1
|
Pathmendra P, Park Y, Enguita FJ, Byrne JA. Publisher Correction: Verification of nucleotide sequence reagent identities in original publications in high impact factor cancer research journals. Naunyn Schmiedebergs Arch Pharmacol 2024:10.1007/s00210-024-02953-8. [PMID: 38225413 DOI: 10.1007/s00210-024-02953-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Affiliation(s)
- Pranujan Pathmendra
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Yasunori Park
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649‑028, Lisbon, Portugal
| | - Jennifer A Byrne
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.
- NSW Health Statewide Biobank, NSW Health Pathology, Camperdown, NSW, 2050, Australia.
| |
Collapse
|
2
|
Pathmendra P, Park Y, Enguita FJ, Byrne JA. Verification of nucleotide sequence reagent identities in original publications in high impact factor cancer research journals. Naunyn Schmiedebergs Arch Pharmacol 2024:10.1007/s00210-023-02846-2. [PMID: 38194106 DOI: 10.1007/s00210-023-02846-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 01/10/2024]
Abstract
Human gene research studies that describe wrongly identified nucleotide sequence reagents have been mostly identified in journals of low to moderate impact factor, where unreliable findings could be considered to have limited influence on future research. This study examined whether papers describing wrongly identified nucleotide sequences are also published in high-impact-factor cancer research journals. We manually verified nucleotide sequence identities in original Molecular Cancer articles published in 2014, 2016, 2018, and 2020, including nucleotide sequence reagents that were claimed to target circRNAs. Using keywords identified in some 2018 and 2020 Molecular Cancer papers, we also verified nucleotide sequence identities in 2020 Oncogene papers that studied miRNA(s) and/or circRNA(s). Overall, 3.8% (251/6647) and 4.0% (47/1165) nucleotide sequences that were verified in Molecular Cancer and Oncogene papers, respectively, were found to be wrongly identified. Wrongly identified nucleotide sequences were distributed across 18% (91/500) original Molecular Cancer papers, including 38% (31/82) Molecular Cancer papers from 2020, and 40% (21/52) selected Oncogene papers from 2020. Original papers with wrongly identified nucleotide sequences were therefore unexpectedly frequent in two high-impact-factor cancer research journals, highlighting the risks of employing journal impact factors or citations as proxies for research quality.
Collapse
Affiliation(s)
- Pranujan Pathmendra
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Yasunori Park
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - Jennifer A Byrne
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.
- NSW Health Statewide Biobank, NSW Health Pathology, Camperdown, NSW, 2050, Australia.
| |
Collapse
|
3
|
Narayanan SA, Jamison DA, Guarnieri JW, Zaksas V, Topper M, Koutnik AP, Park J, Clark KB, Enguita FJ, Leitão AL, Das S, Moraes-Vieira PM, Galeano D, Mason CE, Trovão NS, Schwartz RE, Schisler JC, Coelho-Dos-Reis JGA, Wurtele ES, Beheshti A. A comprehensive SARS-CoV-2 and COVID-19 review, Part 2: host extracellular to systemic effects of SARS-CoV-2 infection. Eur J Hum Genet 2024; 32:10-20. [PMID: 37938797 PMCID: PMC10772081 DOI: 10.1038/s41431-023-01462-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 11/09/2023] Open
Abstract
COVID-19, the disease caused by SARS-CoV-2, has caused significant morbidity and mortality worldwide. The betacoronavirus continues to evolve with global health implications as we race to learn more to curb its transmission, evolution, and sequelae. The focus of this review, the second of a three-part series, is on the biological effects of the SARS-CoV-2 virus on post-acute disease in the context of tissue and organ adaptations and damage. We highlight the current knowledge and describe how virological, animal, and clinical studies have shed light on the mechanisms driving the varied clinical diagnoses and observations of COVID-19 patients. Moreover, we describe how investigations into SARS-CoV-2 effects have informed the understanding of viral pathogenesis and provide innovative pathways for future research on the mechanisms of viral diseases.
Collapse
Affiliation(s)
- S Anand Narayanan
- COVID-19 International Research Team, Medford, MA, 02155, USA.
- Department of Health, Nutrition and Food Sciences, Florida State University, Tallahassee, FL, 32301, USA.
| | - David A Jamison
- COVID-19 International Research Team, Medford, MA, 02155, USA
| | - Joseph W Guarnieri
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Victoria Zaksas
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Center for Translational Data Science, University of Chicago, Chicago, IL, 60637, USA
- Clever Research Lab, Springfield, IL, 62704, USA
| | - Michael Topper
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Departments of Oncology and Medicine and the Sidney Comprehensive Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Andrew P Koutnik
- Human Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, Pensacola, FL, 32502, USA
- Sansum Diabetes Research Institute, Santa Barbara, CA, 93015, USA
| | - Jiwoon Park
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, 10065, USA
| | - Kevin B Clark
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Cures Within Reach, Chicago, IL, 60602, USA
- Campus and Domain Champions Program, Multi-Tier Assistance, Training, and Computational Help (MATCH) Track, National Science Foundation's Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support (ACCESS), Philadelphia, PA, USA
- Expert Network, Penn Center for Innovation, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Biometrics and Nanotechnology Councils, Institute for Electrical and Electronics Engineers, New York, NY, 10016, USA
- Peace Innovation Institute, The Hague 2511, Netherlands and Stanford University, Palo Alto, 94305, CA, USA
| | - Francisco J Enguita
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Ana Lúcia Leitão
- MEtRICs, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Saswati Das
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Atal Bihari Vajpayee Institute of Medical Sciences and Dr Ram Mannohar Lohia Hospital, New Delhi, 110001, India
| | - Pedro M Moraes-Vieira
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC) and Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, Brazil
| | - Diego Galeano
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Facultad de Ingeniería, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Christopher E Mason
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Nídia S Trovão
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert E Schwartz
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan C Schisler
- COVID-19 International Research Team, Medford, MA, 02155, USA
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jordana G A Coelho-Dos-Reis
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Basic and Applied Virology Lab, Department of Microbiology, Institute for Biological Sciences (ICB), Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Genetics Program, Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 90011, USA
- Bioinformatics and Computational Biology Program, Center for Metabolomics, Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 90011, USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA, 02155, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, Santa Clara, CA, 94035, USA.
| |
Collapse
|
4
|
Shiu PKT, DiStefano JK, Alahari SK, Enguita FJ, Feinberg MW, Sideris N, Bayraktar S, Castellano L, Buitrago DL, Caporali A, Mannucci A, Goel A. The Non-Coding RNA Journal Club: Highlights on Recent Papers-13. Noncoding RNA 2023; 9:76. [PMID: 38133210 PMCID: PMC10745700 DOI: 10.3390/ncrna9060076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
We are delighted to share with you our thirteenth Journal Club and highlight some of the most interesting papers published recently [...].
Collapse
Affiliation(s)
- Patrick K. T. Shiu
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Johanna K. DiStefano
- Metabolic Disease Research Unit, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Suresh K. Alahari
- Department of Biochemistry and Molecular Biology, LSUHSC School of Medicine, New Orleans, LA 70112, USA
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Mark W. Feinberg
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nikolaos Sideris
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK (S.B.)
| | - Salih Bayraktar
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK (S.B.)
| | - Leandro Castellano
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK (S.B.)
- Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine (ICTEM), Imperial College London, London W12 0NN, UK
| | - Diana Luna Buitrago
- BHF Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK;
| | - Andrea Caporali
- BHF Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK;
| | - Alessandro Mannucci
- Gastroenterology and Gastrointestinal Endoscopy Unit, IRCCS San Raffaele Scientific Institute, Vita-Salute San Raffaele University, 20132 Milan, Italy;
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Biomedical Research Center, Monrovia, CA 91016, USA
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Biomedical Research Center, Monrovia, CA 91016, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| |
Collapse
|
5
|
Haltom J, Trovao NS, Guarnieri J, Vincent P, Singh U, Tsoy S, O'Leary CA, Bram Y, Widjaja GA, Cen Z, Meller R, Baylin SB, Moss WN, Nikolau BJ, Enguita FJ, Wallace DC, Beheshti A, Schwartz R, Wurtele ES. SARS-CoV-2 Orphan Gene ORF10 Contributes to More Severe COVID-19 Disease. medRxiv 2023:2023.11.27.23298847. [PMID: 38076862 PMCID: PMC10705665 DOI: 10.1101/2023.11.27.23298847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
The orphan gene of SARS-CoV-2, ORF10, is the least studied gene in the virus responsible for the COVID-19 pandemic. Recent experimentation indicated ORF10 expression moderates innate immunity in vitro. However, whether ORF10 affects COVID-19 in humans remained unknown. We determine that the ORF10 sequence is identical to the Wuhan-Hu-1 ancestral haplotype in 95% of genomes across five variants of concern (VOC). Four ORF10 variants are associated with less virulent clinical outcomes in the human host: three of these affect ORF10 protein structure, one affects ORF10 RNA structural dynamics. RNA-Seq data from 2070 samples from diverse human cells and tissues reveals ORF10 accumulation is conditionally discordant from that of other SARS-CoV-2 transcripts. Expression of ORF10 in A549 and HEK293 cells perturbs immune-related gene expression networks, alters expression of the majority of mitochondrially-encoded genes of oxidative respiration, and leads to large shifts in levels of 14 newly-identified transcripts. We conclude ORF10 contributes to more severe COVID-19 clinical outcomes in the human host.
Collapse
Affiliation(s)
- Jeffrey Haltom
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Nidia S Trovao
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Joseph Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Pan Vincent
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Urminder Singh
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
| | - Sergey Tsoy
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Collin A O'Leary
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Gabrielle A Widjaja
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Zimu Cen
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Robert Meller
- Morehouse School of Medicine, Atlanta, GA , 30310-1495, USA
| | - Stephen B Baylin
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231
- Van Andel Research Institute, Grand Rapids, MI 49503
| | - Walter N Moss
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Basil J Nikolau
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA 02155, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Blue Marble Space Institute of Science, Seattle, WA, 98104 USA
| | - Robert Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| |
Collapse
|
6
|
Guarnieri JW, Dybas JM, Fazelinia H, Kim MS, Frere J, Zhang Y, Soto Albrecht Y, Murdock DG, Angelin A, Singh LN, Weiss SL, Best SM, Lott MT, Zhang S, Cope H, Zaksas V, Saravia-Butler A, Meydan C, Foox J, Mozsary C, Bram Y, Kidane Y, Priebe W, Emmett MR, Meller R, Demharter S, Stentoft-Hansen V, Salvatore M, Galeano D, Enguita FJ, Grabham P, Trovao NS, Singh U, Haltom J, Heise MT, Moorman NJ, Baxter VK, Madden EA, Taft-Benz SA, Anderson EJ, Sanders WA, Dickmander RJ, Baylin SB, Wurtele ES, Moraes-Vieira PM, Taylor D, Mason CE, Schisler JC, Schwartz RE, Beheshti A, Wallace DC. Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts. Sci Transl Med 2023; 15:eabq1533. [PMID: 37556555 DOI: 10.1126/scitranslmed.abq1533] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/20/2023] [Indexed: 08/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins bind to host mitochondrial proteins, likely inhibiting oxidative phosphorylation (OXPHOS) and stimulating glycolysis. We analyzed mitochondrial gene expression in nasopharyngeal and autopsy tissues from patients with coronavirus disease 2019 (COVID-19). In nasopharyngeal samples with declining viral titers, the virus blocked the transcription of a subset of nuclear DNA (nDNA)-encoded mitochondrial OXPHOS genes, induced the expression of microRNA 2392, activated HIF-1α to induce glycolysis, and activated host immune defenses including the integrated stress response. In autopsy tissues from patients with COVID-19, SARS-CoV-2 was no longer present, and mitochondrial gene transcription had recovered in the lungs. However, nDNA mitochondrial gene expression remained suppressed in autopsy tissue from the heart and, to a lesser extent, kidney, and liver, whereas mitochondrial DNA transcription was induced and host-immune defense pathways were activated. During early SARS-CoV-2 infection of hamsters with peak lung viral load, mitochondrial gene expression in the lung was minimally perturbed but was down-regulated in the cerebellum and up-regulated in the striatum even though no SARS-CoV-2 was detected in the brain. During the mid-phase SARS-CoV-2 infection of mice, mitochondrial gene expression was starting to recover in mouse lungs. These data suggest that when the viral titer first peaks, there is a systemic host response followed by viral suppression of mitochondrial gene transcription and induction of glycolysis leading to the deployment of antiviral immune defenses. Even when the virus was cleared and lung mitochondrial function had recovered, mitochondrial function in the heart, kidney, liver, and lymph nodes remained impaired, potentially leading to severe COVID-19 pathology.
Collapse
Affiliation(s)
- Joseph W Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Joseph M Dybas
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Hossein Fazelinia
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Man S Kim
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul, South Korea
| | - Justin Frere
- Icahn School of Medicine at Mount Sinai, New York, NY 10023, USA
| | - Yuanchao Zhang
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Yentli Soto Albrecht
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Deborah G Murdock
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessia Angelin
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Scott L Weiss
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sonja M Best
- COVID-19 International Research Team, Medford, MA 02155, USA
- Rocky Mountain Laboratory, National Institute of Allergy and Infectious Disease, NIH, Hamilton, MT 59840, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Henry Cope
- University of Nottingham, Nottingham, UK
| | - Victoria Zaksas
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Chicago, Chicago, IL 60615, USA
- Clever Research Lab, Springfield, IL 62704, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team, Medford, MA 02155, USA
- Logyx, LLC, Mountain View, CA 94043, USA
- NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Cem Meydan
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
| | | | | | - Yaron Bram
- Weill Cornell Medicine, New York, NY 10065, USA
| | - Yared Kidane
- COVID-19 International Research Team, Medford, MA 02155, USA
- Texas Scottish Rite Hospital for Children, Dallas, TX 75219, USA
| | - Waldemar Priebe
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark R Emmett
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert Meller
- COVID-19 International Research Team, Medford, MA 02155, USA
- Morehouse School of Medicine, Atlanta, GA 30310, USA
| | | | | | | | - Diego Galeano
- COVID-19 International Research Team, Medford, MA 02155, USA
- Facultad de Ingeniería, Universidad Nacional de Asunción, San Lorenzo, Central, Paraguay
| | - Francisco J Enguita
- COVID-19 International Research Team, Medford, MA 02155, USA
- Faculdade de Medicina, Universidade de Lisboa, Instituto de Medicina Molecular João Lobo Antunes, 1649-028 Lisboa, Portugal
| | - Peter Grabham
- College of Physicians and Surgeons, Columbia University, New York, NY 19103, USA
| | - Nidia S Trovao
- COVID-19 International Research Team, Medford, MA 02155, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Urminder Singh
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Jeffrey Haltom
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Mark T Heise
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Victoria K Baxter
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Emily A Madden
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - Wes A Sanders
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Stephen B Baylin
- COVID-19 International Research Team, Medford, MA 02155, USA
- Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Pedro M Moraes-Vieira
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Campinas, Campinas, SP, Brazil
| | - Deanne Taylor
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Christopher E Mason
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
- New York Genome Center, New York, NY 10013, USA
| | - Jonathan C Schisler
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert E Schwartz
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA 02155, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Division of Human Genetics, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
7
|
Enguita FJ, Leitão AL, Mattick JS. RNA Regulatory Networks 2.0. Int J Mol Sci 2023; 24:ijms24109001. [PMID: 37240347 DOI: 10.3390/ijms24109001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
The central role of RNA molecules in cell biology has been an expanding subject of study since the proposal of the "RNA world" hypothesis 60 years ago [...].
Collapse
Affiliation(s)
- Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Ana Lúcia Leitão
- Department of Chemistry, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| |
Collapse
|
8
|
Leitão AL, Enguita FJ. Editorial: Secondary metabolism: an unlimited foundation for synthetic biology, volume II. Front Microbiol 2023; 14:1200928. [PMID: 37266013 PMCID: PMC10230052 DOI: 10.3389/fmicb.2023.1200928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/02/2023] [Indexed: 06/03/2023] Open
Affiliation(s)
- Ana Lúcia Leitão
- MEtRICs, Department of Chemistry, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Francisco J. Enguita
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
9
|
Boon PLS, Martins AS, Lim XN, Enguita FJ, Santos NC, Bond PJ, Wan Y, Martins IC, Huber RG. Dengue Virus Capsid Protein Facilitates Genome Compaction and Packaging. Int J Mol Sci 2023; 24:ijms24098158. [PMID: 37175867 PMCID: PMC10179140 DOI: 10.3390/ijms24098158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Dengue virus (DENV) is a single-stranded (+)-sense RNA virus that infects humans and mosquitoes, posing a significant health risk in tropical and subtropical regions. Mature virions are composed of an icosahedral shell of envelope (E) and membrane (M) proteins circumscribing a lipid bilayer, which in turn contains a complex of the approximately 11 kb genomic RNA with capsid (C) proteins. Whereas the structure of the envelope is clearly defined, the structure of the packaged genome in complex with C proteins remains elusive. Here, we investigated the interactions of C proteins with viral RNA, in solution and inside mature virions, via footprinting and cross-linking experiments. We demonstrated that C protein interaction with DENV genomes saturates at an RNA:C protein ratio below 1:250. Moreover, we also showed that the length of the RNA genome interaction sites varies, in a multimodal distribution, consistent with the C protein binding to each RNA site mostly in singlets or pairs (and, in some instances, higher numbers). We showed that interaction sites are preferentially sites with low base pairing, as previously measured by 2'-acetylation analyzed by primer extension (SHAPE) reactivity indicating structuredness. We found a clear association pattern emerged: RNA-C protein binding sites are strongly associated with long-range RNA-RNA interaction sites, particularly inside virions. This, in turn, explains the need for C protein in viral genome packaging: the protein has a chief role in coordinating these key interactions, promoting proper packaging of viral RNA. Such sites are, thus, highly consequential for viral assembly, and, as such, may be targeted in future drug development strategies against these and related viruses.
Collapse
Affiliation(s)
- Priscilla L S Boon
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 16 Science Drive 4, Singapore 117558, Singapore
| | - Ana S Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Xin Ni Lim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 16 Science Drive 4, Singapore 117558, Singapore
| | - Yue Wan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Ivo C Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Roland G Huber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
| |
Collapse
|
10
|
Yazdani B, Sirous H, Enguita FJ, Brogi S, Wing PAC, Fassihi A. Discovery of novel direct small-molecule inhibitors targeting HIF-2α using structure-based virtual screening, molecular dynamics simulation, and MM-GBSA calculations. Mol Divers 2023:10.1007/s11030-023-10650-6. [PMID: 37120484 DOI: 10.1007/s11030-023-10650-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/11/2023] [Indexed: 05/01/2023]
Abstract
Hypoxia-inducible factors (HIFs) are the main regulatory factors implicated in the adaptation of cancer cells to hypoxic stress, which has provoked much interest as an attractive target for the design of promising chemotherapeutic agents. Since indirect HIF inhibitors (HIFIs) lead to the occurrence of various side effects, the need of the hour is to develop direct HIFIs, physically interacting with important functional domains within the HIF protein structure. Accordingly, in the present study, it was attempted to develop an exhaustive structure-based virtual screening (VS) process coupled with molecular docking, molecular dynamic (MD) simulation, and MM-GBSA calculations for the identification of novel direct inhibitors against the HIF-2α subunit. For this purpose, a focused library of over 200,000 compounds from the NCI database was used for VS against the PAS-B domain of the target protein, HIF-2α. This domain was suggested to be a possible ligand-binding site, which is characterized by a large internal hydrophobic cavity, unique to the HIF-2α subunit. The top-ranked compounds, NSC106416, NSC217021, NSC217026, NSC215639, and NSC277811 with the best docking scores were taken up for the subsequent in silico ADME properties and PAINS filtration. The selected drug-like hits were employed for carrying out MD simulation which was followed by MM-GBSA calculations to retrieve the candidates showing the highest in silico binding affinity towards the PAS-B domain of HIF-2α. The analysis of results indicated that all molecules, except the NSC277811, fulfilled necessary drug-likeness properties. Four selected drug-like candidates, NSC106416, NSC217021, NSC217026, and NSC215639 were found to expose the stability profiles within the cavity located inside the PAS-B domain of HIF-2α over simulation time. Finally, the results of the MM-GBSA rescoring method were indicative of the highest binding affinity of NSC217026 for the binding site of the HIF-2α PAS-B domain among selected final hits. Consequently, the hit NSC217026 could serve as a promising scaffold for further optimization toward the design of direct HIF-2α inhibitors for cancer therapy.
Collapse
Affiliation(s)
- Behnaz Yazdani
- Department of Tissue Engineering, Najafabad Branch, Islamic Azad University, Najafabad, Iran
| | - Hajar Sirous
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran.
| | - Francisco J Enguita
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal
| | - Simone Brogi
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran.
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy.
| | - Peter A C Wing
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Afshin Fassihi
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
| |
Collapse
|
11
|
Enguita FJ, Pereira S, Leitão AL. Transcriptomic Analysis of Acetaminophen Biodegradation by Penicillium chrysogenum var. halophenolicum and Insights into Energy and Stress Response Pathways. J Fungi (Basel) 2023; 9:jof9040408. [PMID: 37108863 PMCID: PMC10146002 DOI: 10.3390/jof9040408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
(1) Background: Acetaminophen (APAP), an active component of many analgesic and antipyretic drugs, is one of the most concerning trace contaminants in the environment and is considered as an emergent pollutant of marine and aquatic ecosystems. Despite its biodegradability, APAP has become a recalcitrant compound due to the growth of the global population, the ease of availability, and the inefficient wastewater treatment applied. (2) Methods: In this study, we used a transcriptomic approach to obtain functional and metabolic insights about the metabolization of APAP by a phenol-degrading fungal strain, Penicillium chrysogenum var. halophenolicum. (3) Results: We determined that the transcriptomic profile exhibited by the fungal strain during APAP degradation was very dynamic, being characterized by an abundance of dysregulated transcripts which were proportional to the drug metabolization. Using a systems biology approach, we also inferred the protein functional interaction networks that could be related to APAP degradation. We proposed the involvement of intracellular and extracellular enzymes, such as amidases, cytochrome P450, laccases, and extradiol-dioxygenases, among others. (4) Conclusions: Our data suggested that the fungus could metabolize APAP via a complex metabolic pathway, generating nontoxic metabolites, which demonstrated its potential in the bioremediation of this drug.
Collapse
|
12
|
Rajão-Saraiva J, Dunot J, Ribera A, Temido-Ferreira M, Coelho JE, König S, Moreno S, Enguita FJ, Willem M, Kins S, Marie H, Lopes LV, Pousinha PA. Age-dependent NMDA receptor function is regulated by the amyloid precursor protein. Aging Cell 2023; 22:e13778. [PMID: 36704841 PMCID: PMC10014064 DOI: 10.1111/acel.13778] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/13/2022] [Accepted: 12/21/2022] [Indexed: 01/28/2023] Open
Abstract
N-methyl-D-aspartate receptors (NMDARs) are critical for the maturation and plasticity of glutamatergic synapses. In the hippocampus, NMDARs mainly contain GluN2A and/or GluN2B regulatory subunits. The amyloid precursor protein (APP) has emerged as a putative regulator of NMDARs, but the impact of this interaction to their function is largely unknown. By combining patch-clamp electrophysiology and molecular approaches, we unravel a dual mechanism by which APP controls GluN2B-NMDARs, depending on the life stage. We show that APP is highly abundant specifically at the postnatal postsynapse. It interacts with GluN2B-NMDARs, controlling its synaptic content and mediated currents, both in infant mice and primary neuronal cultures. Upon aging, the APP amyloidogenic-derived C-terminal fragments, rather than APP full-length, contribute to aberrant GluN2B-NMDAR currents. Accordingly, we found that the APP processing is increased upon aging, both in mice and human brain. Interfering with stability or production of the APP intracellular domain normalized the GluN2B-NMDARs currents. While the first mechanism might be essential for synaptic maturation during development, the latter could contribute to age-related synaptic impairments.
Collapse
Affiliation(s)
- Joana Rajão-Saraiva
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisboa, Portugal
| | - Jade Dunot
- University Côte d' Azur, Centre National de la Recherche Scientifique (CNRS) UMR 7275, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Aurore Ribera
- University Côte d' Azur, Centre National de la Recherche Scientifique (CNRS) UMR 7275, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Mariana Temido-Ferreira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisboa, Portugal
| | - Joana E Coelho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisboa, Portugal
| | - Svenja König
- Division of Human Biology and Human Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sébastien Moreno
- University Côte d' Azur, Centre National de la Recherche Scientifique (CNRS) UMR 7275, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisboa, Portugal
| | - Michael Willem
- Biomedical Center (BMC), Division of Metabolic Biochemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stefan Kins
- Division of Human Biology and Human Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Hélène Marie
- University Côte d' Azur, Centre National de la Recherche Scientifique (CNRS) UMR 7275, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Luísa V Lopes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisboa, Portugal
| | - Paula A Pousinha
- University Côte d' Azur, Centre National de la Recherche Scientifique (CNRS) UMR 7275, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| |
Collapse
|
13
|
Martins‐Marques T, Costa MC, Catarino S, Simoes I, Aasen T, Enguita FJ, Girao H. Cx43-mediated sorting of miRNAs into extracellular vesicles. EMBO Rep 2022; 23:e54312. [PMID: 35593040 PMCID: PMC9253745 DOI: 10.15252/embr.202154312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/12/2022] [Accepted: 04/26/2022] [Indexed: 09/23/2023] Open
Abstract
Through the exchange of lipids, proteins, and nucleic acids, extracellular vesicles (EV) allow for cell-cell communication across distant cells and tissues to regulate a wide range of physiological and pathological processes. Although some molecular mediators have been discovered, the mechanisms underlying the selective sorting of miRNAs into EV remain elusive. Previous studies demonstrated that connexin43 (Cx43) forms functional channels at the EV surface, mediating the communication with recipient cells. Here, we show that Cx43 participates in the selective sorting of miRNAs into EV through a process that can also involve RNA-binding proteins. We provide evidence that Cx43 can directly bind to specific miRNAs, namely those containing stable secondary structure elements, including miR-133b. Furthermore, Cx43 facilitates the delivery of EV-miRNAs into recipient cells. Phenotypically, we show that Cx43-mediated EV-miRNAs sorting modulates autophagy. Overall, our study ascribes another biological role to Cx43, that is, the selective incorporation of miRNAs into EV, which potentially modulates multiple biological processes in target cells and may have implications for human health and disease.
Collapse
Affiliation(s)
- Tania Martins‐Marques
- Faculty of MedicineCoimbra Institute for Clinical and Biomedical Research (iCBR)University of CoimbraCoimbraPortugal
- Center for Innovative Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Clinical Academic Centre of Coimbra (CACC)CoimbraPortugal
| | - Marina C Costa
- Faculdade de MedicinaInstituto de Medicina Molecular João Lobo AntunesUniversidade de LisboaLisboaPortugal
| | - Steve Catarino
- Faculty of MedicineCoimbra Institute for Clinical and Biomedical Research (iCBR)University of CoimbraCoimbraPortugal
- Center for Innovative Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Clinical Academic Centre of Coimbra (CACC)CoimbraPortugal
| | - Isaura Simoes
- Center for Innovative Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- CNC‐Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- IIIUC‐Institute of Interdisciplinary ResearchUniversity of CoimbraCoimbraPortugal
| | - Trond Aasen
- Patologia Molecular Translacional, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital UniversitariVall d'Hebron Barcelona Hospital Campus, Passeig Vall d'HebronBarcelonaSpain
- CIBER de Cáncer (CIBERONC)Instituto de Salud Carlos IIIMadridSpain
| | - Francisco J Enguita
- Faculdade de MedicinaInstituto de Medicina Molecular João Lobo AntunesUniversidade de LisboaLisboaPortugal
| | - Henrique Girao
- Faculty of MedicineCoimbra Institute for Clinical and Biomedical Research (iCBR)University of CoimbraCoimbraPortugal
- Center for Innovative Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Clinical Academic Centre of Coimbra (CACC)CoimbraPortugal
| |
Collapse
|
14
|
Leitão AL, Enguita FJ. A Structural View of miRNA Biogenesis and Function. Noncoding RNA 2022; 8:ncrna8010010. [PMID: 35202084 PMCID: PMC8874510 DOI: 10.3390/ncrna8010010] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/16/2022] Open
Abstract
Micro-RNAs (miRNAs) are a class of non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of gene expression. Since their discovery in 1993, they have been the subject of deep study due to their involvement in many important biological processes. Compared with other ncRNAs, miRNAs are generated from devoted transcriptional units which are processed by a specific set of endonucleases. The contribution of structural biology methods for understanding miRNA biogenesis and function has been essential for the dissection of their roles in cell biology and human disease. In this review, we summarize the application of structural biology for the characterization of the molecular players involved in miRNA biogenesis (processors and effectors), starting from the X-ray crystallography methods to the more recent cryo-electron microscopy protocols.
Collapse
Affiliation(s)
- Ana Lúcia Leitão
- MEtRICs, Department of Sciences and Technology of Biomass, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal;
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Correspondence:
| |
Collapse
|
15
|
Pinzon Cortes JA, El-Osta A, Fontemaggi G, Delihas N, Miyazaki K, Goel A, Brazane M, Carré C, Dama P, Bayraktar S, Castellano L, Enguita FJ, Mitic T, Caporali A, Gerber AP, Amodio N. The Non-Coding RNA Journal Club: Highlights on Recent Papers-10. Noncoding RNA 2022; 8:3. [PMID: 35076559 PMCID: PMC8788465 DOI: 10.3390/ncrna8010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/05/2022] [Indexed: 12/05/2022] Open
Abstract
We are delighted to share with you our seventh Journal Club and highlight some of the most interesting papers published recently [...].
Collapse
Affiliation(s)
- Jairo A. Pinzon Cortes
- Epigenetics in Human Health and Disease, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia;
| | - Assam El-Osta
- Epigenetics in Human Health and Disease, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia;
| | - Giulia Fontemaggi
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Nicholas Delihas
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, NY 11794, USA
| | - Katsuki Miyazaki
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Biomedical Research Center, Monrovia, CA 91016, USA;
- Department of Surgery, Tokushima University, Tokushima 7708503, Japan
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Biomedical Research Center, Monrovia, CA 91016, USA;
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Mira Brazane
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, CNRS, Laboratoire Biologie du Développement, Institut de Biologie Paris-Seine, UMR7622, 75005 Paris, France
| | - Clément Carré
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, CNRS, Laboratoire Biologie du Développement, Institut de Biologie Paris-Seine, UMR7622, 75005 Paris, France
| | - Paola Dama
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Salih Bayraktar
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Leandro Castellano
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
- Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine (ICTEM), Imperial College London, London W12 0NN, UK
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Tijana Mitic
- University/British Heart Foundation Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK;
| | - Andrea Caporali
- University/British Heart Foundation Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK;
| | - André P. Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| |
Collapse
|
16
|
Enguita FJ, Leitão AL, McDonald JT, Zaksas V, Das S, Galeano D, Taylor D, Wurtele ES, Saravia-Butler A, Baylin SB, Meller R, Porterfield DM, Wallace DC, Schisler JC, Mason CE, Beheshti A. The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response. Am J Cancer Res 2022; 12:3946-3962. [PMID: 35664076 PMCID: PMC9131284 DOI: 10.7150/thno.73268] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 04/24/2022] [Indexed: 11/29/2022] Open
Abstract
Rationale: Viral infections are complex processes based on an intricate network of molecular interactions. The infectious agent hijacks components of the cellular machinery for its profit, circumventing the natural defense mechanisms triggered by the infected cell. The successful completion of the replicative viral cycle within a cell depends on the function of viral components versus the cellular defenses. Non-coding RNAs (ncRNAs) are important cellular modulators, either promoting or preventing the progression of viral infections. Among these ncRNAs, the long non-coding RNA (lncRNA) family is especially relevant due to their intrinsic functional properties and ubiquitous biological roles. Specific lncRNAs have been recently characterized as modulators of the cellular response during infection of human host cells by single stranded RNA viruses. However, the role of host lncRNAs in the infection by human RNA coronaviruses such as SARS-CoV-2 remains uncharacterized. Methods: In the present work, we have performed a transcriptomic study of a cohort of patients with different SARS-CoV-2 viral load and analyzed the involvement of lncRNAs in supporting regulatory networks based on their interaction with RNA-binding proteins (RBPs). Results: Our results revealed the existence of a SARS-CoV-2 infection-dependent pattern of transcriptional up-regulation in which specific lncRNAs are an integral component. To determine the role of these lncRNAs, we performed a functional correlation analysis complemented with the study of the validated interactions between lncRNAs and RBPs. This combination of in silico functional association studies and experimental evidence allowed us to identify a lncRNA signature composed of six elements - NRIR, BISPR, MIR155HG, FMR1-IT1, USP30-AS1, and U62317.2 - associated with the regulation of SARS-CoV-2 infection. Conclusions: We propose a competition mechanism between the viral RNA genome and the regulatory lncRNAs in the sequestering of specific RBPs that modulates the interferon response and the regulation of RNA surveillance by nonsense-mediated decay (NMD).
Collapse
|
17
|
McDonald JT, Enguita FJ, Taylor D, Griffin RJ, Priebe W, Emmett MR, Sajadi MM, Harris AD, Clement J, Dybas JM, Aykin-Burns N, Guarnieri JW, Singh LN, Grabham P, Baylin SB, Yousey A, Pearson AN, Corry PM, Saravia-Butler A, Aunins TR, Sharma S, Nagpal P, Meydan C, Foox J, Mozsary C, Cerqueira B, Zaksas V, Singh U, Wurtele ES, Costes SV, Davanzo GG, Galeano D, Paccanaro A, Meinig SL, Hagan RS, Bowman NM, Wolfgang MC, Altinok S, Sapoval N, Treangen TJ, Moraes-Vieira PM, Vanderburg C, Wallace DC, Schisler JC, Mason CE, Chatterjee A, Meller R, Beheshti A. Role of miR-2392 in driving SARS-CoV-2 infection. Cell Rep 2021; 37:109839. [PMID: 34624208 PMCID: PMC8481092 DOI: 10.1016/j.celrep.2021.109839] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/13/2021] [Accepted: 09/24/2021] [Indexed: 02/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provide an exciting avenue toward antiviral therapeutics. From patient transcriptomic data, we determined that a circulating miRNA, miR-2392, is directly involved with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) machinery during host infection. Specifically, we show that miR-2392 is key in driving downstream suppression of mitochondrial gene expression, increasing inflammation, glycolysis, and hypoxia, as well as promoting many symptoms associated with coronavirus disease 2019 (COVID-19) infection. We demonstrate that miR-2392 is present in the blood and urine of patients positive for COVID-19 but is not present in patients negative for COVID-19. These findings indicate the potential for developing a minimally invasive COVID-19 detection method. Lastly, using in vitro human and in vivo hamster models, we design a miRNA-based antiviral therapeutic that targets miR-2392, significantly reduces SARS-CoV-2 viability in hamsters, and may potentially inhibit a COVID-19 disease state in humans.
Collapse
Affiliation(s)
- J Tyson McDonald
- COVID-19 International Research Team; Georgetown University School of Medicine, Washington, DC 20007, USA
| | - Francisco J Enguita
- COVID-19 International Research Team; Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Deanne Taylor
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert J Griffin
- COVID-19 International Research Team; University of Arkansas for Medical Sciences, Little Rock, AK 72211, USA
| | - Waldemar Priebe
- COVID-19 International Research Team; University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark R Emmett
- COVID-19 International Research Team; University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | - Anthony D Harris
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jean Clement
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Joseph M Dybas
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Joseph W Guarnieri
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Larry N Singh
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Peter Grabham
- COVID-19 International Research Team; Columbia University, New York, NY 10032, USA
| | - Stephen B Baylin
- COVID-19 International Research Team; Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Aliza Yousey
- COVID-19 International Research Team; Morehouse School of Medicine, Atlanta, GA 30310, USA
| | | | - Peter M Corry
- COVID-19 International Research Team; University of Arkansas for Medical Sciences, Little Rock, AK 72211, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team; Logyx LLC, Mountain View, CA 94043, USA; NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Sadhana Sharma
- University of Colorado Boulder, Boulder, CO 80303, USA; Sachi Bioworks Inc., Boulder, CO 80301, USA
| | - Prashant Nagpal
- Sachi Bioworks Inc., Boulder, CO 80301, USA; Antimicrobial Regeneration Consortium, Boulder Labs, Boulder, CO 80301, USA; Quantum Biology Inc., Boulder, CO 80301, USA
| | - Cem Meydan
- Weill Cornell Medicine, New York, NY 10065, USA
| | | | | | - Bianca Cerqueira
- COVID-19 International Research Team; KBR Space & Science, San Antonio, TX 78235, USA; United States Air Force School of Aerospace Medicine, Lackland AFB, San Antonio, TX 78236, USA
| | - Viktorija Zaksas
- COVID-19 International Research Team; University of Chicago, Chicago, IL 60615, USA
| | - Urminder Singh
- COVID-19 International Research Team; Iowa State University, Ames, IA 50011, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team; Iowa State University, Ames, IA 50011, USA
| | | | | | - Diego Galeano
- COVID-19 International Research Team; Fundação Getulio Vargas, Rio de Janeiro, Brazil; National University of Asuncion, San Lorenzo, Central, Paraguay
| | - Alberto Paccanaro
- COVID-19 International Research Team; Fundação Getulio Vargas, Rio de Janeiro, Brazil; University of London, Egham Hill, Egham, UK
| | - Suzanne L Meinig
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert S Hagan
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie M Bowman
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Selin Altinok
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | | | | | - Douglas C Wallace
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan C Schisler
- COVID-19 International Research Team; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christopher E Mason
- COVID-19 International Research Team; Weill Cornell Medicine, New York, NY 10065, USA; New York Genome Center, New York, NY, USA
| | - Anushree Chatterjee
- COVID-19 International Research Team; University of Colorado Boulder, Boulder, CO 80303, USA; Sachi Bioworks Inc., Boulder, CO 80301, USA; Antimicrobial Regeneration Consortium, Boulder Labs, Boulder, CO 80301, USA
| | - Robert Meller
- COVID-19 International Research Team; Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Afshin Beheshti
- COVID-19 International Research Team; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.
| |
Collapse
|
18
|
Miranda HV, Szegő ÉM, Oliveira LMA, Breda C, Darendelioglu E, de Oliveira RM, Ferreira DG, Gomes MA, Rott R, Oliveira M, Munari F, Enguita FJ, Simões T, Rodrigues EF, Heinrich M, Martins IC, Zamolo I, Riess O, Cordeiro C, Ponces-Freire A, Lashuel HA, Santos NC, Lopes LV, Xiang W, Jovin TM, Penque D, Engelender S, Zweckstetter M, Klucken J, Giorgini F, Quintas A, Outeiro TF. Erratum to: Glycation potentiates α-synuclein-associated neurodegeneration in synucleinopathies. Brain 2021; 144:e58. [PMID: 34100910 DOI: 10.1093/brain/awab175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
19
|
Pereira-da-Silva T, Napoleão P, Costa MC, Gabriel AF, Selas M, Silva F, Enguita FJ, Cruz Ferreira R, Mota Carmo M. Association between miR-146a and Tumor Necrosis Factor Alpha (TNF-α) in Stable Coronary Artery Disease. ACTA ACUST UNITED AC 2021; 57:medicina57060575. [PMID: 34199767 PMCID: PMC8230353 DOI: 10.3390/medicina57060575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022]
Abstract
Background and Objectives: Tumor necrosis factor alpha (TNF-α) is proatherogenic and associated with the risk of acute ischemic events, although the mechanisms that regulate TNF-α expression in stable coronary artery disease (SCAD) are not fully understood. We investigated whether metabolic, inflammatory, and epigenetic (microRNA (miRNA)) markers are associated with TNF-α expression in SCAD. Materials and Methods: Patients with SCAD were prospectively recruited and their metabolic and inflammatory profiles were assessed. TNF-α levels were assessed using an enzyme-linked immunosorbent assay. The relative expression of six circulating miRNAs associated with the regulation of inflammation and/or atherosclerosis was determined. Results: Of the 24 included patients with the mean age of 65 (9) years, 88% were male, and 54% were diabetic. The TNF-α levels were (median (interquartile range)) 1.0 (0.7–1.1) pg/mL. The percentage of glycosylated hemoglobin (r = 0.418, p = 0.042), serum triglyceride levels (r = 0.429, p = 0.037), and C-reactive protein levels (r = 0.407, p = 0.048) were positively correlated with TNF-α levels. Of the candidate miRNAs, miR-146a expression levels were negatively correlated with TNF-α levels (as indicated by r = 0.500, p = 0.035 for correlation between delta cycle threshold (ΔCt) miR-146a and TNF-α levels). In multivariate analysis, serum triglyceride levels and miR-146a expression levels were independently associated with TNF-α levels. miR-146 expression levels were not associated with metabolic or other inflammatory parameters and were negatively correlated with the number of coronary vessels with obstructive disease (as indicated by r = 0.556, p = 0.017 for correlation between ΔCt miR-146a and number of diseased vessels). Conclusions: miR-146a expression levels were negatively correlated with TNF-α levels in patients with SCAD, irrespective of other metabolic or inflammatory markers, and with the severity of coronary artery disease. The results add to the knowledge on the role of miR-146a in TNF-α-based inflammation in SCAD and support future research on the potential therapeutic use of miR-146a in such a clinical scenario.
Collapse
Affiliation(s)
- Tiago Pereira-da-Silva
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
- NOVA Doctoral School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- Correspondence: ; Tel.: +351-919908505
| | - Patrícia Napoleão
- Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
| | - Marina C. Costa
- Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - André F. Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Mafalda Selas
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
| | - Filipa Silva
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Rui Cruz Ferreira
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
| | - Miguel Mota Carmo
- Chronic Diseases Research Center (CEDOC), NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1150-082 Lisbon, Portugal;
| |
Collapse
|
20
|
Miller WB, Enguita FJ, Leitão AL. Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution. Cells 2021; 10:1125. [PMID: 34066959 PMCID: PMC8148535 DOI: 10.3390/cells10051125] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/27/2021] [Accepted: 05/05/2021] [Indexed: 12/16/2022] Open
Abstract
Neo-Darwinism presumes that biological variation is a product of random genetic replication errors and natural selection. Cognition-Based Evolution (CBE) asserts a comprehensive alternative approach to phenotypic variation and the generation of biological novelty. In CBE, evolutionary variation is the product of natural cellular engineering that permits purposive genetic adjustments as cellular problem-solving. CBE upholds that the cornerstone of biology is the intelligent measuring cell. Since all biological information that is available to cells is ambiguous, multicellularity arises from the cellular requirement to maximize the validity of available environmental information. This is best accomplished through collective measurement purposed towards maintaining and optimizing individual cellular states of homeorhesis as dynamic flux that sustains cellular equipoise. The collective action of the multicellular measurement and assessment of information and its collaborative communication is natural cellular engineering. Its yield is linked cellular ecologies and mutualized niche constructions that comprise biofilms and holobionts. In this context, biological variation is the product of collective differential assessment of ambiguous environmental cues by networking intelligent cells. Such concerted action is enabled by non-random natural genomic editing in response to epigenetic impacts and environmental stresses. Random genetic activity can be either constrained or deployed as a 'harnessing of stochasticity'. Therefore, genes are cellular tools. Selection filters cellular solutions to environmental stresses to assure continuous cellular-organismal-environmental complementarity. Since all multicellular eukaryotes are holobionts as vast assemblages of participants of each of the three cellular domains (Prokaryota, Archaea, Eukaryota) and the virome, multicellular variation is necessarily a product of co-engineering among them.
Collapse
Affiliation(s)
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal;
| | - Ana Lúcia Leitão
- MEtRICs, Department of Sciences and Technology of Biomass, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal;
| |
Collapse
|
21
|
Misir S, Hepokur C, Aliyazicioglu Y, Enguita FJ. Biomarker potentials of miRNA-associated circRNAs in breast cancer (MCF-7) cells: an in vitro and in silico study. Mol Biol Rep 2021; 48:2463-2471. [PMID: 33774752 DOI: 10.1007/s11033-021-06281-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/11/2021] [Indexed: 11/28/2022]
Abstract
Breast cancer is a heterogeneous disease, which is the most common malignancy in women. The incidence and mortality rates of breast cancer indicate that it is the leading cause of cancer-related with deaths. circRNAs operate as part of competing endogenous RNAs (ceRNAs) mechanisms, which play critical roles in the different biological processes of breast cancer such as proliferation, migration, and apoptosis. The goal of the present study is to identify the potential predictive biomarker for breast cancer diagnosis in the circRNA network by in vitro and in silico analyzes. 40 miRNAs were obtained from the miRWalk database and their combinatorial target genes (potential ceRNAs) were identified with ComiR. We stated that the cancer-specific circRNA genes in MCF-7 cells using the cancer-specific circRNA (CSDC) database, and obtained the ones showing potential ceRNA activity in our previous analysis among them. Identified genes with remarkable expression differences between BCa and normal breast tissue were determined by the GEPIA database. Moreover, the Spearman correlation test in the GEPIA database was used for the statistical analysis of the relationship between DCAF7 and SOGA1, SOGA1 and AVL 9, DCAF7 and AVL 9 gene pairs. And also, DCAF7, SOGA1, and AVL9 gene expression levels were detected in MCF-7 and MCF-10A cells by RT-qPCR method. DCAF7, SOGA1, and AVL9 gene were significantly more expressed to BCa tissue and MCF-7 cells than normal breast tissue and MCF-10 A cells. And also, DCAF7 and SOGA1, SOGA1 and AVL9, DCAF7 and AVL9 genes pairs were found to be significantly correlated with BCa. These genes may be considered as potential predictive biomarkers to discriminate BCa patients from healthy persons. Our preliminary results can supply a new perspective for in vitro and vivo studies in the future.
Collapse
Affiliation(s)
- Sema Misir
- Department of Biochemistry, Faculty of Pharmacy, Sivas Cumhuriyet University, 58140, Sivas, Turkey.
| | - Ceylan Hepokur
- Department of Biochemistry, Faculty of Pharmacy, Sivas Cumhuriyet University, 58140, Sivas, Turkey
| | - Yuksel Aliyazicioglu
- Department of Medical Biochemistry, Faculty of Medicine, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| |
Collapse
|
22
|
Witek P, Enguita FJ, Grzesiak M, Costa MC, Gabriel A, Koziorowski M, Slomczynska M, Knapczyk-Stwora K. Effects of neonatal exposure to methoxychlor on corpus luteum in gilts: A transcriptomic analysis. Mol Reprod Dev 2021; 88:238-248. [PMID: 33655673 DOI: 10.1002/mrd.23463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/07/2021] [Accepted: 02/20/2021] [Indexed: 11/10/2022]
Abstract
This study investigated the effects of neonatal exposure to methoxychlor (MXC), a synthetic organochlorine used as an insecticide with estrogenic, antiestrogenic, and antiandrogenic activities, on luteal function in pigs. Piglets were injected subcutaneously with MXC (20 μg/kg body weight) or corn oil (control) between postnatal Days 1 and 10 (N = 5/group). Corpora lutea from sexually mature gilts were examined for luteal steroid and prostaglandin concentrations and processed for total RNA isolation and subsequent RNA sequencing. Intra-luteal concentrations of androstenedione and prostaglandin E2 were greater, while that of estrone was lower when compared to control. Fifty-three differentially expressed (DE) microRNAS (miRNAs) (p-adjusted <.05 and log2(fold change) ≥.5) and 359 DE genes (p-adjusted <.05 and log2(fold change) ≥1) were identified in luteal tissue in response to neonatal MXC treatment. MXC was found to affect the expression of genes related to lipogenesis, steroidogenesis, membrane transport, immune response, cell signaling and adhesion. These results suggest an earlier onset of structural luteolysis in pigs caused by MXC actions in neonates. Since negative correlation analysis showed the potential interactions of miRNAs with specific messenger RNAs, we propose that these miRNAs are potential mediators of the long-term MXC effect on the CL function in pigs.
Collapse
Affiliation(s)
- Patrycja Witek
- Department of Endocrinology, Jagiellonian University in Krakow, Krakow, Poland
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Malgorzata Grzesiak
- Department of Endocrinology, Jagiellonian University in Krakow, Krakow, Poland
| | - Marina C Costa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - André Gabriel
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Marek Koziorowski
- Department of Physiology and Reproduction of Animals, Institute of Biotechnology, University of Rzeszow, Kolbuszowa, Poland
| | - Maria Slomczynska
- Department of Endocrinology, Jagiellonian University in Krakow, Krakow, Poland
| | | |
Collapse
|
23
|
Pereira-da-Silva T, Napoleão P, Costa MC, Gabriel AF, Selas M, Silva F, Enguita FJ, Ferreira RC, Carmo MM. Cigarette Smoking, miR-27b Downregulation, and Peripheral Artery Disease: Insights into the Mechanisms of Smoking Toxicity. J Clin Med 2021; 10:jcm10040890. [PMID: 33671744 PMCID: PMC7926909 DOI: 10.3390/jcm10040890] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/14/2021] [Accepted: 02/17/2021] [Indexed: 12/26/2022] Open
Abstract
Cigarette smoking is a risk factor for the development of peripheral artery disease (PAD), although the proatherosclerotic mediators of cigarette smoking are not entirely known. We explored whether circulating microRNAs (miRNAs) are dysregulated in cigarette smokers and associated with the presence of PAD. Ninety-four participants were recruited, including 58 individuals without and 36 with PAD, 51 never smokers, 28 prior smokers, and 15 active smokers. The relative expression of six circulating miRNAs with distinct biological roles (miR-21, miR-27b, miR-29a, miR-126, miR-146, and miR-218) was assessed. Cigarette smoking was associated with the presence of PAD in multivariate analysis. Active smokers, but not prior smokers, presented miR-27b downregulation and higher leukocyte, neutrophil, and lymphocyte counts; miR-27b expression levels were independently associated with active smoking. Considering the metabolic and/or inflammatory abnormalities induced by cigarette smoking, miR-27b was independently associated with the presence of PAD and downregulated in patients with more extensive PAD. In conclusion, the atheroprotective miR-27b was downregulated in active smokers, but not in prior smokers, and miR-27b expression was independently associated with the presence of PAD. These unreported data suggest that the proatherogenic properties of cigarette smoking are mediated by a downregulation of miR-27b, which may be attenuated by smoking cessation.
Collapse
Affiliation(s)
- Tiago Pereira-da-Silva
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
- NOVA Doctoral School, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- Correspondence: ; Tel.: +351-919908505
| | - Patrícia Napoleão
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
| | - Marina C. Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - André F. Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Mafalda Selas
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
| | - Filipa Silva
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Rui Cruz Ferreira
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
| | - Miguel Mota Carmo
- Chronic Diseases Research Center (CEDOC), NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1150-082 Lisbon, Portugal;
| |
Collapse
|
24
|
Pereira-da-Silva T, Napoleão P, Costa MC, Gabriel AF, Selas M, Silva F, Enguita FJ, Ferreira RC, Carmo MM. Circulating miRNAs Are Associated with the Systemic Extent of Atherosclerosis: Novel Observations for miR-27b and miR-146. Diagnostics (Basel) 2021; 11:diagnostics11020318. [PMID: 33669374 PMCID: PMC7920287 DOI: 10.3390/diagnostics11020318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/01/2021] [Accepted: 02/12/2021] [Indexed: 12/18/2022] Open
Abstract
The mechanisms that regulate the systemic extent of atherosclerosis are not fully understood. We investigated whether the expression of circulating miRNAs is associated with the extent of stable atherosclerosis to a single territory or multiple territories (polyvascular) and with the severity of atherosclerosis in each territory. Ninety-four participants were prospectively recruited and divided into five age- and sex-matched groups: presenting no atherosclerosis, isolated coronary atherosclerosis, coronary and lower extremity atherosclerosis, coronary and carotid atherosclerosis, and atherosclerosis of the coronary, lower extremity, and carotid territories. The expression of six circulating miRNAs with distinct biological roles was assessed. The expression of miR-27b and miR-146 differed across groups (p < 0.05), showing a decrease in the presence of atherosclerosis, particularly in the three territories. miR-27b and miR-146 expression decreased in association with a higher severity of coronary, lower extremity, and carotid atherosclerosis. Polyvascular atherosclerosis involving the three territories was independently associated with a decreased miR-27b and miR-146 expression. Both miRNAs presented an area under the curve of ≥0.75 for predicting polyvascular atherosclerosis involving the three territories. To conclude, miR-27b and miR-146 were associated with the presence of severe polyvascular atherosclerosis and with the atherosclerosis severity in each territory. Both are potential biomarkers of severe systemic atherosclerosis.
Collapse
Affiliation(s)
- Tiago Pereira-da-Silva
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
- NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- Correspondence: ; Tel.: +351-919-908-505
| | - Patrícia Napoleão
- Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
| | - Marina C. Costa
- Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - André F. Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Mafalda Selas
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
| | - Filipa Silva
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Rui Cruz Ferreira
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
| | - Miguel Mota Carmo
- Chronic Diseases Research Center (CEDOC), NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1150-082 Lisbon, Portugal;
| |
Collapse
|
25
|
Wang HL, Wang HR, Liang Y, Hu AN, Enguita FJ, Zhou XG, Dong J. Hsa_circ_0006571 promotes spinal metastasis through sponging microRNA-138 to regulate sirtuin 1 expression in lung adenocarcinoma. Transl Lung Cancer Res 2020; 9:2411-2427. [PMID: 33489803 PMCID: PMC7815347 DOI: 10.21037/tlcr-20-1250] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background Circular RNAs (circRNAs) are known to participate in lung cancer. However, their role in spinal metastasis (SM) of lung adenocarcinoma remains elusive. In this study, we determined that hsa_circ_0006571 serves as a sponge for miR-138, which targets sirtuin 1 (Sirt1) in the development of SM. Methods A human circRNA microarray was performed to compare SM and lung adenocarcinoma samples. The expression of hsa_circ_0006571 and miR-138 was determined using quantitative polymerase chain reaction (qPCR) in vitro and in vivo. Cell proliferation was performed by Cell Counting Kit-8 (CCK-8) and apoptosis was analyzed by Annexin V/PI staining. RNA-pulldown and RNA immunoprecipitation (RIP) were used to analyze the interaction between hsa_circ_0006571. Tumor metastasis was determined through a xenograft experiment in vivo. Results Hsa_circ_0006571 was observed to be significantly upregulated in SM tissues through circRNA microarray and qPCR. We detected a lower expression of miR-138 in SM tissues compared with lung adenocarcinoma. Hsa_circ_0006571 silencing suppressed lung cancer cell proliferation and migration while promoting apoptosis. Hsa_circ_0006571 interacted with miR-138 to promote expression of Sirt1, leading to activation of epithelial-mesenchymal transition (EMT). Xenograft experiments showed that downregulation of hsa_circ_0006571 delayed the SM of lung adenocarcinoma cells via the miR-138-Sirt1 axis. Conclusions Hsa_circ_0006571 promoted tumor cell migration and invasion via the miR-138/Sirt1 pathway. Our observations indicate that circRNAs are possible novel therapeutic targets for SM of lung adenocarcinoma.
Collapse
Affiliation(s)
- Hou-Lei Wang
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hui-Ren Wang
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yun Liang
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - An-Nan Hu
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Xiao-Gang Zhou
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Dong
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
26
|
Mello-Vieira J, Enguita FJ, de Koning-Ward TF, Zuzarte-Luís V, Mota MM. Plasmodium translocon component EXP2 facilitates hepatocyte invasion. Nat Commun 2020; 11:5654. [PMID: 33159090 PMCID: PMC7648069 DOI: 10.1038/s41467-020-19492-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022] Open
Abstract
Plasmodium parasites possess a translocon that exports parasite proteins into the infected erythrocyte. Although the translocon components are also expressed during the mosquito and liver stage of infection, their function remains unexplored. Here, using a combination of genetic and chemical assays, we show that the translocon component Exported Protein 2 (EXP2) is critical for invasion of hepatocytes. EXP2 is a pore-forming protein that is secreted from the sporozoite upon contact with the host cell milieu. EXP2-deficient sporozoites are impaired in invasion, which can be rescued by the exogenous administration of recombinant EXP2 and alpha-hemolysin (an S. aureus pore-forming protein), as well as by acid sphingomyelinase. The latter, together with the negative impact of chemical and genetic inhibition of acid sphingomyelinase on invasion, reveals that EXP2 pore-forming activity induces hepatocyte membrane repair, which plays a key role in parasite invasion. Overall, our findings establish a novel and critical function for EXP2 that leads to an active participation of the host cell in Plasmodium sporozoite invasion, challenging the current view of the establishment of liver stage infection. While the role of Plasmodium EXP2 protein as translocon component of blood stage parasites is established, its functional role in liver stage parasites remains unclear. Here, Mello-Vieira et al. reveal that EXP2 pore-forming activity induces hepatocyte membrane repair and hence is critical for hepatocyte invasion.
Collapse
Affiliation(s)
- João Mello-Vieira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | | | - Vanessa Zuzarte-Luís
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisboa, Portugal.
| | - Maria M Mota
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisboa, Portugal.
| |
Collapse
|
27
|
|
28
|
Robinson EL, Pedrosa da Costa Gomes C, Potočnjak I, Hellemans J, Betsou F, de Gonzalo-Calvo D, Stoll M, Birhan Yilmaz M, Ágg B, Beis D, Carmo-Fonseca M, Enguita FJ, Dogan S, Tuna BG, Schroen B, Ammerlaan W, Kuster GM, Carpusca I, Pedrazzini T, Emanueli C, Martelli F, Devaux Y. A Year in the Life of the EU-CardioRNA COST Action: CA17129 Catalysing Transcriptomics Research in Cardiovascular Disease. Noncoding RNA 2020; 6:E17. [PMID: 32443579 PMCID: PMC7345156 DOI: 10.3390/ncrna6020017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023] Open
Abstract
The EU-CardioRNA Cooperation in Science and Technology (COST) Action is a European-wide consortium established in 2018 with 31 European country members and four associate member countries to build bridges between translational researchers from academia and industry who conduct research on non-coding RNAs, cardiovascular diseases and similar research areas. EU-CardioRNA comprises four core working groups (WG1-4). In the first year since its launch, EU-CardioRNA met biannually to exchange and discuss recent findings in related fields of scientific research, with scientific sessions broadly divided up according to WG. These meetings are also an opportunity to establish interdisciplinary discussion groups, brainstorm ideas and make plans to apply for joint research grants and conduct other scientific activities, including knowledge transfer. Following its launch in Brussels in 2018, three WG meetings have taken place. The first of these in Lisbon, Portugal, the second in Istanbul, Turkey, and the most recent in Maastricht, The Netherlands. Each meeting includes a scientific session from each WG. This meeting report briefly describes the highlights and key take-home messages from each WG session in this first successful year of the EU-CardioRNA COST Action.
Collapse
Affiliation(s)
- Emma Louise Robinson
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands;
| | | | - Ines Potočnjak
- Institute for Clinical Medical Research and Education, University Hospital Centre Sisters of Charity, Zagreb 10 000, Croatia;
| | | | - Fay Betsou
- Integrated BioBank of Luxembourg, L-3555 Dudelange, Luxembourg; (F.B.); (W.A.)
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain;
| | - Monika Stoll
- Institute of Human Genetics, Genetic Epidemiology, University of Münster, 48149 Münster, Germany;
| | - Mehmet Birhan Yilmaz
- Department of Cardiology, Faculty of Medicine, Dokuz Eylül University, İzmir 35330, Turkey;
| | - Bence Ágg
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, H-1085 Budapest, Hungary;
- Pharmahungary Group, H-6722 Szeged, Hungary
| | - Dimitris Beis
- Centre for Clinical, Experimental Surgery, & Translational Research, Biomedical Research Foundation, Academy of Athens, 115 27 Athens, Greece;
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (M.C.-F.); (F.J.E.)
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (M.C.-F.); (F.J.E.)
| | - Soner Dogan
- Department of Medical Biology, School of Medicine, Yeditepe University, Istanbul 34755, Turkey;
| | - Bilge G. Tuna
- Department of Biophysics, School of Medicine, Yeditepe University, Istanbul 34755, Turkey
| | - Blanche Schroen
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands;
| | - Wim Ammerlaan
- Integrated BioBank of Luxembourg, L-3555 Dudelange, Luxembourg; (F.B.); (W.A.)
| | - Gabriela M. Kuster
- Department of Biomedicine, University Hospital Basel and University of Basel, 4031 Basel, Switzerland;
| | - Irina Carpusca
- Cardiovascular Research Unit, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (C.P.d.C.G.); (I.C.)
| | - Thierry Pedrazzini
- Department of Medicine, University of Lausanne Medical School, 1005 Lausanne, Switzerland;
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK;
| | - Fabio Martelli
- Molecular Cardiology Laboratory, Policlinico San Donato IRCCS, San Donato Milanese, 20097 Milan, Italy;
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (C.P.d.C.G.); (I.C.)
| | | |
Collapse
|
29
|
Vicente Miranda H, Chegão A, Oliveira MS, Fernandes Gomes B, Enguita FJ, Outeiro TF. Hsp27 reduces glycation-induced toxicity and aggregation of alpha-synuclein. FASEB J 2020; 34:6718-6728. [PMID: 32259355 DOI: 10.1096/fj.201902936r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/02/2020] [Accepted: 03/12/2020] [Indexed: 01/20/2023]
Abstract
α-synuclein (aSyn) is a major player in Parkinson's disease and a group of other disorders collectively known as synucleinopathies, but the precise molecular mechanisms involved are still unclear. aSyn, as virtually all proteins, undergoes a series of posttranslational modifications during its lifetime, which can affect its biology and pathobiology. We recently showed that glycation of aSyn by methylglyoxal (MGO) potentiates its oligomerization and toxicity, induces dopaminergic neuronal cell loss in mice, and affects motor performance in flies. Small heat-shock proteins (sHsps) are molecular chaperones that facilitate the folding of proteins or target misfolded proteins for clearance. Importantly, sHsps were shown to prevent aSyn aggregation and cytotoxicity. Upon treating cells with increasing amounts of methylglyoxal, we found that the levels of Hsp27 decreased in a dose-dependent manner. Therefore, we hypothesized that restoring the levels of Hsp27 in glycating environments could alleviate the pathogenicity of aSyn. Consistently, we found that Hsp27 reduced MGO-induced aSyn aggregation in cells, leading to the formation of nontoxic aSyn species. Remarkably, increasing the levels of Hsp27 suppressed the deleterious effects induced by MGO. Our findings suggest that in glycating environments, the levels of Hsp27 are important for modulating the glycation-associated cellular pathologies in synucleinopathies.
Collapse
Affiliation(s)
- Hugo Vicente Miranda
- CEDOC, Chronic Diseases Research Center, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Ana Chegão
- CEDOC, Chronic Diseases Research Center, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Márcia S Oliveira
- CEDOC, Chronic Diseases Research Center, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Bárbara Fernandes Gomes
- CEDOC, Chronic Diseases Research Center, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Tiago Fleming Outeiro
- CEDOC, Chronic Diseases Research Center, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal.,Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany.,Max Planck Institute for Experimental Medicine, Göttingen, Germany.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| |
Collapse
|
30
|
Leitão AL, Costa MC, Gabriel AF, Enguita FJ. Interspecies Communication in Holobionts by Non-Coding RNA Exchange. Int J Mol Sci 2020; 21:ijms21072333. [PMID: 32230931 PMCID: PMC7177868 DOI: 10.3390/ijms21072333] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/24/2020] [Accepted: 03/26/2020] [Indexed: 12/18/2022] Open
Abstract
Complex organisms are associations of different cells that coexist and collaborate creating a living consortium, the holobiont. The relationships between the holobiont members are essential for proper homeostasis of the organisms, and they are founded on the establishment of complex inter-connections between all the cells. Non-coding RNAs are regulatory molecules that can also act as communication signals between cells, being involved in either homeostasis or dysbiosis of the holobionts. Eukaryotic and prokaryotic cells can transmit signals via non-coding RNAs while using specific extracellular conveyors that travel to the target cell and can be translated into a regulatory response by dedicated molecular machinery. Within holobionts, non-coding RNA regulatory signaling is involved in symbiotic and pathogenic relationships among the cells. This review analyzes current knowledge regarding the role of non-coding RNAs in cell-to-cell communication, with a special focus on the signaling between cells in multi-organism consortia.
Collapse
Affiliation(s)
- Ana Lúcia Leitão
- Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal;
- MEtRICs, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Marina C. Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (M.C.C.); (A.F.G.)
| | - André F. Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (M.C.C.); (A.F.G.)
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (M.C.C.); (A.F.G.)
- Correspondence: ; Tel.: +351-217999480
| |
Collapse
|
31
|
Amado T, Amorim A, Enguita FJ, Romero PV, Inácio D, de Miranda MP, Winter SJ, Simas JP, Krueger A, Schmolka N, Silva-Santos B, Gomes AQ. MicroRNA-181a regulates IFN-γ expression in effector CD8 + T cell differentiation. J Mol Med (Berl) 2020; 98:309-320. [PMID: 32002568 PMCID: PMC7007887 DOI: 10.1007/s00109-019-01865-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/29/2019] [Accepted: 12/06/2019] [Indexed: 12/14/2022]
Abstract
CD8+ T cells are key players in immunity against intracellular infections and tumors. The main cytokine associated with these protective responses is interferon-γ (IFN-γ), whose production is known to be regulated at the transcriptional level during CD8+ T cell differentiation. Here we found that microRNAs constitute a posttranscriptional brake to IFN-γ expression by CD8+ T cells, since the genetic interference with the Dicer processing machinery resulted in the overproduction of IFN-γ by both thymic and peripheral CD8+ T cells. Using a gene reporter mouse for IFN-γ locus activity, we compared the microRNA repertoires associated with the presence or absence of IFN-γ expression. This allowed us to identify a set of candidates, including miR-181a and miR-451, which were functionally tested in overexpression experiments using synthetic mimics in peripheral CD8+ T cell cultures. We found that miR-181a limits IFN-γ production by suppressing the expression of the transcription factor Id2, which in turn promotes the Ifng expression program. Importantly, upon MuHV-4 challenge, miR-181a-deficient mice showed a more vigorous IFN-γ+ CD8+ T cell response and were able to control viral infection significantly more efficiently than control mice. These data collectively establish a novel role for miR-181a in regulating IFN-γ–mediated effector CD8+ T cell responses in vitro and in vivo.
Collapse
Affiliation(s)
- Tiago Amado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Amorim
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Institute of experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Paula V Romero
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Daniel Inácio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Marta Pires de Miranda
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Samantha J Winter
- Institute for Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - J Pedro Simas
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Andreas Krueger
- Institute for Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Nina Schmolka
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. .,Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
| | - Bruno Silva-Santos
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
| | - Anita Q Gomes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. .,H&TRC Health & Technology Research Center, ESTeSL - Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal.
| |
Collapse
|
32
|
Gabriel AF, Costa MC, Enguita FJ. Circular RNA-Centered Regulatory Networks in the Physiopathology of Cardiovascular Diseases. Int J Mol Sci 2020; 21:ijms21020456. [PMID: 31936839 PMCID: PMC7014333 DOI: 10.3390/ijms21020456] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
Non-coding regulatory RNAs are generated as a core output of the eukaryotic genomes, being essential players in cell biology. At the organism level, they are key functional actors in those tissues and organs with limited proliferation capabilities such as the heart. The role of regulatory networks mediated by non-coding RNAs in the pathophysiology of cardiovascular conditions is starting to be unveiled. However, a deeper knowledge of the functional interactions among the diverse non-coding RNA families and their phenotypic consequences is required. This review presents the current knowledge about the functional crosstalk between circRNAs and other biomolecules in the framework of the cardiovascular diseases.
Collapse
Affiliation(s)
- André F. Gabriel
- Instituto de Medicina, Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (A.F.G.); (M.C.C.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Marina C. Costa
- Instituto de Medicina, Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (A.F.G.); (M.C.C.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Francisco J. Enguita
- Instituto de Medicina, Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (A.F.G.); (M.C.C.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Correspondence: ; Tel.: +351-217999480
| |
Collapse
|
33
|
Abstract
The transcriptional complexity generated by the human genomic output is within the core of cell and organ physiology, but also could be in the origin of pathologies. In cardiovascular diseases, the role of specific families of RNA transcripts belonging to the group of the non-coding RNAs started to be unveiled in the last two decades. The knowledge of the functional rules and roles of non-coding RNAs in the context of cardiovascular diseases is an important factor to derive new diagnostic methods, but also to design targeted therapeutic strategies. The characterization and analysis of ncRNA function requires a deep knowledge of the regulatory mechanism of these RNA species that often relies on intricated interaction networks. The use of specific bioinformatic tools to interrogate biological data and to derive functional implications is particularly relevant and needs to be extended to the general practice of translational researchers. This chapter briefly summarizes the bioinformatic tools and strategies that could be used for the characterization and functional analysis of non-coding RNAs, with special emphasis in their applications to the cardiovascular field.
Collapse
Affiliation(s)
- Marina C Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Cardiomics Unit, Centro de Cardiologia da Universidade de Lisboa (CCUL), Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - André F Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Cardiomics Unit, Centro de Cardiologia da Universidade de Lisboa (CCUL), Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. .,Cardiomics Unit, Centro de Cardiologia da Universidade de Lisboa (CCUL), Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
| |
Collapse
|
34
|
Abstract
Non-coding RNAs (ncRNAs) are important regulatory players in human cells that have been shown to modulate different cellular processes and biological functions through controlling gene expression, being also involved in pathological conditions such as cardiovascular diseases. Among them, long non-coding RNAs (lncRNAs) and circular (circRNAs) could act as competing endogenous RNAs (ceRNAs) sequestering other ncRNAs. This entangled network of interactions has been reported to trigger the decay of the targeted ncRNAs having important roles in gene regulation. Growing evidences have been demonstrated that the regulatory mechanism underlying the crosstalk between different ncRNA species, namely lncRNAs, circRNAs and miRNAs has also an important role in the pathophysiological processes of cardiovascular diseases. In this chapter, the main regulatory relationship among lncRNAs, circRNAs and miRNAs were summarized and their role in the control and development of cardiovascular diseases was highlighted.
Collapse
Affiliation(s)
- André F Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Cardiomics Unit, Centro de Cardiologia da Universidade de Lisboa (CCUL), Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Marina C Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Cardiomics Unit, Centro de Cardiologia da Universidade de Lisboa (CCUL), Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. .,Cardiomics Unit, Centro de Cardiologia da Universidade de Lisboa (CCUL), Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
| |
Collapse
|
35
|
Durak-Kozica M, Enguita FJ, Stępień E. Targeting uPAR in diabetic vascular pathologies*. POSTEP HIG MED DOSW 2019. [DOI: 10.5604/01.3001.0013.6909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The uPAR protein is one of the most important elements in fibrinolysis. uPAR is associated with many biological processes, such as cell invasion, angiogenesis and cell proliferation. Because of its multifunctional character, it is difficult to produce an effective inhibitor of uPA-uPAR interactions. The present paper shows the current state of knowledge about the contribution of uPA-uPAR complex in many biological processes and the application of uPAR inhibitors (antibodies, small-molecules, peptides), which might be potentially useful in the treatment of vascular pathologies.
Collapse
Affiliation(s)
- Martyna Durak-Kozica
- Department of Medical Physics, M. Smoluchowski Institute of Physics, Jagiellonian University, Kraków, Poland
| | - Francisco J. Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Ewa Stępień
- Department of Medical Physics, M. Smoluchowski Institute of Physics, Jagiellonian University, Kraków, Poland
| |
Collapse
|
36
|
Gabriel AF, Costa MC, Enguita FJ, Leitão AL. Si vis pacem para bellum: A prospective in silico analysis of miRNA-based plant defenses against fungal infections. Plant Sci 2019; 288:110241. [PMID: 31521215 DOI: 10.1016/j.plantsci.2019.110241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/31/2019] [Accepted: 08/25/2019] [Indexed: 06/10/2023]
Abstract
Fungal pathogens are an important threat for plant crops, being responsible for important reductions of production yields and a consequent economic impact. Among the molecular mediators of fungal infections of plant crops, non-coding RNAs (ncRNAs) have been described as relevant players either in the plant immune responses and mechanism of defense or in the colonization of plant tissues by fungi. Acting as a mechanism of defense, some plant small ncRNAs such as miRNAs and tasiRNAs can be secreted by cells and directed to target the transcriptome of pathogenic fungi, triggering an RNAi-like interference mechanism able to silence the expression of specific fungal genes. The detailed knowledge of this mechanism of defense against fungal pathogens could open new possibilities for the protection of human important crops. To infer putative functional relationships mediated by ncRNA communication, we performed a prospective analysis to determine potential plant miRNAs able to target the genome of fungal pathogens, which resulted in the description of enriched specific plant miRNA families and their putative fungal targets that could be further studied in the context of plant-fungi interactions. The expression profile of specific members of the enriched miRNAs families showed an infection-dependent behavior in laboratory models of infection. Plant miRNAs showed sequence complementarity with coding genes of their cognate fungal pathogens. Plant miRNAs could potentially target fungal genes belonging to functional families related to stress response, membrane architecture, vacuolar transport, membrane traffic, and anabolic processes. Families of specific infection-responsive miRNAs are included in the putative plant defense mechanism.
Collapse
Affiliation(s)
- André F Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Marina C Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal.
| | - Ana Lúcia Leitão
- Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal; MEtRICs, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, Caparica, 2829-516, Portugal.
| |
Collapse
|
37
|
Affiliation(s)
- Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Cardiomics Unit, Centro de Cardiologia da Universidade de Lisboa (CCUL), Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
38
|
Faustino AF, Martins AS, Karguth N, Artilheiro V, Enguita FJ, Ricardo JC, Santos NC, Martins IC. Structural and Functional Properties of the Capsid Protein of Dengue and Related Flavivirus. Int J Mol Sci 2019; 20:E3870. [PMID: 31398956 PMCID: PMC6720645 DOI: 10.3390/ijms20163870] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 02/07/2023] Open
Abstract
Dengue, West Nile and Zika, closely related viruses of the Flaviviridae family, are an increasing global threat, due to the expansion of their mosquito vectors. They present a very similar viral particle with an outer lipid bilayer containing two viral proteins and, within it, the nucleocapsid core. This core is composed by the viral RNA complexed with multiple copies of the capsid protein, a crucial structural protein that mediates not only viral assembly, but also encapsidation, by interacting with host lipid systems. The capsid is a homodimeric protein that contains a disordered N-terminal region, an intermediate flexible fold section and a very stable conserved fold region. Since a better understanding of its structure can give light into its biological activity, here, first, we compared and analyzed relevant mosquito-borne Flavivirus capsid protein sequences and their predicted structures. Then, we studied the alternative conformations enabled by the N-terminal region. Finally, using dengue virus capsid protein as main model, we correlated the protein size, thermal stability and function with its structure/dynamics features. The findings suggest that the capsid protein interaction with host lipid systems leads to minor allosteric changes that may modulate the specific binding of the protein to the viral RNA. Such mechanism can be targeted in future drug development strategies, namely by using improved versions of pep14-23, a dengue virus capsid protein peptide inhibitor, previously developed by us. Such knowledge can yield promising advances against Zika, dengue and closely related Flavivirus.
Collapse
Affiliation(s)
- André F Faustino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Ana S Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Nina Karguth
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Vanessa Artilheiro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Joana C Ricardo
- Centro de Química-Física Molecular, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal.
| | - Ivo C Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal.
| |
Collapse
|
39
|
Baptista R, Marques C, Catarino S, Enguita FJ, Costa MC, Matafome P, Zuzarte M, Castro G, Reis A, Monteiro P, Pêgo M, Pereira P, Girão H. MicroRNA-424(322) as a new marker of disease progression in pulmonary arterial hypertension and its role in right ventricular hypertrophy by targeting SMURF1. Cardiovasc Res 2019; 114:53-64. [PMID: 29016730 DOI: 10.1093/cvr/cvx187] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 09/11/2017] [Indexed: 01/26/2023] Open
Abstract
Aims MicroRNAs (miRNAs) have been implicated in the pathogenesis of pulmonary hypertension (PH), a multifactorial and progressive condition associated with an increased afterload of the right ventricle leading to heart failure and death. The main aim of this study was to correlate the levels of miR-424(322) with the severity and prognosis of PH and with right ventricle hypertrophy progression. Additionally, we intended to evaluate the mechanisms and signalling pathways whereby miR-424(322) secreted by pulmonary arterial endothelial cells (PAECs) impacts cardiomyocytes. Methods and results Using quantitative real-time PCR, we showed that the levels of circulating miR-424(322) are higher in PH patients when compared with healthy subjects. Moreover, we found that miR-424(322) levels correlated with more severe symptoms and haemodynamics. In the subgroup of Eisenmenger syndrome patients, miR-424(322) displayed independent prognostic value. Furthermore, we demonstrated that miR-424(322) targets SMURF1, through which it sustains bone morphogenetic protein receptor 2 signalling. Moreover, we showed that hypoxia induces the secretion of miR-424(322) by PAECs, which after being taken up by cardiomyocytes leads to down-regulation of SMURF1. In the monocrotaline rat model of PH, we found an association between circulating miR-424(322) levels and the stage of right ventricle hypertrophy, as well as an inverse correlation between miR-424(322) and SMURF1 levels in the hypertrophied right ventricle. Conclusions This study shows that miR-424(322) has diagnostic and prognostic value in PH patients, correlating with markers of disease severity. Additionally, miR-424(322) can target proteins with a direct effect on heart function, suggesting that this miRNA can act as a messenger linking pulmonary vascular disease and right ventricle hypertrophy.
Collapse
Affiliation(s)
- Rui Baptista
- Department of Cardiology A, Centro Hospitalar e Universitário de Coimbra, 3000-001 Coimbra, Portugal.,CNC.IBILI, University of Coimbra, Coimbra, Portugal.,Institute for Biomedical Imaging and Life Sciences (IBILI), Faculty of Medicine, University of Coimbra, Azinhaga de Sta Comba, Celas, 3000-354 Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Carla Marques
- CNC.IBILI, University of Coimbra, Coimbra, Portugal.,Institute for Biomedical Imaging and Life Sciences (IBILI), Faculty of Medicine, University of Coimbra, Azinhaga de Sta Comba, Celas, 3000-354 Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Steve Catarino
- CNC.IBILI, University of Coimbra, Coimbra, Portugal.,Institute for Biomedical Imaging and Life Sciences (IBILI), Faculty of Medicine, University of Coimbra, Azinhaga de Sta Comba, Celas, 3000-354 Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, 1649-028 Lisboa, Portugal
| | - Marina C Costa
- Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, 1649-028 Lisboa, Portugal
| | - Paulo Matafome
- CNC.IBILI, University of Coimbra, Coimbra, Portugal.,Institute for Biomedical Imaging and Life Sciences (IBILI), Faculty of Medicine, University of Coimbra, Azinhaga de Sta Comba, Celas, 3000-354 Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,Department of Complementary Sciences, Coimbra Health School (ESTeSC), Instituto Politécnico de Coimbra, 3046-854 Coimbra, Portugal
| | - Mónica Zuzarte
- CNC.IBILI, University of Coimbra, Coimbra, Portugal.,Institute for Biomedical Imaging and Life Sciences (IBILI), Faculty of Medicine, University of Coimbra, Azinhaga de Sta Comba, Celas, 3000-354 Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Graça Castro
- Department of Cardiology A, Centro Hospitalar e Universitário de Coimbra, 3000-001 Coimbra, Portugal
| | - Abílio Reis
- Unidade de Doença Vascular Pulmonar, Departamento de Medicina, Centro Hospitalar do Porto, EPE, 4099-001 Porto, Portugal
| | - Pedro Monteiro
- Department of Cardiology A, Centro Hospitalar e Universitário de Coimbra, 3000-001 Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Mariano Pêgo
- Department of Cardiology A, Centro Hospitalar e Universitário de Coimbra, 3000-001 Coimbra, Portugal
| | - Paulo Pereira
- CNC.IBILI, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,CEDOC, NOVA Medical School, Nova University of Lisbon, 1169-056 Lisboa, Portugal
| | - Henrique Girão
- CNC.IBILI, University of Coimbra, Coimbra, Portugal.,Institute for Biomedical Imaging and Life Sciences (IBILI), Faculty of Medicine, University of Coimbra, Azinhaga de Sta Comba, Celas, 3000-354 Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| |
Collapse
|
40
|
Costa MC, Cortez-Dias N, Gabriel A, de Sousa J, Fiúza M, Gallego J, Nobre Â, Pinto FJ, Enguita FJ. circRNA-miRNA cross-talk in the transition from paroxysmal to permanent atrial fibrillation. Int J Cardiol 2019; 290:134-137. [PMID: 31097202 DOI: 10.1016/j.ijcard.2019.04.072] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/23/2019] [Indexed: 01/11/2023]
Abstract
BACKGROUND Atrial fibrillation (AF) is the most prevalent cardiac arrhythmia in western countries. The factors governing the progression of AF to a permanent chronic condition are still not well characterized. Among epigenetic factors, non-coding RNAs (ncRNAs) such as miRNAs and lncRNAs have been recently described as important players involved in the AF progression. We hypothesize about the existence of additional regulatory layers in AF involving an intricate cross-talk between different ncRNA species, namely miRNAs and circRNAs for the establishment of a chronic AF condition. METHODS AND RESULTS We have performed an unbiased study analyzing the expression profile for miRNAs and circRNAs in left-atrial biopsies from patients with paroxysmal and permanent AF by RNA-seq. The transition from paroxysmal to permanent AF is characterized by a pattern of down-regulated miRNAs, concomitant to the appearance of specific circRNA species. The analysis of the sponging activities of the circRNAs exclusively expressed in permanent AF samples, allowed us to determine that they could be responsible for the downregulation of specific miRNAs in establishment of a permanent AF condition. CONCLUSION Sponging activity of circRNAs sequestering specific miRNAs is an important factor to be considered for the determination of the molecular mechanisms involved in AF progression.
Collapse
Affiliation(s)
- Marina C Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - Nuno Cortez-Dias
- University Hospital Santa Maria, Department of Cardiology, Lisbon Academic Medical Centre, CCUL, Lisbon University, Lisbon, Portugal; Programme for Advanced Medical Education, Fundação Calouste Gulbenkian, Ministry of Health and Foundation for Science and Technology, Lisbon, Portugal
| | - André Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - João de Sousa
- University Hospital Santa Maria, Department of Cardiology, Lisbon Academic Medical Centre, CCUL, Lisbon University, Lisbon, Portugal
| | - Manuela Fiúza
- University Hospital Santa Maria, Department of Cardiology, Lisbon Academic Medical Centre, CCUL, Lisbon University, Lisbon, Portugal
| | - Javier Gallego
- University Hospital Santa Maria, Department of Cardiothoracic Surgery, Lisbon Academic Medical Centre, CCUL, Lisbon University, Lisbon, Portugal
| | - Ângelo Nobre
- University Hospital Santa Maria, Department of Cardiothoracic Surgery, Lisbon Academic Medical Centre, CCUL, Lisbon University, Lisbon, Portugal
| | - Fausto J Pinto
- University Hospital Santa Maria, Department of Cardiology, Lisbon Academic Medical Centre, CCUL, Lisbon University, Lisbon, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisbon, Portugal.
| |
Collapse
|
41
|
Schmolka N, Papotto PH, Romero PV, Amado T, Enguita FJ, Amorim A, Rodrigues AF, Gordon KE, Coroadinha AS, Boldin M, Serre K, Buck AH, Gomes AQ, Silva-Santos B. MicroRNA-146a controls functional plasticity in γδ T cells by targeting NOD1. Sci Immunol 2019; 3:3/23/eaao1392. [PMID: 29728425 DOI: 10.1126/sciimmunol.aao1392] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 02/21/2018] [Indexed: 01/07/2023]
Abstract
γδ T cells are major providers of proinflammatory cytokines. They are preprogrammed in the mouse thymus into distinct subsets producing either interleukin-17 (IL-17) or interferon-γ (IFN-γ), which segregate with CD27 expression. In the periphery, CD27- γδ (γδ27-) T cells can be induced under inflammatory conditions to coexpress IL-17 and IFN-γ; the molecular basis of this functional plasticity remains to be determined. On the basis of differential microRNA (miRNA) expression analysis and modulation in γδ T cell subsets, we identified miR-146a as a thymically imprinted post-transcriptional brake to limit IFN-γ expression in γδ27- T cells in vitro and in vivo. On the basis of biochemical purification of Argonaute 2-bound miR-146a targets, we identified Nod1 to be a relevant mRNA target that regulates γδ T cell plasticity. In line with this, Nod1-deficient mice lacked multifunctional IL-17+ IFN-γ+ γδ27- cells and were more susceptible to Listeria monocytogenes infection. Our studies establish the miR-146a/NOD1 axis as a key determinant of γδ T cell effector functions and plasticity.
Collapse
Affiliation(s)
- Nina Schmolka
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
| | - Pedro H Papotto
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Paula Vargas Romero
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Tiago Amado
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Ana Amorim
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Ana F Rodrigues
- iBET, Instituto de Biologia Experimental e Tecnológica, 2780-157 Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Katrina E Gordon
- Institute of Immunology and Infection and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Ana S Coroadinha
- iBET, Instituto de Biologia Experimental e Tecnológica, 2780-157 Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Mark Boldin
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Karine Serre
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Amy H Buck
- Institute of Immunology and Infection and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Anita Q Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal. .,Escola Superior de Tecnologia da Saúde de Lisboa, 1990-096 Lisboa, Portugal
| | - Bruno Silva-Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
| |
Collapse
|
42
|
Stępień EŁ, Durak-Kozica M, Kamińska A, Targosz-Korecka M, Libera M, Tylko G, Opalińska A, Kapusta M, Solnica B, Georgescu A, Costa MC, Czyżewska-Buczyńska A, Witkiewicz W, Małecki MT, Enguita FJ. Circulating ectosomes: Determination of angiogenic microRNAs in type 2 diabetes. Am J Cancer Res 2018; 8:3874-3890. [PMID: 30083267 PMCID: PMC6071541 DOI: 10.7150/thno.23334] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 05/03/2018] [Indexed: 12/30/2022] Open
Abstract
Ectosomes (Ects) are a subpopulation of extracellular vesicles formed by the process of plasma membrane shedding. In the present study, we profiled ectosome-specific microRNAs (miRNAs) in patients with type 2 diabetes mellitus (T2DM) and analyzed their pro- and anti-angiogenic potential. Methods: We used different approaches for detecting and enumerating Ects, including atomic force microscopy, cryogenic transmission electron microscopy, and nanoparticle tracking analysis. Furthermore, we used bioinformatics tools to analyze functional data obtained from specific miRNA enrichment signatures during angiogenesis and vasculature development. Results: Levels of miR-193b-3p, miR-199a-3p, miR-20a-3p, miR-26b-5p, miR-30b-5p, miR-30c-5p, miR-374a-5p, miR-409-3p, and miR-95-3p were significantly different between Ects obtained from patients with T2DM and those obtained from healthy controls. Conclusion: Our results showed differences in the abundance of pro- and anti-angiogenic miRNAs in Ects of patients with T2DM, and are suggestive of mechanisms underlying the development of vascular complications due to impaired angiogenesis in such patients.
Collapse
|
43
|
Ribeiro-Rodrigues TM, Laundos TL, Pereira-Carvalho R, Batista-Almeida D, Pereira R, Coelho-Santos V, Silva AP, Fernandes R, Zuzarte M, Enguita FJ, Costa MC, Pinto-do-Ó P, Pinto MT, Gouveia P, Ferreira L, Mason JC, Pereira P, Kwak BR, Nascimento DS, Girão H. Exosomes secreted by cardiomyocytes subjected to ischaemia promote cardiac angiogenesis. Cardiovasc Res 2018; 113:1338-1350. [PMID: 28859292 DOI: 10.1093/cvr/cvx118] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 06/15/2017] [Indexed: 12/31/2022] Open
Abstract
Aims Myocardial infarction (MI) is the leading cause of morbidity and mortality worldwide and results from an obstruction in the blood supply to a region of the heart. In an attempt to replenish oxygen and nutrients to the deprived area, affected cells release signals to promote the development of new vessels and confer protection against MI. However, the mechanisms underlying the growth of new vessels in an ischaemic scenario remain poorly understood. Here, we show that cardiomyocytes subjected to ischaemia release exosomes that elicit an angiogenic response of endothelial cells (ECs). Methods and results Exosomes secreted by H9c2 myocardial cells and primary cardiomyocytes, cultured either in control or ischaemic conditions were isolated and added to ECs. We show that ischaemic exosomes, in comparison with control exosomes, confer protection against oxidative-induced lesion, promote proliferation, and sprouting of ECs, stimulate the formation of capillary-like structures and strengthen adhesion complexes and barrier properties. Moreover, ischaemic exosomes display higher levels of metalloproteases (MMP) and promote the secretion of MMP by ECs. We demonstrate that miR-222 and miR-143, the relatively most abundant miRs in ischaemic exosomes, partially recapitulate the angiogenic effect of exosomes. Additionally, we show that ischaemic exosomes stimulate the formation of new functional vessels in vivo using in ovo and Matrigel plug assays. Finally, we demonstrate that intramyocardial delivery of ischaemic exosomes improves neovascularization following MI. Conclusions This study establishes that exosomes secreted by cardiomyocytes under ischaemic conditions promote heart angiogenesis, which may pave the way towards the development of add-on therapies to enhance myocardial blood supply.
Collapse
Affiliation(s)
- Teresa M Ribeiro-Rodrigues
- Institute for Biomedical Imaging and Life Sciences (IBILI), University of Coimbra, Azinhaga de Sta Comba, 3000-354 Coimbra, Portugal.,CNC.IBILI, University of Coimbra, Portugal
| | - Tiago L Laundos
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,INEB-Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Rita Pereira-Carvalho
- Institute for Biomedical Imaging and Life Sciences (IBILI), University of Coimbra, Azinhaga de Sta Comba, 3000-354 Coimbra, Portugal.,CNC.IBILI, University of Coimbra, Portugal
| | - Daniela Batista-Almeida
- Institute for Biomedical Imaging and Life Sciences (IBILI), University of Coimbra, Azinhaga de Sta Comba, 3000-354 Coimbra, Portugal.,CNC.IBILI, University of Coimbra, Portugal
| | - Ricardo Pereira
- Institute for Biomedical Imaging and Life Sciences (IBILI), University of Coimbra, Azinhaga de Sta Comba, 3000-354 Coimbra, Portugal.,CNC.IBILI, University of Coimbra, Portugal
| | - Vanessa Coelho-Santos
- Institute for Biomedical Imaging and Life Sciences (IBILI), University of Coimbra, Azinhaga de Sta Comba, 3000-354 Coimbra, Portugal.,CNC.IBILI, University of Coimbra, Portugal.,Institute of Pharmacology and Experimental Therapeutics, University of Coimbra, Azinhaga de Sta Comba, 3000-354 Coimbra, Portugal
| | - Ana P Silva
- Institute for Biomedical Imaging and Life Sciences (IBILI), University of Coimbra, Azinhaga de Sta Comba, 3000-354 Coimbra, Portugal.,CNC.IBILI, University of Coimbra, Portugal.,Institute of Pharmacology and Experimental Therapeutics, University of Coimbra, Azinhaga de Sta Comba, 3000-354 Coimbra, Portugal
| | - Rosa Fernandes
- Institute for Biomedical Imaging and Life Sciences (IBILI), University of Coimbra, Azinhaga de Sta Comba, 3000-354 Coimbra, Portugal.,CNC.IBILI, University of Coimbra, Portugal
| | - Monica Zuzarte
- Institute for Biomedical Imaging and Life Sciences (IBILI), University of Coimbra, Azinhaga de Sta Comba, 3000-354 Coimbra, Portugal.,CNC.IBILI, University of Coimbra, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, 1649-028 Lisboa, Portugal
| | - Marina C Costa
- Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, 1649-028 Lisboa, Portugal
| | - Perpetua Pinto-do-Ó
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,INEB-Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Marta T Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology (Ipatimup), University of Porto, Portugal
| | - Pedro Gouveia
- CNC.IBILI, University of Coimbra, Portugal.,CNC-Center for Neurosciences and Cell Biology, University of Coimbra, 3000 Coimbra, Portugal
| | - Lino Ferreira
- CNC.IBILI, University of Coimbra, Portugal.,CNC-Center for Neurosciences and Cell Biology, University of Coimbra, 3000 Coimbra, Portugal
| | - Justin C Mason
- Vascular Sciences Unit, Imperial Centre for Translational & Experimental Medicine, Imperial College London, London, UK
| | - Paulo Pereira
- Institute for Biomedical Imaging and Life Sciences (IBILI), University of Coimbra, Azinhaga de Sta Comba, 3000-354 Coimbra, Portugal.,CNC.IBILI, University of Coimbra, Portugal.,CEDOC, NOVA Medical School, NOVA University of Lisbon, Lisboa 1169-056, Portugal
| | - Brenda R Kwak
- Department of Pathology and Immunology, and Department of Medical Specialties-Cardiology, University of Geneva, CH-1211 Geneva, Switzerland
| | - Diana S Nascimento
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,INEB-Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | - Henrique Girão
- Institute for Biomedical Imaging and Life Sciences (IBILI), University of Coimbra, Azinhaga de Sta Comba, 3000-354 Coimbra, Portugal.,CNC.IBILI, University of Coimbra, Portugal
| |
Collapse
|
44
|
Gacoń J, Badacz R, Stępień E, Karch I, Enguita FJ, Żmudka K, Przewłocki T, Kabłak-Ziembicka A. Diagnostic and prognostic micro-RNAs in ischaemic stroke due to carotid artery stenosis and in acute coronary syndrome: a four-year prospective study. Kardiol Pol 2018; 76:362-369. [PMID: 29350392 DOI: 10.5603/kp.a2017.0243] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 10/09/2017] [Accepted: 11/16/2017] [Indexed: 11/25/2022]
Abstract
BACKGROUND Circulating microRNAs (miRs) levels are potentially important diagnostic and prognostic biomarkers in acute coronary syndrome (ACS) or cerebral ischaemic events (CIE) resulting from internal carotid artery stenosis (ICAS). AIM This four-year prospective study aimed to compare the levels of circulating miRs in ACS vs. CIE patients, and investigate miRs potentially associated with risk of recurrent cardiovascular events. METHODS The circulating miRs levels (miR-1-3p, miR-16-5p, miR-34a-5p, mir-122-5p, miR-124-3p, miR-133a-3p, miR-133b, miR-134-5p, miR-208b-3p, miR-375, and miR-499-5p) were compared in 43 (34 men, 57.6 ± 10.1 years) patients with ACS, and in 71 (47 men, 69.5 ± 9.6 years) with CIE due to ICAS. A four-year prospective evaluation of miRs associated with risk of cardiovascular death (CVD), myocardial infarction (MI), CIE, or all (CVD/MI/CIE) was performed. RESULTS In ACS vs. CIE patients, the levels of miR-124-3p (p < 0.001), miR-134-5p (p = 0.012), miR-208b-3p (p < 0.001), miR-34a-5p (p < 0.001), and miR-499-5p (p < 0.001) were higher, while levels of miR-16-5p (p < 0.001) and miR-122-5p (p < 0.001) were lower. Levels of miR-1-3p (p = 0.195), miR-133a-3p (p = 0.333), miR-133b (p = 0.056), and miR-375 (p = 0.055) were non-statistically different. During follow-up (median 57 months, Q1-Q3: 54-60), CVD/MI/CIE occurred in 23 subjects, including eight CVDs, five non-fatal CIEs, and 10 non-fatal MIs. The multivariate Cox proportional hazard analysis (relative risk [RR]; 95% confidence interval [CI]) revealed that miR-208b-3p (1.225; 1.092-1.375), miR-34a-5p (0.963; 0.935-0.992), and miR-499-5p (0.077; 0.025-0.239) were independently associated with risk of CVD/MI/CIE, as well as risk of each event. Furthermore, miR-133b (1.009; 1.003-1.015) was associated with risk of CVD. CONCLUSIONS This study shows that although most investigated miRs levels differ significantly between patients with ACS and CIE, similar levels of circulating miR-1-3p, miR-133a-3p, miR-133b, and miR-375 were observed; furthermore, we identified several common miRs as possible risk factors for recurrent cardiovascular events.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Anna Kabłak-Ziembicka
- Department of Interventional Cardiology, Jagiellonian University School of Medicine, John Paul II Hospital, Krakow, Poland.
| |
Collapse
|
45
|
Levene M, Enguita FJ, Bax BE. Discovery profiling and bioinformatics analysis of serum microRNA in Mitochondrial NeuroGastroIntestinal Encephalomyopathy (MNGIE). Nucleosides Nucleotides Nucleic Acids 2018; 37:618-629. [PMID: 30587073 DOI: 10.1080/15257770.2018.1492138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is a rare and fatal inherited metabolic disorder due to mutations in the nuclear TYMP gene and leads to a deficiency in the enzyme thymidine phosphorylase. This results in an accumulation of the deoxynucleosides, thymidine and deoxyuridine in the cellular and extracellular compartments, ultimately leading to mitochondrial failure. The understanding of the precise molecular mechanisms that underlie the disease pathology is limited, being hampered by the rarity of the disorder. Expression profiling of serum based mircoRNAs and subsequent bioinformatical analyses provide an approach to facilitate the identity of dysregulated genes and signalling pathways potentially involved in the pathogenesis of MNGIE.
Collapse
Affiliation(s)
- Michelle Levene
- a Cell Biology and Genetics Research Centre , St George's University of London, Molecular and Cell Sciences Institute , London , United Kingdom
| | - Francisco J Enguita
- b Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa , Lisboa , Portugal
| | - Bridget E Bax
- a Cell Biology and Genetics Research Centre , St George's University of London, Molecular and Cell Sciences Institute , London , United Kingdom
| |
Collapse
|
46
|
Esteves JV, Yonamine CY, Pinto-Junior DC, Gerlinger-Romero F, Enguita FJ, Machado UF. Diabetes Modulates MicroRNAs 29b-3p, 29c-3p, 199a-5p and 532-3p Expression in Muscle: Possible Role in GLUT4 and HK2 Repression. Front Endocrinol (Lausanne) 2018; 9:536. [PMID: 30258406 PMCID: PMC6143689 DOI: 10.3389/fendo.2018.00536] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/23/2018] [Indexed: 12/16/2022] Open
Abstract
The reduced expression of solute carrier family 2, facilitated glucose transporter member 4 (GLUT4) and hexokinase-2 (HK2) in skeletal muscle participates in insulin resistance of diabetes mellitus (DM). MicroRNAs (miRNAs) have emerged as important modulators of mRNA/protein expression, but their role in DM is unclear. We investigated miRNAs hypothetically involved in GLUT4/HK2 expression in soleus muscle of type 1 diabetes-like rats. In silico analysis revealed 651 miRNAs predicted to regulate solute carrier family 2 member 4 (Slc2a4) mRNA, several of them also predicted to regulate Hk2 mRNA, and 16 miRNAs were selected for quantification. Diabetes reduced Slc2a4/GLUT4 and Hk2/HK2 expression (50-77%), upregulated miR-29b-3p and miR-29c-3p (50-100%), and downregulated miR-93-5p, miR-150-5p, miR-199a-5p, miR-345-3p, and miR-532-3p (~30%) expression. Besides, GLUT4 and HK2 proteins correlated (P < 0.05) negatively with miR-29b-3p and miR-29c-3p and positively with miR-199a-5p and miR-532-3p, suggesting that these miRNAs could be markers of alterations in GLUT4 and HK2 expression. Additionally, diabetes increased the nuclear factor kappa B subunit 1 protein (p50) expression, a repressor of Slc2a4, which was also predicted as a target for miR-199a-5p and miR-532-3p. Correlations were also detected between these miRNAs and blood glucose, 24-h glycosuria and plasma fructosamine, and insulin therapy reversed most of the alterations. In sum, we report that diabetes altered miR-29b-3p, miR-29c-3p, miR-199a-5p and miR-532-3p expression in muscle of male rats, where their predicted targets Slc2a4/GLUT4 and Hk2/HK2 are repressed. These data shed light on these miRNAs as a markers of impaired skeletal muscle glucose disposal, and, consequently, glycemic control in diabetes.
Collapse
Affiliation(s)
- João V. Esteves
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- *Correspondence: João V. Esteves
| | - Caio Y. Yonamine
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Danilo C. Pinto-Junior
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Frederico Gerlinger-Romero
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Francisco J. Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Ubiratan F. Machado
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
47
|
Kamińska A, Enguita FJ, Stępień EŁ. Lactadherin: An unappreciated haemostasis regulator and potential therapeutic agent. Vascul Pharmacol 2017; 101:21-28. [PMID: 29169950 DOI: 10.1016/j.vph.2017.11.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/19/2017] [Accepted: 11/18/2017] [Indexed: 01/01/2023]
Abstract
Lactadherin is a small (53-66kDa) multifunctional glycoprotein belonging to the secreted extracellular matrix protein family. It has a multi-domain structure and is involved in many biological and physiological processes, including phagocytosis, angiogenesis, atherosclerosis, tissue remodeling, and haemostasis regulation. Lactadherin binds phosphatidylserine (PS)-enriched cell surfaces in a receptor-independent manner. Interaction between lactadherin and PS is crucial for regulation of blood coagulation processes. This review summarizes recent knowledge on the possible role of lactadherin in haemostasis control, emphasizing the great significance of the interaction between lactadherin and PS expressed on activated platelets and extracellular vesicles. The possible role of lactadherin as a therapeutic target and biomarker is also discussed.
Collapse
Affiliation(s)
- Agnieszka Kamińska
- Department of Medical Physics, Marian Smoluchowski Institute of Physics, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Prof. Stanisława Łojasiewicza 11 Street, Kraków 30-348, Poland.
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa 1649-028, Portugal.
| | - Ewa Ł Stępień
- Department of Medical Physics, Marian Smoluchowski Institute of Physics, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Prof. Stanisława Łojasiewicza 11 Street, Kraków 30-348, Poland.
| |
Collapse
|
48
|
Vicente Miranda H, Szego ÉM, Oliveira LMA, Breda C, Darendelioglu E, de Oliveira RM, Ferreira DG, Gomes MA, Rott R, Oliveira M, Munari F, Enguita FJ, Simões T, Rodrigues EF, Heinrich M, Martins IC, Zamolo I, Riess O, Cordeiro C, Ponces-Freire A, Lashuel HA, Santos NC, Lopes LV, Xiang W, Jovin TM, Penque D, Engelender S, Zweckstetter M, Klucken J, Giorgini F, Quintas A, Outeiro TF. Glycation potentiates α-synuclein-associated neurodegeneration in synucleinopathies. Brain 2017; 140:1399-1419. [PMID: 28398476 DOI: 10.1093/brain/awx056] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 01/20/2017] [Indexed: 12/15/2022] Open
Abstract
α-Synuclein misfolding and aggregation is a hallmark in Parkinson's disease and in several other neurodegenerative diseases known as synucleinopathies. The toxic properties of α-synuclein are conserved from yeast to man, but the precise underpinnings of the cellular pathologies associated are still elusive, complicating the development of effective therapeutic strategies. Combining molecular genetics with target-based approaches, we established that glycation, an unavoidable age-associated post-translational modification, enhanced α-synuclein toxicity in vitro and in vivo, in Drosophila and in mice. Glycation affected primarily the N-terminal region of α-synuclein, reducing membrane binding, impaired the clearance of α-synuclein, and promoted the accumulation of toxic oligomers that impaired neuronal synaptic transmission. Strikingly, using glycation inhibitors, we demonstrated that normal clearance of α-synuclein was re-established, aggregation was reduced, and motor phenotypes in Drosophila were alleviated. Altogether, our study demonstrates glycation constitutes a novel drug target that can be explored in synucleinopathies as well as in other neurodegenerative conditions.
Collapse
Affiliation(s)
- Hugo Vicente Miranda
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Éva M Szego
- Department of Neurodegeneration and Restorative Research, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Waldweg 33, 37073 Göttingen, Germany
| | - Luís M A Oliveira
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Superior de Ciências da Saúde Egas Moniz, 2829-511 Monte de Caparica, Caparica, Portugal.,Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Carlo Breda
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Ekrem Darendelioglu
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK.,Bingol University, Science and Letters Faculty, Molecular Biology and Genetics Department, 12000, Bingol, Turkey
| | - Rita M de Oliveira
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Diana G Ferreira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Department of Neurodegeneration and Restorative Research, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Waldweg 33, 37073 Göttingen, Germany
| | - Marcos A Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Ruth Rott
- Department of Biochemistry, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Márcia Oliveira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Francesca Munari
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Tânia Simões
- Laboratório de Proteómica, Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, 1649-016 Lisboa, Portugal
| | - Eva F Rodrigues
- Department of Neurodegeneration and Restorative Research, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Waldweg 33, 37073 Göttingen, Germany
| | - Michael Heinrich
- Department of Molecular Neurology, University Hospital Erlangen, Schwabachanlage 6, 91054 Erlangen, Germany
| | - Ivo C Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Irina Zamolo
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72074 Tuebingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72074 Tuebingen, Germany
| | - Carlos Cordeiro
- Enzymology Group, Departamento de Quimica e Bioquimica, Centro de Quimica e Bioquimica, Faculdade de Ciencias da Universidade de Lisboa, Campo Grande, Edificio C8, 1749-016, Lisboa, Portugal
| | - Ana Ponces-Freire
- Enzymology Group, Departamento de Quimica e Bioquimica, Centro de Quimica e Bioquimica, Faculdade de Ciencias da Universidade de Lisboa, Campo Grande, Edificio C8, 1749-016, Lisboa, Portugal
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Swiss Federal Institute of Technology Lausanne (EPFL), FSV-BMI AI 2137.1, Station 15, CH-1015 Lausanne, Switzerland
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Luisa V Lopes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Wei Xiang
- Institute for Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Thomas M Jovin
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Deborah Penque
- Laboratório de Proteómica, Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, 1649-016 Lisboa, Portugal
| | - Simone Engelender
- Department of Biochemistry, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Markus Zweckstetter
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany.,Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center, 37075 Göttingen, Germany
| | - Jochen Klucken
- Department of Molecular Neurology, University Hospital Erlangen, Schwabachanlage 6, 91054 Erlangen, Germany
| | - Flaviano Giorgini
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Alexandre Quintas
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Superior de Ciências da Saúde Egas Moniz, 2829-511 Monte de Caparica, Caparica, Portugal
| | - Tiago F Outeiro
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal.,Department of Neurodegeneration and Restorative Research, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Waldweg 33, 37073 Göttingen, Germany.,Max Plank Institute for Experimental Medicine, Goettingen, Germany
| |
Collapse
|
49
|
Mendes de Almeida R, Tavares J, Martins S, Carvalho T, Enguita FJ, Brito D, Carmo-Fonseca M, Lopes LR. Whole gene sequencing identifies deep-intronic variants with potential functional impact in patients with hypertrophic cardiomyopathy. PLoS One 2017; 12:e0182946. [PMID: 28797094 PMCID: PMC5552324 DOI: 10.1371/journal.pone.0182946] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/27/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND High throughput sequencing technologies have revolutionized the identification of mutations responsible for genetic diseases such as hypertrophic cardiomyopathy (HCM). However, approximately 50% of individuals with a clinical diagnosis of HCM have no causal mutation identified. This may be due to the presence of pathogenic mutations located deep within the introns, which are not detected by conventional sequencing analysis restricted to exons and exon-intron boundaries. OBJECTIVE The aim of this study was to develop a whole-gene sequencing strategy to prioritize deep intronic variants that may play a role in HCM pathogenesis. METHODS AND RESULTS The full genomic DNA sequence of 26 genes previously associated with HCM was analysed in 16 unrelated patients. We identified likely pathogenic deep intronic variants in VCL, PRKAG2 and TTN genes. These variants, which are predicted to act through disruption of either splicing or transcription factor binding sites, are 3-fold more frequent in our cohort of probands than in normal European populations. Moreover, we found a patient that is compound heterozygous for a splice site mutation in MYBPC3 and the deep intronic VCL variant. Analysis of family members revealed that carriers of the MYBPC3 mutation alone do not manifest the disease, while family members that are compound heterozygous are clinically affected. CONCLUSION This study provides a framework for scrutinizing variation along the complete intronic sequence of HCM-associated genes and prioritizing candidates for mechanistic and functional analysis. Our data suggest that deep intronic variation contributes to HCM phenotype.
Collapse
Affiliation(s)
- Rita Mendes de Almeida
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Joana Tavares
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Sandra Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Teresa Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Francisco J. Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Dulce Brito
- Departamento de Cardiologia, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
- Centro Cardiovascular da Universidade de Lisboa, Lisbon, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Luís Rocha Lopes
- Centro Cardiovascular da Universidade de Lisboa, Lisbon, Portugal
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| |
Collapse
|
50
|
Cortez-Dias N, Costa MC, Carrilho-Ferreira P, Silva D, Jorge C, Calisto C, Pessoa T, Robalo Martins S, de Sousa JC, da Silva PC, Fiúza M, Diogo AN, Pinto FJ, Enguita FJ. CORRIGENDUM: Circulating miR-122-5p/miR-133b Ratio Is a Specific Early Prognostic Biomarker in Acute Myocardial Infarction. Circ J 2017; 81:613. [PMID: 28344209 DOI: 10.1253/circj.cj-66-0140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|