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Makarova J, Maltseva D, Tonevitsky A. Challenges in characterization of transcriptomes of extracellular vesicles and non-vesicular extracellular RNA carriers. Front Mol Biosci 2023; 10:1327985. [PMID: 38116380 PMCID: PMC10729812 DOI: 10.3389/fmolb.2023.1327985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
Since its original discovery over a decade ago, extracellular RNA (exRNA) has been found in all biological fluids. Furthermore, extracellular microRNA has been shown to be involved in communication between various cell types. Importantly, the exRNA is protected from RNases degradation by certain carriers including membrane vesicles and non-vesicular protein nanoparticles. Each type of carrier has its unique exRNA profile, which may vary depending on cell type and physiological conditions. To clarify putative mechanisms of intercellular communication mediated by exRNA, the RNA profile of each carrier has to be characterized. While current methods of biofluids fractionation are continuously improving, they fail to completely separate exRNA carriers. Likewise, most popular library preparation approaches for RNA sequencing do not allow obtaining exhaustive and unbiased data on exRNA transcriptome. In this mini review we discuss ongoing progress in the field of exRNA, with the focus on exRNA carriers, analyze the key methodological challenges and provide recommendations on how the latter could be overcome.
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Affiliation(s)
- Julia Makarova
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Diana Maltseva
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- Hertsen Moscow Oncology Research Center, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- Art Photonics GmbH, Berlin, Germany
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2
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Qin W, Wan Q, Yan J, Han X, Lu W, Ma Z, Ye T, Li Y, Li C, Wang C, Tay FR, Niu L, Jiao K. Effect of Extracellular Ribonucleic Acids on Neurovascularization in Osteoarthritis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301763. [PMID: 37395388 PMCID: PMC10502862 DOI: 10.1002/advs.202301763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/14/2023] [Indexed: 07/04/2023]
Abstract
Osteoarthritis is a degenerative disease characterized by abnormal neurovascularization at the osteochondral junctions, the regulatory mechanisms of which remain poorly understood. In the present study, a murine osteoarthritic model with augmented neurovascularization at the osteochondral junction is used to examine this under-evaluated facet of degenerative joint dysfunction. Increased extracellular RNA (exRNA) content is identified in neurovascularized osteoarthritic joints. It is found that the amount of exRNA is positively correlated with the extent of neurovascularization and the expression of vascular endothelial growth factor (VEGF). In vitro binding assay and molecular docking demonstrate that synthetic RNAs bind to VEGF via electrostatic interactions. The RNA-VEGF complex promotes the migration and function of endothelial progenitor cells and trigeminal ganglion cells. The use of VEGF and VEGFR2 inhibitors significantly inhibits the amplification of the RNA-VEGF complex. Disruption of the RNA-VEGF complex by RNase and polyethyleneimine reduces its in vitro activities, as well as prevents excessive neurovascularization and osteochondral deterioration in vivo. The results of the present study suggest that exRNAs may be potential targets for regulating nerve and blood vessel ingrowth under physiological and pathological joint conditions.
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Affiliation(s)
- Wen‐pin Qin
- Department of StomatologyTangdu hospitalThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Qian‐Qian Wan
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Jian‐Fei Yan
- Department of StomatologyTangdu hospitalThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Xiao‐Xiao Han
- Department of StomatologyTangdu hospitalThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Wei‐Cheng Lu
- Department of StomatologyTangdu hospitalThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Zhang‐Yu Ma
- Department of StomatologyTangdu hospitalThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Tao Ye
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Yu‐Tao Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Chang‐Jun Li
- Department of EndocrinologyEndocrinology Research CenterThe Xiangya Hospital of Central South UniversityChangshaHunan410008P. R. China
| | - Chen Wang
- Department of StomatologyThe Eighth Medical Center of PLA General HospitalHaidian DistrictBeijingP. R. China100091
| | - Franklin R. Tay
- Dental College of GeorgiaAugusta UniversityAugustaGA30912USA
| | - Li‐Na Niu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Kai Jiao
- Department of StomatologyTangdu hospitalThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
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3
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Chai P, Lebedenko CG, Flynn RA. RNA Crossing Membranes: Systems and Mechanisms Contextualizing Extracellular RNA and Cell Surface GlycoRNAs. Annu Rev Genomics Hum Genet 2023; 24:85-107. [PMID: 37068783 DOI: 10.1146/annurev-genom-101722-101224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
The subcellular localization of a biopolymer often informs its function. RNA is traditionally confined to the cytosolic and nuclear spaces, where it plays critical and conserved roles across nearly all biochemical processes. Our recent observation of cell surface glycoRNAs may further explain the extracellular role of RNA. While cellular membranes are efficient gatekeepers of charged polymers such as RNAs, a large body of research has demonstrated the accumulation of specific RNA species outside of the cell, termed extracellular RNAs (exRNAs). Across various species and forms of life, protein pores have evolved to transport RNA across membranes, thus providing a mechanistic path for exRNAs to achieve their extracellular topology. Here, we review types of exRNAs and the pores capable of RNA transport to provide a logical and testable path toward understanding the biogenesis and regulation of cell surface glycoRNAs.
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Affiliation(s)
- Peiyuan Chai
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Charlotta G Lebedenko
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
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4
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Bao ZD, Wan J, Zhu W, Shen JX, Yang Y, Zhou XY. Differentially Expressed Circulating Long-Noncoding RNAS in Premature Infants with Respiratory Distress Syndrome. Balkan J Med Genet 2023; 26:11-20. [PMID: 37576795 PMCID: PMC10413991 DOI: 10.2478/bjmg-2023-0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
Abstract
Purpose Recent studies have addressed the association between lung development and long-noncoding RNAs (lncRNAs). But few studies have investigated the role of lncRNAs in neonatal respiratory distress syndrome (RDS). Thus, this study aimed to compare the expression profile of circulating lncRNAs between RDS infants and controls. Methods 10 RDS infants and 5 controls were enrolled. RDS patients were further divided into mild and severe RDS subgroups. Blood samples were collected for the lncRNA expression profile. Subsequently, differentially expressed lncRNAs were screened out. Bioinformatics analysis was applied to establish a co-expression network of differential lncRNAs and mRNAs, and predict the underlying biological functions. Results A total of 135 differentially expressed lncRNAs were identified, including 108 upregulated and 27 downregulated lncRNAs (fold-change>2 and P<0.05) among the three groups (non-RDS, mild RDS and severe RDS groups). Of these lncRNAs, four were selected as showing higher fold changes and validated by qRT-PCR. ENST00000470527.1, ENST00000504497.1, ENST00000417781.5, and ENST00000440408.5 were increased not only in the plasma of total RDS patients but also in the severe RDS subgroup. Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses showed that differentially expressed lncRNAs may play important roles in RDS through regulating PI3KAkt, RAS, MAPK, and TGF-β signaling pathways. Conclusion The present results found that ENST00000470527.1, ENST00000504497.1, ENST00000417781.5, and ENST00000440408.5 may be invol ved in RDS. This could provide new insight into research of the potential pathophysiological mechanisms of preterm RDS.
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Affiliation(s)
- ZD Bao
- Department of Neonatology, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu210008, P.R. China
- Department of Neonatology, Jiangyin People’s Hospital of Nantong University, Jiangyin, Jiangsu214400, P.R. China
| | - J Wan
- Department of Neonatology, Jiangyin People’s Hospital of Nantong University, Jiangyin, Jiangsu214400, P.R. China
| | - W Zhu
- Department of Neonatology, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu210008, P.R. China
| | - JX Shen
- Department of Neonatology, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu210008, P.R. China
| | - Y Yang
- Department of Neonatology, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu210008, P.R. China
| | - XY Zhou
- Department of Neonatology, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu210008, P.R. China
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5
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Sharma H, Yadav V, D'Souza-Schorey C, Go DB, Senapati S, Chang HC. A Scalable High-Throughput Isoelectric Fractionation Platform for Extracellular Nanocarriers: Comprehensive and Bias-Free Isolation of Ribonucleoproteins from Plasma, Urine, and Saliva. ACS NANO 2023; 17:9388-9404. [PMID: 37071723 PMCID: PMC10756736 DOI: 10.1021/acsnano.3c01340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Extracellular nanocarriers (extracellular vesicles (EVs), lipoproteins, and ribonucleoproteins) of protein and nucleic acids mediate intercellular communication and are clinically adaptable as distinct circulating biomarkers. However, the overlapping size and density of the nanocarriers have so far prevented their efficient physical fractionation, thus impeding independent downstream molecular assays. Here, we report a bias-free high-throughput and high-yield continuous isoelectric fractionation nanocarrier fractionation technique based on their distinct isoelectric points. This nanocarrier fractionation platform is enabled by a robust and tunable linear pH profile provided by water-splitting at a bipolar membrane and stabilized by flow without ampholytes. The linear pH profile that allows easy tuning is a result of rapid equilibration of the water dissociation reaction and stabilization by flow. The platform is automated with a machine learning procedure to allow recalibration for different physiological fluids and nanocarriers. The optimized technique has a resolution of 0.3 ΔpI, sufficient to separate all nanocarriers and even subclasses of nanocarriers. Its performance is then evaluated with several biofluids, including plasma, urine, and saliva samples. Comprehensive, high-purity (plasma: >93%, urine: >95% and saliva: >97%), high-yield (plasma: >78%, urine: >87% and saliva: >96%), and probe-free isolation of ribonucleoproteins in 0.75 mL samples of various biofluids in 30 min is demonstrated, significantly outperforming affinity-based and highly biased gold standards having low yield and day-long protocols. Binary fractionation of EVs and different lipoproteins is also achieved with similar performance.
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Affiliation(s)
- Himani Sharma
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Vivek Yadav
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Crislyn D'Souza-Schorey
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - David B Go
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Satyajyoti Senapati
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
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López-Cepeda L, Castro JD, Aristizábal-Pachón AF, González-Giraldo Y, Pinzón A, Puentes-Rozo PJ, González J. Modulation of Small RNA Signatures by Astrocytes on Early Neurodegeneration Stages; Implications for Biomarker Discovery. Life (Basel) 2022; 12:1720. [PMID: 36362875 PMCID: PMC9696502 DOI: 10.3390/life12111720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/01/2022] [Accepted: 10/12/2022] [Indexed: 04/04/2024] Open
Abstract
Diagnosis of neurodegenerative disease (NDD) is complex, therefore simpler, less invasive, more accurate biomarkers are needed. small non-coding RNA (sncRNA) dysregulates in NDDs and sncRNA signatures have been explored for the diagnosis of NDDs, however, the performance of previous biomarkers is still better. Astrocyte dysfunction promotes neurodegeneration and thus derived scnRNA signatures could provide a more precise way to identify of changes related to NDD course and pathogenesis, and it could be useful for the dissection of mechanistic insights operating in NDD. Often sncRNA are transported outside the cell by the action of secreted particles such as extracellular vesicles (EV), which protect sncRNA from degradation. Furthermore, EV associated sncRNA can cross the BBB to be found in easier to obtain peripheral samples, EVs also inherit cell-specific surface markers that can be used for the identification of Astrocyte Derived Extracellular Vesicles (ADEVs) in a peripheral sample. By the study of the sncRNA transported in ADEVs it is possible to identify astrocyte specific sncRNA signatures that could show astrocyte dysfunction in a more simpler manner than previous methods. However, sncRNA signatures in ADEV are not a copy of intracellular transcriptome and methodological aspects such as the yield of sncRNA produced in ADEV or the variable amount of ADEV captured after separation protocols must be considered. Here we review the role as signaling molecules of ADEV derived sncRNA dysregulated in conditions associated with risk of neurodegeneration, providing an explanation of why to choose ADEV for the identification of astrocyte-specific transcriptome. Finally, we discuss possible limitations of this approach and the need to improve the detection limits of sncRNA for the use of ADEV derived sncRNA signatures.
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Affiliation(s)
- Leonardo López-Cepeda
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Juan David Castro
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | | | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Andrés Pinzón
- Laboratorio de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Pedro J. Puentes-Rozo
- Grupo de Neurociencias del Caribe, Unidad de Neurociencias Cognitivas, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Grupo de Neurociencias del Caribe, Universidad del Atlántico, Barranquilla 080007, Colombia
| | - Janneth González
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
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Ward Z, Schmeier S, Pearson J, Cameron VA, Frampton CM, Troughton RW, Doughty RN, Richards AM, Pilbrow AP. Identifying Candidate Circulating RNA Markers for Coronary Artery Disease by Deep RNA-Sequencing in Human Plasma. Cells 2022; 11:3191. [PMID: 36291058 PMCID: PMC9599983 DOI: 10.3390/cells11203191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2023] Open
Abstract
Advances in RNA sequencing (RNA-Seq) have facilitated transcriptomic analysis of plasma for the discovery of new diagnostic and prognostic markers for disease. We aimed to develop a short-read RNA-Seq protocol to detect mRNAs, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in plasma for the discovery of novel markers for coronary artery disease (CAD) and heart failure (HF). Circulating cell-free RNA from 59 patients with stable CAD (half of whom developed HF within 3 years) and 30 controls was sequenced to a median depth of 108 paired reads per sample. We identified fragments from 3986 messenger RNAs (mRNAs), 164 long non-coding RNAs (lncRNAs), 405 putative novel lncRNAs and 227 circular RNAs in plasma. Circulating levels of 160 mRNAs, 10 lncRNAs and 2 putative novel lncRNAs were altered in patients compared with controls (absolute fold change >1.2, p < 0.01 adjusted for multiple comparisons). The most differentially abundant transcripts were enriched in mRNAs encoded by the mitochondrial genome. We did not detect any differences in the plasma RNA profile between patients who developed HF compared with those who did not. In summary, we show that mRNAs, lncRNAs and circular RNAs can be reliably detected in plasma by deep RNA-Seq. Multiple coding and non-coding transcripts were altered in association with CAD, including several mitochondrial mRNAs, which may indicate underlying myocardial ischaemia and oxidative stress. If validated, circulating levels of these transcripts could potentially be used to help identify asymptomatic individuals with established CAD prior to an acute coronary event.
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Affiliation(s)
- Zoe Ward
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Sebastian Schmeier
- School of Natural and Computational Sciences, Massey University, Auckland 0632, New Zealand
- Evotec SE, Essener Bogen 7, 22419 Hamburg, Germany
| | - John Pearson
- Biostatistics and Computational Biology Unit, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Vicky A Cameron
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Chris M Frampton
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Richard W Troughton
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Rob N Doughty
- Heart Health Research Group, University of Auckland, Auckland 1023, New Zealand
| | - A. Mark Richards
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
- Cardiovascular Research Institute, National University of Singapore, Singapore 119228, Singapore
| | - Anna P Pilbrow
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
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Liu Z, Wang T, Yang X, Zhou Q, Zhu S, Zeng J, Chen H, Sun J, Li L, Xu J, Geng C, Xu X, Wang J, Yang H, Zhu S, Chen F, Wang WJ. Polyadenylation ligation-mediated sequencing (PALM-Seq) characterizes cell-free coding and non-coding RNAs in human biofluids. Clin Transl Med 2022; 12:e987. [PMID: 35858042 PMCID: PMC9299576 DOI: 10.1002/ctm2.987] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/16/2022] [Accepted: 07/03/2022] [Indexed: 11/16/2022] Open
Abstract
Background Cell‐free messenger RNA (cf‐mRNA) and long non‐coding RNA (cf‐lncRNA) are becoming increasingly important in liquid biopsy by providing biomarkers for disease prediction, diagnosis and prognosis, but the simultaneous characterization of coding and non‐coding RNAs in human biofluids remains challenging. Methods Here, we developed polyadenylation ligation‐mediated sequencing (PALM‐Seq), an RNA sequencing strategy employing treatment of RNA with T4 polynucleotide kinase to generate cell‐free RNA (cfRNA) fragments with 5′ phosphate and 3′ hydroxyl and RNase H to deplete abundant RNAs, achieving simultaneous quantification and characterization of cfRNAs. Results Using PALM‐Seq, we successfully identified well‐known differentially abundant mRNA, lncRNA and microRNA in the blood plasma of pregnant women. We further characterized cfRNAs in blood plasma, saliva, urine, seminal plasma and amniotic fluid and found that the detected numbers of different RNA biotypes varied with body fluids. The profiles of cf‐mRNA reflected the function of originated tissues, and immune cells significantly contributed RNA to blood plasma and saliva. Short fragments (<50 nt) of mRNA and lncRNA were major in biofluids, whereas seminal plasma and amniotic fluid tended to retain long RNA. Body fluids showed distinct preferences of pyrimidine at the 3′ end and adenine at the 5′ end of cf‐mRNA and cf‐lncRNA, which were correlated with the proportions of short fragments. Conclusion Together, PALM‐Seq enables a simultaneous characterization of cf‐mRNA and cf‐lncRNA, contributing to elucidating the biology and promoting the application of cfRNAs.
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Affiliation(s)
| | | | - Xi Yang
- BGI-Shenzhen, Shenzhen, China
| | | | - Sujun Zhu
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Juan Zeng
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | | | - Jinghua Sun
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | | | | | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
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9
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Differential expression of serum extracellular vesicle microRNAs and analysis of target-gene pathways in major depressive disorder. Biomark Neuropsychiatry 2022. [DOI: 10.1016/j.bionps.2022.100049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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10
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Almeida A, Gabriel M, Firlej V, Martin‐Jaular L, Lejars M, Cipolla R, Petit F, Vogt N, San‐Roman M, Dingli F, Loew D, Destouches D, Vacherot F, de la Taille A, Théry C, Morillon A. Urinary extracellular vesicles contain mature transcriptome enriched in circular and long noncoding RNAs with functional significance in prostate cancer. J Extracell Vesicles 2022; 11:e12210. [PMID: 35527349 PMCID: PMC9081490 DOI: 10.1002/jev2.12210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/22/2022] [Accepted: 03/15/2022] [Indexed: 12/14/2022] Open
Abstract
Long noncoding (lnc)RNAs modulate gene expression alongside presenting unexpected source of neoantigens. Despite their immense interest, their ability to be transferred and control adjacent cells is unknown. Extracellular Vesicles (EVs) offer a protective environment for nucleic acids, with pro and antitumourigenic functions by controlling the immune response. In contrast to extracellular nonvesicular RNA, few studies have addressed the full RNA content within human fluids' EVs and have compared them with their tissue of origin. Here, we performed Total RNA-Sequencing on six Formalin-Fixed-Paraffin-Embedded (FFPE) prostate cancer (PCa) tumour tissues and their paired urinary (u)EVs to provide the first whole transcriptome comparison from the same patients. UEVs contain simplified transcriptome with intron-free cytoplasmic transcripts and enriched lnc/circular (circ)RNAs, strikingly common to an independent 20 patients' urinary cohort. Our full cellular and EVs transcriptome comparison within three PCa cell lines identified a set of overlapping 14 uEV-circRNAs characterized as essential for prostate cell proliferation in vitro and 28 uEV-lncRNAs belonging to the cancer-related lncRNA census (CLC2). In addition, we found 15 uEV-lncRNAs, predicted to encode 768 high-affinity neoantigens, and for which three of the encoded-ORF produced detectable unmodified peptides by mass spectrometry. Our dual analysis of EVs-lnc/circRNAs both in urines' and in vitro's EVs provides a fundamental resource for future uEV-lnc/circRNAs phenotypic characterization involved in PCa.
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Affiliation(s)
- Anna Almeida
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
- Departement de Recherche TranslationnellePSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Marc Gabriel
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Virginie Firlej
- AP‐HPHôpital H. MondorPlateforme de Ressources BiologiquesCréteilFrance
- Univ Paris Est CreteilUR TRePCaCréteilFrance
| | - Lorena Martin‐Jaular
- INSERM U932PSL UniversityInstitut Curie, Centre de RechercheParisFrance
- Curie Core Tech Extracellular VesiclesInstitut Curie, Centre de RechercheParisFrance
| | - Matthieu Lejars
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Rocco Cipolla
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Floriane Petit
- Tumour BiologyINSERM U820, Sorbonne Université, PSL University, Institut CurieCentre de RechercheParisFrance
| | - Nicolas Vogt
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Mabel San‐Roman
- CNRS UMR3215, Sorbonne Université, PSL University, Institut CurieCentre de RechercheParisFrance
| | - Florent Dingli
- Laboratoire de Spectrométrie de Masse ProtéomiquePSL Research University, Institut Curie Centre de RechercheParisFrance
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse ProtéomiquePSL Research University, Institut Curie Centre de RechercheParisFrance
| | | | | | | | - Clotilde Théry
- INSERM U932PSL UniversityInstitut Curie, Centre de RechercheParisFrance
- Curie Core Tech Extracellular VesiclesInstitut Curie, Centre de RechercheParisFrance
| | - Antonin Morillon
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
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11
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Zhao Y, Liu P, Tan H, Chen X, Wang Q, Chen T. Exosomes as Smart Nanoplatforms for Diagnosis and Therapy of Cancer. Front Oncol 2021; 11:743189. [PMID: 34513718 PMCID: PMC8427309 DOI: 10.3389/fonc.2021.743189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/09/2021] [Indexed: 12/17/2022] Open
Abstract
Exosomes are composed of a lipid bilayer membrane, containing proteins, nucleic acids, DNA, RNA, etc., derived from donor cells. They have a size range of approximately 30-150 nm. The intrinsic characteristics of exosomes, including efficient cellular uptake, low immunogenicity, low toxicity, intrinsic ability to traverse biological barriers, and inherent targeting ability, facilitate their application to the drug delivery system. Here, we review the generation, uptake, separation, and purification methods of exosomes, focusing on their application as carriers in tumor diagnosis and treatment, especially in brain tumors, as well as the patent applications of exosomes in recent years.
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Affiliation(s)
- Yuying Zhao
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Mammary Disease, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Piaoxue Liu
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hanxu Tan
- School of Fundamental Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaojia Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Qi Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Tongkai Chen
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
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12
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Otsuka K, Ochiya T. Possible connection between diet and microRNA in cancer scenario. Semin Cancer Biol 2021; 73:4-18. [DOI: 10.1016/j.semcancer.2020.11.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/30/2020] [Accepted: 11/16/2020] [Indexed: 02/06/2023]
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13
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Veerman RE, Teeuwen L, Czarnewski P, Güclüler Akpinar G, Sandberg A, Cao X, Pernemalm M, Orre LM, Gabrielsson S, Eldh M. Molecular evaluation of five different isolation methods for extracellular vesicles reveals different clinical applicability and subcellular origin. J Extracell Vesicles 2021; 10:e12128. [PMID: 34322205 PMCID: PMC8298890 DOI: 10.1002/jev2.12128] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/21/2021] [Accepted: 07/13/2021] [Indexed: 12/14/2022] Open
Abstract
Extracellular vesicles (EVs) are increasingly tested as therapeutic vehicles and biomarkers, but still EV subtypes are not fully characterised. To isolate EVs with few co-isolated entities, a combination of methods is needed. However, this is time-consuming and requires large sample volumes, often not feasible in most clinical studies or in studies where small sample volumes are available. Therefore, we compared EVs rendered by five commonly used methods based on different principles from conditioned cell medium and 250 μl or 3 ml plasma, that is, precipitation (ExoQuick ULTRA), membrane affinity (exoEasy Maxi Kit), size-exclusion chromatography (qEVoriginal), iodixanol gradient (OptiPrep), and phosphatidylserine affinity (MagCapture). EVs were characterised by electron microscopy, Nanoparticle Tracking Analysis, Bioanalyzer, flow cytometry, and LC-MS/MS. The different methods yielded samples of different morphology, particle size, and proteomic profile. For the conditioned medium, Izon 35 isolated the highest number of EV proteins followed by exoEasy, which also isolated fewer non-EV proteins. For the plasma samples, exoEasy isolated a high number of EV proteins and few non-EV proteins, while Izon 70 isolated the most EV proteins. We conclude that no method is perfect for all studies, rather, different methods are suited depending on sample type and interest in EV subtype, in addition to sample volume and budget.
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Affiliation(s)
- Rosanne E. Veerman
- Department of Clinical Immunology and Transfusion Medicine and Division of Immunology and Allergy, Department of Medicine SolnaKarolinska University Hospital and Karolinska InstitutetStockholmSweden
| | - Loes Teeuwen
- Department of Clinical Immunology and Transfusion Medicine and Division of Immunology and Allergy, Department of Medicine SolnaKarolinska University Hospital and Karolinska InstitutetStockholmSweden
| | - Paulo Czarnewski
- Science for Life LaboratoryDepartment of Biochemistry and BiophysicsNational Bioinformatics Infrastructure SwedenStockholm UniversitySolnaSweden
| | - Gözde Güclüler Akpinar
- Department of Clinical Immunology and Transfusion Medicine and Division of Immunology and Allergy, Department of Medicine SolnaKarolinska University Hospital and Karolinska InstitutetStockholmSweden
| | - AnnSofi Sandberg
- Department of Oncology and PathologyKarolinska InstitutetScience for Life LaboratorySolnaSweden
| | - Xiaofang Cao
- Department of Oncology and PathologyKarolinska InstitutetScience for Life LaboratorySolnaSweden
| | - Maria Pernemalm
- Department of Oncology and PathologyKarolinska InstitutetScience for Life LaboratorySolnaSweden
| | - Lukas M. Orre
- Department of Oncology and PathologyKarolinska InstitutetScience for Life LaboratorySolnaSweden
| | - Susanne Gabrielsson
- Department of Clinical Immunology and Transfusion Medicine and Division of Immunology and Allergy, Department of Medicine SolnaKarolinska University Hospital and Karolinska InstitutetStockholmSweden
| | - Maria Eldh
- Department of Clinical Immunology and Transfusion Medicine and Division of Immunology and Allergy, Department of Medicine SolnaKarolinska University Hospital and Karolinska InstitutetStockholmSweden
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14
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Han X, Li T, Fan Y, Wang X, Gu W, Lu W, Yin Y, Meng Q, Zhang W, Zhao J, Zhang F, Fu Y. Screening of 20 Mycobacterium tuberculosis sRNAs in plasma for detection of active pulmonary tuberculosis. Tuberculosis (Edinb) 2021; 129:102086. [PMID: 34051642 DOI: 10.1016/j.tube.2021.102086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/24/2021] [Accepted: 05/04/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND Mycobacterium tuberculosis (MTB) sRNAs are abundant. However, the level of MTB sRNA in peripheral blood remains elusive. METHODS Twenty MTB sRNAs annotated in the reference genome of H37Rv were detected in the plasma of 170 active pulmonary tuberculosis patients and 124 healthy people by qRT-PCR detection system. The differential expression of sRNAs were analyzed in two groups. The value of sRNAs for diagnosis of active tuberculosis were evaluated by ROC curve analysis. RESULTS Eight of the 20 sRNAs (MTS2823, MTS0997, MTS1338, ASdes, G2, C8, mcr15 and MTS1082) were found in at least 50% of the samples detected. The relative expression levels of MTS2823, MTS0997, MTS1338 and ASdes in plasma of tuberculosis patients were statistically higher than those in healthy controls. ROC curve analysis showed that the AUC of MTS0997, MTS1338, MTS2823 and ASdes were 0.8935 (95% CI 0.8109-0.9760), 0.8722 (95% CI 0.7862-0.9581), 0.8208 (95% CI 0.7246-0.9170) and 0.5792 (95% CI 0.4240-0.7344), respectively. The AUC value of combination of MTS0997, MTS1338 and MTS2823 was 0.914 (95% CI 0.8281-0.9926). CONCLUSIONS MTB sRNAs MTS2823, MTS0997 and MTS1338 have the potential to be plasma biomarkers for active pulmonary tuberculosis.
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Affiliation(s)
- Xue Han
- Wu Lien-Teh Institute, Department of Microbiology, Harbin Medical University, 194, Xuefu Road, Nangang District, Harbin, 150081, China.
| | - Ting Li
- Wu Lien-Teh Institute, Department of Microbiology, Harbin Medical University, 194, Xuefu Road, Nangang District, Harbin, 150081, China.
| | - Yunfan Fan
- Wu Lien-Teh Institute, Department of Microbiology, Harbin Medical University, 194, Xuefu Road, Nangang District, Harbin, 150081, China.
| | - Xinyang Wang
- Wu Lien-Teh Institute, Department of Microbiology, Harbin Medical University, 194, Xuefu Road, Nangang District, Harbin, 150081, China.
| | - Wei Gu
- Wu Lien-Teh Institute, Department of Microbiology, Harbin Medical University, 194, Xuefu Road, Nangang District, Harbin, 150081, China.
| | - Weinan Lu
- Wu Lien-Teh Institute, Department of Microbiology, Harbin Medical University, 194, Xuefu Road, Nangang District, Harbin, 150081, China.
| | - Yian Yin
- Wu Lien-Teh Institute, Department of Microbiology, Harbin Medical University, 194, Xuefu Road, Nangang District, Harbin, 150081, China.
| | - Qingtai Meng
- Wu Lien-Teh Institute, Department of Microbiology, Harbin Medical University, 194, Xuefu Road, Nangang District, Harbin, 150081, China.
| | - Wenli Zhang
- Wu Lien-Teh Institute, Department of Microbiology, Harbin Medical University, 194, Xuefu Road, Nangang District, Harbin, 150081, China.
| | - Jizi Zhao
- Wu Lien-Teh Institute, Department of Microbiology, Harbin Medical University, 194, Xuefu Road, Nangang District, Harbin, 150081, China.
| | - Fengmin Zhang
- Wu Lien-Teh Institute, Department of Microbiology, Harbin Medical University, 194, Xuefu Road, Nangang District, Harbin, 150081, China; Heilongjiang Provincial Key Laboratory of Infection and Immunity, Pathogen Biology, Harbin, China.
| | - Yingmei Fu
- Wu Lien-Teh Institute, Department of Microbiology, Harbin Medical University, 194, Xuefu Road, Nangang District, Harbin, 150081, China; Heilongjiang Provincial Key Laboratory of Infection and Immunity, Pathogen Biology, Harbin, China.
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15
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Neuberger EWI, Hillen B, Mayr K, Simon P, Krämer-Albers EM, Brahmer A. Kinetics and Topology of DNA Associated with Circulating Extracellular Vesicles Released during Exercise. Genes (Basel) 2021; 12:522. [PMID: 33918465 PMCID: PMC8065814 DOI: 10.3390/genes12040522] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 12/22/2022] Open
Abstract
Although it is widely accepted that cancer-derived extracellular vesicles (EVs) carry DNA cargo, the association of cell-free circulating DNA (cfDNA) and EVs in plasma of healthy humans remains elusive. Using a physiological exercise model, where EVs and cfDNA are synchronously released, we aimed to characterize the kinetics and localization of DNA associated with EVs. EVs were separated from human plasma using size exclusion chromatography or immuno-affinity capture for CD9+, CD63+, and CD81+ EVs. DNA was quantified with an ultra-sensitive qPCR assay targeting repetitive LINE elements, with or without DNase digestion. This model shows that a minute part of circulating cell-free DNA is associated with EVs. During rest and following exercise, only 0.12% of the total cfDNA occurs in association with CD9+/CD63+/CD81+EVs. DNase digestion experiments indicate that the largest part of EV associated DNA is sensitive to DNase digestion and only ~20% are protected within the lumen of the separated EVs. A single bout of running or cycling exercise increases the levels of EVs, cfDNA, and EV-associated DNA. While EV surface DNA is increasing, DNAse-resistant DNA remains at resting levels, indicating that EVs released during exercise (ExerVs) do not contain DNA. Consequently, DNA is largely associated with the outer surface of circulating EVs. ExerVs recruit cfDNA to their corona, but do not carry DNA in their lumen.
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Affiliation(s)
- Elmo W. I. Neuberger
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (B.H.); (P.S.)
| | - Barlo Hillen
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (B.H.); (P.S.)
| | - Katharina Mayr
- Institute of Developmental Biology and Neurobiology, Extracellular Vesicles Research Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (K.M.); (E.-M.K.-A.)
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (B.H.); (P.S.)
| | - Eva-Maria Krämer-Albers
- Institute of Developmental Biology and Neurobiology, Extracellular Vesicles Research Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (K.M.); (E.-M.K.-A.)
| | - Alexandra Brahmer
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (B.H.); (P.S.)
- Institute of Developmental Biology and Neurobiology, Extracellular Vesicles Research Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (K.M.); (E.-M.K.-A.)
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16
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Abstract
The discovery that all cells secrete extracellular vesicles (EVs) to shuttle proteins and nucleic acids to recipient cells suggested they play an important role in intercellular communication. EVs are widely distributed in many body fluids, including blood, cerebrospinal fluid, urine and saliva. Exosomes are nano-sized EVs of endosomal origin that regulate many pathophysiological processes including immune responses, inflammation, tumour growth, and infection. Healthy individuals release exosomes with a cargo of different RNA, DNA, and protein contents into the circulation, which can be measured non-invasively as biomarkers of healthy and diseased states. Cancer-derived exosomes carry a unique set of DNA, RNA, protein and lipid reflecting the stage of tumour progression, and may serve as diagnostic and prognostic biomarkers for various cancers. However, many gaps in knowledge and technical challenges in EVs and extracellular RNA (exRNA) biology, such as mechanisms of EV biogenesis and uptake, exRNA cargo selection, and exRNA detection remain. The NIH Common Fund-supported exRNA Communication Consortium was launched in 2013 to address major scientific challenges in this field. This review focuses on scientific highlights in biomarker discovery of exosome-based exRNA in cancer and its possible clinical application as cancer biomarkers.
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Affiliation(s)
- Christine Happel
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aniruddha Ganguly
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute at the National Institutes of Health, Bethesda, MD 20892, USA
| | - Danilo A Tagle
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
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17
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Almiñana C, Rudolf Vegas A, Tekin M, Hassan M, Uzbekov R, Fröhlich T, Bollwein H, Bauersachs S. Isolation and Characterization of Equine Uterine Extracellular Vesicles: A Comparative Methodological Study. Int J Mol Sci 2021; 22:ijms22020979. [PMID: 33478136 PMCID: PMC7835857 DOI: 10.3390/ijms22020979] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 12/14/2022] Open
Abstract
Extracellular vesicles (EVs) have been identified in the uterine fluid in different species and have been pointed as key players in the embryo-maternal dialogue, maternal recognition of pregnancy and establishment of pregnancy. However, little is known about the uterine EVs in the mare. Therefore, the present study aimed at characterizing EVs from uterine lavage of cyclic mares by comparing five EVs isolation methods and the combination of them: (1) ultracentrifugation (UC); (2) concentration of lavage volume by Centricon ultrafiltration (CE); (3) the use of CE with different washing steps (phosphate-buffered saline with or without trehalose); (4) size-exclusion chromatography with iZON-qEV columns, and (5) a combination of the methods with best results based on EVs yield, purity, and protein cargo profiles. Transmission electron microscopy and Western blotting confirmed the isolation of EVs by all methods but with quantitative and qualitative differences. Mass spectrometry provided differences in protein profiles between methods, number of identified proteins, and protein classes. Our results indicate that the combination of CE/trehalose/iZON/UC is an optimal method to isolate equine uterine EVs with good yield and purity that can be applied in future studies to determine the role of equine uterine EVs in embryo-maternal interactions.
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Affiliation(s)
- Carmen Almiñana
- Functional Genomics Group, Institute of Veterinary Anatomy, Vetsuisse Faculty Zurich, University of Zurich, 8315 Lindau, Switzerland; (A.R.V.); (S.B.)
- UMR85 PRC, INRAE, CNRS 7247, Université de Tours, IFCE, 37380 Nouzilly, France
- Correspondence:
| | - Alba Rudolf Vegas
- Functional Genomics Group, Institute of Veterinary Anatomy, Vetsuisse Faculty Zurich, University of Zurich, 8315 Lindau, Switzerland; (A.R.V.); (S.B.)
- Clinic of Reproductive Medicine, Department for Farm Animals, Vetsuisse-Faculty, University of Zurich, 8057 Zurich, Switzerland; (M.T.); (M.H.); (H.B.)
| | - Muhittin Tekin
- Clinic of Reproductive Medicine, Department for Farm Animals, Vetsuisse-Faculty, University of Zurich, 8057 Zurich, Switzerland; (M.T.); (M.H.); (H.B.)
| | - Mubbashar Hassan
- Clinic of Reproductive Medicine, Department for Farm Animals, Vetsuisse-Faculty, University of Zurich, 8057 Zurich, Switzerland; (M.T.); (M.H.); (H.B.)
| | - Rustem Uzbekov
- Laboratoire Biologie Cellulaire et Microscopie Electronique, Faculté de Médecine, Université de Tours, 37032 Tours, France;
- Faculty of Bioengineering and Bioinformatics, Moscow State University, 119992 Moscow, Russia
| | - Thomas Fröhlich
- Gene Center, Laboratory for Functional Genome Analysis, LMU Munich, 81377 Munich, Germany;
| | - Heinrich Bollwein
- Clinic of Reproductive Medicine, Department for Farm Animals, Vetsuisse-Faculty, University of Zurich, 8057 Zurich, Switzerland; (M.T.); (M.H.); (H.B.)
| | - Stefan Bauersachs
- Functional Genomics Group, Institute of Veterinary Anatomy, Vetsuisse Faculty Zurich, University of Zurich, 8315 Lindau, Switzerland; (A.R.V.); (S.B.)
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18
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Heiss M, Hagelskamp F, Marchand V, Motorin Y, Kellner S. Cell culture NAIL-MS allows insight into human tRNA and rRNA modification dynamics in vivo. Nat Commun 2021; 12:389. [PMID: 33452242 PMCID: PMC7810713 DOI: 10.1038/s41467-020-20576-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 12/04/2020] [Indexed: 12/16/2022] Open
Abstract
Recently, studies about RNA modification dynamics in human RNAs are among the most controversially discussed. As a main reason, we identified the unavailability of a technique which allows the investigation of the temporal processing of RNA transcripts. Here, we present nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS) for efficient, monoisotopic stable isotope labeling in both RNA and DNA in standard cell culture. We design pulse chase experiments and study the temporal placement of modified nucleosides in tRNAPhe and 18S rRNA. In existing RNAs, we observe a time-dependent constant loss of modified nucleosides which is masked by post-transcriptional methylation mechanisms and thus undetectable without NAIL-MS. During alkylation stress, NAIL-MS reveals an adaptation of tRNA modifications in new transcripts but not existing ones. Overall, we present a fast and reliable stable isotope labeling strategy which allows in-depth study of RNA modification dynamics in human cell culture.
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Affiliation(s)
- Matthias Heiss
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Felix Hagelskamp
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Virginie Marchand
- Université de Lorraine, CNRS, Inserm, UMS2008/US40 IBSLor and UMR7365 IMoPA, F-54000, Nancy, France
| | - Yuri Motorin
- Université de Lorraine, CNRS, Inserm, UMS2008/US40 IBSLor and UMR7365 IMoPA, F-54000, Nancy, France
| | - Stefanie Kellner
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str, 9, 60438, Frankfurt, Germany.
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19
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Marchand V, Galvanin A, Motorin Y. Isolation, Extraction and Deep-Sequencing Analysis of Extracellular RNAs (exRNAs) from Human Plasma. Methods Mol Biol 2021; 2300:165-182. [PMID: 33792880 DOI: 10.1007/978-1-0716-1386-3_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Extracellular RNAs (exRNAs) are secreted by nearly all cell types and are now known to play multiple physiological roles. Human plasma, a readily available sample for biomedical analysis, was reported to contain various subpopulations of exRNA, some of which are most likely components of plasma ribonucleoproteins (RNPs), while others are encapsulated into extracellular vesicles (EVs) of different size, origin, and composition. Unbiased analysis of exRNA composition can be performed with prefractionation of plasma exRNA followed by library preparation, sequencing, and bioinformatics analysis. In addition to "mature," adaptor ligation-competent RNA species (5'-P/3'-OH), human plasma contains a substantial proportion of degraded RNA fragments, featuring 5'-OH/3'-P or cyclophosphate extremities, which can be made competent for ligation using appropriate treatment. Polyethylene glycol (PEG)-based precipitation kits for EV isolation yield a fraction that is highly contaminated by large RNPs and EV-associated RNAs. Purer EV preparations are obtained by using Proteinase K and RNase A treatment, as well as by size-exclusion chromatography (SEC).
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Affiliation(s)
- Virginie Marchand
- Université de Lorraine, CNRS, INSERM, IBSLOR, F-54000 Nancy, France.
| | | | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, IBSLOR, F-54000 Nancy, France.,Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
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20
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Extracellular RNAs in Bacterial Infections: From Emerging Key Players on Host-Pathogen Interactions to Exploitable Biomarkers and Therapeutic Targets. Int J Mol Sci 2020; 21:ijms21249634. [PMID: 33348812 PMCID: PMC7766527 DOI: 10.3390/ijms21249634] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/04/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are key regulators of post-transcriptional gene expression in prokaryotic and eukaryotic organisms. These molecules can interact with mRNAs or proteins, affecting a variety of cellular functions. Emerging evidence shows that intra/inter-species and trans-kingdom regulation can also be achieved with exogenous RNAs, which are exported to the extracellular medium, mainly through vesicles. In bacteria, membrane vesicles (MVs) seem to be the more common way of extracellular communication. In several bacterial pathogens, MVs have been described as a delivery system of ncRNAs that upon entry into the host cell, regulate their immune response. The aim of the present work is to review this recently described mode of host-pathogen communication and to foster further research on this topic envisaging their exploitation in the design of novel therapeutic and diagnostic strategies to fight bacterial infections.
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21
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Veziroglu EM, Mias GI. Characterizing Extracellular Vesicles and Their Diverse RNA Contents. Front Genet 2020; 11:700. [PMID: 32765582 PMCID: PMC7379748 DOI: 10.3389/fgene.2020.00700] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/09/2020] [Indexed: 12/15/2022] Open
Abstract
Cells release nanometer-scale, lipid bilayer-enclosed biomolecular packages (extracellular vesicles; EVs) into their surrounding environment. EVs are hypothesized to be intercellular communication agents that regulate physiological states by transporting biomolecules between near and distant cells. The research community has consistently advocated for the importance of RNA contents in EVs by demonstrating that: (1) EV-related RNA contents can be detected in a liquid biopsy, (2) disease states significantly alter EV-related RNA contents, and (3) sensitive and specific liquid biopsies can be implemented in precision medicine settings by measuring EV-derived RNA contents. Furthermore, EVs have medical potential beyond diagnostics. Both natural and engineered EVs are being investigated for therapeutic applications such as regenerative medicine and as drug delivery agents. This review focuses specifically on EV characterization, analysis of their RNA content, and their functional implications. The NIH extracellular RNA communication (ERC) program has catapulted human EV research from an RNA profiling standpoint by standardizing the pipeline for working with EV transcriptomics data, and creating a centralized database for the scientific community. There are currently thousands of RNA-sequencing profiles hosted on the Extracellular RNA Atlas alone (Murillo et al., 2019), encompassing a variety of human biofluid types and health conditions. While a number of significant discoveries have been made through these studies individually, integrative analyses of these data have thus far been limited. A primary focus of the ERC program over the next five years is to bring higher resolution tools to the EV research community so that investigators can isolate and analyze EV sub-populations, and ultimately single EVs sourced from discrete cell types, tissues, and complex biofluids. Higher resolution techniques will be essential for evaluating the roles of circulating EVs at a level which impacts clinical decision making. We expect that advances in microfluidic technologies will drive near-term innovation and discoveries about the diverse RNA contents of EVs. Long-term translation of EV-based RNA profiling into a mainstay medical diagnostic tool will depend upon identifying robust patterns of circulating genetic material that correlate with a change in health status.
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Affiliation(s)
- Eren M. Veziroglu
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States
| | - George I. Mias
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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22
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Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles. Sci Rep 2019; 9:17574. [PMID: 31772251 PMCID: PMC6879519 DOI: 10.1038/s41598-019-53892-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/06/2019] [Indexed: 12/16/2022] Open
Abstract
RNA profiling has emerged as a powerful tool to investigate the biomarker potential of human biofluids. However, despite enormous interest in extracellular nucleic acids, RNA sequencing methods to quantify the total RNA content outside cells are rare. Here, we evaluate the performance of the SMARTer Stranded Total RNA-Seq method in human platelet-rich plasma, platelet-free plasma, urine, conditioned medium, and extracellular vesicles (EVs) from these biofluids. We found the method to be accurate, precise, compatible with low-input volumes and able to quantify a few thousand genes. We picked up distinct classes of RNA molecules, including mRNA, lncRNA, circRNA, miscRNA and pseudogenes. Notably, the read distribution and gene content drastically differ among biofluids. In conclusion, we are the first to show that the SMARTer method can be used for unbiased unraveling of the complete transcriptome of a wide range of biofluids and their extracellular vesicles.
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