G.-S.); (P.M.-R.); (M.A.J.-S.); (S.R.)
| | - Celia Crespo-Bermejo
- Laboratory of Reference and Research on Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, 28220 Majadahonda, Madrid, Spain; (C.C.-B.); (V.B.)
| | - Claudia Palladino
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal;
| | - María Muñoz-Muñoz
- Department of Animal Genetics, Instituto Nacional de Investigación y Alimentación Agraria y Alimentaria (INIA), 28040 Madrid, Spain;
| | - María A. Jiménez-Sousa
- Unit of Viral Infection and Immunity, National Center for Microbiology, Institute of Health Carlos III, 28220 Majadahonda, Madrid, Spain; (D.V.-M.); (Ó.B.-K.); (A.G.-S.); (P.M.-R.); (M.A.J.-S.); (S.R.)
| | - Salvador Resino
- Unit of Viral Infection and Immunity, National Center for Microbiology, Institute of Health Carlos III, 28220 Majadahonda, Madrid, Spain; (D.V.-M.); (Ó.B.-K.); (A.G.-S.); (P.M.-R.); (M.A.J.-S.); (S.R.)
| | - Verónica Briz
- Laboratory of Reference and Research on Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, 28220 Majadahonda, Madrid, Spain; (C.C.-B.); (V.B.)
| | - Amanda Fernández-Rodríguez
- Unit of Viral Infection and Immunity, National Center for Microbiology, Institute of Health Carlos III, 28220 Majadahonda, Madrid, Spain; (D.V.-M.); (Ó.B.-K.); (A.G.-S.); (P.M.-R.); (M.A.J.-S.); (S.R.)
- Faculty of Medicine, Universidad Alfonso X el Sabio, Avenida Universidad 1, 28691 Villanueva de la Cañada, Madrid, Spain
- Correspondence: ; Tel.: +34-918-223-892
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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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Plasma microRNA expression levels in HIV-1-positive patients receiving antiretroviral therapy. Biosci Rep 2021; 40:222736. [PMID: 32319513 PMCID: PMC7225415 DOI: 10.1042/bsr20194433] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs/miRs) may serve as therapeutic agents or targets in diseases in which the expression of proteins plays an important role. The aim of the present study was to compare the expression levels of specific miRNAs, as well as their correlation with markers of response to antiretroviral (ARV) therapy, in patients with human immunodeficiency virus type 1 (HIV-1) infection with and without resistance to highly active antiretroviral therapy (HAART). Methods: miRNA assays were performed on plasma samples obtained from 20 HIV-1-positive patients. A total of ten patients were divided into two groups: HAART-responsive and HAART-resistant (n=5 per group). Commercial arrays were subsequently used to identify 84 miRNAs. A total of three differentially expressed miRNAs were selected and analyzed by quantitative PCR (qPCR). Five other patients were subsequently added to each group for a new relative expression analysis. The absolute expression level of the two miRNAs was obtained and compared using the Student’s t test. Receiver operating characteristic (ROC) curves were used to identify patients with antiretroviral therapy (ART) resistance. Results: The array analysis revealed that miR-15b-5p, miR-16-5p, miR-20a-5p, miR-26a-5p, miR-126-3p and miR-150-5p were down-regulated in patients with HAART-resistance comparing with HAART-responsive. The expression levels of miR-16-5p, miR-26a-5p and miR-150-5p were confirmed using qPCR. The area under the ROC curve was 1.0 for the three miRNAs. Conclusions: The lower expression levels of miR-16-5p and miR-26a-5p in patients with HAART-resistance suggested that these may serve as potential biomarkers for the identification of HAART-responsive patients.
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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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Rosca A, Anton G, Botezatu A, Temereanca A, Ene L, Achim C, Ruta S. miR-29a associates with viro-immunological markers of HIV infection in treatment experienced patients. J Med Virol 2016; 88:2132-2137. [PMID: 27232693 DOI: 10.1002/jmv.24586] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2016] [Indexed: 01/05/2023]
Abstract
MicroRNAs (miRNAs) are small, non-coding RNA species essential for the post-translational regulation of gene expression. Several miRNA have been proposed to contribute to Human immunodeficiency virus-1 (HIV-1) infection establishment, progression and latency. Among them, miR-29a seems to be of particular interest. The aim of this study was to investigate the association between miR-29a expression and immunologic and virologic markers of HIV infection progression in long-term antiretroviral-treated individuals. In a homogenous group of 165 young adults, with chronic HIV infection, parenterally acquired during childhood, the expression level of miR-29a was found to be inversely correlated with HIV viral load and the degree of immunosuppression, expressed by both CD4 cell count and the CD4/CD8 ratio. There was a significant difference in miR-29a expression according to the patient's response to treatment, with the lowest levels expressed by patients with treatment failure, defined as detectable viremia and CD4 < 350 cells/mm3 . No significant correlation was found between miRNA level and the nadir CD4 count or zenith HIV viral load. This study establishes the association between miR-29a expression and markers of HIV infection in long-term survivors, treatment-experienced patients, suggesting its potential use as an indicator for the on-treatment disease evolution. J. Med. Virol. 88:2132-2137, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Adelina Rosca
- Virology Chair, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Stefan S. Nicolau Virology Institute, Bucharest, Romania
| | - Gabriela Anton
- Stefan S. Nicolau Virology Institute, Bucharest, Romania
| | - Anca Botezatu
- Stefan S. Nicolau Virology Institute, Bucharest, Romania
| | - Aura Temereanca
- Virology Chair, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Stefan S. Nicolau Virology Institute, Bucharest, Romania
| | - Luminita Ene
- Victor Babes Hospital for Infectious and Tropical Diseases, Bucharest, Romania
| | | | - Simona Ruta
- Virology Chair, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania. .,Stefan S. Nicolau Virology Institute, Bucharest, Romania.
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