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Welsh JA, Goberdhan DCI, O'Driscoll L, Buzas EI, Blenkiron C, Bussolati B, Cai H, Di Vizio D, Driedonks TAP, Erdbrügger U, Falcon‐Perez JM, Fu Q, Hill AF, Lenassi M, Lim SK, Mahoney MG, Mohanty S, Möller A, Nieuwland R, Ochiya T, Sahoo S, Torrecilhas AC, Zheng L, Zijlstra A, Abuelreich S, Bagabas R, Bergese P, Bridges EM, Brucale M, Burger D, Carney RP, Cocucci E, Colombo F, Crescitelli R, Hanser E, Harris AL, Haughey NJ, Hendrix A, Ivanov AR, Jovanovic‐Talisman T, Kruh‐Garcia NA, Ku'ulei‐Lyn Faustino V, Kyburz D, Lässer C, Lennon KM, Lötvall J, Maddox AL, Martens‐Uzunova ES, Mizenko RR, Newman LA, Ridolfi A, Rohde E, Rojalin T, Rowland A, Saftics A, Sandau US, Saugstad JA, Shekari F, Swift S, Ter‐Ovanesyan D, Tosar JP, Useckaite Z, Valle F, Varga Z, van der Pol E, van Herwijnen MJC, Wauben MHM, Wehman AM, Williams S, Zendrini A, Zimmerman AJ, MISEV Consortium, Théry C, Witwer KW. Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches. J Extracell Vesicles 2024; 13:e12404. [PMID: 38326288 PMCID: PMC10850029 DOI: 10.1002/jev2.12404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 02/09/2024] Open
Abstract
Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly.
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Affiliation(s)
- Joshua A. Welsh
- Translational Nanobiology Section, Laboratory of PathologyNational Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Deborah C. I. Goberdhan
- Nuffield Department of Women's and Reproductive HealthUniversity of Oxford, Women's Centre, John Radcliffe HospitalOxfordUK
| | - Lorraine O'Driscoll
- School of Pharmacy and Pharmaceutical SciencesTrinity College DublinDublinIreland
- Trinity Biomedical Sciences InstituteTrinity College DublinDublinIreland
- Trinity St. James's Cancer InstituteTrinity College DublinDublinIreland
| | - Edit I. Buzas
- Department of Genetics, Cell‐ and ImmunobiologySemmelweis UniversityBudapestHungary
- HCEMM‐SU Extracellular Vesicle Research GroupSemmelweis UniversityBudapestHungary
- HUN‐REN‐SU Translational Extracellular Vesicle Research GroupSemmelweis UniversityBudapestHungary
| | - Cherie Blenkiron
- Faculty of Medical and Health SciencesThe University of AucklandAucklandNew Zealand
| | - Benedetta Bussolati
- Department of Molecular Biotechnology and Health SciencesUniversity of TurinTurinItaly
| | | | - Dolores Di Vizio
- Department of Surgery, Division of Cancer Biology and TherapeuticsCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Tom A. P. Driedonks
- Department CDL ResearchUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Uta Erdbrügger
- University of Virginia Health SystemCharlottesvilleVirginiaUSA
| | - Juan M. Falcon‐Perez
- Exosomes Laboratory, Center for Cooperative Research in BiosciencesBasque Research and Technology AllianceDerioSpain
- Metabolomics Platform, Center for Cooperative Research in BiosciencesBasque Research and Technology AllianceDerioSpain
- IKERBASQUE, Basque Foundation for ScienceBilbaoSpain
| | - Qing‐Ling Fu
- Otorhinolaryngology Hospital, The First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Extracellular Vesicle Research and Clinical Translational CenterThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Andrew F. Hill
- Institute for Health and SportVictoria UniversityMelbourneAustralia
| | - Metka Lenassi
- Faculty of MedicineUniversity of LjubljanaLjubljanaSlovenia
| | - Sai Kiang Lim
- Institute of Molecular and Cell Biology (IMCB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Paracrine Therapeutics Pte. Ltd.SingaporeSingapore
- Department of Surgery, YLL School of MedicineNational University SingaporeSingaporeSingapore
| | - Mỹ G. Mahoney
- Thomas Jefferson UniversityPhiladelphiaPennsylvaniaUSA
| | - Sujata Mohanty
- Stem Cell FacilityAll India Institute of Medical SciencesNew DelhiIndia
| | - Andreas Möller
- Chinese University of Hong KongHong KongHong Kong S.A.R.
- QIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Rienk Nieuwland
- Laboratory of Experimental Clinical Chemistry, Amsterdam University Medical Centers, Location AMCUniversity of AmsterdamAmsterdamThe Netherlands
- Amsterdam Vesicle Center, Amsterdam University Medical Centers, Location AMCUniversity of AmsterdamAmsterdamThe Netherlands
| | | | - Susmita Sahoo
- Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Ana C. Torrecilhas
- Laboratório de Imunologia Celular e Bioquímica de Fungos e Protozoários, Departamento de Ciências Farmacêuticas, Instituto de Ciências Ambientais, Químicas e FarmacêuticasUniversidade Federal de São Paulo (UNIFESP) Campus DiademaDiademaBrazil
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Andries Zijlstra
- Department of PathologyVanderbilt University Medical CenterNashvilleTennesseeUSA
- GenentechSouth San FranciscoCaliforniaUSA
| | - Sarah Abuelreich
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Reem Bagabas
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Paolo Bergese
- Department of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
- Center for Colloid and Surface Science (CSGI)FlorenceItaly
- National Center for Gene Therapy and Drugs based on RNA TechnologyPaduaItaly
| | - Esther M. Bridges
- Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Marco Brucale
- Consiglio Nazionale delle Ricerche ‐ Istituto per lo Studio dei Materiali NanostrutturatiBolognaItaly
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande InterfaseFlorenceItaly
| | - Dylan Burger
- Kidney Research CentreOttawa Hopsital Research InstituteOttawaCanada
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaCanada
- School of Pharmaceutical SciencesUniversity of OttawaOttawaCanada
| | - Randy P. Carney
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCaliforniaUSA
| | - Emanuele Cocucci
- Division of Pharmaceutics and Pharmacology, College of PharmacyThe Ohio State UniversityColumbusOhioUSA
- Comprehensive Cancer CenterThe Ohio State UniversityColumbusOhioUSA
| | - Federico Colombo
- Division of Pharmaceutics and Pharmacology, College of PharmacyThe Ohio State UniversityColumbusOhioUSA
| | - Rossella Crescitelli
- Sahlgrenska Center for Cancer Research, Department of Surgery, Institute of Clinical SciencesSahlgrenska Academy, University of GothenburgGothenburgSweden
- Wallenberg Centre for Molecular and Translational Medicine, Institute of Clinical SciencesSahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Edveena Hanser
- Department of BiomedicineUniversity Hospital BaselBaselSwitzerland
- Department of BiomedicineUniversity of BaselBaselSwitzerland
| | | | - Norman J. Haughey
- Departments of Neurology and PsychiatryJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Human Structure and RepairGhent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Alexander R. Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Tijana Jovanovic‐Talisman
- Department of Cancer Biology and Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Nicole A. Kruh‐Garcia
- Bio‐pharmaceutical Manufacturing and Academic Resource Center (BioMARC)Infectious Disease Research Center, Colorado State UniversityFort CollinsColoradoUSA
| | - Vroniqa Ku'ulei‐Lyn Faustino
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Diego Kyburz
- Department of BiomedicineUniversity of BaselBaselSwitzerland
- Department of RheumatologyUniversity Hospital BaselBaselSwitzerland
| | - Cecilia Lässer
- Krefting Research Centre, Department of Internal Medicine and Clinical NutritionInstitute of Medicine at Sahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Kathleen M. Lennon
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Jan Lötvall
- Krefting Research Centre, Institute of Medicine at Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Adam L. Maddox
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Elena S. Martens‐Uzunova
- Erasmus MC Cancer InstituteUniversity Medical Center Rotterdam, Department of UrologyRotterdamThe Netherlands
| | - Rachel R. Mizenko
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCaliforniaUSA
| | - Lauren A. Newman
- College of Medicine and Public HealthFlinders UniversityAdelaideAustralia
| | - Andrea Ridolfi
- Department of Physics and Astronomy, and LaserLaB AmsterdamVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Eva Rohde
- Department of Transfusion Medicine, University HospitalSalzburger Landeskliniken GmbH of Paracelsus Medical UniversitySalzburgAustria
- GMP Unit, Paracelsus Medical UniversitySalzburgAustria
- Transfer Centre for Extracellular Vesicle Theralytic Technologies, EV‐TTSalzburgAustria
| | - Tatu Rojalin
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCaliforniaUSA
- Expansion Therapeutics, Structural Biology and BiophysicsJupiterFloridaUSA
| | - Andrew Rowland
- College of Medicine and Public HealthFlinders UniversityAdelaideAustralia
| | - Andras Saftics
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Ursula S. Sandau
- Department of Anesthesiology & Perioperative MedicineOregon Health & Science UniversityPortlandOregonUSA
| | - Julie A. Saugstad
- Department of Anesthesiology & Perioperative MedicineOregon Health & Science UniversityPortlandOregonUSA
| | - Faezeh Shekari
- Department of Stem Cells and Developmental Biology, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
- Celer DiagnosticsTorontoCanada
| | - Simon Swift
- Waipapa Taumata Rau University of AucklandAucklandNew Zealand
| | - Dmitry Ter‐Ovanesyan
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMassachusettsUSA
| | - Juan P. Tosar
- Universidad de la RepúblicaMontevideoUruguay
- Institut Pasteur de MontevideoMontevideoUruguay
| | - Zivile Useckaite
- College of Medicine and Public HealthFlinders UniversityAdelaideAustralia
| | - Francesco Valle
- Consiglio Nazionale delle Ricerche ‐ Istituto per lo Studio dei Materiali NanostrutturatiBolognaItaly
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande InterfaseFlorenceItaly
| | - Zoltan Varga
- Biological Nanochemistry Research GroupInstitute of Materials and Environmental Chemistry, Research Centre for Natural SciencesBudapestHungary
- Department of Biophysics and Radiation BiologySemmelweis UniversityBudapestHungary
| | - Edwin van der Pol
- Amsterdam Vesicle Center, Amsterdam University Medical Centers, Location AMCUniversity of AmsterdamAmsterdamThe Netherlands
- Biomedical Engineering and Physics, Amsterdam UMC, location AMCUniversity of AmsterdamAmsterdamThe Netherlands
- Laboratory of Experimental Clinical Chemistry, Amsterdam UMC, location AMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Martijn J. C. van Herwijnen
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Marca H. M. Wauben
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | | | | | - Andrea Zendrini
- Department of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
- Center for Colloid and Surface Science (CSGI)FlorenceItaly
| | - Alan J. Zimmerman
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | | | - Clotilde Théry
- Institut Curie, INSERM U932PSL UniversityParisFrance
- CurieCoreTech Extracellular Vesicles, Institut CurieParisFrance
| | - Kenneth W. Witwer
- Department of Molecular and Comparative PathobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- EV Core Facility “EXCEL”, Institute for Basic Biomedical SciencesJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer's DiseaseJohns Hopkins University School of MedicineBaltimoreMarylandUSA
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Saftics A, Abuelreich S, Romano E, Ghaeli I, Jiang N, Spanos M, Lennon KM, Singh G, Das S, Van Keuren‐Jensen K, Jovanovic‐Talisman T. Single Extracellular VEsicle Nanoscopy. J Extracell Vesicles 2023; 12:e12346. [PMID: 37422692 PMCID: PMC10329735 DOI: 10.1002/jev2.12346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/26/2023] [Accepted: 06/23/2023] [Indexed: 07/10/2023] Open
Abstract
Extracellular vesicles (EVs) and their cargo constitute novel biomarkers. EV subpopulations have been defined not only by abundant tetraspanins (e.g., CD9, CD63 and CD81) but also by specific markers derived from their source cells. However, it remains a challenge to robustly isolate and characterize EV subpopulations. Here, we combined affinity isolation with super-resolution imaging to comprehensively assess EV subpopulations from human plasma. Our Single Extracellular VEsicle Nanoscopy (SEVEN) assay successfully quantified the number of affinity-isolated EVs, their size, shape, molecular tetraspanin content, and heterogeneity. The number of detected tetraspanin-enriched EVs positively correlated with sample dilution in a 64-fold range (for SEC-enriched plasma) and a 50-fold range (for crude plasma). Importantly, SEVEN robustly detected EVs from as little as ∼0.1 μL of crude plasma. We further characterized the size, shape and molecular tetraspanin content (with corresponding heterogeneities) for CD9-, CD63- and CD81-enriched EV subpopulations. Finally, we assessed EVs from the plasma of four pancreatic ductal adenocarcinoma patients with resectable disease. Compared to healthy plasma, CD9-enriched EVs from patients were smaller while IGF1R-enriched EVs from patients were larger, rounder and contained more tetraspanin molecules, suggestive of a unique pancreatic cancer-enriched EV subpopulation. This study provides the method validation and demonstrates that SEVEN could be advanced into a platform for characterizing both disease-associated and organ-associated EV subpopulations.
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Affiliation(s)
- Andras Saftics
- Department of Cancer Biology and Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Sarah Abuelreich
- Department of Cancer Biology and Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Eugenia Romano
- Department of Cancer Biology and Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Ima Ghaeli
- Department of Cancer Biology and Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Nan Jiang
- Department of Cancer Biology and Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Michail Spanos
- Cardiology Division and Corrigan Minehan Heart CenterMassachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Kathleen M. Lennon
- Department of Cancer Biology and Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Gagandeep Singh
- Department of SurgeryCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Saumya Das
- Cardiology Division and Corrigan Minehan Heart CenterMassachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | | | - Tijana Jovanovic‐Talisman
- Department of Cancer Biology and Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
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Asim MN, Ibrahim MA, Imran Malik M, Dengel A, Ahmed S. Advances in Computational Methodologies for Classification and Sub-Cellular Locality Prediction of Non-Coding RNAs. Int J Mol Sci 2021; 22:8719. [PMID: 34445436 PMCID: PMC8395733 DOI: 10.3390/ijms22168719] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 02/06/2023] Open
Abstract
Apart from protein-coding Ribonucleic acids (RNAs), there exists a variety of non-coding RNAs (ncRNAs) which regulate complex cellular and molecular processes. High-throughput sequencing technologies and bioinformatics approaches have largely promoted the exploration of ncRNAs which revealed their crucial roles in gene regulation, miRNA binding, protein interactions, and splicing. Furthermore, ncRNAs are involved in the development of complicated diseases like cancer. Categorization of ncRNAs is essential to understand the mechanisms of diseases and to develop effective treatments. Sub-cellular localization information of ncRNAs demystifies diverse functionalities of ncRNAs. To date, several computational methodologies have been proposed to precisely identify the class as well as sub-cellular localization patterns of RNAs). This paper discusses different types of ncRNAs, reviews computational approaches proposed in the last 10 years to distinguish coding-RNA from ncRNA, to identify sub-types of ncRNAs such as piwi-associated RNA, micro RNA, long ncRNA, and circular RNA, and to determine sub-cellular localization of distinct ncRNAs and RNAs. Furthermore, it summarizes diverse ncRNA classification and sub-cellular localization determination datasets along with benchmark performance to aid the development and evaluation of novel computational methodologies. It identifies research gaps, heterogeneity, and challenges in the development of computational approaches for RNA sequence analysis. We consider that our expert analysis will assist Artificial Intelligence researchers with knowing state-of-the-art performance, model selection for various tasks on one platform, dominantly used sequence descriptors, neural architectures, and interpreting inter-species and intra-species performance deviation.
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Affiliation(s)
- Muhammad Nabeel Asim
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Muhammad Ali Ibrahim
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Muhammad Imran Malik
- National Center for Artificial Intelligence (NCAI), National University of Sciences and Technology, Islamabad 44000, Pakistan;
- School of Electrical Engineering & Computer Science, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Andreas Dengel
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- DeepReader GmbH, Trippstadter Str. 122, 67663 Kaiserslautern, Germany
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Lang F, Contreras-Gerenas MF, Gelléri M, Neumann J, Kröger O, Sadlo F, Berniak K, Marx A, Cremer C, Wagenknecht HA, Allgayer H. Tackling Tumour Cell Heterogeneity at the Super-Resolution Level in Human Colorectal Cancer Tissue. Cancers (Basel) 2021; 13:cancers13153692. [PMID: 34359592 PMCID: PMC8345115 DOI: 10.3390/cancers13153692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Tumour cell heterogeneity is the most fundamental problem in cancer diagnosis and therapy. Micro-diagnostic technologies able to differentiate the heterogeneous molecular, especially metastatic, potential of single cells or cell clones already within early primary tumours of carcinoma patients would be of utmost importance. Single molecule localisation microscopy (SMLM) has recently allowed the imaging of subcellular features at the nanoscale. However, the technology has mostly been limited to cultured cell lines only. We introduce a first-in-field approach for quantitative SMLM-analysis of chromatin nanostructure in individual cells in resected, routine-pathology colorectal carcinoma patient tissue sections, illustrating, as a first example, changes in nuclear chromatin nanostructure and microRNA intracellular distribution within carcinoma cells as opposed to normal cells, chromatin accessibility and microRNAs having been shown to be critical in gene regulation and metastasis. We believe this technology to have an enormous potential for future differential diagnosis between individual cells in the tissue context. Abstract Tumour cell heterogeneity, and its early individual diagnosis, is one of the most fundamental problems in cancer diagnosis and therapy. Single molecule localisation microscopy (SMLM) resolves subcellular features but has been limited to cultured cell lines only. Since nuclear chromatin architecture and microRNAs are critical in metastasis, we introduce a first-in-field approach for quantitative SMLM-analysis of chromatin nanostructure in individual cells in resected, routine-pathology colorectal carcinoma (CRC) patient tissue sections. Chromatin density profiles proved to differ for cells in normal and carcinoma colorectal tissues. In tumour sections, nuclear size and chromatin compaction percentages were significantly different in carcinoma versus normal epithelial and other cells of colorectal tissue. SMLM analysis in nuclei from normal colorectal tissue revealed abrupt changes in chromatin density profiles at the nanoscale, features not detected by conventional widefield microscopy. SMLM for microRNAs relevant for metastasis was achieved in colorectal cancer tissue at the nuclear level. Super-resolution microscopy with quantitative image evaluation algorithms provide powerful tools to analyse chromatin nanostructure and microRNAs of individual cells from normal and tumour tissue at the nanoscale. Our new perspectives improve the differential diagnosis of normal and (metastatically relevant) tumour cells at the single-cell level within the heterogeneity of primary tumours of patients.
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Affiliation(s)
- Fabian Lang
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, Campus Süd, 76131 Karlsruhe, Germany; (F.L.); (H.-A.W.)
| | - María F. Contreras-Gerenas
- Department of Experimental Surgery—Cancer Metastasis, Mannheim Medical Faculty, Ruprecht-Karls University of Heidelberg, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany;
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
| | - Márton Gelléri
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
| | - Jan Neumann
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
| | - Ole Kröger
- Interdisciplinary Centre for Scientific Computing (IWR), University Heidelberg, Mathematikon B, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany; (O.K.); (F.S.)
| | - Filip Sadlo
- Interdisciplinary Centre for Scientific Computing (IWR), University Heidelberg, Mathematikon B, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany; (O.K.); (F.S.)
| | - Krzysztof Berniak
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7 Street, 30-387 Krakow, Poland;
| | - Alexander Marx
- Institute of Pathology, Mannheim Medical Faculty, Ruprecht-Karls University of Heidelberg, Theodor-Kutzer-Ufer 1, 68167 Mannheim, Germany;
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
- Interdisciplinary Centre for Scientific Computing (IWR), University Heidelberg, Mathematikon B, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany; (O.K.); (F.S.)
- Institute of Pharmacy & Molecular Biotechnology, Ruprecht-Karls University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, Campus Süd, 76131 Karlsruhe, Germany; (F.L.); (H.-A.W.)
| | - Heike Allgayer
- Department of Experimental Surgery—Cancer Metastasis, Mannheim Medical Faculty, Ruprecht-Karls University of Heidelberg, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany;
- Correspondence: ; Tel.: +49-(0)621-383-71630/-1406/-71635; Fax: +49-(0)621-383-71631
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Bordanaba-Florit G, Royo F, Kruglik SG, Falcón-Pérez JM. Using single-vesicle technologies to unravel the heterogeneity of extracellular vesicles. Nat Protoc 2021; 16:3163-3185. [PMID: 34135505 DOI: 10.1038/s41596-021-00551-z] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/31/2021] [Indexed: 12/12/2022]
Abstract
Extracellular vesicles (EVs) are heterogeneous lipid containers with a complex molecular cargo comprising several populations with unique roles in biological processes. These vesicles are closely associated with specific physiological features, which makes them invaluable in the detection and monitoring of various diseases. EVs play a key role in pathophysiological processes by actively triggering genetic or metabolic responses. However, the heterogeneity of their structure and composition hinders their application in medical diagnosis and therapies. This diversity makes it difficult to establish their exact physiological roles, and the functions and composition of different EV (sub)populations. Ensemble averaging approaches currently employed for EV characterization, such as western blotting or 'omics' technologies, tend to obscure rather than reveal these heterogeneities. Recent developments in single-vesicle analysis have made it possible to overcome these limitations and have facilitated the development of practical clinical applications. In this review, we discuss the benefits and challenges inherent to the current methods for the analysis of single vesicles and review the contribution of these approaches to the understanding of EV biology. We describe the contributions of these recent technological advances to the characterization and phenotyping of EVs, examination of the role of EVs in cell-to-cell communication pathways and the identification and validation of EVs as disease biomarkers. Finally, we discuss the potential of innovative single-vesicle imaging and analysis methodologies using microfluidic devices, which promise to deliver rapid and effective basic and practical applications for minimally invasive prognosis systems.
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Affiliation(s)
- Guillermo Bordanaba-Florit
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.
| | - Félix Royo
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Madrid, Spain
| | - Sergei G Kruglik
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin, Paris, France
| | - Juan M Falcón-Pérez
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Madrid, Spain. .,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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6
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Exploring interactions between extracellular vesicles and cells for innovative drug delivery system design. Adv Drug Deliv Rev 2021; 173:252-278. [PMID: 33798644 DOI: 10.1016/j.addr.2021.03.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/15/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023]
Abstract
Extracellular vesicles (EVs) are submicron cell-secreted structures containing proteins, nucleic acids and lipids. EVs can functionally transfer these cargoes from one cell to another to modulate physiological and pathological processes. Due to their presumed biocompatibility and capacity to circumvent canonical delivery barriers encountered by synthetic drug delivery systems, EVs have attracted considerable interest as drug delivery vehicles. However, it is unclear which mechanisms and molecules orchestrate EV-mediated cargo delivery to recipient cells. Here, we review how EV properties have been exploited to improve the efficacy of small molecule drugs. Furthermore, we explore which EV surface molecules could be directly or indirectly involved in EV-mediated cargo transfer to recipient cells and discuss the cellular reporter systems with which such transfer can be studied. Finally, we elaborate on currently identified cellular processes involved in EV cargo delivery. Through these topics, we provide insights in critical effectors in the EV-cell interface which may be exploited in nature-inspired drug delivery strategies.
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7
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Sung BH, Parent CA, Weaver AM. Extracellular vesicles: Critical players during cell migration. Dev Cell 2021; 56:1861-1874. [PMID: 33811804 DOI: 10.1016/j.devcel.2021.03.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/09/2021] [Accepted: 03/12/2021] [Indexed: 12/13/2022]
Abstract
Cell migration is essential for the development and maintenance of multicellular organisms, contributing to embryogenesis, wound healing, immune response, and other critical processes. It is also involved in the pathogenesis of many diseases, including immune deficiency disorders and cancer metastasis. Recently, extracellular vesicles (EVs) have been shown to play important roles in cell migration. Here, we review recent studies describing the functions of EVs in multiple aspects of cell motility, including directional sensing, cell adhesion, extracellular matrix (ECM) degradation, and leader-follower behavior. We also discuss the role of EVs in migration during development and disease and the utility of imaging tools for studying the role of EVs in cell migration.
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Affiliation(s)
- Bong Hwan Sung
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 1161 Medical Center Dr, Nashville, TN 37232, USA
| | - Carole A Parent
- Department of Pharmacology, University of Michigan, 500 S. State Street, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan, 500 S. State Street, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, 500 S. State Street, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, 500 S. State Street, Ann Arbor, MI 48109, USA
| | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 1161 Medical Center Dr, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1211 Medical Center Dr, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2220 Pierce Ave, Nashville, TN 37232, USA.
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8
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Cardoen B, Yedder HB, Sharma A, Chou KC, Nabi IR, Hamarneh G. ERGO: Efficient Recurrent Graph Optimized Emitter Density Estimation in Single Molecule Localization Microscopy. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:1942-1956. [PMID: 31880546 DOI: 10.1109/tmi.2019.2962361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Single molecule localization microscopy (SMLM) allows unprecedented insight into the three-dimensional organization of proteins at the nanometer scale. The combination of minimal invasive cell imaging with high resolution positions SMLM at the forefront of scientific discovery in cancer, infectious, and degenerative diseases. By stochastic temporal and spatial separation of light emissions from fluorescent labelled proteins, SMLM is capable of nanometer scale reconstruction of cellular structures. Precise localization of proteins in 3D astigmatic SMLM is dependent on parameter sensitive preprocessing steps to select regions of interest. With SMLM acquisition highly variable over time, it is non-trivial to find an optimal static parameter configuration. The high emitter density required for reconstruction of complex protein structures can compromise accuracy and introduce artifacts. To address these problems, we introduce two modular auto-tuning pre-processing methods: adaptive signal detection and learned recurrent signal density estimation that can leverage the information stored in the sequence of frames that compose the SMLM acquisition process. We show empirically that our contributions improve accuracy, precision and recall with respect to the state of the art. Both modules auto-tune their hyper-parameters to reduce the parameter space for practitioners, improve robustness and reproducibility, and are validated on a reference in silico dataset. Adaptive signal detection and density prediction can offer a practitioner, in addition to informed localization, a tool to tune acquisition parameters ensuring improved reconstruction of the underlying protein complex. We illustrate the challenges faced by practitioners in applying SMLM algorithms on real world data markedly different from the data used in development and show how ERGO can be run on new datasets without retraining while motivating the need for robust transfer learning in SMLM.
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9
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RNA delivery by extracellular vesicles in mammalian cells and its applications. Nat Rev Mol Cell Biol 2020; 21:585-606. [PMID: 32457507 PMCID: PMC7249041 DOI: 10.1038/s41580-020-0251-y] [Citation(s) in RCA: 921] [Impact Index Per Article: 230.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
The term 'extracellular vesicles' refers to a heterogeneous population of vesicular bodies of cellular origin that derive either from the endosomal compartment (exosomes) or as a result of shedding from the plasma membrane (microvesicles, oncosomes and apoptotic bodies). Extracellular vesicles carry a variety of cargo, including RNAs, proteins, lipids and DNA, which can be taken up by other cells, both in the direct vicinity of the source cell and at distant sites in the body via biofluids, and elicit a variety of phenotypic responses. Owing to their unique biology and roles in cell-cell communication, extracellular vesicles have attracted strong interest, which is further enhanced by their potential clinical utility. Because extracellular vesicles derive their cargo from the contents of the cells that produce them, they are attractive sources of biomarkers for a variety of diseases. Furthermore, studies demonstrating phenotypic effects of specific extracellular vesicle-associated cargo on target cells have stoked interest in extracellular vesicles as therapeutic vehicles. There is particularly strong evidence that the RNA cargo of extracellular vesicles can alter recipient cell gene expression and function. During the past decade, extracellular vesicles and their RNA cargo have become better defined, but many aspects of extracellular vesicle biology remain to be elucidated. These include selective cargo loading resulting in substantial differences between the composition of extracellular vesicles and source cells; heterogeneity in extracellular vesicle size and composition; and undefined mechanisms for the uptake of extracellular vesicles into recipient cells and the fates of their cargo. Further progress in unravelling the basic mechanisms of extracellular vesicle biogenesis, transport, and cargo delivery and function is needed for successful clinical implementation. This Review focuses on the current state of knowledge pertaining to packaging, transport and function of RNAs in extracellular vesicles and outlines the progress made thus far towards their clinical applications.
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10
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Panagopoulou MS, Wark AW, Birch DJS, Gregory CD. Phenotypic analysis of extracellular vesicles: a review on the applications of fluorescence. J Extracell Vesicles 2020; 9:1710020. [PMID: 32002172 PMCID: PMC6968689 DOI: 10.1080/20013078.2019.1710020] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/18/2019] [Accepted: 12/21/2019] [Indexed: 12/22/2022] Open
Abstract
Extracellular vesicles (EVs) have numerous potential applications in the field of healthcare and diagnostics, and research into their biological functions is rapidly increasing. Mainly because of their small size and heterogeneity, there are significant challenges associated with their analysis and despite overt evidence of the potential of EVs in clinical diagnostic practice, guidelines for analytical procedures have not yet been properly established. Here, we present an overview of the main methods for studying the properties of EVs based on the principles of fluorescence. Setting aside the isolation, purification and physicochemical characterization strategies which answer questions about the size, surface charge and stability of EVs (reviewed elsewhere), we focus on available optical tools that enable the direct analysis of phenotype and mechanisms of interaction with tissues. In brief, the topics on which we elaborate range from the most popular approaches such as nanoparticle tracking analysis and flow cytometry, to less commonly used techniques such as fluorescence depolarization and microarrays as well as emerging areas such as fast fluorescence lifetime imaging microscopy (FLIM). We highlight that understanding the strengths and limitations of each method is essential for choosing the most appropriate combination of analytical tools. Finally, future directions of this rapidly developing area of medical diagnostics are discussed.
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Affiliation(s)
- Maria S. Panagopoulou
- University of Edinburgh Centre for Inflammation Research, The Queen’s Medical Research Institute, Edinburgh, UK
| | - Alastair W. Wark
- Centre for Molecular Nanometrology, Technology and Innovation Centre, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - David J S Birch
- Photophysics Group, Department of Physics, SUPA, University of Strathclyde, Glasgow, UK
| | - Christopher D. Gregory
- University of Edinburgh Centre for Inflammation Research, The Queen’s Medical Research Institute, Edinburgh, UK
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11
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Allgayer H, Leupold JH, Patil N. Defining the "Metastasome": Perspectives from the genome and molecular landscape in colorectal cancer for metastasis evolution and clinical consequences. Semin Cancer Biol 2019; 60:1-13. [PMID: 31362074 DOI: 10.1016/j.semcancer.2019.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 02/07/2023]
Abstract
Metastasis still poses the highest challenge for personalized therapy in cancer, partly due to a still incomplete understanding of its molecular evolution. We recently presented the most comprehensive whole-genome study of colorectal metastasis vs. matched primary tumors and suggested novel components of disease progression and metastasis evolution, some of them potentially relevant for targeted therapy. In this review, we try to put these findings into perspective with latest discoveries of colleagues and recent literature, and propose a systematic international team effort to collectively define the "metastasome", a term we introduce to summarize all genomic, epigenomic, transcriptomic, further -omic, molecular and functional characteristics rendering metastases different from primary tumors. Based on recent discoveries, we propose a revised metastasis model for colorectal cancer which is based on a common ancestor clone, early dissemination but flexible early or late stage clonal separation paralleling stromal interactions. Furthermore, we discuss hypotheses on site-specific metastasis, colorectal cancer progression, metastasis-targeted diagnosis and therapy, and metastasis prevention based on latest metastasome data.
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Affiliation(s)
- Heike Allgayer
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Theodor Kutzer Ufer 1-3, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany; Centre for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ludolf-Krehl-Str. 6, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany.
| | - Jörg H Leupold
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Theodor Kutzer Ufer 1-3, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany; Centre for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ludolf-Krehl-Str. 6, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany
| | - Nitin Patil
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Theodor Kutzer Ufer 1-3, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany; Centre for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ludolf-Krehl-Str. 6, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany
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12
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Bovaird S, Patel D, Padilla JCA, Lécuyer E. Biological functions, regulatory mechanisms, and disease relevance of RNA localization pathways. FEBS Lett 2018; 592:2948-2972. [PMID: 30132838 DOI: 10.1002/1873-3468.13228] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/06/2018] [Accepted: 08/17/2018] [Indexed: 12/12/2022]
Abstract
The asymmetric subcellular distribution of RNA molecules from their sites of transcription to specific compartments of the cell is an important aspect of post-transcriptional gene regulation. This involves the interplay of intrinsic cis-regulatory elements within the RNA molecules with trans-acting RNA-binding proteins and associated factors. Together, these interactions dictate the intracellular localization route of RNAs, whose downstream impacts have wide-ranging implications in cellular physiology. In this review, we examine the mechanisms underlying RNA localization and discuss their biological significance. We also review the growing body of evidence pointing to aberrant RNA localization pathways in the development and progression of diseases.
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Affiliation(s)
- Samantha Bovaird
- Institut de recherches cliniques de Montréal (IRCM), QC, Canada.,Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Dhara Patel
- Institut de recherches cliniques de Montréal (IRCM), QC, Canada.,Molecular Biology Program, Faculty of Medicine, Université de Montréal, QC, Canada
| | - Juan-Carlos Alberto Padilla
- Institut de recherches cliniques de Montréal (IRCM), QC, Canada.,Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Eric Lécuyer
- Institut de recherches cliniques de Montréal (IRCM), QC, Canada.,Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada.,Molecular Biology Program, Faculty of Medicine, Université de Montréal, QC, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, QC, Canada
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13
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Malandrino A, Kamm RD, Moeendarbary E. In Vitro Modeling of Mechanics in Cancer Metastasis. ACS Biomater Sci Eng 2018; 4:294-301. [PMID: 29457129 PMCID: PMC5811931 DOI: 10.1021/acsbiomaterials.7b00041] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 05/16/2017] [Indexed: 02/06/2023]
Abstract
In addition to a multitude of genetic and biochemical alterations, abnormal morphological, structural, and mechanical changes in cells and their extracellular environment are key features of tumor invasion and metastasis. Furthermore, it is now evident that mechanical cues alongside biochemical signals contribute to critical steps of cancer initiation, progression, and spread. Despite its importance, it is very challenging to study mechanics of different steps of metastasis in the clinic or even in animal models. While considerable progress has been made in developing advanced in vitro models for studying genetic and biological aspects of cancer, less attention has been paid to models that can capture both biological and mechanical factors realistically. This is mainly due to lack of appropriate models and measurement tools. After introducing the central role of mechanics in cancer metastasis, we provide an outlook on the emergence of novel in vitro assays and their combination with advanced measurement technologies to probe and recapitulate mechanics in conditions more relevant to the metastatic disease.
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Affiliation(s)
- Andrea Malandrino
- Department of Mechanical Engineering and Department of Biological
Engineering, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
- Institute
for Bioengineering of Catalonia, Barcelona 08028, Spain
| | - Roger D. Kamm
- Department of Mechanical Engineering and Department of Biological
Engineering, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Emad Moeendarbary
- Department of Mechanical Engineering and Department of Biological
Engineering, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
- Department
of Mechanical Engineering, University College
London, London WC1E 6BT, United Kingdom
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14
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Barteneva NS, Baiken Y, Fasler-Kan E, Alibek K, Wang S, Maltsev N, Ponomarev ED, Sautbayeva Z, Kauanova S, Moore A, Beglinger C, Vorobjev IA. Extracellular vesicles in gastrointestinal cancer in conjunction with microbiota: On the border of Kingdoms. Biochim Biophys Acta Rev Cancer 2017; 1868:372-393. [DOI: 10.1016/j.bbcan.2017.06.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/26/2017] [Accepted: 06/26/2017] [Indexed: 12/16/2022]
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15
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Schillaci O, Fontana S, Monteleone F, Taverna S, Di Bella MA, Di Vizio D, Alessandro R. Exosomes from metastatic cancer cells transfer amoeboid phenotype to non-metastatic cells and increase endothelial permeability: their emerging role in tumor heterogeneity. Sci Rep 2017; 7:4711. [PMID: 28680152 PMCID: PMC5498501 DOI: 10.1038/s41598-017-05002-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/23/2017] [Indexed: 01/03/2023] Open
Abstract
The goal of this study was to understand if exosomes derived from high-metastatic cells may influence the behavior of less aggressive cancer cells and the properties of the endothelium. We found that metastatic colon cancer cells are able to transfer their amoeboid phenotype to isogenic primary cancer cells through exosomes, and that this morphological transition is associated with the acquisition of a more aggressive behavior. Moreover, exosomes from the metastatic line (SW620Exos) exhibited higher ability to cause endothelial hyperpermeability than exosomes from the non metastatic line (SW480Exos). SWATH-based quantitative proteomic analysis highlighted that SW620Exos are significantly enriched in cytoskeletal-associated proteins including proteins activating the RhoA/ROCK pathway, known to induce amoeboid properties and destabilization of endothelial junctions. In particular, thrombin was identified as a key mediator of the effects induced by SW620Exos in target cells, in which we also found a significant increase of RhoA activity. Overall, our results demonstrate that in a heterogeneous context exosomes released by aggressive sub-clones can contribute to accelerate tumor progression by spreading malignant properties that affect both the tumor cell plasticity and the endothelial cell behavior.
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Affiliation(s)
- Odessa Schillaci
- Department of Biopathology and Medical Biotechnologies, University of Palermo, Palermo, Italy
| | - Simona Fontana
- Department of Biopathology and Medical Biotechnologies, University of Palermo, Palermo, Italy.
| | - Francesca Monteleone
- Department of Biopathology and Medical Biotechnologies, University of Palermo, Palermo, Italy
| | - Simona Taverna
- Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council, Palermo, Italy
| | | | - Dolores Di Vizio
- Division of Cancer Biology and Therapeutics, Departments of Surgery, Biomedical Sciences and Pathology and Laboratory Medicine, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA
| | - Riccardo Alessandro
- Department of Biopathology and Medical Biotechnologies, University of Palermo, Palermo, Italy
- Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council, Palermo, Italy
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16
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Cremer C, Szczurek A, Schock F, Gourram A, Birk U. Super-resolution microscopy approaches to nuclear nanostructure imaging. Methods 2017; 123:11-32. [PMID: 28390838 DOI: 10.1016/j.ymeth.2017.03.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/23/2017] [Indexed: 12/14/2022] Open
Abstract
The human genome has been decoded, but we are still far from understanding the regulation of all gene activities. A largely unexplained role in these regulatory mechanisms is played by the spatial organization of the genome in the cell nucleus which has far-reaching functional consequences for gene regulation. Until recently, it appeared to be impossible to study this problem on the nanoscale by light microscopy. However, novel developments in optical imaging technology have radically surpassed the limited resolution of conventional far-field fluorescence microscopy (ca. 200nm). After a brief review of available super-resolution microscopy (SRM) methods, we focus on a specific SRM approach to study nuclear genome structure at the single cell/single molecule level, Spectral Precision Distance/Position Determination Microscopy (SPDM). SPDM, a variant of localization microscopy, makes use of conventional fluorescent proteins or single standard organic fluorophores in combination with standard (or only slightly modified) specimen preparation conditions; in its actual realization mode, the same laser frequency can be used for both photoswitching and fluorescence read out. Presently, the SPDM method allows us to image nuclear genome organization in individual cells down to few tens of nanometer (nm) of structural resolution, and to perform quantitative analyses of individual small chromatin domains; of the nanoscale distribution of histones, chromatin remodeling proteins, and transcription, splicing and repair related factors. As a biomedical research application, using dual-color SPDM, it became possible to monitor in mouse cardiomyocyte cells quantitatively the effects of ischemia conditions on the chromatin nanostructure (DNA). These novel "molecular optics" approaches open an avenue to study the nuclear landscape directly in individual cells down to the single molecule level and thus to test models of functional genome architecture at unprecedented resolution.
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Affiliation(s)
- Christoph Cremer
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany; Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany. http://www.optics.imb-mainz.de
| | - Aleksander Szczurek
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Florian Schock
- Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany
| | - Amine Gourram
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Udo Birk
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany; Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany
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17
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Abba ML, Patil N, Leupold JH, Moniuszko M, Utikal J, Niklinski J, Allgayer H. MicroRNAs as novel targets and tools in cancer therapy. Cancer Lett 2017; 387:84-94. [DOI: 10.1016/j.canlet.2016.03.043] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/24/2016] [Accepted: 03/29/2016] [Indexed: 02/07/2023]
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18
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Bohländer PR, Abba ML, Bestvater F, Allgayer H, Wagenknecht HA. Two wavelength-shifting molecular beacons for simultaneous and selective imaging of vesicular miRNA-21 and miRNA-31 in living cancer cells. Org Biomol Chem 2016; 14:5001-6. [PMID: 27114268 DOI: 10.1039/c6ob00691d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two molecular beacons were designed as complementary fluorescent imaging probes for miRNA-21 and miRNA-31. Both beacons were prepared by a combination of solid-phase protocol and Cu(i)-catalyzed cycloaddition chemistry. The four photostable and bright fluorophores were attached to 2'-positions in the stem part of the two beacons. One beacon was labeled by a green-to-red emitting and the other by a blue-to-yellow emitting energy transfer pair. This two by two combination yields the four color emission readout. In vitro experiments demonstrate rapid and highly selective opening of both molecular beacons upon addition of the complementary target RNA and excellent green : red and blue : yellow emission color contrasts. Confocal microscopy of selected cancer cell lines provides evidence that a four color imaging of versicular miRNA-21 and miRNA-31 can be achieved both selectively and simultaneously upon transfection by the beacons, and that the fluorescent readouts track well with miRNA levels determined by PCR.
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Affiliation(s)
- Peggy R Bohländer
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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19
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Abba ML, Patil N, Leupold JH, Allgayer H. MicroRNA Regulation of Epithelial to Mesenchymal Transition. J Clin Med 2016; 5:jcm5010008. [PMID: 26784241 PMCID: PMC4730133 DOI: 10.3390/jcm5010008] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 12/18/2015] [Accepted: 01/05/2016] [Indexed: 02/07/2023] Open
Abstract
Epithelial to mesenchymal transition (EMT) is a central regulatory program that is similar in many aspects to several steps of embryonic morphogenesis. In addition to its physiological role in tissue repair and wound healing, EMT contributes to chemo resistance, metastatic dissemination and fibrosis, amongst others. Classically, the morphological change from epithelial to mesenchymal phenotype is characterized by the appearance or loss of a group of proteins which have come to be recognized as markers of the EMT process. As with all proteins, these molecules are controlled at the transcriptional and translational level by transcription factors and microRNAs, respectively. A group of developmental transcription factors form the backbone of the EMT cascade and a large body of evidence shows that microRNAs are heavily involved in the successful coordination of mesenchymal transformation and vice versa, either by suppressing the expression of different groups of transcription factors, or otherwise acting as their functional mediators in orchestrating EMT. This article dissects the contribution of microRNAs to EMT and analyzes the molecular basis for their roles in this cellular process. Here, we emphasize their interaction with core transcription factors like the zinc finger enhancer (E)-box binding homeobox (ZEB), Snail and Twist families as well as some pluripotency transcription factors.
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Affiliation(s)
- Mohammed L Abba
- Department of Experimental Surgery, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ruprecht Karl University of Heidelberg, Ludolf-Krehl-Str. 6, 68135 Mannheim, Germany.
| | - Nitin Patil
- Department of Experimental Surgery, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ruprecht Karl University of Heidelberg, Ludolf-Krehl-Str. 6, 68135 Mannheim, Germany.
| | - Jörg Hendrik Leupold
- Department of Experimental Surgery, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ruprecht Karl University of Heidelberg, Ludolf-Krehl-Str. 6, 68135 Mannheim, Germany.
| | - Heike Allgayer
- Department of Experimental Surgery, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ruprecht Karl University of Heidelberg, Ludolf-Krehl-Str. 6, 68135 Mannheim, Germany.
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