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Chen T, Ellman DG, Fang S, Bak ST, Nørgård MØ, Svenningsen P, Andersen DC. Transfer of cardiomyocyte-derived extracellular vesicles to neighboring cardiac cells requires tunneling nanotubes during heart development. Theranostics 2024; 14:3843-3858. [PMID: 38994028 PMCID: PMC11234280 DOI: 10.7150/thno.91604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 05/26/2024] [Indexed: 07/13/2024] Open
Abstract
Rationale: Extracellular vesicles (EVs) are thought to mediate intercellular communication during development and disease. Yet, biological insight to intercellular EV transfer remains elusive, also in the heart, and is technically challenging to demonstrate. Here, we aimed to investigate biological transfer of cardiomyocyte-derived EVs in the neonatal heart. Methods: We exploited CD9 as a marker of EVs, and generated two lines of cardiomyocyte specific EV reporter mice: Tnnt2-Cre; double-floxed inverted CD9/EGFP and αMHC-MerCreMer; double-floxed inverted CD9/EGFP. The two mouse lines were utilized to determine whether developing cardiomyocytes transfer EVs to other cardiac cells (non-myocytes and cardiomyocytes) in vitro and in vivo and investigate the intercellular transport pathway of cardiomyocyte-derived EVs. Results: Genetic tagging of cardiomyocytes was confirmed in both reporter mouse lines and proof of concept in the postnatal heart showed that, a fraction of EGFP+/MYH1- non-myocytes exist firmly demonstrating in vivo cardiomyocyte-derived EV transfer. However, two sets of direct and indirect EGFP +/- cardiac cell co-cultures showed that cardiomyocyte-derived EGFP+ EV transfer requires cell-cell contact and that uptake of EGFP+ EVs from the medium is limited. The same was observed when co-cultiring with mouse macrophages. Further mechanistic insight showed that cardiomyocyte EV transfer occurs through type I tunneling nanotubes. Conclusion: While the current notion assumes that EVs are transferred through secretion to the surroundings, our data show that cardiomyocyte-derived EV transfer in the developing heart occurs through nanotubes between neighboring cells. Whether these data are fundamental and relate to adult hearts and other organs remains to be determined, but they imply that the normal developmental process of EV transfer goes through cell-cell contact rather than through the extracellular compartment.
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Affiliation(s)
- Ting Chen
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Urology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Ditte Gry Ellman
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Shu Fang
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Sara Thornby Bak
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mikkel Ørnfeldt Nørgård
- Department of Molecular Medicine, Unit of Cardiovascular and Renal Research, University of Southern Denmark, Odense, Denmark
| | - Per Svenningsen
- Department of Molecular Medicine, Unit of Cardiovascular and Renal Research, University of Southern Denmark, Odense, Denmark
| | - Ditte Caroline Andersen
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
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2
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Castellano M, Blanco V, Calzi ML, Costa B, Witwer K, Hill M, Cayota A, Segovia M, Tosar JP. Ribonuclease activity undermines immune sensing of naked extracellular RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590771. [PMID: 38712104 PMCID: PMC11071435 DOI: 10.1101/2024.04.23.590771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The plasma membrane and the membrane of endosomal vesicles are considered physical barriers preventing extracellular RNA uptake. While naked RNA can be spontaneously internalized by certain cells types, functional delivery of naked RNA into the cytosol has been rarely observed. Here we show that extracellular ribonucleases, mainly derived from cell culture supplements, have so far hindered the study of extracellular RNA functionality. In the presence of active ribonuclease inhibitors (RI), naked bacterial RNA is pro-inflammatory when spiked in the media of dendritic cells and macrophages. In murine cells, this response mainly depends on the action of endosomal Toll-like receptors. However, we also show that naked RNA can perform endosomal escape and engage with cytosolic RNA sensors and ribosomes. For example, naked mRNAs encoding reporter proteins can be spontaneously internalized and translated by a variety of cell types, in an RI-dependent manner. In vivo, RI co-injection enhances the activation induced by naked extracellular RNA on splenic lymphocytes and myeloid-derived leukocytes. Furthermore, naked extracellular RNA is inherently pro-inflammatory in ribonuclease-poor compartments such as the peritoneal cavity. Overall, these results demonstrate that naked RNA is bioactive and does not need encapsulation inside synthetic or biological lipid vesicles for functional uptake, making a case for nonvesicular extracellular RNA-mediated intercellular communication.
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Affiliation(s)
- Mauricio Castellano
- Functional Genomics Laboratory, Institut Pasteur Montevideo, Uruguay
- Immunoregulation and Inflammation Laboratory, Institut Pasteur Montevideo, Uruguay
| | - Valentina Blanco
- Functional Genomics Laboratory, Institut Pasteur Montevideo, Uruguay
| | - Marco Li Calzi
- Functional Genomics Laboratory, Institut Pasteur Montevideo, Uruguay
| | - Bruno Costa
- Functional Genomics Laboratory, Institut Pasteur Montevideo, Uruguay
- Analytical Biochemistry Unit, School of Science, Universidad de la República, Uruguay
| | - Kenneth Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- EV Core Facility “EXCEL”, Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Marcelo Hill
- Immunoregulation and Inflammation Laboratory, Institut Pasteur Montevideo, Uruguay
- Academic Unit of Immunobiology, School of Medicine, Universidad de la República, Uruguay
| | - Alfonso Cayota
- Functional Genomics Laboratory, Institut Pasteur Montevideo, Uruguay
- Hospital de Clínicas, Universidad de la República, Uruguay
| | - Mercedes Segovia
- Immunoregulation and Inflammation Laboratory, Institut Pasteur Montevideo, Uruguay
- Academic Unit of Immunobiology, School of Medicine, Universidad de la República, Uruguay
| | - Juan Pablo Tosar
- Functional Genomics Laboratory, Institut Pasteur Montevideo, Uruguay
- Analytical Biochemistry Unit, School of Science, Universidad de la República, Uruguay
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3
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Zirak B, Naghipourfar M, Saberi A, Pouyabahar D, Zarezadeh A, Luo L, Fish L, Huh D, Navickas A, Sharifi-Zarchi A, Goodarzi H. Revealing the grammar of small RNA secretion using interpretable machine learning. CELL GENOMICS 2024; 4:100522. [PMID: 38460515 PMCID: PMC11019361 DOI: 10.1016/j.xgen.2024.100522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 11/02/2023] [Accepted: 02/12/2024] [Indexed: 03/11/2024]
Abstract
Small non-coding RNAs can be secreted through a variety of mechanisms, including exosomal sorting, in small extracellular vesicles, and within lipoprotein complexes. However, the mechanisms that govern their sorting and secretion are not well understood. Here, we present ExoGRU, a machine learning model that predicts small RNA secretion probabilities from primary RNA sequences. We experimentally validated the performance of this model through ExoGRU-guided mutagenesis and synthetic RNA sequence analysis. Additionally, we used ExoGRU to reveal cis and trans factors that underlie small RNA secretion, including known and novel RNA-binding proteins (RBPs), e.g., YBX1, HNRNPA2B1, and RBM24. We also developed a novel technique called exoCLIP, which reveals the RNA interactome of RBPs within the cell-free space. Together, our results demonstrate the power of machine learning in revealing novel biological mechanisms. In addition to providing deeper insight into small RNA secretion, this knowledge can be leveraged in therapeutic and synthetic biology applications.
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Affiliation(s)
- Bahar Zirak
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US
| | - Mohsen Naghipourfar
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Ali Saberi
- Department of Electrical and Computer Engineering, McGill University, Montreal, QC H3A 0E9, Canada; McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, 740 Dr Penfield Avenue, Montreal, QC H3A 0G1, Canada
| | - Delaram Pouyabahar
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Amirhossein Zarezadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Lixi Luo
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US; Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lisa Fish
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US
| | - Doowon Huh
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Albertas Navickas
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US; Institut Curie, CNRS UMR3348, INSERM U1278, Orsay, France.
| | - Ali Sharifi-Zarchi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran.
| | - Hani Goodarzi
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US.
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4
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Shi Y, Yang W, Lin H, Han L, Cai AJ, Saraf R, Lei Y, Zhang C. Identification of RNA-based cell-type markers for stem-cell manufacturing systems with a statistical scoring function. GENE REPORTS 2024; 34:101869. [PMID: 38351912 PMCID: PMC10861185 DOI: 10.1016/j.genrep.2023.101869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Cell-type biomarkers are useful in stem-cell manufacturing to monitor cell purity, quantity, and quality. However, the study on cell-type markers, specifically for stem cell manufacture, is limited. Emerging questions include which RNA transcripts can serve as biomarkers during stem cell culture and how to discover these biomarkers efficiently and precisely. We developed a scoring function system to identify RNA biomarkers with RNA-seq data for systems that have a limited number of cell types. We applied the method to two data sets, one for extracellular RNAs (ex-RNAs) and the other for intracellular microRNAs (miRNAs). The first data set has RNA-seq data of ex-RNAs from cell culture media for six different types of cells, including human embryonic stem cells. To get the RNA-seq data from intracellular miRNAs, we cultured three types of cells: human embryonic stem cells (H9), neural stem cells (NSC), hESC-derived endothelial cells (EC) and conducted small RNA-seq to their intracellular miRNAs. Using these data, we identified a set of ex-RNAs/smRNAs as candidates of biomarkers for different types of cells for cell manufacture. The validity of these findings was confirmed by the utilization of additional data sets and experimental procedures. We also used deep-learning-based prediction methods and simulated data to validate these discovered biomarkers.
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Affiliation(s)
- Yu Shi
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Weilong Yang
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Haishuang Lin
- Department of Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, NE, USA
| | - Li Han
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Alyssa J. Cai
- Newark Academy, 91 W S Orange Ave, Livingston, NJ, USA
| | - Ravi Saraf
- Department of Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, NE, USA
| | - Yuguo Lei
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
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5
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Longjohn MN, Hudson JABJ, Peña-Castillo L, Cormier RPJ, Hannay B, Chacko S, Lewis SM, Moorehead PC, Christian SL. Extracellular vesicle small RNA cargo discriminates non-cancer donors from pediatric B-lymphoblastic leukemia patients. Front Oncol 2023; 13:1272883. [PMID: 38023151 PMCID: PMC10679349 DOI: 10.3389/fonc.2023.1272883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Pediatric B-acute lymphoblastic leukemia (B-ALL) is a disease of abnormally growing B lymphoblasts. Here we hypothesized that extracellular vesicles (EVs), which are nanosized particles released by all cells (including cancer cells), could be used to monitor B-ALL severity and progression by sampling plasma instead of bone marrow. EVs are especially attractive as they are present throughout the circulation regardless of the location of the originating cell. First, we used nanoparticle tracking analysis to compare EVs between non-cancer donor (NCD) and B-ALL blood plasma; we found that B-ALL plasma contains more EVs than NCD plasma. We then isolated EVs from NCD and pediatric B-ALL peripheral blood plasma using a synthetic peptide-based isolation technique (Vn96), which is clinically amenable and isolates a broad spectrum of EVs. RNA-seq analysis of small RNAs contained within the isolated EVs revealed a signature of differentially packaged and exclusively packaged RNAs that distinguish NCD from B-ALL. The plasma EVs contain a heterogenous mixture of miRNAs and fragments of long non-coding RNA (lncRNA) and messenger RNA (mRNA). Transcripts packaged in B-ALL EVs include those involved in negative cell cycle regulation, potentially suggesting that B-ALL cells may use EVs to discard gene sequences that control growth. In contrast, NCD EVs carry sequences representative of multiple organs, including brain, muscle, and epithelial cells. This signature could potentially be used to monitor B-ALL disease burden in pediatric B-ALL patients via blood draws instead of invasive bone marrow aspirates.
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Affiliation(s)
- Modeline N. Longjohn
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Jo-Anna B. J. Hudson
- Discipline of Pediatrics, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Lourdes Peña-Castillo
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
- Department of Computer Science, Memorial University of Newfoundland, St. John’s, NL, Canada
| | | | | | - Simi Chacko
- Atlantic Cancer Research Institute, Moncton, NB, Canada
| | - Stephen M. Lewis
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
- Atlantic Cancer Research Institute, Moncton, NB, Canada
- Department of Chemistry & Biochemistry, Université de Moncton, Moncton, NB, Canada
| | - Paul C. Moorehead
- Discipline of Pediatrics, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Sherri L. Christian
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
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6
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Oshchepkova A, Zenkova M, Vlassov V. Extracellular Vesicles for Therapeutic Nucleic Acid Delivery: Loading Strategies and Challenges. Int J Mol Sci 2023; 24:ijms24087287. [PMID: 37108446 PMCID: PMC10139028 DOI: 10.3390/ijms24087287] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Extracellular vesicles (EVs) are membrane vesicles released into the extracellular milieu by cells of various origins. They contain different biological cargoes, protecting them from degradation by environmental factors. There is an opinion that EVs have a number of advantages over synthetic carriers, creating new opportunities for drug delivery. In this review, we discuss the ability of EVs to function as carriers for therapeutic nucleic acids (tNAs), challenges associated with the use of such carriers in vivo, and various strategies for tNA loading into EVs.
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Affiliation(s)
- Anastasiya Oshchepkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
| | - Marina Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
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7
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Korvenlaita N, Gómez‐Budia M, Scoyni F, Pistono C, Giudice L, Eamen S, Loppi S, de Sande AH, Huremagic B, Bouvy‐Liivrand M, Heinäniemi M, Kaikkonen MU, Cheng L, Hill AF, Kanninen KM, Jenster GW, van Royen ME, Ramiro L, Montaner J, Batkova T, Mikulik R, Giugno R, Jolkkonen J, Korhonen P, Malm T. Dynamic release of neuronal extracellular vesicles containing miR-21a-5p is induced by hypoxia. J Extracell Vesicles 2023; 12:e12297. [PMID: 36594832 PMCID: PMC9809533 DOI: 10.1002/jev2.12297] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Hypoxia induces changes in the secretion of extracellular vesicles (EVs) in several non-neuronal cells and pathological conditions. EVs are packed with biomolecules, such as microRNA(miR)-21-5p, which respond to hypoxia. However, the true EV association of miR-21-5p, and its functional or biomarker relevance, are inadequately characterised. Neurons are extremely sensitive cells, and it is not known whether the secretion of neuronal EVs and miR-21-5p are altered upon hypoxia. Here, we characterised the temporal EV secretion profile and cell viability of neurons under hypoxia. Hypoxia induced a rapid increase of miR-21a-5p secretion in the EVs, which preceded the elevation of hypoxia-induced tissue or cellular miR-21a-5p. Prolonged hypoxia induced cell death and the release of morphologically distinct EVs. The EVs protected miR-21a-5p from enzymatic degradation but a remarkable fraction of miR-21a-5p remained fragile and non-EV associated. The increase in miR-21a-5p secretion may have biomarker potential, as high blood levels of miR-21-5p in stroke patients were associated with significant disability at hospital discharge. Our data provides an understanding of the dynamic regulation of EV secretion from neurons under hypoxia and provides a candidate for the prediction of recovery from ischemic stroke.
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Affiliation(s)
- Nea Korvenlaita
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Mireia Gómez‐Budia
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Flavia Scoyni
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Cristiana Pistono
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Luca Giudice
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland,Department of Computer ScienceUniversity of VeronaVeronaVenetoItaly
| | - Shaila Eamen
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Sanna Loppi
- Department of ImmunologyUniversity of ArizonaTucsonArizonaUSA
| | - Ana Hernández de Sande
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Benjamin Huremagic
- Department of Computer ScienceUniversity of VeronaVeronaVenetoItaly,Department of Human GeneticsKU LeuvenLeuvenFlandersBelgium
| | | | | | - Minna U. Kaikkonen
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Lesley Cheng
- Department of Biochemistry and ChemistrySchool of Agriculture Biomedicine & EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
| | - Andrew F. Hill
- Department of Biochemistry and ChemistrySchool of Agriculture Biomedicine & EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia,La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia,Institute for Health and SportVictoria UniversityMelbourneVictoriaAustralia
| | - Katja M. Kanninen
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Guido W. Jenster
- Department of UrologyErasmus University Medical CenterRotterdamThe Netherlands
| | - Martin E. van Royen
- Department of PathologyErasmus University Medical CenterRotterdamThe Netherlands
| | - Laura Ramiro
- Neurovascular Research LaboratoryVall d'Hebron Institute of Research (VHIR)Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Joan Montaner
- Neurovascular Research LaboratoryVall d'Hebron Institute of Research (VHIR)Universitat Autònoma de BarcelonaBarcelonaSpain,Institute de Biomedicine of SevilleIBiS/Hospital Universitario Virgen del Rocío/CSIC/University of Seville & Department of NeurologyHospital Universitario Virgen MacarenaSevilleAndalucíaSpain
| | - Tereza Batkova
- BioVendor‐laboratorni medicina a.s.BrnoCzech Republic,International Clinical Research CenterNeurological DepartmentSt. Anne's University Hospital and Masaryk UniversityBrnoCzech Republic
| | - Robert Mikulik
- International Clinical Research CenterNeurological DepartmentSt. Anne's University Hospital and Masaryk UniversityBrnoCzech Republic
| | - Rosalba Giugno
- Department of Computer ScienceUniversity of VeronaVeronaVenetoItaly
| | - Jukka Jolkkonen
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Paula Korhonen
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Tarja Malm
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
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8
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Panio A, Cava C, D’Antona S, Bertoli G, Porro D. Diagnostic Circulating miRNAs in Sporadic Amyotrophic Lateral Sclerosis. Front Med (Lausanne) 2022; 9:861960. [PMID: 35602517 PMCID: PMC9121628 DOI: 10.3389/fmed.2022.861960] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by the neurodegeneration of motoneurons. About 10% of ALS is hereditary and involves mutation in 25 different genes, while 90% of the cases are sporadic forms of ALS (sALS). The diagnosis of ALS includes the detection of early symptoms and, as disease progresses, muscle twitching and then atrophy spreads from hands to other parts of the body. The disease causes high disability and has a high mortality rate; moreover, the therapeutic approaches for the pathology are not effective. miRNAs are small non-coding RNAs, whose activity has a major impact on the expression levels of coding mRNA. The literature identifies several miRNAs with diagnostic abilities on sALS, but a unique diagnostic profile is not defined. As miRNAs could be secreted, the identification of specific blood miRNAs with diagnostic ability for sALS could be helpful in the identification of the patients. In the view of personalized medicine, we performed a meta-analysis of the literature in order to select specific circulating miRNAs with diagnostic properties and, by bioinformatics approaches, we identified a panel of 10 miRNAs (miR-193b, miR-3911, miR-139-5p, miR-193b-1, miR-338-5p, miR-3911-1, miR-455-3p, miR-4687-5p, miR-4745-5p, and miR-4763-3p) able to classify sALS patients by blood analysis. Among them, the analysis of expression levels of the couple of blood miR-193b/miR-4745-5p could be translated in clinical practice for the diagnosis of sALS.
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9
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Corrado C, Barreca MM, Zichittella C, Alessandro R, Conigliaro A. Molecular Mediators of RNA Loading into Extracellular Vesicles. Cells 2021; 10:cells10123355. [PMID: 34943863 PMCID: PMC8699260 DOI: 10.3390/cells10123355] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 12/16/2022] Open
Abstract
In the last decade, an increasing number of studies have demonstrated that non-coding RNA (ncRNAs) cooperate in the gene regulatory networks with other biomolecules, including coding RNAs, DNAs and proteins. Among them, microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are involved in transcriptional and translation regulation at different levels. Intriguingly, ncRNAs can be packed in vesicles, released in the extracellular space, and finally internalized by receiving cells, thus affecting gene expression also at distance. This review focuses on the mechanisms through which the ncRNAs can be selectively packaged into extracellular vesicles (EVs).
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Affiliation(s)
- Chiara Corrado
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Biology and Genetics, University of Palermo, 90133 Palermo, Italy; (C.C.); (M.M.B.); (C.Z.); (R.A.)
| | - Maria Magdalena Barreca
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Biology and Genetics, University of Palermo, 90133 Palermo, Italy; (C.C.); (M.M.B.); (C.Z.); (R.A.)
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Chiara Zichittella
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Biology and Genetics, University of Palermo, 90133 Palermo, Italy; (C.C.); (M.M.B.); (C.Z.); (R.A.)
| | - Riccardo Alessandro
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Biology and Genetics, University of Palermo, 90133 Palermo, Italy; (C.C.); (M.M.B.); (C.Z.); (R.A.)
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), 90146 Palermo, Italy
| | - Alice Conigliaro
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Biology and Genetics, University of Palermo, 90133 Palermo, Italy; (C.C.); (M.M.B.); (C.Z.); (R.A.)
- Correspondence:
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10
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Ligustrazine Attenuates Gastric Inflammation and Apoptosis in Helicobacter pylori-induced Gastric Epithelial Cells. Jundishapur J Microbiol 2021. [DOI: 10.5812/jjm.116612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Stomach disorders, including gastric cancer and gastritis, are associated with the pathogenic bacterium Helicobacter pylori. Enhanced inflammation is the characteristic of H. pylori-induced gastritis. Ligustrazine exerts anti-inflammatory properties in mouse asthma models and acute kidney injury. Objectives: To determine the role of ligustrazine in H. pylori-induced gastritis. Methods: Normal gastric epithelial cell line (GES-1) was cultured with H. pylori at a multiplicity of infection (MOI) of 100: 1 for 24 hours. GES-1 cell line under H. pylori condition was incubated with 100 or 200 μM ligustrazine for 24 hours. Cell viability and apoptosis were investigated by MTT and flow cytometry assays, respectively. Inflammation was assessed by determining the levels and mRNA expression of interleukins (IL)-6/8, tumor necrosis factor-α (TNF-α), and monocyte chemotactic protein 1 (MCP-1) using ELISA and qRT-PCR analysis, respectively. Results: Helicobacter pylori infection reduced the viability and promoted the apoptosis of GES-1 cell line, accompanied by the enhanced activities of caspases 3 and 9. However, ligustrazine reversed the H. pylori-induced infection decreased viability, while increased apoptosis and caspases 3/9 activities in GES-1 cell line. Moreover, ligustrazine attenuated H. pylori-induced secretions of pro-inflammatory factors, IL-6/8, TNF-α, and MCP-1, in GES-1 cell line. The protein expression of inhibitor of NF-κB (IκBα) was downregulated in GES-1 cell line after H. pylori infection, while the protein expression levels of p65 and phosphorylation of IκBα were upregulated by H. pylori infection. On the contrary, ligustrazine decreased H. pylori-induced protein expression of IκBα, whereas increased protein expression of p65 and phosphorylation of IκBα. Conclusions: Ligustrazine exerted protective effects on H. pylori-induced gastric epithelial cells through inhibition of gastric inflammation and apoptosis and inactivation of NF-κB pathway.
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