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Bhavsar V, Sahu A, Taware R. Stress-induced extracellular vesicles: insight into their altered proteomic composition and probable physiological role in cancer. Mol Cell Biochem 2024:10.1007/s11010-024-05121-x. [PMID: 39302488 DOI: 10.1007/s11010-024-05121-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 09/09/2024] [Indexed: 09/22/2024]
Abstract
EVs (extracellular vesicles) are phospholipid bilayer vesicles that can be released by both prokaryotic and eukaryotic cells in normal as well as altered physiological conditions. These vesicles also termed as signalosomes, possess a distinctive cargo comprising nucleic acids, proteins, lipids, and metabolites, enabling them to play a pivotal role in both local and long-distance intercellular communication. The composition, origin, and release of EVs can be influenced by different physiological conditions and a variety of stress factors, consequently affecting the contents carried within these vesicles. Therefore, identifying the modified contents of EVs can provide valuable insights into their functional role in stress-triggered communication. Particularly, this is important when EVs released from tumor microenvironment are investigated for their role in the development and dissemination of cancer. This review article emphasizes the importance of differential EV shedding and altered proteomic content in response to reduced oxygen concentration, altered levels of glucose and glutamine, pH variations, oxidative stress and Ca2+ ion concertation and it is subsequent effects on the behavior of recipient cells.
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Affiliation(s)
- Vaidehi Bhavsar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Ahmedabad, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Ashish Sahu
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Ahmedabad, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Ravindra Taware
- Department of Natural Products, National Institute of Pharmaceutical Education and Research-Ahmedabad, Palaj, Gandhinagar, Gujarat, 382355, India.
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2
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Ong JLK, Jalaludin NFF, Wong MK, Tan SH, Angelina C, Sukhatme SA, Yeo T, Lim CT, Lee YT, Soh SY, Lim TKH, Tay TKY, Chang KTE, Chen ZX, Loh AH. Exosomal mRNA Cargo are biomarkers of tumor and immune cell populations in pediatric osteosarcoma. Transl Oncol 2024; 46:102008. [PMID: 38852279 PMCID: PMC11220529 DOI: 10.1016/j.tranon.2024.102008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/04/2024] [Accepted: 05/22/2024] [Indexed: 06/11/2024] Open
Abstract
Osteosarcoma is the commonest malignant bone tumor of children and adolescents and is characterized by a high risk of recurrence despite multimodal therapy, especially in metastatic disease. This suggests the presence of clinically undetected cancer cells that persist, leading to cancer recurrence. We sought to evaluate the utility of peripheral blood exosomes as a more sensitive yet minimally invasive blood test that could aid in evaluating treatment response and surveillance for potential disease recurrence. We extracted exosomes from the blood of pediatric osteosarcoma patients at diagnosis (n=7) and after neoadjuvant chemotherapy (n=5 subset), as well as from age-matched cancer-free controls (n=3). We also obtained matched tumor biopsy samples (n=7) from the cases. Exosome isolation was verified by CD9 immunoblot and characterized on electron microscopy. Profiles of 780 cancer-related transcripts were analysed in mRNA from exosomes of osteosarcoma patients at diagnosis and control patients, matched post-chemotherapy samples, and matched primary tumor samples. Peripheral blood exosomes of osteosarcoma patients at diagnosis were significantly smaller than those of controls and overexpressed extracellular matrix protein gene THBS1 and B cell markers MS4A1 and TCL1A. Immunohistochemical staining of corresponding tumor samples verified the expression of THBS1 on tumor cells and osteoid matrix, and its persistence in a treatment-refractory patient, as well as the B cell origin of the latter. These hold potential as liquid biopsy biomarkers of disease burden and host immune response in osteosarcoma. Our findings suggest that exosomes may provide novel and clinically-important insights into the pathophysiology of cancers such as osteosarcoma.
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Affiliation(s)
| | | | - Meng Kang Wong
- VIVA-KKH Paediatric Brain and Solid Tumor Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore
| | - Sheng Hui Tan
- VIVA-KKH Paediatric Brain and Solid Tumor Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore
| | - Clara Angelina
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sarvesh A Sukhatme
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Trifanny Yeo
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore; Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore; Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore
| | - Chwee Teck Lim
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore; Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore; Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore
| | - York Tien Lee
- Duke NUS Medical School, Singapore, Singapore; VIVA-KKH Paediatric Brain and Solid Tumor Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore; Department of Paediatric Surgery, KK Women's and Children's Hospital, Singapore, Singapore
| | - Shui Yen Soh
- Duke NUS Medical School, Singapore, Singapore; VIVA-KKH Paediatric Brain and Solid Tumor Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore; Department of Paediatric Subspecialties Haematology/Oncology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Tony K H Lim
- Duke NUS Medical School, Singapore, Singapore; Department of Anatomic Pathology, Singapore General Hospital, Singapore, Singapore
| | - Timothy Kwang Yong Tay
- Duke NUS Medical School, Singapore, Singapore; Department of Anatomic Pathology, Singapore General Hospital, Singapore, Singapore
| | - Kenneth Tou En Chang
- Duke NUS Medical School, Singapore, Singapore; VIVA-KKH Paediatric Brain and Solid Tumor Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore; Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, Singapore
| | - Zhi Xiong Chen
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; VIVA-KKH Paediatric Brain and Solid Tumor Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore; National University Cancer Institute, National University Health System, Singapore, Singapore; NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Amos Hp Loh
- Duke NUS Medical School, Singapore, Singapore; VIVA-KKH Paediatric Brain and Solid Tumor Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore; Department of Paediatric Surgery, KK Women's and Children's Hospital, Singapore, Singapore.
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Chabronova A, Holmes TL, Hoang DM, Denning C, James V, Smith JGW, Peffers MJ. SnoRNAs in cardiovascular development, function, and disease. Trends Mol Med 2024; 30:562-578. [PMID: 38523014 DOI: 10.1016/j.molmed.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
Small nucleolar RNAs (snoRNAs) are emerging as important regulators of cardiovascular (patho)biology. Several roles of snoRNAs have recently been identified in heart development and congenital heart diseases, as well as their dynamic regulation in hypertrophic and dilated cardiomyopathies, coronary heart disease (CHD), myocardial infarction (MI), cardiac fibrosis, and heart failure. Furthermore, reports of changes in vesicular snoRNA expression and altered levels of circulating snoRNAs in response to cardiac stress suggest that snoRNAs also function in cardiac signaling and intercellular communication. In this review, we summarize and discuss key findings and outline the clinical potential of snoRNAs considering current challenges and gaps in the field of cardiovascular diseases (CVDs).
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Affiliation(s)
- Alzbeta Chabronova
- Department of Musculoskeletal Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, L7 8TX, UK.
| | - Terri L Holmes
- Centre for Metabolic Health, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Duc M Hoang
- Department of Stem Cell Biology, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Chris Denning
- Department of Stem Cell Biology, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Victoria James
- School of Veterinary Medicine and Science, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - James G W Smith
- Centre for Metabolic Health, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Mandy J Peffers
- Department of Musculoskeletal Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, L7 8TX, UK
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Zirak B, Naghipourfar M, Saberi A, Pouyabahar D, Zarezadeh A, Luo L, Fish L, Huh D, Navickas A, Sharifi-Zarchi A, Goodarzi H. Revealing the grammar of small RNA secretion using interpretable machine learning. CELL GENOMICS 2024; 4:100522. [PMID: 38460515 PMCID: PMC11019361 DOI: 10.1016/j.xgen.2024.100522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 11/02/2023] [Accepted: 02/12/2024] [Indexed: 03/11/2024]
Abstract
Small non-coding RNAs can be secreted through a variety of mechanisms, including exosomal sorting, in small extracellular vesicles, and within lipoprotein complexes. However, the mechanisms that govern their sorting and secretion are not well understood. Here, we present ExoGRU, a machine learning model that predicts small RNA secretion probabilities from primary RNA sequences. We experimentally validated the performance of this model through ExoGRU-guided mutagenesis and synthetic RNA sequence analysis. Additionally, we used ExoGRU to reveal cis and trans factors that underlie small RNA secretion, including known and novel RNA-binding proteins (RBPs), e.g., YBX1, HNRNPA2B1, and RBM24. We also developed a novel technique called exoCLIP, which reveals the RNA interactome of RBPs within the cell-free space. Together, our results demonstrate the power of machine learning in revealing novel biological mechanisms. In addition to providing deeper insight into small RNA secretion, this knowledge can be leveraged in therapeutic and synthetic biology applications.
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Affiliation(s)
- Bahar Zirak
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US
| | - Mohsen Naghipourfar
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Ali Saberi
- Department of Electrical and Computer Engineering, McGill University, Montreal, QC H3A 0E9, Canada; McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, 740 Dr Penfield Avenue, Montreal, QC H3A 0G1, Canada
| | - Delaram Pouyabahar
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Amirhossein Zarezadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Lixi Luo
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US; Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lisa Fish
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US
| | - Doowon Huh
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Albertas Navickas
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US; Institut Curie, CNRS UMR3348, INSERM U1278, Orsay, France.
| | - Ali Sharifi-Zarchi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran.
| | - Hani Goodarzi
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US.
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Ibrahim P, Denniston R, Mitsuhashi H, Yang J, Fiori LM, Żurawek D, Mechawar N, Nagy C, Turecki G. Profiling Small RNA From Brain Extracellular Vesicles in Individuals With Depression. Int J Neuropsychopharmacol 2024; 27:pyae013. [PMID: 38457375 PMCID: PMC10946232 DOI: 10.1093/ijnp/pyae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/07/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Major depressive disorder (MDD) is a leading cause of disability with significant mortality risk. Despite progress in our understanding of the etiology of MDD, the underlying molecular changes in the brain remain poorly understood. Extracellular vesicles (EVs) are lipid-bound particles that can reflect the molecular signatures of the tissue of origin. We aimed to optimize a streamlined EV isolation protocol from postmortem brain tissue and determine whether EV RNA cargo, particularly microRNAs (miRNAs), have an MDD-specific profile. METHODS EVs were isolated from postmortem human brain tissue. Quality was assessed using western blots, transmission electron microscopy, and microfluidic resistive pulse sensing. EV RNA was extracted and sequenced on Illumina platforms. Functional follow-up was performed in silico. RESULTS Quality assessment showed an enrichment of EV markers, as well as a size distribution of 30 to 200 nm in diameter, and no contamination with cellular debris. Small RNA profiling indicated the presence of several RNA biotypes, with miRNAs and transfer RNAs being the most prominent. Exploring miRNA levels between groups revealed decreased expression of miR-92a-3p and miR-129-5p, which was validated by qPCR and was specific to EVs and not seen in bulk tissue. Finally, in silico functional analyses indicate potential roles for these 2 miRNAs in neurotransmission and synaptic plasticity. CONCLUSION We provide a streamlined isolation protocol that yields EVs of high quality that are suitable for molecular follow-up. Our findings warrant future investigations into brain EV miRNA dysregulation in MDD.
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Affiliation(s)
- Pascal Ibrahim
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec, Canada
| | - Ryan Denniston
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec, Canada
| | - Haruka Mitsuhashi
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec, Canada
| | - Jennie Yang
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec, Canada
| | - Laura M Fiori
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec, Canada
| | - Dariusz Żurawek
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec, Canada
| | - Naguib Mechawar
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Corina Nagy
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Gustavo Turecki
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec, Canada
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Cao THM, Le APH, Tran TT, Huynh VK, Pham BH, Le TM, Nguyen QL, Tran TC, Tong TM, Than THN, Nguyen TTT, Ha HTT. Plasma cell-free RNA profiling of Vietnamese Alzheimer's patients reveals a linkage with chronic inflammation and apoptosis: a pilot study. Front Mol Neurosci 2023; 16:1308610. [PMID: 38178908 PMCID: PMC10764507 DOI: 10.3389/fnmol.2023.1308610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
Introduction Circulating cell-free RNA (cfRNA) is a potential hallmark for early diagnosis of Alzheimer's Disease (AD) as it construes the genetic expression level, giving insights into the pathological progress from the outset. Profiles of cfRNA in Caucasian AD patients have been investigated thoroughly, yet there was no report exploring cfRNAs in the ASEAN groups. This study examined the gap, expecting to support the development of point-of-care AD diagnosis. Methods cfRNA profiles were characterized from 20 Vietnamese plasma samples (10 probable AD and 10 age-matched controls). RNA reads were subjected to differential expression (DE) analysis. Weighted gene correlation network analysis (WGCNA) was performed to identify gene modules that were significantly co-expressed. These modules' expression profiles were then correlated with AD status to identify relevant modules. Genes with the highest intramodular connectivity (module membership) were selected as hub genes. Transcript counts of differentially expressed genes were correlated with key AD measures-MMSE and MTA scores-to identify potential biomarkers. Results 136 genes were identified as significant AD hallmarks (p < 0.05), with 52 downregulated and 84 upregulated in the AD cohort. 45.6% of these genes are highly expressed in the hippocampus, cerebellum, and cerebral cortex. Notably, all markers related to chronic inflammation were upregulated, and there was a significant shift in all apoptotic markers. Three co-expressed modules were found to be significantly correlated with Alzheimer's status (p < 0.05; R2> 0.5). Functional enrichment analysis on these modules reveals an association with focal adhesion, nucleocytoplasmic transport, and metal ion response leading to apoptosis, suggesting the potential participation of these pathways in AD pathology. 47 significant hub genes were found to be differentially expressed genes with the highest connectivity. Six significant hub genes (CREB1, YTHDC1, IL1RL1, PHACTR2, ANKRD36B, RNF213) were found to be significantly correlated with MTA and MMSE scores. Other significant transcripts (XRN1, UBB, CHP1, THBS1, S100A9) were found to be involved in inflammation and neuronal death. Overall, we have identified candidate transcripts in plasma cf-RNA that are differentially expressed and are implicated in inflammation and apoptosis, which can jumpstart further investigations into applying cf-RNA as an AD biomarker in Vietnam and ASEAN countries.
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Affiliation(s)
- Thien Hoang Minh Cao
- School of Biomedical Engineering, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Anh Phuc Hoang Le
- School of Biomedical Engineering, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Tai Tien Tran
- Department of Physiology, Pathophysiology and Immunology, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Vy Kim Huynh
- School of Biomedical Engineering, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Bao Hoai Pham
- School of Biomedical Engineering, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Thao Mai Le
- School of Biomedical Engineering, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Quang Lam Nguyen
- School of Biomedical Engineering, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Thang Cong Tran
- Department of Neurology, Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Trang Mai Tong
- Department of Neurology, University Medical Center, Ho Chi Minh City, Vietnam
| | - The Ha Ngoc Than
- Department of Geriatrics, Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
- Department of Geriatrics and Palliative Care, University Medical Center, Ho Chi Minh City, Vietnam
| | - Tran Tran To Nguyen
- Department of Geriatrics, Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Huong Thi Thanh Ha
- School of Biomedical Engineering, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
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Prosdocimi F, Cortines JR, José MV, Farias ST. Decoding viruses: An alternative perspective on their history, origins and role in nature. Biosystems 2023; 231:104960. [PMID: 37437771 DOI: 10.1016/j.biosystems.2023.104960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/14/2023]
Abstract
This article provides an alternative perspective on viruses, exploring their origins, ecology, and evolution. Viruses are recognized as the most prevalent biological entities on Earth, permeating nearly all environments and forming the virosphere-a significant biological layer. They play a crucial role in regulating bacterial populations within ecosystems and holobionts, influencing microbial communities and nutrient recycling. Viruses are also key drivers of molecular evolution, actively participating in the maintenance and regulation of ecosystems and cellular organisms. Many eukaryotic genomes contain genomic elements with viral origins, which contribute to organismal equilibrium and fitness. Viruses are involved in the generation of species-specific orphan genes, facilitating adaptation and the development of unique traits in biological lineages. They have been implicated in the formation of vital structures like the eukaryotic nucleus and the mammalian placenta. The presence of virus-specific genes absent in cellular organisms suggests that viruses may pre-date cellular life. Like progenotes, viruses are ribonucleoprotein entities with simpler capsid architectures compared to proteolipidic membranes. This article presents a comprehensive scenario describing major transitions in prebiotic evolution and proposes that viruses emerged prior to the Last Universal Common Ancestor (LUCA) during the progenote era. However, it is important to note that viruses do not form a monophyletic clade, and many viral taxonomic groups originated more recently as reductions of cellular structures. Thus, viral architecture should be seen as an ancient and evolutionarily stable strategy adopted by biological systems. The goal of this article is to reshape perceptions of viruses, highlighting their multifaceted significance in the complex tapestry of life and fostering a deeper understanding of their origins, ecological impact, and evolutionary dynamics.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Juliana Reis Cortines
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Brazil
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, CDMX, Mexico
| | - Sávio Torres Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil; Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds, LS7 3RB, UK
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8
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Zhu Y, Shen L, Xia Q, Tao H, Liu Z, Wang M, Zhang X, Zhang J, Lv J. Extracellular vesicle-derived circHIPK3: Novel diagnostic biomarker for lung cancer. Adv Med Sci 2023; 68:426-432. [PMID: 37866205 DOI: 10.1016/j.advms.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/15/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023]
Abstract
PURPOSE Lung cancer (LC) is a common malignancy worldwide. A great number of circular RNAs (circRNAs) have been identified that serve crucial roles in cancer development. Extracellular vesicles (EVs) and their contents have been shown to be biomarkers for the diagnosis and prognosis of LC. Thus, we intended to clarify the functional role of EVs-derived circRNA homology domain interacting protein kinase 3 (EVs-circHIPK3) and its underlying mechanism of action. MATERIAL AND METHODS Bioinformatics analysis was performed to validate the potential of partially circulating HIPK3 in LC diagnosis. EVs were isolated by polyethylene glycol (PEG) precipitation from plasma of 52 LC patients and 30 healthy controls. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was employed to evaluate the expressions of candidate circRNAs (circHIPK3) and microRNA-637 (miR-637, a target of circHIPK3). RESULTS CircHIPK3 is significantly up-regulated in LC, while miR-637 expression is significantly reduced (p < 0.05). Receiver operating characteristic (ROC) curve analysis, based on the expression of EVs-circHIPK3, allowed us to distinguish LC from healthy controls (area under the curve, AUC 0.897). CONCLUSIONS Taken together, our study shows that EV-derived circHIPK3 can serve as a promising biomarker for LC patient diagnosis. However, the downstream mRNA of the circHIPK3/miR-637 axis requires further exploration to enrich our understanding of circHIPK3's mechanism in LC.
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Affiliation(s)
- Yingying Zhu
- Department of Oncology, Affiliated Aoyang Hospital of Jiangsu University, Jiangsu, China
| | - Li Shen
- Department of Oncology, Affiliated Aoyang Hospital of Jiangsu University, Jiangsu, China
| | - Qiuyan Xia
- Department of Oncology, Affiliated Aoyang Hospital of Jiangsu University, Jiangsu, China
| | - Heyun Tao
- Department of Oncology, Affiliated Aoyang Hospital of Jiangsu University, Jiangsu, China
| | - Zhanguo Liu
- Department of Oncology, Affiliated Aoyang Hospital of Jiangsu University, Jiangsu, China
| | - Mengdie Wang
- Department of Oncology, Affiliated Aoyang Hospital of Jiangsu University, Jiangsu, China
| | - Xiaomin Zhang
- Department of Oncology, Affiliated Aoyang Hospital of Jiangsu University, Jiangsu, China
| | - Jun Zhang
- Department of Oncology, Affiliated Aoyang Hospital of Jiangsu University, Jiangsu, China.
| | - Jian Lv
- Department of Thoracic Surgery, Affiliated Changzheng Hospital, Second Military Medical University, Shanghai, China.
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9
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Elshafie NO, Gribskov M, Lichti NI, Sayedahmed EE, Childress MO, dos Santos AP. miRNome expression analysis in canine diffuse large B-cell lymphoma. Front Oncol 2023; 13:1238613. [PMID: 37711209 PMCID: PMC10499539 DOI: 10.3389/fonc.2023.1238613] [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: 06/12/2023] [Accepted: 08/04/2023] [Indexed: 09/16/2023] Open
Abstract
Introduction Lymphoma is a common canine cancer with translational relevance to human disease. Diffuse large B-cell lymphoma (DLBCL) is the most frequent subtype, contributing to almost fifty percent of clinically recognized lymphoma cases. Identifying new biomarkers capable of early diagnosis and monitoring DLBCL is crucial for enhancing remission rates. This research seeks to advance our knowledge of the molecular biology of DLBCL by analyzing the expression of microRNAs, which regulate gene expression by negatively impacting gene expression via targeted RNA degradation or translational repression. The stability and accessibility of microRNAs make them appropriate biomarkers for the diagnosis, prognosis, and monitoring of diseases. Methods We extracted and sequenced microRNAs from ten fresh-frozen lymph node tissue samples (six DLBCL and four non-neoplastic). Results Small RNA sequencing data analysis revealed 35 differently expressed miRNAs (DEMs) compared to controls. RT-qPCR confirmed that 23/35 DEMs in DLBCL were significantly upregulated (n = 14) or downregulated (n = 9). Statistical significance was determined by comparing each miRNA's average expression fold-change (2-Cq) between the DLCBL and healthy groups by applying the unpaired parametric Welch's 2-sample t-test and false discovery rate (FDR). The predicted target genes of the DEMs were mainly enriched in the PI3K-Akt-MAPK pathway. Discussion Our data point to the potential value of miRNA signatures as diagnostic biomarkers and serve as a guideline for subsequent experimental studies to determine the targets and functions of these altered miRNAs in canine DLBCL.
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Affiliation(s)
- Nelly O. Elshafie
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | - Michael Gribskov
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Nathanael I. Lichti
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, United States
| | - Ekramy. E. Sayedahmed
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | - Michael O. Childress
- Department of Veterinary Clinical Sciences, Purdue University, West Lafayette, IN, United States
| | - Andrea P. dos Santos
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
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10
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Kurtulmuş A, Koçana CÇ, Toprak SF, Sözer S. The role of Extracellular Genomic Materials (EGMs) in psychiatric disorders. Transl Psychiatry 2023; 13:262. [PMID: 37464177 PMCID: PMC10354097 DOI: 10.1038/s41398-023-02549-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023] Open
Abstract
Extracellular Genomic Materials (EGMs) are the nucleic acids secreted or released from all types of cells by endogenous or exogenous stimuli through varying mechanisms into the extracellular region and inevitably to all biological fluids. EGMs could be found as free, protein-bound, and/ or with vesicles. EGMs can potentially have immunophenotypic and/or genotypic characteristics of a cell of origin, travel to distant organs, and interact with the new microenvironment. To achieve all, EGMs might bi-directionally transit through varying membranes, including the blood-brain barrier. Such ability provides the transfer of any information related to the pathophysiological changes in psychiatric disorders in the brain to the other distant organ systems or vice versa. In this article, many aspects of EGMs have been elegantly reviewed, including their potential in diagnosis as biomarkers, application in treatment modalities, and functional effects in the pathophysiology of psychiatric disorders. The psychiatric disorders were studied under subgroups of Schizophrenia spectrum disorders, bipolar disorder, depressive disorders, and an autism spectrum disorders. EGMs provide a robust and promising tool in clinics for prognosis and diagnosis. The successful application of EGMs into treatment modalities might further provide encouraging outcomes for researchers and clinicians in psychiatric disorders.
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Affiliation(s)
- Ayşe Kurtulmuş
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
- Institute of Health Sciences, Istanbul University, Istanbul, Turkey
- Istanbul Göztepe Prof.Dr.Süleyman Yalçın City Hospital, Department of Psychiatry, Istanbul, Turkey
| | - Cemal Çağıl Koçana
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
- Institute of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Selin Fulya Toprak
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
- Institute of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Selçuk Sözer
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
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11
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Xing J, Zhang M, Zhao S, Lu M, Lin L, Chen L, Gao W, Li W, Shang J, Zhou J, Zhu X. EIF4A3-Induced Exosomal circLRRC8A Alleviates Granulosa Cells Senescence Via the miR-125a-3p/NFE2L1 axis. Stem Cell Rev Rep 2023:10.1007/s12015-023-10564-8. [PMID: 37243831 PMCID: PMC10390409 DOI: 10.1007/s12015-023-10564-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2023] [Indexed: 05/29/2023]
Abstract
Premature ovarian failure (POF) is an important cause of female infertility and seriously impacts the physical and psychological health of patients. Mesenchymal stromal cells-derived exosomes (MSCs-Exos) have an essential role in the treatment of reproductive disorders, particularly POF. However, the biological function and therapeutic mechanism of MSCs exosomal circRNAs in POF remain to be determined. Here, with bioinformatics analysis and functional assays, circLRRC8A was found to be downregulated in senescent granulosa cells (GCs) and acted as a crucial factor in MSCs-Exos for oxidative damage protection and anti-senescence of GCs in vitro and in vivo. Mechanistic investigations revealed that circLRRC8A served as an endogenous miR-125a-3p sponge to downregulate NFE2L1 expression. Moreover, eukaryotic initiation factor 4A3 (EIF4A3), acting as a pre-mRNA splicing factor, promoted circLRRC8A cyclization and expression by directly binding to the LRRC8A mRNA transcript. Notably, EIF4A3 silencing reduced circLRRC8A expression and attenuated the therapeutic effect of MSCs-Exos on oxidatively damaged GCs. This study demonstrates a new therapeutic pathway for cellular senescence protection against oxidative damage by delivering circLRRC8A-enriched exosomes through the circLRRC8A/miR-125a-3p/NFE2L1 axis and paves the way for the establishment of a cell-free therapeutic approach for POF. CircLRRC8A may be a promising circulating biomarker for diagnosis and prognosis and an exceptional candidate for further therapeutic exploration.
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Affiliation(s)
- Jie Xing
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Mengxue Zhang
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Shijie Zhao
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Mingjun Lu
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Li Lin
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Lu Chen
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Wujiang Gao
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Wenxin Li
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Junyu Shang
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Jiamin Zhou
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Xiaolan Zhu
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China.
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China.
- Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China.
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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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Cognitive impairments correlate with increased central nervous system immune activation after allogeneic haematopoietic stem cell transplantation. Leukemia 2023; 37:888-900. [PMID: 36792657 PMCID: PMC10079537 DOI: 10.1038/s41375-023-01840-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/17/2023]
Abstract
Murine studies indicate that, after allogeneic haematopoietic stem cell transplantation (aHSCT), donor-derived macrophages replace damaged microglia and alloreactive T-cells invade the central nervous system (CNS). The clinical relevance of this is unknown. We assessed CNS immune surveillance and metabolic activity involved in neuronal survival, in relation to fatigue and cognitive dysfunction in 25 long-term survivors after aHSCT. Patients with cognitive dysfunction exhibited increased proportions of activated T-cells and CD16 + NK-cells in the cerebrospinal fluid (CSF). Immune cell activation was paralleled with reduced levels of anti-inflammatory factors involved in T-cell suppression (transforming growth factor-β, programmed death ligand-1), NK-cell regulation (poliovirus receptor, nectin-2), and macrophage and microglia activation (CD200, chemokine [C-X3-C motif] ligand-1). Additionally, the CSF mRNA expression pattern was associated with neuroinflammation and oxidative stress. Furthermore, proteomic, and transcriptomic studies demonstrated decreased levels of neuroprotective factors, and an upregulation of apoptosis pathway genes. The kynurenine pathway of tryptophan metabolism was activated in the CNS of all aHSCT patients, resulting in accumulation of neurotoxic and pro-inflammatory metabolites. Cognitive decline and fatigue are overlooked but frequent complications of aHSCT. This study links post-transplant CNS inflammation and neurotoxicity to our previously reported hypoactivation in the prefrontal cortex during cognitive testing, suggesting novel treatment targets.
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Rybarczyk A, Lehmann T, Iwańczyk-Skalska E, Juzwa W, Pławski A, Kopciuch K, Blazewicz J, Jagodziński PP. In silico and in vitro analysis of the impact of single substitutions within EXO-motifs on Hsa-MiR-1246 intercellular transfer in breast cancer cell. J Appl Genet 2023; 64:105-124. [PMID: 36394782 PMCID: PMC9837009 DOI: 10.1007/s13353-022-00730-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/19/2022]
Abstract
MiR-1246 has recently gained much attention and many studies have shown its oncogenic role in colorectal, breast, lung, and ovarian cancers. However, miR-1246 processing, stability, and mechanisms directing miR-1246 into neighbor cells remain still unclear. In this study, we aimed to determine the role of single-nucleotide substitutions within short exosome sorting motifs - so-called EXO-motifs: GGAG and GCAG present in miR-1246 sequence on its intracellular stability and extracellular transfer. We applied in silico methods such as 2D and 3D structure analysis and modeling of protein interactions. We also performed in vitro validation through the transfection of fluorescently labeled miRNA to MDA-MB-231 cells, which we analyzed by flow cytometry and fluorescent microscopy. Our results suggest that nucleotides alterations that disturbed miR-1246 EXO-motifs were able to modulate miRNA-1246 stability and its transfer level to the neighboring cells, suggesting that the molecular mechanism of RNA stability and intercellular transfer can be closely related.
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Affiliation(s)
- Agnieszka Rybarczyk
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
| | - Tomasz Lehmann
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Fredry 10, 61-701 Poznan, Poland
| | - Ewa Iwańczyk-Skalska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Fredry 10, 61-701 Poznan, Poland
| | - Wojciech Juzwa
- Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-627 Poznan, Poland
| | - Andrzej Pławski
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznan, Poland
| | - Kamil Kopciuch
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
| | - Jacek Blazewicz
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paweł P. Jagodziński
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Fredry 10, 61-701 Poznan, Poland
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Yin S, Chen A, Ding Y, Song J, Chen R, Zhang P, Yang C. Recent advances in exosomal RNAs analysis towards diagnostic and therapeutic applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Levy K, Fishman B, Barnea A, Ayali A, Tauber E. Transcriptional Response of Circadian Clock Genes to an ‘Artificial Light at Night’ Pulse in the Cricket Gryllus bimaculatus. Int J Mol Sci 2022; 23:ijms231911358. [PMID: 36232659 PMCID: PMC9570371 DOI: 10.3390/ijms231911358] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/22/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
Light is the major signal entraining the circadian clock that regulates physiological and behavioral rhythms in most organisms, including insects. Artificial light at night (ALAN) disrupts the natural light–dark cycle and negatively impacts animals at various levels. We simulated ALAN using dim light stimuli and tested their impact on gene expression in the cricket Gryllus bimaculatus, a model of insect physiology and chronobiology. At night, adult light–dark-regime-raised crickets were exposed for 30 min to a light pulse of 2–40 lx. The relative expression of five circadian-clock-associated genes was compared using qPCR. A dim ALAN pulse elicited tissue-dependent differential expression in some of these genes. The strongest effect was observed in the brain and in the optic lobe, the cricket’s circadian pacemaker. The expression of opsin-Long Wave (opLW) was upregulated, as well as cryptochrome1-2 (cry) and period (per). Our findings demonstrate that even a dim ALAN exposure may affect insects at the molecular level, underscoring the impact of ALAN on the circadian clock system.
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Affiliation(s)
- Keren Levy
- School of Zoology, Tel Aviv University, Tel-Aviv 6997801, Israel
| | - Bettina Fishman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa 3498838, Israel
| | - Anat Barnea
- Department of Natural and Life Sciences, The Open University of Israel, Raanana 4353701, Israel
| | - Amir Ayali
- School of Zoology, Tel Aviv University, Tel-Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel-Aviv 6997801, Israel
- Correspondence: (A.A.); (E.T.)
| | - Eran Tauber
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa 3498838, Israel
- Correspondence: (A.A.); (E.T.)
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Comfort N, Wu H, De Hoff P, Vuppala A, Vokonas PS, Spiro A, Weisskopf M, Coull BA, Laurent LC, Baccarelli AA, Schwartz J. Extracellular microRNA and cognitive function in a prospective cohort of older men: The Veterans Affairs Normative Aging Study. Aging (Albany NY) 2022; 14:6859-6886. [PMID: 36069796 PMCID: PMC9512498 DOI: 10.18632/aging.204268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/17/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Aging-related cognitive decline is an early symptom of Alzheimer's disease and other dementias, and on its own can have substantial consequences on an individual's ability to perform important everyday functions. Despite increasing interest in the potential roles of extracellular microRNAs (miRNAs) in central nervous system (CNS) pathologies, there has been little research on extracellular miRNAs in early stages of cognitive decline. We leverage the longitudinal Normative Aging Study (NAS) cohort to investigate associations between plasma miRNAs and cognitive function among cognitively normal men. METHODS This study includes data from up to 530 NAS participants (median age: 71.0 years) collected from 1996 to 2013, with a total of 1,331 person-visits (equal to 2,471 years of follow up). Global cognitive function was assessed using the Mini-Mental State Examination (MMSE). Plasma miRNAs were profiled using small RNA sequencing. Associations of expression of 381 miRNAs with current cognitive function and rate of change in cognitive function were assessed using linear regression (N = 457) and linear mixed models (N = 530), respectively. RESULTS In adjusted models, levels of 2 plasma miRNAs were associated with higher MMSE scores (p < 0.05). Expression of 33 plasma miRNAs was associated with rate of change in MMSE scores over time (p < 0.05). Enriched KEGG pathways for miRNAs associated with concurrent MMSE and MMSE trajectory included Hippo signaling and extracellular matrix-receptor interactions. Gene targets of miRNAs associated with MMSE trajectory were additionally associated with prion diseases and fatty acid biosynthesis. CONCLUSIONS Circulating miRNAs were associated with both cross-sectional cognitive function and rate of change in cognitive function among cognitively normal men. Further research is needed to elucidate the potential functions of these miRNAs in the CNS and investigate relationships with other neurological outcomes.
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Affiliation(s)
- Nicole Comfort
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Haotian Wu
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Peter De Hoff
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Aishwarya Vuppala
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Pantel S. Vokonas
- VA Normative Aging Study, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Avron Spiro
- Massachusetts Veterans Epidemiology and Research Information Center, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Marc Weisskopf
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Brent A. Coull
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Joel Schwartz
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
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Yi X, Chen J, Huang D, Feng S, Yang T, Li Z, Wang X, Zhao M, Wu J, Zhong T. Current perspectives on clinical use of exosomes as novel biomarkers for cancer diagnosis. Front Oncol 2022; 12:966981. [PMID: 36119470 PMCID: PMC9472136 DOI: 10.3389/fonc.2022.966981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/01/2022] [Indexed: 12/11/2022] Open
Abstract
Exosomes are a heterogeneous subset of extracellular vesicles (EVs) that biogenesis from endosomes. Besides, exosomes contain a variety of molecular cargoes including proteins, lipids and nucleic acids, which play a key role in the mechanism of exosome formation. Meanwhile, exosomes are involved with physiological and pathological conditions. The molecular profile of exosomes reflects the type and pathophysiological status of the originating cells so could potentially be exploited for diagnostic of cancer. This review aims to describe important molecular cargoes involved in exosome biogenesis. In addition, we highlight exogenous factors, especially autophagy, hypoxia and pharmacology, that regulate the release of exosomes and their corresponding cargoes. Particularly, we also emphasize exosome molecular cargoes as potential biomarkers in liquid biopsy for diagnosis of cancer.
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Affiliation(s)
- Xiaomei Yi
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Jie Chen
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Defa Huang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Shuo Feng
- English Teaching and Research Section, Gannan Healthcare Vocational College, Ganzhou, China
| | - Tong Yang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Zhengzhe Li
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xiaoxing Wang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Minghong Zhao
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Jiyang Wu
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Tianyu Zhong
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- *Correspondence: Tianyu Zhong,
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Sohail AM, Khawar MB, Afzal A, Hassan A, Shahzaman S, Ali A. Multifaceted roles of extracellular RNAs in different diseases. Mil Med Res 2022; 9:43. [PMID: 35948986 PMCID: PMC9367134 DOI: 10.1186/s40779-022-00405-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 07/26/2022] [Indexed: 11/10/2022] Open
Abstract
Extracellular RNAs (exRNAs) are novel circulating factors that can be used as biomarkers in various diseases. Their unique and diverse kinds, as well as their role as biomarkers, make them significant biomarkers. There has been immense work carried out since the discovery of exRNAs in circulation and other biological fluids to catalog and determine whether exRNAs may be utilized as indicators for health and illness. In this review, we aim to understand the current state of exRNAs in relation to various diseases and their potential as biomarkers. We will also review current issues and challenges faced in using exRNAs, with clinical and lab trials, that can be used as viable markers for different diseases.
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Affiliation(s)
- Abdullah Muhammad Sohail
- Molecular Medicine and Cancer Therapeutics Lab, Department of Zoology, Faculty of Sciences, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Babar Khawar
- Applied Molecular Biology and Biomedicine Lab, Department of Zoology, University of Narowal, Narowal, Pakistan.
| | - Ali Afzal
- Molecular Medicine and Cancer Therapeutics Lab, Department of Zoology, Faculty of Sciences, University of Central Punjab, Lahore, Pakistan
| | - Ali Hassan
- Molecular Medicine and Cancer Therapeutics Lab, Department of Zoology, Faculty of Sciences, University of Central Punjab, Lahore, Pakistan
| | - Sara Shahzaman
- Molecular Medicine and Cancer Therapeutics Lab, Department of Zoology, Faculty of Sciences, University of Central Punjab, Lahore, Pakistan
| | - Ahmed Ali
- Molecular Medicine and Cancer Therapeutics Lab, Department of Zoology, Faculty of Sciences, University of Central Punjab, Lahore, Pakistan
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20
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Roganović J, Petrović N. Clinical Perspectives of Non-Coding RNA in Oral Inflammatory Diseases and Neuropathic Pain: A Narrative Review. Int J Mol Sci 2022; 23:ijms23158278. [PMID: 35955417 PMCID: PMC9368403 DOI: 10.3390/ijms23158278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 02/07/2023] Open
Abstract
Non-coding RNAs (ncRNAs) represent a research hotspot by playing a key role in epigenetic and transcriptional regulation of diverse biological functions and due to their involvement in different diseases, including oral inflammatory diseases. Based on ncRNAs’ suitability for salivary biomarkers and their involvement in neuropathic pain and tissue regeneration signaling pathways, the present narrative review aims to highlight the potential clinical applications of ncRNAs in oral inflammatory diseases, with an emphasis on salivary diagnostics, regenerative dentistry, and precision medicine for neuropathic orofacial pain.
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Affiliation(s)
- Jelena Roganović
- Department of Pharmacology in Dentistry, School of Dental Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Correspondence: ; Tel.: +381-641976330
| | - Nina Petrović
- Department of Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia;
- Institute for Oncology and Radiology of Serbia, 11000 Belgrade, Serbia
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21
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Kakouri AC, Koutalianos D, Koutsoulidou A, Oulas A, Tomazou M, Nikolenko N, Turner C, Roos A, Lusakowska A, Janiszewska K, Papadimas GK, Papadopoulos C, Kararizou E, Papanicolaou EZ, Gorman G, Lochmüller H, Spyrou GM, Phylactou LA. Circulating small RNA signatures differentiate accurately the subtypes of muscular dystrophies: small-RNA next-generation sequencing analytics and functional insights. RNA Biol 2022; 19:507-518. [PMID: 35388741 PMCID: PMC8993092 DOI: 10.1080/15476286.2022.2058817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Muscular dystrophies are a group of rare and severe inherited disorders mainly affecting the muscle tissue. Duchene Muscular Dystrophy, Myotonic Dystrophy types 1 and 2, Limb Girdle Muscular Dystrophy and Facioscapulohumeral Muscular Dystrophy are some of the members of this family of disorders. In addition to the current diagnostic tools, there is an increasing interest for the development of novel non-invasive biomarkers for the diagnosis and monitoring of these diseases. miRNAs are small RNA molecules characterized by high stability in blood thus making them ideal biomarker candidates for various diseases. In this study, we present the first genome-wide next-generation small RNA sequencing in serum samples of five different types of muscular dystrophy patients and healthy individuals. We identified many small RNAs including miRNAs, lncRNAs, tRNAs, snoRNAs and snRNAs, that differentially discriminate the muscular dystrophy patients from the healthy individuals. Further analysis of the identified miRNAs showed that some miRNAs can distinguish the muscular dystrophy patients from controls and other miRNAs are specific to the type of muscular dystrophy. Bioinformatics analysis of the target genes for the most significant miRNAs and the biological role of these genes revealed different pathways that the dysregulated miRNAs are involved in each type of muscular dystrophy investigated. In conclusion, this study shows unique signatures of small RNAs circulating in five types of muscular dystrophy patients and provides a useful resource for future studies for the development of miRNA biomarkers in muscular dystrophies and for their involvement in the pathogenesis of the disorders.
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Affiliation(s)
- Andrea C Kakouri
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Demetris Koutalianos
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Andrie Koutsoulidou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Anastasis Oulas
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marios Tomazou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Department of Neurogenetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Nikoletta Nikolenko
- National Hospital for Neurology and Neurosurgery, Queen Square, University College London Hospitals NHS Foundation Trust, London, UK
| | - Chris Turner
- National Hospital for Neurology and Neurosurgery, Queen Square, University College London Hospitals NHS Foundation Trust, London, UK
| | - Andreas Roos
- Department of Neuropediatrics, University Hospital Essen, Duisburg-Essen University, Germany.,Division of Neurology, Department of Medicine, Childrens Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Anna Lusakowska
- Department of Neurology, Medical University of Warsaw, Warsaw, Poland
| | | | - George K Papadimas
- Department of Neurology, Eginitio hospital, Medical School of Athens, Athens, Greece
| | | | - Evangelia Kararizou
- Department of Neurology, Eginitio hospital, Medical School of Athens, Athens, Greece
| | | | - Grainne Gorman
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, University of Newcastle, Newcastle, UK
| | - Hanns Lochmüller
- Division of Neurology, Department of Medicine, Childrens Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada.,Centro Nacional de AnálisisGenómico, Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (Bist), Barcelona, Spain
| | - George M Spyrou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Leonidas A Phylactou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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22
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Zhou H, Zhu L, Song J, Wang G, Li P, Li W, Luo P, Sun X, Wu J, Liu Y, Zhu S, Zhang Y. Liquid biopsy at the frontier of detection, prognosis and progression monitoring in colorectal cancer. Mol Cancer 2022; 21:86. [PMID: 35337361 PMCID: PMC8951719 DOI: 10.1186/s12943-022-01556-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/02/2022] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide and a leading cause of carcinogenic death. To date, surgical resection is regarded as the gold standard by the operator for clinical decisions. Because conventional tissue biopsy is invasive and only a small sample can sometimes be obtained, it is unable to represent the heterogeneity of tumor or dynamically monitor tumor progression. Therefore, there is an urgent need to find a new minimally invasive or noninvasive diagnostic strategy to detect CRC at an early stage and monitor CRC recurrence. Over the past years, a new diagnostic concept called “liquid biopsy” has gained much attention. Liquid biopsy is noninvasive, allowing repeated analysis and real-time monitoring of tumor recurrence, metastasis or therapeutic responses. With the advanced development of new molecular techniques in CRC, circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), exosomes, and tumor-educated platelet (TEP) detection have achieved interesting and inspiring results as the most prominent liquid biopsy markers. In this review, we focused on some clinical applications of CTCs, ctDNA, exosomes and TEPs and discuss promising future applications to solve unmet clinical needs in CRC patients.
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Affiliation(s)
- Hui Zhou
- Department of General Surgery, Third Xiangya Hospital, Central South University, Changsha, 410013, China.,Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Liyong Zhu
- Department of General Surgery, Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Jun Song
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Guohui Wang
- Department of General Surgery, Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Pengzhou Li
- Department of General Surgery, Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Weizheng Li
- Department of General Surgery, Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Ping Luo
- Department of General Surgery, Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Xulong Sun
- Department of General Surgery, Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Jin Wu
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Yunze Liu
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Shaihong Zhu
- Department of General Surgery, Third Xiangya Hospital, Central South University, Changsha, 410013, China.
| | - Yi Zhang
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China.
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23
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Famta P, Shah S, Khatri DK, Guru SK, Singh SB, Srivastava S. Enigmatic role of exosomes in breast cancer progression and therapy. Life Sci 2022; 289:120210. [PMID: 34875250 DOI: 10.1016/j.lfs.2021.120210] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 12/17/2022]
Abstract
Breast cancer (BC) is reported to be the leading cause of mortality in females worldwide. At the beginning of the year 2021, about 7.8 million women were diagnosed with BC in past 5 years. High prevalence and poor neoadjuvant chemotherapeutic efficacy has motivated the scientists around the globe to investigate alternative management strategies. In recent years, there has been an exponential rise in the scientific studies reporting the role of tumor derived exosomes (TDEs) in the BC pathophysiology and management. TDEs play an important role in the intercellular communication and transportation of biomolecules. This manuscript reviews the role of exosomes in the BC pathophysiology, diagnosis, and therapy. Role of TDEs in the mechanistic pathways of BC metastasis, immunosuppression, migration, dormancy and chemo-resistance is extensively reviewed. We have also highlighted the epigenetic modulations orchestrated by exosomal miRNAs and long noncoding RNAs (lnc RNAs) in the BC environment. Liquid biopsies analyzing blood circulating exosomes for early and accurate detection of the BC have been discussed. Characterization of exosomes, strategies to use them in BC chemotherapy, BC immunotherapy and potential challenges that will present themselves in translating exosomes based technologies to market are discussed.
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Affiliation(s)
- Paras Famta
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Saurabh Shah
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Dharmendra Kumar Khatri
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Santosh Kumar Guru
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Shashi Bala Singh
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Saurabh Srivastava
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India.
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24
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Yazdanpanah Z, Kazemipour N, Kalantar SM, Vahidi Mehrjardi MY. Plasma miR-21 as a potential predictor in prediabetic individuals with a positive family history of type 2 diabetes mellitus. Physiol Rep 2022; 10:e15163. [PMID: 35076188 PMCID: PMC8787720 DOI: 10.14814/phy2.15163] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 04/18/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a heritable metabolic perturbation, rapidly growing across the world. Primary recognition of susceptible individuals with a family history of type 2 diabetes (FHD) in the prediabetes stage could delay the onset of T2DM or reduce complications induced by diabetes. This study aims to evaluate the expression levels of miR-21, miR-126 as noninvasive predictive biomarkers in individuals with genetic predisposition and investigate the correlation of miRNAs and cardiometabolic risk factors. Our study demonstrated that miR-21 expression has a notable elevate in both groups of T2DM and pre-T2DM. miR-21 expression was distinguished in the pre-T2DM and T2DM from the nondiabetic individuals by ROC curve analysis with AUC of 0.77 (95% CI 0.65-0.90; p = 0.0004) and AUC of 0.78 (95% CI 0.64-0.92; p = 0.0042), respectively. The relative gene expression of miR-126 was nearly equal among groups. miR-21 expression was positively associated with glycosylated hemoglobin (HbA1c), fasting blood sugar (FBS), and triglyceride (TG) and might have diagnostic value for T2DM and pre-T2DM. This study has revealed that the expression level of miR-21 can be considered as a non-invasive and rapid tool for distinguishing pre-T2DM and T2DM counterparts from healthy individuals.
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Affiliation(s)
- Zakieh Yazdanpanah
- Biochemistry DivisionDepartment of Basic ScienceSchool of Veterinary Medicine, Shiraz UniversityShirazIran
| | - Nasrin Kazemipour
- Biochemistry DivisionDepartment of Basic ScienceSchool of Veterinary Medicine, Shiraz UniversityShirazIran
| | - Seyed Mehdi Kalantar
- Department of Medical GeneticMedical SchoolShahid Sadoughi University of Medical ScienceYazdIran
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25
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The Role of Exosomes and Their Applications in Cancer. Int J Mol Sci 2021; 22:ijms222212204. [PMID: 34830085 PMCID: PMC8622108 DOI: 10.3390/ijms222212204] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 02/06/2023] Open
Abstract
Exosomes are very small extracellular vesicles secreted by multiple cell types and are extensively distributed in various biological fluids. Recent research indicated that exosomes can participate in regulating the tumor microenvironment and impacting tumor proliferation and progression. Due to the extensive enrollment in cancer development, exosomes have become a focus of the search for a new therapeutic method for cancer. Exosomes can be utilized for the therapeutic delivery of small molecules, proteins and RNAs to target cancer cells with a high efficiency. Exosome-carried proteins, lipids and nucleic acids are being tested as promising biomarkers for cancer diagnosis and prognosis, even as potential treatment targets for cancer. Moreover, different sources of exosomes exhibit multiple performances in cancer applications. In this review, we elaborate on the specific mechanism by which exosomes affect the communication between tumors and the microenvironment and state the therapeutic and diagnostic applications of exosomes in cancers.
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26
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Zhou J, Flores-Bellver M, Pan J, Benito-Martin A, Shi C, Onwumere O, Mighty J, Qian J, Zhong X, Hogue T, Amponsah-Antwi B, Einbond L, Gharbaran R, Wu H, Chen BJ, Zheng Z, Tchaikovskaya T, Zhang X, Peinado H, Canto-Soler MV, Redenti S. Human retinal organoids release extracellular vesicles that regulate gene expression in target human retinal progenitor cells. Sci Rep 2021; 11:21128. [PMID: 34702879 PMCID: PMC8548301 DOI: 10.1038/s41598-021-00542-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/07/2021] [Indexed: 01/23/2023] Open
Abstract
The mechanisms underlying retinal development have not been completely elucidated. Extracellular vesicles (EVs) are novel essential mediators of cell-to-cell communication with emerging roles in developmental processes. Nevertheless, the identification of EVs in human retinal tissue, characterization of their cargo, and analysis of their potential role in retina development has not been accomplished. Three-dimensional retinal tissue derived from human induced pluripotent stem cells (hiPSC) provide an ideal developmental system to achieve this goal. Here we report that hiPSC-derived retinal organoids release exosomes and microvesicles with small noncoding RNA cargo. EV miRNA cargo-predicted targetome correlates with Gene Ontology (GO) pathways involved in mechanisms of retinogenesis relevant to specific developmental stages corresponding to hallmarks of native human retina development. Furthermore, uptake of EVs by human retinal progenitor cells leads to changes in gene expression correlated with EV miRNA cargo predicted gene targets, and mechanisms involved in retinal development, ganglion cell and photoreceptor differentiation and function.
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Affiliation(s)
- Jing Zhou
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Miguel Flores-Bellver
- CellSight Ocular Stem Cell and Regeneration Program, Department of Ophthalmology, Sue Anschutz- Rodgers Eye Center, University of Colorado, 12800 East 19th Avenue, Aurora, CO, 80045, USA
| | - Jianbo Pan
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Alberto Benito-Martin
- Departments of Pediatrics, Hematology/Oncology Division, Weill Medical College of Cornell University, 413 E. 69th St., New York, NY, 10021, USA
| | - Cui Shi
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
| | | | - Jason Mighty
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Xiufeng Zhong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Tasmim Hogue
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
| | | | - Linda Einbond
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
| | | | - Hao Wu
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Bo-Juen Chen
- New York Genome Center, New York, NY, 10013, USA
| | - Zhiliang Zheng
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
| | - Tatyana Tchaikovskaya
- Department of Medicine, Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Xusheng Zhang
- Department of Medicine, Computational Genomics Core in Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hector Peinado
- Microenvironment and Metastasis Laboratory, Department of Molecular Oncology, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Maria Valeria Canto-Soler
- CellSight Ocular Stem Cell and Regeneration Program, Department of Ophthalmology, Sue Anschutz- Rodgers Eye Center, University of Colorado, 12800 East 19th Avenue, Aurora, CO, 80045, USA.
| | - Stephen Redenti
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA.
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA.
- Biochemistry Doctoral Program, The Graduate School, City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA.
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27
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Killingsworth B, Welsh JA, Jones JC. EV Translational Horizons as Viewed Across the Complex Landscape of Liquid Biopsies. Front Cell Dev Biol 2021; 9:556837. [PMID: 34616722 PMCID: PMC8488153 DOI: 10.3389/fcell.2021.556837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 03/04/2021] [Indexed: 12/16/2022] Open
Abstract
Extracellular Vesicle (EV)-based diagnostic and therapeutic tools are an area of intensive study and substantial promise, but EVs as liquid biopsies have advanced years ahead of EVs as therapeutic tools. EVs are emerging as a promising approach for detecting tumors, evaluating the molecular profiles of known disease, and monitoring treatment responses. Although correlative assays based on liquid biopsies are already having an impact on translational studies and clinical practice, much remains to be learned before these assays will be optimized for clinical correlations, functional biological studies, and therapeutic use. What follows is an overview of current evidence supporting the investigation and use of liquid biopsies, organized by specific liquid biopsy components available for analysis, along with a summary of what challenges must be overcome before these assays will provide functional biological insights into the pathogenesis and treatment of disease. The same challenges must also be overcome before it will be feasible to measure and monitor the dosing, distribution, pharmacokinetics, and delivery of EV therapeutics and their cargo in complex biofluids where EVs and circulate with and are co-isolated with a number of other nanoscale materials, including lipoproteins (LPPs), ribonucleoprotein complexes (RNPs), and cell free nucleic acids (cfNA).
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Affiliation(s)
- Bryce Killingsworth
- Translational Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Joshua A Welsh
- Translational Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jennifer C Jones
- Translational Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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28
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Liu J, Ren L, Li S, Li W, Zheng X, Yang Y, Fu W, Yi J, Wang J, Du G. The biology, function, and applications of exosomes in cancer. Acta Pharm Sin B 2021; 11:2783-2797. [PMID: 34589397 PMCID: PMC8463268 DOI: 10.1016/j.apsb.2021.01.001] [Citation(s) in RCA: 225] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/30/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023] Open
Abstract
Exosomes are cell-derived nanovesicles with diameters from 30 to 150 nm, released upon fusion of multivesicular bodies with the cell surface. They can transport nucleic acids, proteins, and lipids for intercellular communication and activate signaling pathways in target cells. In cancers, exosomes may participate in growth and metastasis of tumors by regulating the immune response, blocking the epithelial-mesenchymal transition, and promoting angiogenesis. They are also involved in the development of resistance to chemotherapeutic drugs. Exosomes in liquid biopsies can be used as non-invasive biomarkers for early detection and diagnosis of cancers. Because of their amphipathic structure, exosomes are natural drug delivery vehicles for cancer therapy.
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Key Words
- ABCA3, ATP-binding cassette transporter A3
- APCs, antigen-presenting cells
- Biomarkers
- CAFs, cancer-associated fibroblasts
- CCRCC, clear-cell renal cell carcinoma
- CD-UPRT, cytosine deaminase-uracil phosphoribosyltransferase
- CDH3, cadherin 3
- CRC, colorectal cancer
- DC, dendritic cells
- DEXs, DC-derived exosomes
- DLBCL, diffuse large B-cell lymphoma
- DNM3, dynamin 3
- Del-1, developmental endothelial locus-1
- Drug delivery
- Drug resistance
- ECM, extracellular matrix
- EMT, epithelial–mesenchymal transition
- ESCRT, endosomal sorting complex required for transport
- Exosomes
- GPC1, glypican-1
- HA, hyaluronic acid
- HCC, hepatocellular carcinoma
- HIF1, hypoxia-inducible factor 1
- HTR, hormone therapy-resistant
- HUVECs, human umbilical vein endothelial cells
- ILVs, intraluminal vesicles
- MDSCs, myeloid-derived suppressor cells
- MIF, migration inhibitory factor
- MSC, mesenchymal stem cells
- MVB, multivesicular body
- NKEXOs, natural killer cell-derived exosomes
- NNs, nanoparticles
- NSCLC, non-small cell lung cancer
- PA, phosphatidic acid
- PCC, pheochromocytoma
- PD-L1, programmed cell death receptor ligand 1
- PDAC, pancreatic ductal adenocarcinoma
- PGL, paraganglioma
- PI, phosphatidylinositol
- PS, phosphatidylserine
- PTRF, polymerase I and transcript release factor
- RCC, renal cell carcinoma
- SM, sphingomyelin
- SNARE, soluble NSF-attachment protein receptor
- TEX, tumor-derived exosomes
- TSG101, tumor susceptibility gene 101
- Tumor immunity
- Tumor metastasis
- circRNAs, circular RNAs
- dsDNA, double stranded DNA
- hTERT, human telomerase reverse transcriptase
- lamp2b, lysosome-associated membrane glycoprotein 2b
- lncRNAs, long non-coding RNAs
- miRNA, microRNA
- mtDNA, mitochondrial DNA
- ncRNA, non-coding RNAs
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Affiliation(s)
- Jinyi Liu
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Liwen Ren
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Sha Li
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Wan Li
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Xiangjin Zheng
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Yihui Yang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Weiqi Fu
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Jie Yi
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Beijing 100730, China
| | - Jinhua Wang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Guanhua Du
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
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29
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Mahjoor M, Afkhami H, Mollaei M, Nasr A, Shahriary S, Khorrami S. MicroRNA-30c delivered by bone marrow-mesenchymal stem cells induced apoptosis and diminished cell invasion in U-251 glioblastoma cell line. Life Sci 2021; 279:119643. [PMID: 34048811 DOI: 10.1016/j.lfs.2021.119643] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/10/2021] [Accepted: 05/14/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Glioblastoma multiform (GBM) is the most belligerent and prevalent brain malignancy among adults. Due to the blood-brain barrier (BBB), drug administration is confronted by massive challenges, making resectional surgery the only treatment pipeline. MicroRNAs have recently absorbed the attention of studies for correlating with the progression of various malignancies. miR-30c has been reported to play a role in cell proliferation, metabolism, and apoptosis process. For instance, miR-30c has been reported to regulate apoptosis through the TNF-related apoptosis-inducing ligand (TRAIL). miR-30c also targets IL-6, which further induces apoptosis. Besides, miR-30c inhibits glioma proliferation and its migratory ability. Besides, the overexpression of miR-30c arrested cells at G0 as well as dampening their migration and invasion. However, it has been shown that the expression level of miR-30c was low in glioma. MSCs can migrate toward tumor cells which is called tumor-tropism, in which they are capable of delivering engineered miR-30c based on gap junction and non-intimacy mechanisms. MATERIAL AND METHODS MiR-30c was cloned into pCDH-CMV-MCS-EF1-copGFP vector utilizing XbaI and EcoRI in order to construct pCDH-miR-30c. Then psPAX2, pMD2.G, and pCDH-miR-30c were co-transfected into Hek-293T to yield lenti-miR-30c virus particles. Next, bone marrow-mesenchymal stem cells (BM-MSCs) were Transduced with lenti-miR-30c. Thereafter, we co-cultured U-251 cell line with BM-MCSs-miR-30c and evaluated the apoptosis rate and the relative expression level of IL-6, Klf4, Sox2, c-Myc, and Oct4 using Real-Time PCR and flow cytometry. RESULTS Wound healing assays represented low migratory ability in U-251 cells treated with BM-MSCs-miR-30c. Plus, apoptosis assay using Annexin V/7AAD showed an increased number of apoptotic U-251 cells following the treatment. miR-30 targeted IL-6 and induced apoptosis. It also impacted on the self-renewal and the anti-apoptotic cluster of genes, namely Klf4, Sox2, c-Myc, and Oct4, to induce apoptosis and dwindle the migration and invasion.
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Affiliation(s)
- Mohamad Mahjoor
- Department of Immunology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamed Afkhami
- Department of Medical Microbiology, Faculty of Medicine, Shahed University of Medical Sciences, Tehran, Iran
| | - Mojtaba Mollaei
- Department of Immunology, School of Medicine, Tarbiat Modares University, Tehran, Iran
| | - Atieh Nasr
- Bachelor Student of Biochemistry, Department of Biochemistry, Islamic Azad University of Najafabad, Esfahan, Iran
| | - Shamin Shahriary
- Bachelor Student of Microbiology, Department of Microbiology, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Samaneh Khorrami
- Department of Immunology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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30
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Torres AG, Martí E. Toward an Understanding of Extracellular tRNA Biology. Front Mol Biosci 2021; 8:662620. [PMID: 33937338 PMCID: PMC8082309 DOI: 10.3389/fmolb.2021.662620] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022] Open
Abstract
Extracellular RNAs (exRNAs) including abundant full length tRNAs and tRNA fragments (tRFs) have recently garnered attention as a promising source of biomarkers and a novel mediator in cell-to-cell communication in eukaryotes. Depending on the physiological state of cells, tRNAs/tRFs are released to the extracellular space either contained in extracellular vesicles (EVs) or free, through a mechanism that is largely unknown. In this perspective article, we propose that extracellular tRNAs (ex-tRNAs) and/or extracellular tRFs (ex-tRFs) are relevant paracrine signaling molecules whose activity depends on the mechanisms of release by source cells and capture by recipient cells. We speculate on how ex-tRNA/ex-tRFs orchestrate the effects in target cells, depending on the type of sequence and the mechanisms of uptake. We further propose that tRNA modifications may be playing important roles in ex-tRNA biology.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eulàlia Martí
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Epidemiología y Salud Pública, Madrid, Spain
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31
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Abstract
Damage-associated molecular patterns (DAMPs) are endogenous molecules which foment inflammation and are associated with disorders in sepsis and cancer. Thus, therapeutically targeting DAMPs has potential to provide novel and effective treatments. When establishing anti-DAMP strategies, it is important not only to focus on the DAMPs as inflammatory mediators but also to take into account the underlying mechanisms of their release from cells and tissues. DAMPs can be released passively by membrane rupture due to necrosis/necroptosis, although the mechanisms of release appear to differ between the DAMPs. Other types of cell death, such as apoptosis, pyroptosis, ferroptosis and NETosis, can also contribute to DAMP release. In addition, some DAMPs can be exported actively from live cells by exocytosis of secretory lysosomes or exosomes, ectosomes, and activation of cell membrane channel pores. Here we review the shared and DAMP-specific mechanisms reported in the literature for high mobility group box 1, ATP, extracellular cold-inducible RNA-binding protein, histones, heat shock proteins, extracellular RNAs and cell-free DNA.
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Affiliation(s)
- Atsushi Murao
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, 350 Community Dr., Manhasset, NY, 11030, USA
| | - Monowar Aziz
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, 350 Community Dr., Manhasset, NY, 11030, USA
| | - Haichao Wang
- Center for Biomedical Science, The Feinstein Institutes for Medical Research, Manhasset, NY, USA.,Department of Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - Max Brenner
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, 350 Community Dr., Manhasset, NY, 11030, USA. .,Department of Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA.
| | - Ping Wang
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, 350 Community Dr., Manhasset, NY, 11030, USA. .,Department of Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA. .,Department of Surgery, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA.
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32
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Berg MD, Brandl CJ. Transfer RNAs: diversity in form and function. RNA Biol 2021; 18:316-339. [PMID: 32900285 PMCID: PMC7954030 DOI: 10.1080/15476286.2020.1809197] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/08/2020] [Indexed: 12/11/2022] Open
Abstract
As the adaptor that decodes mRNA sequence into protein, the basic aspects of tRNA structure and function are central to all studies of biology. Yet the complexities of their properties and cellular roles go beyond the view of tRNAs as static participants in protein synthesis. Detailed analyses through more than 60 years of study have revealed tRNAs to be a fascinatingly diverse group of molecules in form and function, impacting cell biology, physiology, disease and synthetic biology. This review analyzes tRNA structure, biosynthesis and function, and includes topics that demonstrate their diversity and growing importance.
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Affiliation(s)
- Matthew D. Berg
- Department of Biochemistry, The University of Western Ontario, London, Canada
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33
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Dong L, Huang CY, Johnson EJ, Yang L, Zieren RC, Horie K, Kim CJ, Warren S, Amend SR, Xue W, Pienta KJ. High-Throughput Simultaneous mRNA Profiling Using nCounter Technology Demonstrates That Extracellular Vesicles Contain Different mRNA Transcripts Than Their Parental Prostate Cancer Cells. Anal Chem 2021; 93:3717-3725. [PMID: 33596381 PMCID: PMC7944479 DOI: 10.1021/acs.analchem.0c03185] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Extracellular
vesicles (EVs) are nano-sized lipid bilayer encapsulated
particles with a molecular cargo that appears to play important roles
within the human body, such as in cell-to-cell communication. Unraveling
the composition of EV cargos remains one of the most fundamental steps
toward understanding the role of EVs in intercellular communication
and the discovery of new biomarkers. One of the unmet needs in this
field is the lack of a robust, sensitive, and multiplexed method for
EV mRNA profiling. We established a new protocol using the NanoString
low RNA input nCounter assay by which the targeted mRNA transcripts
in EVs can be efficiently and specifically amplified and then assayed
for 770 mRNAs in one reaction. Prostate cancer cells with epithelial
(PC3-Epi) or mesenchymal (PC3-EMT) phenotypes and their progeny EVs
were analyzed by the same panel. Among these mRNAs, 157 were detected
in PC3-Epi EVs and 564 were detected in PC3-EMT EVs. NOTCH1 was the
most significantly abundant mRNA transcripts in PC3-EMT EVs compared
to PC3-Epi EVs. Our results demonstrated that when cells undergo epithelial-to-mesenchymal
transition (EMT), a more active loading of cancer progression-related
mRNA transcripts may occur. The mRNA cargos of EVs derived from mesenchymal
prostate cancer cells may contribute to the pro-EMT function. We found
that mRNA transcripts are different in progeny EVs compared to parental
cells. EV cargos are not completely reflective of their cell origin,
and the underlying mechanism of cargo sorting is complicated and needs
to be further elucidated.
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Affiliation(s)
- Liang Dong
- The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, United States.,Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200072, China
| | - Chung-Ying Huang
- NanoString Technologies, Inc., Seattle, Washington 98109, United States
| | - Eric J Johnson
- NanoString Technologies, Inc., Seattle, Washington 98109, United States
| | - Lei Yang
- NanoString Technologies, Inc., Seattle, Washington 98109, United States
| | - Richard C Zieren
- The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, United States.,Department of Urology, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands
| | - Kengo Horie
- The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, United States.,Department of Urology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Chi-Ju Kim
- The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, United States.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sarah Warren
- NanoString Technologies, Inc., Seattle, Washington 98109, United States
| | - Sarah R Amend
- The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, United States
| | - Wei Xue
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200072, China
| | - Kenneth J Pienta
- The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, United States
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34
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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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35
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Elshafie NO, Nascimento NCD, Lichti NI, Kasinski AL, Childress MO, Santos APD. MicroRNA Biomarkers in Canine Diffuse Large B-Cell Lymphoma. Vet Pathol 2020; 58:34-41. [PMID: 33287683 DOI: 10.1177/0300985820967902] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Lymphoma is among the most common cancer in dogs. Diffuse large B-cell lymphoma (DLBCL) is the predominant type, accounting for up to half of all cases. Definitive diagnosis of DLBCL relies on cytologic evaluation with immunophenotyping, or histopathology and immunohistochemistry when needed. A rapid and specific molecular test aiding in the diagnosis could be beneficial. Noncoding microRNAs (miRNAs) are regulators of gene expression involved in a variety of cellular processes, including cell differentiation, cell cycle progression, and apoptosis. Not surprisingly, miRNA expression is aberrant in diseases such as cancers. Their high stability and abundance in tissues make them promising biomarkers for diagnosing and monitoring diseases. This study aimed to identify miRNA signatures of DLBCL to develop ancillary molecular diagnostic tools. miRNA was isolated from formalin-fixed, paraffin-embedded lymph node tissue from 22 DLBCL and 14 nonneoplastic controls. Relative gene expression of 8 tumor-regulating miRNAs was achieved by RT-qPCR (reverse transcriptase quantitative polymerase chain reaction). The results showed downregulation of the let-7 family of miRNAs and miR-155, whereas miR-34a was upregulated in DLBCL compared to the controls. We demonstrated that the combination of expression levels of miR-34a and let-7f or of let-7b and let-7f achieved 100% differentiation between DLBCL and controls. Furthermore, let-7f alone discriminated DLBCL from nonneoplastic tissue in 97% of cases. Our results represent one step forward in search of a rapid and accurate ancillary diagnostic test for DLBCL in dogs.
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36
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Nevalainen T, Autio A, Puhka M, Jylhä M, Hurme M. Composition of the whole transcriptome in the human plasma: Cellular source and modification by aging. Exp Gerontol 2020; 143:111119. [PMID: 33086079 DOI: 10.1016/j.exger.2020.111119] [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] [Received: 03/17/2020] [Revised: 09/10/2020] [Accepted: 10/11/2020] [Indexed: 11/30/2022]
Abstract
Plasma contains several bioactive molecules (RNA, DNA, proteins, lipids, and metabolites), which are well preserved in extracellular vesicles, that are involved in many types of cell-to-cell interactions, and are capable of modifying biological processes in recipient cells. To obtain information about the source of mRNA molecules present in the plasma, we analyzed the plasma extracellular RNA (exRNA) of healthy individuals using RNA-sequencing and compared it to that of the peripheral blood mononuclear cell (PBMCs) of the same individual. The resultant data indicates that large proportion of the transcripts in plasma are derived from cell types other than PBMCs. To assess aging-associated changes in the plasma exRNA composition, gene ontology enrichment analysis was performed, revealing a functional decline in biological processes as a result of aging. Additionally, plasma RNA levels were analyzed with differential expression analysis, revealing 10 transcripts with significant aging-associated changes. Thus, it seems that the plasma exRNA is not fully derived from the PBMCs. Instead, other cell types supply RNAs to constitute the plasma exRNA compartment. This was true in both the young and elderly individuals that were tested. Furthermore, the RNA content of the plasma showed significant changes due to aging, affecting important biological processes.
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Affiliation(s)
- Tapio Nevalainen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Gerontology Research Center, Tampere University, Tampere, Finland.
| | - Arttu Autio
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Gerontology Research Center, Tampere University, Tampere, Finland; Science Centre, Pirkanmaa Hospital District, Tampere, Finland.
| | - Maija Puhka
- HiPrep and EV Core, Institute for Molecular Medicine Finland FIMM, University of Helsinki, Finland.
| | - Marja Jylhä
- Faculty of Social Sciences, Tampere University, Tampere, Finland; Gerontology Research Center, Tampere University, Tampere, Finland.
| | - Mikko Hurme
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Gerontology Research Center, Tampere University, Tampere, Finland.
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37
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O'Brien K, Breyne K, Ughetto S, Laurent LC, Breakefield XO. 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: 968] [Impact Index Per Article: 242.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [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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Affiliation(s)
- Killian O'Brien
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Koen Breyne
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stefano Ughetto
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Oncology, University of Turin, Candiolo, Italy
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Xandra O Breakefield
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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38
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Abstract
Small RNAs (sRNAs), including microRNAs (miRNAs), are noncoding RNA (ncRNA) molecules involved in gene regulation. sRNAs play important roles in development; however, their significance in nutritional control and as metabolic modulators is still emerging. The mechanisms by which diet impacts metabolic genes through miRNAs remain an important area of inquiry. Recent work has established how miRNAs are transported in body fluids often within exosomes, which are small cell-derived vesicles that function in intercellular communication. The abundance of other recently identified ncRNAs and new insights regarding ncRNAs as dietary bioactive compounds could remodel our understanding about how foods impact gene expression. Although controversial, some groups have shown that dietary RNAs from plants and animals (i.e., milk) are functional in consumers. In the future, regulating sRNAs either directly through dietary delivery or indirectly by altered expression of endogenous sRNA may be part of nutritional interventions for regulating metabolism.
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Affiliation(s)
- Elizabeth M McNeill
- Department of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011, USA
| | - Kendal D Hirschi
- Departments of Pediatrics and Human and Molecular Genetics, Children's Nutrition Research Center, Baylor College of Medicine, Houston, Texas 77030, USA;
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39
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Murao A, Brenner M, Aziz M, Wang P. Exosomes in Sepsis. Front Immunol 2020; 11:2140. [PMID: 33013905 PMCID: PMC7509534 DOI: 10.3389/fimmu.2020.02140] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
Sepsis is a severe state of infection with high mortality. Pathogen-associated molecular patterns and damage-associated molecular patterns (DAMPs) initiate dysregulated systemic inflammation upon binding to pattern recognition receptors. Exosomes are endosome-derived vesicles, which carry proteins, lipids and nucleic acids, and facilitate intercellular communications. Studies have shown altered contents and function of exosomes during sepsis. In sepsis, exosomes carry increased levels of cytokines and DAMPs to induce inflammation. Exosomal DAMPs include, but are not limited to, high mobility group box 1, heat shock proteins, histones, adenosine triphosphate, and extracellular RNA. Exosomes released during sepsis have impact on multiple organs, including the lungs, kidneys, liver, cardiovascular system, and central nervous system. Here, we review the mechanisms of inflammation caused by exosomes, and their contribution to multiple organ dysfunction in sepsis.
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Affiliation(s)
- Atsushi Murao
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Max Brenner
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States.,Department of Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, United States
| | - Monowar Aziz
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Ping Wang
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States.,Department of Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, United States.,Department of Surgery, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, United States
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40
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Extracellular RNA: Emerging roles in cancer cell communication and biomarkers. Cancer Lett 2020; 495:33-40. [PMID: 32916182 DOI: 10.1016/j.canlet.2020.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/15/2020] [Accepted: 09/02/2020] [Indexed: 01/05/2023]
Abstract
Extracellular RNAs (exRNAs) are a type of RNA molecules that present in various biological fluids. exRNAs are heterogenous populations including small (e.g., miRNA) and long non-coding RNAs and coding RNAs (e.g., mRNA). They can exist in a free form or associate with carriers range from lipo- and ribo-proteins to extracellular vesicles such as exosomes in the extracellular fluids. exRNAs participate in cell-to-cell communication to regulate a broad array of physiological and pathological processes. exRNAs have been widely studied as a biomarker for cancer and other diseases. In this review, we will discuss the sorts of exRNAs with potential carriers as well as their roles in cancer.
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41
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Hallal S, Ebrahim Khani S, Wei H, Lee MYT, Sim HW, Sy J, Shivalingam B, Buckland ME, Alexander-Kaufman KL. Deep Sequencing of Small RNAs from Neurosurgical Extracellular Vesicles Substantiates miR-486-3p as a Circulating Biomarker that Distinguishes Glioblastoma from Lower-Grade Astrocytoma Patients. Int J Mol Sci 2020; 21:ijms21144954. [PMID: 32668808 PMCID: PMC7404297 DOI: 10.3390/ijms21144954] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/01/2020] [Accepted: 07/07/2020] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs) play key roles in glioblastoma (GBM; astrocytoma grade IV) biology and are novel sources of biomarkers. EVs released from GBM tumors can cross the blood-brain-barrier into the periphery carrying GBM molecules, including small non-coding RNA (sncRNA). Biomarkers cargoed in circulating EVs have shown great promise for assessing the molecular state of brain tumors in situ. Neurosurgical aspirate fluids captured during tumor resections are a rich source of GBM-EVs isolated directly from tumor microenvironments. Using density gradient ultracentrifugation, EVs were purified from cavitron ultrasonic surgical aspirate (CUSA) washings from GBM (n = 12) and astrocytoma II-III (GII-III, n = 5) surgeries. The sncRNA contents of surgically captured EVs were profiled using the Illumina® NextSeqTM 500 NGS System. Differential expression analysis identified 27 miRNA and 10 piRNA species in GBM relative to GII-III CUSA-EVs. Resolved CUSA-EV sncRNAs could discriminate serum-EV sncRNA profiles from GBM and GII-III patients and healthy controls and 14 miRNAs (including miR-486-3p and miR-106b-3p) and cancer-associated piRNAs (piR_016658, _016659, _020829 and _204090) were also significantly expressed in serum-EVs. Circulating EV markers that correlate with histological, neuroradiographic and clinical parameters will provide objective measures of tumor activity and improve the accuracy of GBM tumor surveillance.
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Affiliation(s)
- Susannah Hallal
- Department of Neurosurgical Services, Chris O’Brien Lifehouse, Camperdown 2050, Australia; (S.H.); (B.S.)
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Camperdown 2006, Australia; (S.E.K.); (M.E.B.)
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
| | - Saeideh Ebrahim Khani
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Camperdown 2006, Australia; (S.E.K.); (M.E.B.)
| | - Heng Wei
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
| | - Maggie Yuk Ting Lee
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
| | - Hao-Wen Sim
- Department of Medical Oncology and NHMRC Clinical Trials Centre, Chris O’Brien Lifehouse, Camperdown 2050, Australia;
- Central Clinical School, The University of Sydney, Camperdown 2006, Australia
- The Kinghorn Cancer Centre, St Vincent’s Hospital, Darlinghurst 2010, Australia
| | - Joanne Sy
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
| | - Brindha Shivalingam
- Department of Neurosurgical Services, Chris O’Brien Lifehouse, Camperdown 2050, Australia; (S.H.); (B.S.)
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
| | - Michael E. Buckland
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Camperdown 2006, Australia; (S.E.K.); (M.E.B.)
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
| | - Kimberley L. Alexander-Kaufman
- Department of Neurosurgical Services, Chris O’Brien Lifehouse, Camperdown 2050, Australia; (S.H.); (B.S.)
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Camperdown 2006, Australia; (S.E.K.); (M.E.B.)
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
- Correspondence: ; Tel.: +61-2-8514-0675
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42
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Extracellular vesicle-mediated nucleic acid transfer and reprogramming in the tumor microenvironment. Cancer Lett 2020; 482:33-43. [DOI: 10.1016/j.canlet.2020.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/19/2020] [Accepted: 04/03/2020] [Indexed: 02/06/2023]
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43
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Lu Y, Liu D, Feng Q, Liu Z. Diabetic Nephropathy: Perspective on Extracellular Vesicles. Front Immunol 2020; 11:943. [PMID: 32582146 PMCID: PMC7283536 DOI: 10.3389/fimmu.2020.00943] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
Diabetic nephropathy (DN) is a major microvascular complication of diabetes mellitus. It is the most frequent cause of end-stage renal disease with no definitive therapy available so far. Extracellular vesicles (EVs), including exosomes, microvesicles, and apoptotic bodies, are nano- and micron-sized heterogeneous vesicles that can be secreted by almost all cell types. Importantly, EVs contain many biologically active materials, such as RNAs, DNAs, proteins, and lipids, from their parental cells, which can be transported to their recipient cells to mediate intercellular communication and signaling. Accumulating studies demonstrated that EVs, mainly exosomes and microvesicles, participated in the pathophysiological process of DN. Recently emerging studies also found that the contents of EVs in the urine (miRNAs, mRNAs, and proteins) could be used as potential biomarkers for DN. Therefore, in this mini-review, the generation, isolation methods, and biological function of EVs were introduced, and then the current information about the mechanism and the diagnostic value in the development of DN was summarized. Moreover, the review also discussed the future challenges of exploring the role of EVs in kidney disease.
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Affiliation(s)
- Yanfang Lu
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China.,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China.,Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou, China
| | - Dongwei Liu
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China.,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China.,Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou, China
| | - Qi Feng
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China.,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China.,Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou, China
| | - Zhangsuo Liu
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China.,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China.,Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou, China
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44
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snoRNAs Offer Novel Insight and Promising Perspectives for Lung Cancer Understanding and Management. Cells 2020; 9:cells9030541. [PMID: 32111002 PMCID: PMC7140444 DOI: 10.3390/cells9030541] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/29/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are non-coding RNAs localized in the nucleolus, where they participate in the cleavage and chemical modification of ribosomal RNAs. Their biogenesis and molecular functions have been extensively studied since their identification in the 1960s. However, their role in cancer has only recently started to emerge. In lung cancer, efforts to profile snoRNA expression have enabled the definition of snoRNA-related signatures, not only in tissues but also in biological fluids, exposing these small RNAs as potential non-invasive biomarkers. Moreover, snoRNAs appear to be essential actors of lung cancer onset and dissemination. They affect diverse cellular functions, from regulation of the cell proliferation/death balance to promotion of cancer cell plasticity. snoRNAs display both oncogenic and tumor suppressive activities that are pivotal in lung cancer tumorigenesis and progression. Altogether, we review how further insight into snoRNAs may improve our understanding of basic lung cancer biology and the development of innovative diagnostic tools and therapies.
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45
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Wang Z, Yang H, Ma D, Mu Y, Tan X, Hao Q, Feng L, Liang J, Xin W, Chen Y, Wu Y, Jia Y, Zhao H. Serum PIWI-Interacting RNAs piR-020619 and piR-020450 Are Promising Novel Biomarkers for Early Detection of Colorectal Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:990-998. [PMID: 32066615 DOI: 10.1158/1055-9965.epi-19-1148] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/27/2019] [Accepted: 02/07/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Early diagnosis can significantly reduce colorectal cancer deaths. We sought to identify serum PIWI-interacting RNAs (piRNAs) that could serve as sensitive and specific noninvasive biomarkers for early colorectal cancer detection. METHODS We screened the piRNA expression profile in sera from 7 patients with colorectal cancer and 7 normal controls using small RNA sequencing. Differentially expressed piRNAs were measured in a training cohort of 140 patients with colorectal cancer and 140 normal controls using reverse transcription quantitative PCR. The identified piRNAs were evaluated in two independent validation cohorts of 180 patients with colorectal cancer and 180 normal controls. Finally, the diagnostic value of the identified piRNAs for colorectal adenoma (CRA) was assessed, and their expression was measured in 50 patients with lung cancer, 50 with breast cancer, and 50 with gastric cancer. RESULTS The piRNAs piR-020619 and piR-020450 were consistently elevated in sera of patients with colorectal cancer as compared with controls. A predicative panel based on the two piRNAs was established that displayed high diagnostic accuracy for colorectal cancer detection. The two-piRNA panel could detect small-size and early-stage colorectal cancer with an area under the ROC curve of 0.863 and 0.839, respectively. Combined use of the two piRNAs could effectively distinguish CRA from controls. Aberrant elevation of the two piRNAs was not observed in sera of patients with lung, breast, and gastric cancer. CONCLUSIONS Serum piR-020619 and piR-020450 show a strong potential as colorectal cancer-specific early detection biomarkers. IMPACT The field of circulating piRNAs could allow for novel tumor biomarker development.
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Affiliation(s)
- Zhenfei Wang
- The Laboratory for Tumor Molecular Diagnosis, Affiliated People's Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Hao Yang
- Department of Radiotherapy, Affiliated People's Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Daguang Ma
- Department of Thoracic Surgery, Affiliated People's Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Yongping Mu
- The Laboratory for Tumor Molecular Diagnosis, Affiliated People's Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Xiaohui Tan
- College of Traditional Chinese Medicine, Inner Mongolia Medical University, Huhhot, China
| | - Qin Hao
- Department of Gastrointestinal Surgery, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Li Feng
- Department of Abdominal Tumor Surgery, Affiliated People's Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Junqing Liang
- The Laboratory for Tumor Molecular Diagnosis, Affiliated People's Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Wen Xin
- TransGen Biotech Co. Ltd., Beijing, China
| | - Yongxia Chen
- The Laboratory for Tumor Molecular Diagnosis, Affiliated People's Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Yingcai Wu
- The Laboratory for Tumor Molecular Diagnosis, Affiliated People's Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Yongfeng Jia
- The Laboratory for Tumor Molecular Diagnosis, Affiliated People's Hospital of Inner Mongolia Medical University, Huhhot, China. .,Basic Medicine College, Inner Mongolia Medical University, Huhhot, China
| | - Haiping Zhao
- Department of Abdominal Tumor Surgery, Affiliated People's Hospital of Inner Mongolia Medical University, Huhhot, China.
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46
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Han W, Cui H, Liang J, Su X. Role of MicroRNA-30c in cancer progression. J Cancer 2020; 11:2593-2601. [PMID: 32201529 PMCID: PMC7066027 DOI: 10.7150/jca.38449] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/21/2020] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) is a non-coding small RNA of a type of 18~24 nucleotide-regulated gene that has been discovered in recent years. It mainly degrades the target gene mRNA or inhibits its translation process through the complete or incomplete bindings with 3'UTR of target genes, followed by the regulation of individual development, apoptosis, proliferation, differentiation and other life activities through the post-transcriptional regulation. Among many miRNAs, the microRNA family, miR-30, plays diverse roles in these key process of neoplastic transformation, metastasis, and clinical outcomes in different cancer progression. As key member of miR-30, miR-30c is regulated by oncogenic transcription factors and cancer progression related genes. Recently, numerous studies have demonstrated that the aberrant expression of miR-30c was significantly associated with the majority of human cancer progression. In this review, the diverse roles of miR-30c in different cancer progression such as the cellular and molecular mechanisms, the potential applications in clinics were summarized to speculate the benefits of miR-30c over-expression in cancer treatment and prognosis.
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Affiliation(s)
- Wenyan Han
- Laboratory of the Second Affiliated Hospital of Inner Mongolia Medical University.No.1 Yingfang Road, Huimin District, Hohhot, Inner Mongolia, China
| | - Hongwei Cui
- Clinical Medical Research Center of the Affiliated Hospital/Inner Mongolia Key Laboratory of Medical Cellular Biology, Inner Mongolia Medical University, Hohhot, 010050, Inner Mongolia, P.R. China
| | - Junqing Liang
- Department of Breast Oncology, Inner Mongolia Autonomous Region Cancer Hospital, Hohhot, 010000, Inner Mongolia, P.R. China
| | - Xiulan Su
- Clinical Medical Research Center of the Affiliated Hospital/Inner Mongolia Key Laboratory of Medical Cellular Biology, Inner Mongolia Medical University, Hohhot, 010050, Inner Mongolia, P.R. China
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47
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Advances in the study of exosomal lncRNAs in tumors and the selection of research methods. Biomed Pharmacother 2019; 123:109716. [PMID: 31896067 DOI: 10.1016/j.biopha.2019.109716] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/19/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023] Open
Abstract
Exosomes are endosome-derived extracellular vesicles that are released upon the fusion of multivesicular bodies with the plasma membrane. These vesicles contain proteins, lipids, and nucleic acids and are found in various human body fluids. Exosomes can transfer bioactive molecules to nearby or distant recipient cells, thereby affecting their function. Recently, exosomes have gained importance as a medium of communication between tumor cells. An increasing number of studies have found that non-coding RNAs in tumor cell-derived exosomes can regulate tumor microenvironments, inhibit immune cell function, promote the growth and invasion of tumor cells, and impart resistance to chemicals in tumor cells. In this review, we focus on the effects of exosomal long non-coding RNAs (lncRNAs) on tumors. As exosomes and their parent cells have similar biological characteristics and coated lncRNAs can exist stably in vivo without being degraded by RNases, exosomal lncRNAs have emerged as novel non-invasive tumor biomarkers for use in the early diagnosis and evaluation of prognosis of tumors. Advancements in the field have led to the development of a variety of techniques in exosomal non-coding RNA research. Currently, most methods include the separation and purification of exosomes, followed by RNA extraction, reverse transcription, and subsequent analyses; thus, these processes are very tedious and vulnerable to contamination and could lead to inaccurate and inconsistent results. Thus, there has been an increase in the development of detection methods for exosomal RNAs. Here, we discuss the existing research methods, their advantages and disadvantages, and a few new techniques.
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48
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Gotte G, Menegazzi M. Biological Activities of Secretory RNases: Focus on Their Oligomerization to Design Antitumor Drugs. Front Immunol 2019; 10:2626. [PMID: 31849926 PMCID: PMC6901985 DOI: 10.3389/fimmu.2019.02626] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/22/2019] [Indexed: 12/11/2022] Open
Abstract
Ribonucleases (RNases) are a large number of enzymes gathered into different bacterial or eukaryotic superfamilies. Bovine pancreatic RNase A, bovine seminal BS-RNase, human pancreatic RNase 1, angiogenin (RNase 5), and amphibian onconase belong to the pancreatic type superfamily, while binase and barnase are in the bacterial RNase N1/T1 family. In physiological conditions, most RNases secreted in the extracellular space counteract the undesired effects of extracellular RNAs and become protective against infections. Instead, if they enter the cell, RNases can digest intracellular RNAs, becoming cytotoxic and having advantageous effects against malignant cells. Their biological activities have been investigated either in vitro, toward a number of different cancer cell lines, or in some cases in vivo to test their potential therapeutic use. However, immunogenicity or other undesired effects have sometimes been associated with their action. Nevertheless, the use of RNases in therapy remains an appealing strategy against some still incurable tumors, such as mesothelioma, melanoma, or pancreatic cancer. The RNase inhibitor (RI) present inside almost all cells is the most efficacious sentry to counteract the ribonucleolytic action against intracellular RNAs because it forms a tight, irreversible and enzymatically inactive complex with many monomeric RNases. Therefore, dimerization or multimerization could represent a useful strategy for RNases to exert a remarkable cytotoxic activity by evading the interaction with RI by steric hindrance. Indeed, the majority of the mentioned RNases can hetero-dimerize with antibody derivatives, or even homo-dimerize or multimerize, spontaneously or artificially. This can occur through weak interactions or upon introducing covalent bonds. Immuno-RNases, in particular, are fusion proteins representing promising drugs by combining high target specificity with easy delivery in tumors. The results concerning the biological features of many RNases reported in the literature are described and discussed in this review. Furthermore, the activities displayed by some RNases forming oligomeric complexes, the mechanisms driving toward these supramolecular structures, and the biological rebounds connected are analyzed. These aspects are offered with the perspective to suggest possible efficacious therapeutic applications for RNases oligomeric derivatives that could contemporarily lack, or strongly reduce, immunogenicity and other undesired side-effects.
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Affiliation(s)
- Giovanni Gotte
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Marta Menegazzi
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
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49
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Diversity and heterogeneity of extracellular RNA in human plasma. Biochimie 2019; 164:22-36. [PMID: 31108123 DOI: 10.1016/j.biochi.2019.05.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/14/2019] [Indexed: 12/15/2022]
Abstract
Extracellular RNAs (exRNAs) are secreted by nearly all cell types and are now known to play multiple physiological roles. In humans, exRNA populations are found in nearly any physiological liquid and are attracting growing interest as a potential source for biomarker discovery. Human plasma, a readily available sample for biomedical analysis, 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. This variation explains the extreme complexity of the human exRNA fraction in plasma. In this work, we aimed to characterize exRNA species from blood samples of healthy human donors to achieve the most comprehensive overview of the species, sizes and origins of the exRNA present in plasma fractions. Unbiased analysis of exRNA composition was performed with prefractionation of plasma exRNA followed by library preparation, sequencing and bioinformatics analysis. Our results demonstrate that, in addition to "mature", adaptor ligation-competent RNA species (5'-P/3'-OH), human plasma contains a substantial proportion of degraded RNA fragments (5'-OH/3'-P or cycloP), which can be made competent for ligation using appropriate treatments. These degraded RNAs represent the major fraction in the overall population and mostly correspond to rRNA, in contrast to mature products, which mostly contain miRNAs and hY4 RNA fragments. Precipitation polyethylene glycol (PEG)-based kits for EV isolation yield a fraction that is highly contaminated by large RNPs and by RNA loosely bound to EVs. Purer EV preparations are obtained by using proteinase K and RNase A treatment, as well as by size-exclusion chromatography (SEC). These samples have rather distinct RNA compositions compared to PEG-precipitated EV preparations and contain a substantial proportion of exRNA of non-human origin, arising from human skin and gut microbiota, including viral microbiota. These exogenous exRNAs represent up to 75-80% of total RNA reads in highly purified extracellular vesicles, paving the way for biomedical exploitation of these non-human biomarkers.
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50
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Turchinovich A, Drapkina O, Tonevitsky A. Transcriptome of Extracellular Vesicles: State-of-the-Art. Front Immunol 2019; 10:202. [PMID: 30873152 PMCID: PMC6404625 DOI: 10.3389/fimmu.2019.00202] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/23/2019] [Indexed: 12/21/2022] Open
Abstract
Exosomes and microvesicles are two major categories of extracellular vesicles (EVs) released by almost all cell types and are highly abundant in biological fluids. Both the molecular composition of EVs and their release are thought to be strictly regulated by external stimuli. Multiple studies have consistently demonstrated that EVs transfer proteins, lipids and RNA between various cell types, thus mediating intercellular communication, and signaling. Importantly, small non-coding RNAs within EVs are thought to be major contributors to the molecular events occurring in the recipient cell. Furthermore, RNA cargo in exosomes and microvesicles could hold tremendous potential as non-invasive biomarkers for multiple disorders, including pathologies of the immune system. This mini-review is aimed to provide the state-of-the-art in the EVs-associated RNA transcriptome field, as well as the comprehensive analysis of previous studies characterizing RNA content within EVs released by various cells using next-generation sequencing. Finally, we highlight the technical challenges associated with obtaining pure EVs and deep sequencing of the EV-associated RNAs.
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Affiliation(s)
- Andrey Turchinovich
- SciBerg e.Kfm, Mannheim, Germany.,Molecular Epidemiology C080, German Cancer Research Center, Heidelberg, Germany
| | - Oxana Drapkina
- National Medical Research Center for Preventive Medicine, Moscow, Russia
| | - Alexander Tonevitsky
- Department of Cell Biology, Higher School of Economics, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,SRC BioClinicum, Moscow, Russia
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