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Hasan MDN, Rahman MDM, Husna AA, Kato D, Nakagawa T, Arif M, Miura N. Hypoxia-related Y RNA fragments as a novel potential biomarker for distinguishing metastatic oral melanoma from non-metastatic oral melanoma in dogs. Vet Q 2024; 44:1-8. [PMID: 38288969 PMCID: PMC10829814 DOI: 10.1080/01652176.2023.2300943] [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: 07/28/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024] Open
Abstract
Hypoxia may promote tumor progression, and hypoxically altered noncoding RNA (ncRNA) expression may play a role in metastasis. Canine oral melanoma (COM) frequently metastasizes, and ncRNA expression under hypoxia may be clinically significant. We aimed to elucidate ncRNA fragments whose expression is altered by hypoxia in COM-derived primary KMeC and metastatic LMeC cell lines using next-generation sequencing to validate these results in qRT-PCR, and then compare expression between metastatic and non-metastatic COM. The NGS analysis and subsequent qRT-PCR validation were performed using hypoxic and normoxic KMeC and LMeC cells, and clinical samples [tumor tissue, plasma, and plasma-derived extracellular vesicles] obtained from dogs with metastatic or non-metastatic melanoma were analyzed with qRT-PCR. Y RNA was significantly decreased in metastatic LMeC cells versus primary KMeC cells in hypoxic and normoxic conditions. The expression of Y RNA was decreased in dogs with metastatic melanoma versus those with non-metastatic melanoma for all clinical sample types, reflecting the pattern found with hypoxia. Receiver operating characteristic analysis demonstrated that Y RNA level is a promising biomarker for discriminating metastatic from non-metastatic melanoma in plasma [area under the curve (AUC) = 0.993, p < 0.0001] and plasma-derived extracellular vesicles (AUC = 0.981, p = 0.0002). Overall, Y RNA may be more resistant to hypoxic stress in the metastatic than the non-metastatic state for COM. However, further investigation is required to elucidate the biological functions of Y RNA under hypoxic conditions.
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Affiliation(s)
- MD Nazmul Hasan
- Joint Graduate School of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Japan
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Kagoshima, Japan
| | - MD Mahfuzur Rahman
- Department of Human Oncology, University of WI School of Medicine and Public Health, Madison, WI, USA
| | - Al Asmaul Husna
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Kagoshima, Japan
| | - Daiki Kato
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Takayuki Nakagawa
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Mohammad Arif
- Joint Graduate School of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Naoki Miura
- Joint Graduate School of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Japan
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Kagoshima, Japan
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2
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Stewart JM. RNA nanotechnology on the horizon: Self-assembly, chemical modifications, and functional applications. Curr Opin Chem Biol 2024; 81:102479. [PMID: 38889473 DOI: 10.1016/j.cbpa.2024.102479] [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: 04/01/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/20/2024]
Abstract
RNA nanotechnology harnesses the unique chemical and structural properties of RNA to build nanoassemblies and supramolecular structures with dynamic and functional capabilities. This review focuses on design and assembly approaches to building RNA structures, the RNA chemical modifications used to enhance stability and functionality, and modern-day applications in therapeutics, biosensing, and bioimaging.
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3
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Ciullo A, Li L, Li C, Tsi K, Farrell C, Pellegrini M, Marbán E, Ibrahim AGE. Non-coding RNA yREX3 from human extracellular vesicles exerts macrophage-mediated cardioprotection via a novel gene-methylating mechanism. Eur Heart J 2024:ehae357. [PMID: 38865332 DOI: 10.1093/eurheartj/ehae357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/22/2024] [Accepted: 05/21/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND AND AIMS Extracellular vesicles (EVs) secreted by cardiosphere-derived cells exert immunomodulatory effects through the transmission of small non-coding RNAs. METHODS The mechanism and role of yREX3, a small Y RNA abundant in EVs in myocardial injury, was investigated. RESULTS yREX3 attenuates cardiac ischaemic injury by selective DNA methylation. Synthetic yREX3 encapsulated in lipid nanoparticles triggers broad transcriptomic changes in macrophages, localizes to the nucleus, and mediates epigenetic silencing of protein interacting with C kinase-1 (Pick1) through methylation of upstream CpG sites. Moreover, yREX3 interacts with polypyrimidine tract binding protein 3 (PTBP3) to methylate the Pick1 gene locus in a DNA methyltransferase-dependent manner. Suppression of Pick1 in macrophages potentiates Smad3 signalling and enhances efferocytosis, minimizing heart necrosis in rats with myocardial infarction. Adoptive transfer of Pick1-deficient macrophages recapitulates the cardioprotective effects of yREX3 in vivo. CONCLUSIONS These findings highlight the role of a small Y RNA mined from EVs with a novel gene-methylating mechanism.
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Affiliation(s)
- Alessandra Ciullo
- Cedars-Sinai Medical Center, Smidt Heart Institute, 8700 Beverly Blvd, 1090 Davis Bldg, Los Angeles, CA 90048, USA
| | - Liang Li
- Cedars-Sinai Medical Center, Smidt Heart Institute, 8700 Beverly Blvd, 1090 Davis Bldg, Los Angeles, CA 90048, USA
| | - Chang Li
- Cedars-Sinai Medical Center, Smidt Heart Institute, 8700 Beverly Blvd, 1090 Davis Bldg, Los Angeles, CA 90048, USA
| | - Kara Tsi
- Cedars-Sinai Medical Center, Smidt Heart Institute, 8700 Beverly Blvd, 1090 Davis Bldg, Los Angeles, CA 90048, USA
| | - Colin Farrell
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Eduardo Marbán
- Cedars-Sinai Medical Center, Smidt Heart Institute, 8700 Beverly Blvd, 1090 Davis Bldg, Los Angeles, CA 90048, USA
| | - Ahmed G E Ibrahim
- Cedars-Sinai Medical Center, Smidt Heart Institute, 8700 Beverly Blvd, 1090 Davis Bldg, Los Angeles, CA 90048, USA
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Velázquez-Flores MÁ, Ruiz Esparza-Garrido R. Fragments derived from non-coding RNAs: how complex is genome regulation? Genome 2024. [PMID: 38684113 DOI: 10.1139/gen-2023-0136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The human genome is highly dynamic and only a small fraction of it codes for proteins, but most of the genome is transcribed, highlighting the importance of non-coding RNAs on cellular functions. In addition, it is now known the generation of non-coding RNA fragments under particular cellular conditions and their functions have revealed unexpected mechanisms of action, converging, in some cases, with the biogenic pathways and action machineries of microRNAs or Piwi-interacting RNAs. This led us to the question why the cell produces so many apparently redundant molecules to exert similar functions and regulate apparently convergent processes? However, non-coding RNAs fragments can also function similarly to aptamers, with secondary and tertiary conformations determining their functions. In the present work, it was reviewed and analyzed the current information about the non-coding RNAs fragments, describing their structure and biogenic pathways, with special emphasis on their cellular functions.
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Affiliation(s)
- Miguel Ángel Velázquez-Flores
- Laboratorio de RNAs No Codificantes de la Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX, México
| | - Ruth Ruiz Esparza-Garrido
- Investigadora por México, Laboratorio de RNAs No Codificantes de la Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX, México
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5
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Bryl R, Kulus M, Bryja A, Domagała D, Mozdziak P, Antosik P, Bukowska D, Zabel M, Dzięgiel P, Kempisty B. Cardiac progenitor cell therapy: mechanisms of action. Cell Biosci 2024; 14:30. [PMID: 38444042 PMCID: PMC10913616 DOI: 10.1186/s13578-024-01211-x] [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: 07/01/2023] [Accepted: 02/17/2024] [Indexed: 03/07/2024] Open
Abstract
Heart failure (HF) is an end-stage of many cardiac diseases and one of the main causes of death worldwide. The current management of this disease remains suboptimal. The adult mammalian heart was considered a post-mitotic organ. However, several reports suggest that it may possess modest regenerative potential. Adult cardiac progenitor cells (CPCs), the main players in the cardiac regeneration, constitute, as it may seem, a heterogenous group of cells, which remain quiescent in physiological conditions and become activated after an injury, contributing to cardiomyocytes renewal. They can mediate their beneficial effects through direct differentiation into cardiac cells and activation of resident stem cells but majorly do so through paracrine release of factors. CPCs can secrete cytokines, chemokines, and growth factors as well as exosomes, rich in proteins, lipids and non-coding RNAs, such as miRNAs and YRNAs, which contribute to reparation of myocardium by promoting angiogenesis, cardioprotection, cardiomyogenesis, anti-fibrotic activity, and by immune modulation. Preclinical studies assessing cardiac progenitor cells and cardiac progenitor cells-derived exosomes on damaged myocardium show that administration of cardiac progenitor cells-derived exosomes can mimic effects of cell transplantation. Exosomes may become new promising therapeutic strategy for heart regeneration nevertheless there are still several limitations as to their use in the clinic. Key questions regarding their dosage, safety, specificity, pharmacokinetics, pharmacodynamics and route of administration remain outstanding. There are still gaps in the knowledge on basic biology of exosomes and filling them will bring as closer to translation into clinic.
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Affiliation(s)
- Rut Bryl
- Section of Regenerative Medicine and Cancer Research, Natural Sciences Club, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznan, 61-614, Poland
| | - Magdalena Kulus
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University, Torun, 87-100, Poland
| | - Artur Bryja
- Department of Human Morphology and Embryology, Division of Anatomy, Wroclaw Medical University, Wroclaw, 50-367, Poland
| | - Dominika Domagała
- Department of Human Morphology and Embryology, Division of Anatomy, Wroclaw Medical University, Wroclaw, 50-367, Poland
| | - Paul Mozdziak
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, 27695, USA
- Physiology Graduate Faculty, North Carolina State University, Raleigh, NC, 27695, USA
| | - Paweł Antosik
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University, Torun, 87-100, Poland
| | - Dorota Bukowska
- Department of Diagnostics and Clinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Maciej Zabel
- Division of Anatomy and Histology, University of Zielona Góra, Zielona Góra, 65-046, Poland
- Department of Human Morphology and Embryology, Division of Histology and Embryology, Wroclaw Medical University, Wroclaw, 50-368, Poland
| | - Piotr Dzięgiel
- Department of Human Morphology and Embryology, Division of Histology and Embryology, Wroclaw Medical University, Wroclaw, 50-368, Poland
| | - Bartosz Kempisty
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University, Torun, 87-100, Poland.
- Department of Human Morphology and Embryology, Division of Anatomy, Wroclaw Medical University, Wroclaw, 50-367, Poland.
- Physiology Graduate Faculty, North Carolina State University, Raleigh, NC, 27695, USA.
- Department of Obstetrics and Gynaecology, University Hospital and Masaryk University, Brno, 62500, Czech Republic.
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6
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Michael FS, Hamouda MB, Stupak J, Li J, Pearson A, Sauvageau J. Identification of glycosylated nucleosides in small synthetic glyco-RNAs. Chembiochem 2024; 25:e202300784. [PMID: 38116890 DOI: 10.1002/cbic.202300784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
Recently, the post-transcriptional modification of RNA with N-glycans was reported, changing the paradigm that RNAs are not commonly N-glycosylated. Moreover, glycan modifications of RNA are investigated for therapeutic targeting purposes. But the glyco-RNA field is in its infancy with many challenges to overcome. One question is how to accurately characterize glycosylated RNA constructs. Thus, we generated glycosylated forms of Y5 RNA mimics, a short non-coding RNA. The simple glycans lactose and sialyllactose were attached to the RNA backbone using azide-alkyne cycloadditions. Using nuclease digestion followed by LC-MS, we confirmed the presence of the glycosylated nucleosides, and characterized the chemical linkage. Next, we probed if glycosylation would affect the cellular response to Y5 RNA. We treated human foreskin fibroblasts in culture with the generated compounds. Key transcripts in the innate immune response were quantified by RT-qPCR. We found that under our experimental conditions, exposure of cells to the Y5 RNA did not trigger an interferon response, and glycosylation of this RNA did not have an impact. Thus, we have identified a successful approach to chemically characterize synthetic glyco-RNAs, which will be critical for further studies to elucidate how the presence of complex glycans on RNA affects the cellular response.
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Affiliation(s)
- Frank St Michael
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
| | - Maha Ben Hamouda
- INRS-Centre Armand-Frappier Santé Biotechnologie, 531, boul. des Prairies, Laval, Québec, H7V 1B7, Canada
| | - Jacek Stupak
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
| | - Jianjun Li
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
| | - Angela Pearson
- INRS-Centre Armand-Frappier Santé Biotechnologie, 531, boul. des Prairies, Laval, Québec, H7V 1B7, Canada
| | - Janelle Sauvageau
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
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7
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Babington S, Tilbrook AJ, Maloney SK, Fernandes JN, Crowley TM, Ding L, Fox AH, Zhang S, Kho EA, Cozzolino D, Mahony TJ, Blache D. Finding biomarkers of experience in animals. J Anim Sci Biotechnol 2024; 15:28. [PMID: 38374201 PMCID: PMC10877933 DOI: 10.1186/s40104-023-00989-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/28/2023] [Indexed: 02/21/2024] Open
Abstract
At a time when there is a growing public interest in animal welfare, it is critical to have objective means to assess the way that an animal experiences a situation. Objectivity is critical to ensure appropriate animal welfare outcomes. Existing behavioural, physiological, and neurobiological indicators that are used to assess animal welfare can verify the absence of extremely negative outcomes. But welfare is more than an absence of negative outcomes and an appropriate indicator should reflect the full spectrum of experience of an animal, from negative to positive. In this review, we draw from the knowledge of human biomedical science to propose a list of candidate biological markers (biomarkers) that should reflect the experiential state of non-human animals. The proposed biomarkers can be classified on their main function as endocrine, oxidative stress, non-coding molecular, and thermobiological markers. We also discuss practical challenges that must be addressed before any of these biomarkers can become useful to assess the experience of an animal in real-life.
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Affiliation(s)
- Sarah Babington
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Alan J Tilbrook
- Centre for Animal Science, The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
- School of Veterinary Science, The University of Queensland, Gatton, QLD, 4343, Australia
| | - Shane K Maloney
- School of Human Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Jill N Fernandes
- School of Veterinary Science, The University of Queensland, Gatton, QLD, 4343, Australia
| | - Tamsyn M Crowley
- School of Medicine, Deakin University, Geelong, VIC, 3217, Australia
- Poultry Hub Australia, University of New England, Armidale, NSW, 2350, Australia
| | - Luoyang Ding
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Archa H Fox
- School of Human Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Song Zhang
- School of Human Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Elise A Kho
- Centre for Animal Science, The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Daniel Cozzolino
- Centre for Nutrition and Food Sciences, The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Timothy J Mahony
- Centre for Animal Science, The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Dominique Blache
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia.
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
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8
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Bai Z, Zhang D, Gao Y, Tao B, Bao S, Enninful A, Zhang D, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu ML, Fan R. Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579143. [PMID: 38370833 PMCID: PMC10871202 DOI: 10.1101/2024.02.06.579143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Spatial transcriptomics has emerged as a powerful tool for dissecting spatial cellular heterogeneity but as of today is largely limited to gene expression analysis. Yet, the life of RNA molecules is multifaceted and dynamic, requiring spatial profiling of different RNA species throughout the life cycle to delve into the intricate RNA biology in complex tissues. Human disease-relevant tissues are commonly preserved as formalin-fixed and paraffin-embedded (FFPE) blocks, representing an important resource for human tissue specimens. The capability to spatially explore RNA biology in FFPE tissues holds transformative potential for human biology research and clinical histopathology. Here, we present Patho-DBiT combining in situ polyadenylation and deterministic barcoding for spatial full coverage transcriptome sequencing, tailored for probing the diverse landscape of RNA species even in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for five years. Furthermore, genome-wide single nucleotide RNA variants can be captured to distinguish different malignant clones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA-mRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis trajectory. High resolution Patho-DBiT at the cellular level reveals a spatial neighborhood and traces the spatiotemporal kinetics driving tumor progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to study human tissue biology and aid in clinical pathology evaluation.
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Affiliation(s)
- Zhiliang Bai
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Dingyao Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yan Gao
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bo Tao
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shuozhen Bao
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Archibald Enninful
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Daiwei Zhang
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Xiaolong Tian
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Ningning Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yang Xiao
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Yang Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mark Gerstein
- Section on Biomedical Informatics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jun Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mina L. Xu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA
- Human and Translational Immunology, Yale University School of Medicine, New Haven, CT 06520, USA
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9
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Hasan MN, Rahman MM, Husna AA, Nozaki N, Yamato O, Miura N. YRNA and tRNA fragments can differentiate benign from malignant canine mammary gland tumors. Biochem Biophys Res Commun 2024; 691:149336. [PMID: 38039834 DOI: 10.1016/j.bbrc.2023.149336] [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: 09/25/2023] [Accepted: 11/23/2023] [Indexed: 12/03/2023]
Abstract
Mammary gland tumors (MGT) are the most common tumors in sexually intact female dogs. The functional regulation of miRNAs, a type of noncoding RNAs (ncRNAs), in canine MGT has been extensively investigated. However, the expression of other ncRNAs, such as YRNAs and transfer RNA-derived fragments (tRFs) in canine MGT is unknown. We investigated ncRNAs other than miRNAs from our small RNA project (PRJNA716131) in different canine MGT histologic subtypes. This study included benign tumors (benign mixed tumor, complex adenoma) and malignant tumors (carcinoma in benign tumor and carcinoma with metastasis) samples. Aberrantly expressed ncRNAs were examined by comparisons among MGT subtypes. The relative expression trends were validated in canine MGT tissues, plasma, extracellular vesicles, and MGT cell lines using quantitative reverse transcription PCR. Three aberrantly expressed ncRNAs were identified by comparisons among MGT subtypes. YRNA and tRNA-Gly-GCC distinguished benign mixed tumor from other MGT histologic subtypes, while tRNA-Val differentiated complex adenoma, carcinoma in benign tumors, and carcinoma with metastasis. The ROC curve of the three ncRNAs showed they might be potential biomarkers to discriminate malignant from benign MGT. YRNA and tRFs expression levels were decreased in metastatic compared with primary canine MGT cell lines. To the best of our knowledge, this is the first investigation of YRNA and tRFs in canine MGT. The three identified ncRNAs may be biomarkers for differentiating MGT histologic subtypes. Suggested Reviewers: Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporatio.
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Affiliation(s)
- Md Nazmul Hasan
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan; Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan.
| | - Md Mahfuzur Rahman
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Al Asmaul Husna
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan.
| | - Nobuhiro Nozaki
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan.
| | - Osamu Yamato
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan; Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan.
| | - Naoki Miura
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan; Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan.
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10
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Elzer D, Bremser M, Zischler H. Human sperm heads harbor modified YsRNA as transgenerationally inherited non-coding RNAs. Front Genet 2023; 14:1294389. [PMID: 38162679 PMCID: PMC10756665 DOI: 10.3389/fgene.2023.1294389] [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: 09/14/2023] [Accepted: 11/23/2023] [Indexed: 01/03/2024] Open
Abstract
Most epigenetic information is reprogrammed during gametogenesis and early development. However, some epigenetic information persists and can be inherited, a phenomenon that is common in plants. On the other hand, there are increasing examples of epigenetic inheritance in metazoans, especially for small non-coding RNAs. The presence of regulatory important RNAs in oocytes is undisputed, whereas the corresponding RNA payload in spermatozoa and its regulatory influence in the zygote and early embryogenesis is largely enigmatic. For humans, we herein describe small YRNA fragments (YsRNA) as a paternal contribution to the zygote. First, we trace the biogenesis of these YsRNAs from the source YRNAs with respect to the 5' and 3' modifications. Both the length and modifications make these YsRNAs reminiscent of canonical piRNAs that are not derived from piRNA clusters. Second, from the early stages of spermatogenesis to maturation in the epididymis, we observe distinct YsRNA profile dynamics in the male germline. We detected YsRNAs exclusively in mature sperm heads, the precursor of the male pronucleus in the zygote, suggesting an important role of the epididymis as a site for transmitting and modification of epigenetic information in the form of YsRNA between soma and germline in humans. Since this YsRNA-based epigenetic mechanism is effective across generations, we wondered whether this phenomenon of epigenetic inheritance has an adaptive value. Full-length YRNAs bind to Ro60, an RNA chaperone that additionally binds to non-coding RNAs. We described the profiles of non-coding RNAs bound to Ro60 in the human sperm head and detected specific binding profiles of RNA to Ro60 but no YRNA bound to Ro60. We hypothesize that the sperm head Ro60 system is functional. An adaptive phenotype mediated by the presence of a large amount of YsRNA in the sperm head, and thus as a paternal contribution in the zygote, might be related to an association of YsRNA with YRNA that prevents the adoption of a YRNA secondary structure capable of binding to Ro60. We hypothesize that preventing YRNAs from acting as Ro60-associated gatekeepers for misfolded RNAs in the zygote and early development may enhance RNA chaperoning and, thus, represent the adaptive molecular phenotype.
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Affiliation(s)
- Darja Elzer
- Division of Anthropology, Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Hans Zischler
- Division of Anthropology, Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
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11
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Akins RB, Ostberg K, Cherlin T, Tsiouplis NJ, Loher P, Rigoutsos I. The Typical tRNA Co-Expresses Multiple 5' tRNA Halves Whose Sequences and Abundances Depend on Isodecoder and Isoacceptor and Change with Tissue Type, Cell Type, and Disease. Noncoding RNA 2023; 9:69. [PMID: 37987365 PMCID: PMC10660753 DOI: 10.3390/ncrna9060069] [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] [Received: 08/15/2023] [Revised: 10/02/2023] [Accepted: 10/12/2023] [Indexed: 11/22/2023] Open
Abstract
Transfer RNA-derived fragments (tRFs) are noncoding RNAs that arise from either mature transfer RNAs (tRNAs) or their precursors. One important category of tRFs comprises the tRNA halves, which are generated through cleavage at the anticodon. A given tRNA typically gives rise to several co-expressed 5'-tRNA halves (5'-tRHs) that differ in the location of their 3' ends. These 5'-tRHs, even though distinct, have traditionally been treated as indistinguishable from one another due to their near-identical sequences and lengths. We focused on co-expressed 5'-tRHs that arise from the same tRNA and systematically examined their exact sequences and abundances across 10 different human tissues. To this end, we manually curated and analyzed several hundred human RNA-seq datasets from NCBI's Sequence Run Archive (SRA). We grouped datasets from the same tissue into their own collection and examined each group separately. We found that a given tRNA produces different groups of co-expressed 5'-tRHs in different tissues, different cell lines, and different diseases. Importantly, the co-expressed 5'-tRHs differ in their sequences, absolute abundances, and relative abundances, even among tRNAs with near-identical sequences from the same isodecoder or isoacceptor group. The findings suggest that co-expressed 5'-tRHs that are produced from the same tRNA or closely related tRNAs have distinct, context-dependent roles. Moreover, our analyses show that cell lines modeling the same tissue type and disease may not be interchangeable when it comes to experimenting with tRFs.
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Affiliation(s)
| | | | | | | | | | - Isidore Rigoutsos
- Computational Medical Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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12
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Ushio N, Hasan MN, Arif M, Miura N. Novel Y RNA-Derived Fragments Can Differentiate Canine Hepatocellular Carcinoma from Hepatocellular Adenoma. Animals (Basel) 2023; 13:3054. [PMID: 37835660 PMCID: PMC10571523 DOI: 10.3390/ani13193054] [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: 08/14/2023] [Revised: 09/16/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Hepatocellular carcinomas (HCC) are common tumors, whereas hepatocellular adenomas (HCA) are rare, benign tumors in dogs. The aberrant expression of noncoding RNAs (ncRNAs) plays a pivotal role in HCC tumorigenesis and progression. Among ncRNAs, micro RNAs have been widely researched in human HCC, but much less widely in canine HCC. However, Y RNA-derived fragments have yet to be investigated in canine HCC and HCA. This study targeted canine HCC and HCA patients. We used qRT-PCR to determine Y RNA expression in clinical tissues, plasma, and plasma extracellular vesicles, and two HCC cell lines (95-1044 and AZACH). Y RNA was significantly decreased in tissue, plasma, and plasma extracellular vesicles for canine HCC versus canine HCA and healthy controls. Y RNA was decreased in 95-1044 and AZACH cells versus normal liver tissue and in AZACH versus 95-1044 cells. In plasma samples, Y RNA levels were decreased in HCC versus HCA and Healthy controls and increased in HCA versus Healthy controls. Receiver operating characteristic analysis showed that Y RNA could be a promising biomarker for distinguishing HCC from HCA and healthy controls. Overall, the dysregulated expression of Y RNA can distinguish canine HCC from HCA. However, further research is necessary to elucidate the underlying Y RNA-related molecular mechanisms in hepatocellular neoplastic diseases. To the best of our knowledge, this is the first report on the relative expression of Y RNA in canine HCC and HCA.
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Affiliation(s)
- Norio Ushio
- United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-0841, Japan;
| | - Md Nazmul Hasan
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; (M.N.H.); (M.A.)
| | - Mohammad Arif
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; (M.N.H.); (M.A.)
| | - Naoki Miura
- United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-0841, Japan;
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; (M.N.H.); (M.A.)
- Clinical Veterinary Division, Faculty of Veterinary Medicine, Airlangga University, Mulyorejo, Surabaya 60115, Indonesia
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13
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Zhou S, Van Bortle K. The Pol III transcriptome: Basic features, recurrent patterns, and emerging roles in cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1782. [PMID: 36754845 PMCID: PMC10498592 DOI: 10.1002/wrna.1782] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/10/2023]
Abstract
The RNA polymerase III (Pol III) transcriptome is universally comprised of short, highly structured noncoding RNA (ncRNA). Through RNA-protein interactions, the Pol III transcriptome actuates functional activities ranging from nuclear gene regulation (7SK), splicing (U6, U6atac), and RNA maturation and stability (RMRP, RPPH1, Y RNA), to cytoplasmic protein targeting (7SL) and translation (tRNA, 5S rRNA). In higher eukaryotes, the Pol III transcriptome has expanded to include additional, recently evolved ncRNA species that effectively broaden the footprint of Pol III transcription to additional cellular activities. Newly evolved ncRNAs function as riboregulators of autophagy (vault), immune signaling cascades (nc886), and translation (Alu, BC200, snaR). Notably, upregulation of Pol III transcription is frequently observed in cancer, and multiple ncRNA species are linked to both cancer progression and poor survival outcomes among cancer patients. In this review, we outline the basic features and functions of the Pol III transcriptome, and the evidence for dysregulation and dysfunction for each ncRNA in cancer. When taken together, recurrent patterns emerge, ranging from shared functional motifs that include molecular scaffolding and protein sequestration, overlapping protein interactions, and immunostimulatory activities, to the biogenesis of analogous small RNA fragments and noncanonical miRNAs, augmenting the function of the Pol III transcriptome and further broadening its role in cancer. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Processing of Small RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Sihang Zhou
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kevin Van Bortle
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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14
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van Zonneveld AJ, Zhao Q, Rotmans JI, Bijkerk R. Circulating non-coding RNAs in chronic kidney disease and its complications. Nat Rev Nephrol 2023; 19:573-586. [PMID: 37286733 DOI: 10.1038/s41581-023-00725-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2023] [Indexed: 06/09/2023]
Abstract
Post-transcriptional regulation by non-coding RNAs (ncRNAs) can modulate the expression of genes involved in kidney physiology and disease. A large variety of ncRNA species exist, including microRNAs, long non-coding RNAs, piwi-interacting RNAs, small nucleolar RNAs, circular RNAs and yRNAs. Despite early assumptions that some of these species may exist as by-products of cell or tissue injury, a growing body of literature suggests that these ncRNAs are functional and participate in a variety of processes. Although they function intracellularly, ncRNAs are also present in the circulation, where they are carried by extracellular vesicles, ribonucleoprotein complexes or lipoprotein complexes such as HDL. These systemic, circulating ncRNAs are derived from specific cell types and can be directly transferred to a variety of cells, including endothelial cells of the vasculature and virtually any cell type in the kidney, thereby affecting the function of the host cell and/or its response to injury. Moreover, chronic kidney disease itself, as well as injury states associated with transplantation and allograft dysfunction, is associated with a shift in the distribution of circulating ncRNAs. These findings may provide opportunities for the identification of biomarkers with which to monitor disease progression and/or the development of therapeutic interventions.
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Affiliation(s)
- Anton Jan van Zonneveld
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Qiao Zhao
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Joris I Rotmans
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Roel Bijkerk
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands.
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands.
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15
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Cross T, Haug KBF, Brusletto BS, Ommundsen SK, Trøseid AMS, Aspelin T, Olstad OK, Aass HCD, Galtung HK, Utheim TP, Jensen JL, Øvstebø R. Non-Coding RNA in Salivary Extracellular Vesicles: A New Frontier in Sjögren's Syndrome Diagnostics? Int J Mol Sci 2023; 24:13409. [PMID: 37686214 PMCID: PMC10488010 DOI: 10.3390/ijms241713409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Sjögren's syndrome is an autoimmune rheumatic disease characterized by inflammation of the salivary and lacrimal glands, often manifesting as dry mouth and dry eyes. To simplify diagnostics of primary Sjögren's syndrome (pSS), a non-invasive marker is needed. The aim of the study was to compare the RNA content of salivary extracellular vesicles (EVs) between patients with pSS and healthy controls using microarray technology. Stimulated whole saliva was collected from 11 pSS patients and 11 age-matched controls. EV-RNA was isolated from the saliva samples using a Qiagen exoRNeasy Midi Kit and analyzed using Affymetrix Clariom D™ microarrays. A one-way ANOVA test was used to compare the mean signal values of each transcript between the two groups. A total of 9307 transcripts, coding and non-coding RNA, were detected in all samples. Of these transcripts, 1475 showed statistically significant differential abundance between the pSS and the control groups, generating two distinct EV-RNA patterns. In particular, tRNAs were downregulated in pSS patients, with the transcript tRNA-Ile-AAT-2-1 showing a 2-fold difference, and a promise as a potential biomarker candidate. This study therein demonstrates the potential for using salivary EV-RNA in pSS diagnostics.
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Affiliation(s)
- Tanya Cross
- The Regenerative Medicine Unit, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Kari Bente Foss Haug
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Berit Sletbakk Brusletto
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Stine Kamilla Ommundsen
- The Regenerative Medicine Unit, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Anne-Marie Siebke Trøseid
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Trude Aspelin
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Ole Kristoffer Olstad
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | | | - Hilde Kanli Galtung
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
| | - Tor Paaske Utheim
- The Regenerative Medicine Unit, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, 0372 Oslo, Norway
- Department of Ophthalmology, Oslo University Hospital, 0450 Oslo, Norway
- Department of Ophthalmology, Sørlandet Hospital Arendal, 4838 Arendal, Norway
- Department of Ophthalmology, Vestre Viken Hospital Trust, 3004 Drammen, Norway
- The Norwegian Dry Eye Clinic, 0369 Oslo, Norway
| | - Janicke Liaaen Jensen
- Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, University of Oslo, 0455 Oslo, Norway
| | - Reidun Øvstebø
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
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16
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Olliff NS, Hunt MA, Paudel SS, Nguyen KN, Delcher HA, DeMeis JD, Roberts JT, Fouty BW, Audia JP, Kim JH, Borchert GM. Human YRNA 4 (HY4) plasma levels are a prognostic indicator of SARS-CoV-2 infection clinical severity. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000925. [PMID: 37662051 PMCID: PMC10474479 DOI: 10.17912/micropub.biology.000925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
SARS-CoV-2 infection can result in a range of outcomes from asymptomatic/mild disease to severe COVID-19/fatality. In this study, we investigated the differential expression of small noncoding RNAs (sncRNAs) between patient cohorts defined by disease severity. We collected plasma samples, stratified these based on clinical outcomes, and sequenced their circulating sncRNAs. Excitingly, we found YRNA HY4 displays significant differential expression (p=0.025) between patients experiencing mild and severe disease. In agreement with recent reports identifying plasma YRNAs as indicators of influenza infection severity, our results strongly suggest that circulating HY4 levels represent a powerful prognostic indicator of likely SARS-CoV-2 patient infection outcome.
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Affiliation(s)
| | - Miles A. Hunt
- Biology, Howard University, Washington, Washington, D.C., United States
| | - Sunita S. Paudel
- Pharmacology, University of South Alabama, Mobile, Alabama, United States
| | - Kevin N. Nguyen
- Pharmacology, University of South Alabama, Mobile, Alabama, United States
| | - Haley A. Delcher
- Pharmacology, University of South Alabama, Mobile, Alabama, United States
| | - Jeffrey D. DeMeis
- Pharmacology, University of South Alabama, Mobile, Alabama, United States
| | - Justin T. Roberts
- Pharmacology, University of South Alabama, Mobile, Alabama, United States
| | - Brian W. Fouty
- Pharmacology, University of South Alabama, Mobile, Alabama, United States
- Internal Medicine, University of South Alabama, Mobile, Alabama, United States
| | - Jonathon P. Audia
- Microbiology & Immunology, University of South Alabama, Mobile, Alabama, United States
| | - Jin H. Kim
- Microbiology & Immunology, University of South Alabama, Mobile, Alabama, United States
| | - Glen M. Borchert
- Pharmacology, University of South Alabama, Mobile, Alabama, United States
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17
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Shin HC, Bochkov YA, Kim K, Gern JE, Jarjour NN, Esnault S. A motif in the 5'untranslated region of messenger RNAs regulates protein synthesis in a S6 kinase-dependent manner. Adv Biol Regul 2023; 89:100975. [PMID: 37302177 PMCID: PMC10735251 DOI: 10.1016/j.jbior.2023.100975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023]
Abstract
The 5' untranslated regions (UTRs) in messenger RNAs (mRNAs) play an important role in the regulation of protein synthesis. We had previously identified a group of mRNAs that includes human semaphorin 7A (SEMA7A) whose translation is upregulated by the Erk/p90S6K pathway in human eosinophils, with a potential negative impact in asthma and airway inflammation. In the current study, we aimed to find a common 5'UTR regulatory cis-element, and determine its impact on protein synthesis. We identified a common and conserved 5'UTR motif GGCTG-[(C/G)T(C/G)]n-GCC that was present in this group of mRNAs. Mutations of the first two GG bases in this motif in SEMA7A 5'UTR led to a complete loss of S6K activity dependence for maximal translation. In conclusion, the newly identified 5'UTR motif present in SEMA7A has a critical role in regulating S6K-dependent protein synthesis.
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Affiliation(s)
- Hyun-Chul Shin
- Department of Chemistry Education, Korea National University of Education, Cheongju-si, Chungcheonbuk-do, Republic of Korea
| | - Yury A Bochkov
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Kangsan Kim
- Department of Chemistry Education, Korea National University of Education, Cheongju-si, Chungcheonbuk-do, Republic of Korea
| | - James E Gern
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA; Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Nizar N Jarjour
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Stephane Esnault
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA.
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18
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Xiong Q, Zhang Y. Small RNA modifications: regulatory molecules and potential applications. J Hematol Oncol 2023; 16:64. [PMID: 37349851 PMCID: PMC10286502 DOI: 10.1186/s13045-023-01466-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/14/2023] [Indexed: 06/24/2023] Open
Abstract
Small RNAs (also referred to as small noncoding RNAs, sncRNA) are defined as polymeric ribonucleic acid molecules that are less than 200 nucleotides in length and serve a variety of essential functions within cells. Small RNA species include microRNA (miRNA), PIWI-interacting RNA (piRNA), small interfering RNA (siRNA), tRNA-derived small RNA (tsRNA), etc. Current evidence suggest that small RNAs can also have diverse modifications to their nucleotide composition that affect their stability as well as their capacity for nuclear export, and these modifications are relevant to their capacity to drive molecular signaling processes relevant to biogenesis, cell proliferation and differentiation. In this review, we highlight the molecular characteristics and cellular functions of small RNA and their modifications, as well as current techniques for their reliable detection. We also discuss how small RNA modifications may be relevant to the clinical applications for the diagnosis and treatment of human health conditions such as cancer.
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Affiliation(s)
- Qunli Xiong
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics and Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
- Abdominal Oncology Ward, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yaguang Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics and Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
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19
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Zauner R, Wimmer M, Atzmueller S, Proell J, Niklas N, Ablinger M, Reisenberger M, Lettner T, Illmer J, Dorfer S, Koller U, Guttmann-Gruber C, Hofbauer JP, Bauer JW, Wally V. Biomarker Discovery in Rare Malignancies: Development of a miRNA Signature for RDEB-cSCC. Cancers (Basel) 2023; 15:3286. [PMID: 37444397 DOI: 10.3390/cancers15133286] [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: 04/13/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
Machine learning has been proven to be a powerful tool in the identification of diagnostic tumor biomarkers but is often impeded in rare cancers due to small patient numbers. In patients suffering from recessive dystrophic epidermolysis bullosa (RDEB), early-in-life development of particularly aggressive cutaneous squamous-cell carcinomas (cSCCs) represents a major threat and timely detection is crucial to facilitate prompt tumor excision. As miRNAs have been shown to hold great potential as liquid biopsy markers, we characterized miRNA signatures derived from cultured primary cells specific for the potential detection of tumors in RDEB patients. To address the limitation in RDEB-sample accessibility, we analyzed the similarity of RDEB miRNA profiles with other tumor entities derived from the Cancer Genome Atlas (TCGA) repository. Due to the similarity in miRNA expression with RDEB-SCC, we used HN-SCC data to train a tumor prediction model. Three models with varying complexity using 33, 10 and 3 miRNAs were derived from the elastic net logistic regression model. The predictive performance of all three models was determined on an independent HN-SCC test dataset (AUC-ROC: 100%, 83% and 96%), as well as on cell-based RDEB miRNA-Seq data (AUC-ROC: 100%, 100% and 91%). In addition, the ability of the models to predict tumor samples based on RDEB exosomes (AUC-ROC: 100%, 93% and 100%) demonstrated the potential feasibility in a clinical setting. Our results support the feasibility of this approach to identify a diagnostic miRNA signature, by exploiting publicly available data and will lay the base for an improvement of early RDEB-SCC detection.
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Affiliation(s)
- Roland Zauner
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology & Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Monika Wimmer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology & Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Sabine Atzmueller
- Center for Medical Research, Medical Faculty, Johannes-Kepler-University, 4020 Linz, Austria
| | - Johannes Proell
- Center for Medical Research, Medical Faculty, Johannes-Kepler-University, 4020 Linz, Austria
| | - Norbert Niklas
- Red Cross Transfusion Service of Upper Austria, 4020 Linz, Austria
| | - Michael Ablinger
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology & Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Manuela Reisenberger
- Department of Dermatology & Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Thomas Lettner
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology & Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Julia Illmer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology & Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Sonja Dorfer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology & Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology & Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Christina Guttmann-Gruber
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology & Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Josefina Piñón Hofbauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology & Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Johann W Bauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology & Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
- Department of Dermatology & Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Verena Wally
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology & Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
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20
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Stott J, Wright T, Holmes J, Wilson J, Griffiths-Jones S, Foster D, Wright B. A systematic review of non-coding RNA genes with differential expression profiles associated with autism spectrum disorders. PLoS One 2023; 18:e0287131. [PMID: 37319303 PMCID: PMC10270643 DOI: 10.1371/journal.pone.0287131] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/30/2023] [Indexed: 06/17/2023] Open
Abstract
AIMS To identify differential expression of shorter non-coding RNA (ncRNA) genes associated with autism spectrum disorders (ASD). BACKGROUND ncRNA are functional molecules that derive from non-translated DNA sequence. The HUGO Gene Nomenclature Committee (HGNC) have approved ncRNA gene classes with alignment to the reference human genome. One subset is microRNA (miRNA), which are highly conserved, short RNA molecules that regulate gene expression by direct post-transcriptional repression of messenger RNA. Several miRNA genes are implicated in the development and regulation of the nervous system. Expression of miRNA genes in ASD cohorts have been examined by multiple research groups. Other shorter classes of ncRNA have been examined less. A comprehensive systematic review examining expression of shorter ncRNA gene classes in ASD is timely to inform the direction of research. METHODS We extracted data from studies examining ncRNA gene expression in ASD compared with non-ASD controls. We included studies on miRNA, piwi-interacting RNA (piRNA), small NF90 (ILF3) associated RNA (snaR), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), transfer RNA (tRNA), vault RNA (vtRNA) and Y RNA. The following electronic databases were searched: Cochrane Library, EMBASE, PubMed, Web of Science, PsycINFO, ERIC, AMED and CINAHL for papers published from January 2000 to May 2022. Studies were screened by two independent investigators with a third resolving discrepancies. Data was extracted from eligible papers. RESULTS Forty-eight eligible studies were included in our systematic review with the majority examining miRNA gene expression alone. Sixty-four miRNA genes had differential expression in ASD compared to controls as reported in two or more studies, but often in opposing directions. Four miRNA genes had differential expression in the same direction in the same tissue type in at least 3 separate studies. Increased expression was reported in miR-106b-5p, miR-155-5p and miR-146a-5p in blood, post-mortem brain, and across several tissue types, respectively. Decreased expression was reported in miR-328-3p in bloods samples. Seven studies examined differential expression from other classes of ncRNA, including piRNA, snRNA, snoRNA and Y RNA. No individual ncRNA genes were reported in more than one study. Six studies reported differentially expressed snoRNA genes in ASD. A meta-analysis was not possible because of inconsistent methodologies, disparate tissue types examined, and varying forms of data presented. CONCLUSION There is limited but promising evidence associating the expression of certain miRNA genes and ASD, although the studies are of variable methodological quality and the results are largely inconsistent. There is emerging evidence associating differential expression of snoRNA genes in ASD. It is not currently possible to say whether the reports of differential expression in ncRNA may relate to ASD aetiology, a response to shared environmental factors linked to ASD such as sleep and nutrition, other molecular functions, human diversity, or chance findings. To improve our understanding of any potential association, we recommend improved and standardised methodologies and reporting of raw data. Further high-quality research is required to shine a light on possible associations, which may yet yield important information.
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Affiliation(s)
- Jon Stott
- Child Oriented Mental Health Intervention Collaborative (COMIC), University of York in Collaboration with Leeds and York Partnership NHS Foundation Trust, York, United Kingdom
- Tees, Esk & Wear Valleys NHS Foundation Trust, Foss Park Hospital, York, United Kingdom
| | - Thomas Wright
- Manchester Centre for Genomic Medicine, Clinical Genetics Service, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Jannah Holmes
- Child Oriented Mental Health Intervention Collaborative (COMIC), University of York in Collaboration with Leeds and York Partnership NHS Foundation Trust, York, United Kingdom
- Hull York Medical School, University of York, Heslington, York, United Kingdom
| | - Julie Wilson
- Department of Mathematics, University of York, Heslington, York, United Kingdom
| | - Sam Griffiths-Jones
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Deborah Foster
- Tees, Esk & Wear Valleys NHS Foundation Trust, Foss Park Hospital, York, United Kingdom
| | - Barry Wright
- Child Oriented Mental Health Intervention Collaborative (COMIC), University of York in Collaboration with Leeds and York Partnership NHS Foundation Trust, York, United Kingdom
- Hull York Medical School, University of York, Heslington, York, United Kingdom
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21
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Farina FM, Weber C, Santovito D. The emerging landscape of non-conventional RNA functions in atherosclerosis. Atherosclerosis 2023; 374:74-86. [PMID: 36725418 DOI: 10.1016/j.atherosclerosis.2023.01.009] [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: 08/02/2022] [Revised: 12/15/2022] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Most of the human genome is transcribed into non-coding RNAs (ncRNAs), which encompass a heterogeneous family of transcripts including microRNAs (miRNAs), long ncRNAs (lncRNAs), circular RNAs (circRNAs), and others. Although the detailed modes of action of some classes are not fully elucidated, the common notion is that ncRNAs contribute to sculpting gene expression of eukaryotic cells at multiple levels. These range from the regulation of chromatin remodeling and transcriptional activity to post-transcriptional regulation of messenger RNA splicing, stability, and decay. Many of these functions ultimately govern the expression of coding and non-coding genes to affect diverse physiological and pathological mechanisms in vascular biology and beyond. As such, different classes of ncRNAs emerged as crucial regulators of vascular integrity as well as active players in the pathophysiology of atherosclerosis from the early stages of endothelial dysfunction to the clinically relevant complications. However, research in recent years revealed unexpected findings such as small ncRNAs being able to biophysically regulate protein function, the glycosylation of ncRNAs to be exposed on the cell surface, the release of ncRNAs in the extracellular space to act as ligands of receptors, and even the ability of non-coding portion of messenger RNAs to mediate structural functions. This evidence expanded the functional repertoire of ncRNAs far beyond gene regulation and highlighted an additional layer of biological control of cell function. In this Review, we will discuss these emerging aspects of ncRNA biology, highlight the implications for the mechanisms of vascular biology and atherosclerosis, and discuss possible translational implications.
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Affiliation(s)
- Floriana Maria Farina
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU), Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU), Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany; Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| | - Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU), Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany; Institute for Genetic and Biomedical Research (IRGB), Unit of Milan, National Research Council, Milan, Italy.
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22
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Naesens L, Haerynck F, Gack MU. The RNA polymerase III-RIG-I axis in antiviral immunity and inflammation. Trends Immunol 2023; 44:435-449. [PMID: 37149405 PMCID: PMC10461603 DOI: 10.1016/j.it.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 05/08/2023]
Abstract
Nucleic acid sensors survey subcellular compartments for atypical or mislocalized RNA or DNA, ultimately triggering innate immune responses. Retinoic acid-inducible gene-I (RIG-I) is part of the family of cytoplasmic RNA receptors that can detect viruses. A growing literature demonstrates that mammalian RNA polymerase III (Pol III) transcribes certain viral or cellular DNA sequences into immunostimulatory RIG-I ligands, which elicits antiviral or inflammatory responses. Dysregulation of the Pol III-RIG-I sensing axis can lead to human diseases including severe viral infection outcomes, autoimmunity, and tumor progression. Here, we summarize the newly emerging role of viral and host-derived Pol III transcripts in immunity and also highlight recent advances in understanding how mammalian cells prevent unwanted immune activation by these RNAs to maintain homeostasis.
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Affiliation(s)
- Leslie Naesens
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA.
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23
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Straub S, Sampaio NG. Activation of cytosolic RNA sensors by endogenous ligands: roles in disease pathogenesis. Front Immunol 2023; 14:1092790. [PMID: 37292201 PMCID: PMC10244536 DOI: 10.3389/fimmu.2023.1092790] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/15/2023] [Indexed: 06/10/2023] Open
Abstract
Early detection of infection is a central and critical component of our innate immune system. Mammalian cells have developed specialized receptors that detect RNA with unusual structures or of foreign origin - a hallmark of many virus infections. Activation of these receptors induces inflammatory responses and an antiviral state. However, it is increasingly appreciated that these RNA sensors can also be activated in the absence of infection, and that this 'self-activation' can be pathogenic and promote disease. Here, we review recent discoveries in sterile activation of the cytosolic innate immune receptors that bind RNA. We focus on new aspects of endogenous ligand recognition uncovered in these studies, and their roles in disease pathogenesis.
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Affiliation(s)
- Sarah Straub
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, School of Clinical Sciences, Monash University, Clayton, VIC, Australia
| | - Natalia G. Sampaio
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, School of Clinical Sciences, Monash University, Clayton, VIC, Australia
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24
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Mármol-Sánchez E, Heidemann PL, Gredal H, Cirera S. MicroRNA profiling of cerebrospinal fluid from dogs with steroid responsive meningitis-arteritis and meningoencephalitis of unknown origin. Front Vet Sci 2023; 10:1144084. [PMID: 37215481 PMCID: PMC10196361 DOI: 10.3389/fvets.2023.1144084] [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: 01/13/2023] [Accepted: 03/28/2023] [Indexed: 05/24/2023] Open
Abstract
Introduction Non-infectious inflammatory diseases of the central nervous system in dogs, such as steroid responsive meningitis-arteritis (SRMA) and meningoencephalitis of unknown origin (MUO), represent a common clinical challenge that needs extensive and multimodal work-up to reach a presumptive diagnosis. Both diseases are presumably caused by dysregulations of the immune system, but further research is needed in order to understand the molecular mechanisms behind each disease and to optimize treatment. Methods By next-generation sequencing and subsequent quantitative real-time PCR (qPCR) verification, we designed a prospective case-control pilot study to analyze the small RNA profiles of cerebrospinal fluid from dogs suffering from MUO (N = 5), dogs suffering from SRMA (N = 8), and healthy dogs (N = 5) presented for elective euthanasia used as the Control group. Results Our results showed an overall enrichment in Y-RNA fragments across all samples, followed by microRNAs (miRNAs) and ribosomal RNAs as the major findings. Additional traces of short RNA reads mapped to long non-coding RNAs and protein-coding genes were also found. From the detected canine miRNAs, miR-21, miR-486, miR-148a, miR-99a, miR-191 and miR-92a were among the most abundant. Dogs with SRMA showed higher differences in miRNA abundance than dogs with MUO when compared to healthy dogs, and miR-142-3p was consistently detected as differentially upregulated in both diseases, although at a low concentration. Moreover, miR-405-5p and miR-503-5p showed different profiles between SRMA and MUO dogs. Subsequent qPCR analyses confirmed miR-142-5p, miR-191-5p and miR-92a-3p as significantly upregulated miRNAs in dogs with SRMA and/or MUO. Discussion Cerebrospinal fluid is a challenging biological material to use for profiling miRNAs due to the low content of circulating RNAs. Despite this, we could confirm several miRNAs being differentially abundant when comparing healthy dogs and dogs with MUO and SRMA, respectively. The results of this study indicate a potential role of miRNAs in the underlying molecular mechanisms of these diseases and establish the basis for further studies.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Centre for Paleogenetics, Stockholm University, Stockholm, Sweden
| | - Pernille Lindholm Heidemann
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hanne Gredal
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Susanna Cirera
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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25
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Cimmino G, Conte S, Palumbo D, Sperlongano S, Torella M, Della Corte A, Golino P. The Novel Role of Noncoding RNAs in Modulating Platelet Function: Implications in Activation and Aggregation. Int J Mol Sci 2023; 24:ijms24087650. [PMID: 37108819 PMCID: PMC10144470 DOI: 10.3390/ijms24087650] [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: 03/12/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
It is currently believed that plaque complication, with the consequent superimposed thrombosis, is a key factor in the clinical occurrence of acute coronary syndromes (ACSs). Platelets are major players in this process. Despite the considerable progress made by the new antithrombotic strategies (P2Y12 receptor inhibitors, new oral anticoagulants, thrombin direct inhibitors, etc.) in terms of a reduction in major cardiovascular events, a significant number of patients with previous ACSs treated with these drugs continue to experience events, indicating that the mechanisms of platelet remain largely unknown. In the last decade, our knowledge of platelet pathophysiology has improved. It has been reported that, in response to physiological and pathological stimuli, platelet activation is accompanied by de novo protein synthesis, through a rapid and particularly well-regulated translation of resident mRNAs of megakaryocytic derivation. Although the platelets are anucleate, they indeed contain an important fraction of mRNAs that can be quickly used for protein synthesis following their activation. A better understanding of the pathophysiology of platelet activation and the interaction with the main cellular components of the vascular wall will open up new perspectives in the treatment of the majority of thrombotic disorders, such as ACSs, stroke, and peripheral artery diseases before and after the acute event. In the present review, we will discuss the novel role of noncoding RNAs in modulating platelet function, highlighting the possible implications in activation and aggregation.
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Affiliation(s)
- Giovanni Cimmino
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
- Cardiology Unit, Azienda Ospedaliera Universitaria Luigi Vanvitelli, Piazza Miraglia, 80138 Naples, Italy
| | - Stefano Conte
- Department of Translational Medical Sciences, Section of Lung Diseases, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
| | - Domenico Palumbo
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
| | - Simona Sperlongano
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
- Cardiology Unit, Azienda Ospedaliera Universitaria Luigi Vanvitelli, Piazza Miraglia, 80138 Naples, Italy
| | - Michele Torella
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
| | - Alessandro Della Corte
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
| | - Paolo Golino
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
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26
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The Impact of YRNAs on HNSCC and HPV Infection. Biomedicines 2023; 11:biomedicines11030681. [PMID: 36979661 PMCID: PMC10045647 DOI: 10.3390/biomedicines11030681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/20/2023] [Accepted: 02/17/2023] [Indexed: 02/27/2023] Open
Abstract
HPV infection is one of the most important risk factors for head and neck squamous cell carcinoma among younger patients. YRNAs are short non-coding RNAs involved in DNA replication. YRNAs have been found to be dysregulated in many cancers, including head and neck squamous cell carcinoma (HNSCC). In this study, we investigated the role of YRNAs in HPV-positive HNSCC using publicly available gene expression datasets from HNSCC tissue, where expression patterns of YRNAs in HPV(+) and HPV(−) HNSCC samples significantly differed. Additionally, HNSCC cell lines were treated with YRNA1-overexpressing plasmid and RNA derived from these cell lines was used to perform a NGS analysis. Additionally, a deconvolution analysis was performed to determine YRNA1’s impact on immune cells. YRNA expression levels varied according to cancer pathological and clinical stages, and correlated with more aggressive subtypes. YRNAs were mostly associated with more advanced cancer stages in the HPV(+) group, and YRNA3 and YRNA1 expression levels were found to be correlated with more advanced clinical stages despite HPV infection status, showing that they may function as potential biomarkers of more advanced stages of the disease. YRNA5 was associated with less-advanced cancer stages in the HPV(−) group. Overall survival and progression-free survival analyses showed opposite results between the HPV groups. The expression of YRNAs, especially YRNA1, correlated with a vast number of proteins and cellular processes associated with viral infections and immunologic responses to viruses. HNSCC-derived cell lines overexpressing YRNA1 were then used to determine the correlation of YRNA1 and the expression of genes associated with HPV infections. Taken together, our results highlight the potential of YRNAs as possible HNSCC biomarkers and new molecular targets.
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27
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Almandil NB, Alismail MA, Alsuwat HS, AlSulaiman A, AbdulAzeez S, Borgio JF. Exome-wide analysis identify multiple variations in olfactory receptor genes ( OR12D2 and OR5V1) associated with autism spectrum disorder in Saudi females. Front Med (Lausanne) 2023; 10:1051039. [PMID: 36817779 PMCID: PMC9928728 DOI: 10.3389/fmed.2023.1051039] [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: 09/22/2022] [Accepted: 01/13/2023] [Indexed: 02/04/2023] Open
Abstract
Background Autism Spectrum Disorder (ASD) is a multifactorial, neurodevelopmental disorder, characterized by deficits in communication, restricted and repetitive behaviors. ASD is highly heritable in Saudi Arabia; indecencies of affected individuals are increasing. Objectives To identify the most significant genes and SNPs associated with the increased risk of ASD in Saudi females to give an insight for early diagnosis. Methods Pilot case-control study mostly emphasized on the significant SNPs and haplotypes contributing to Saudi females with ASD patients (n = 22) compared to controls (n = 51) without ASD. With the use of allelic association analysis tools, 243,345 SNPs were studied systematically and classified according to their significant association. The significant SNPs and their genes were selected for further investigation for mapping of ASD candidate causal variants and functional impact. Results In females, five risk SNPs at p ≤ 2.32 × 10-05 was identified in association with autism. The most significant exonic variants at chromosome 6p22.1 with olfactory receptor genes (OR12D2 and OR5V1) clustered with high linkage disequilibrium through haplotyping analysis. Comparison between highly associated genes (56 genes) of male and female autistic patients with female autistic samples revealed that 39 genes are unique biomarkers for Saudi females with ASD. Conclusion Multiple variations in olfactory receptor genes (OR5V1 and OR12D2) and single variations on SPHK1, PLCL2, AKAP9 and LOC107984893 genes are contributing to ASD in females of Arab origin. Accumulation of these multiple predisposed coding SNPs can increase the possibility of developing ASD in Saudi females.
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Affiliation(s)
- Noor B. Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia,*Correspondence: Noor B Almandil,
| | - Maram Adnan Alismail
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia,College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Hind Saleh Alsuwat
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Abdulla AlSulaiman
- Department of Neurology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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28
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Xia L, Guo H, Wu X, Xu Y, Zhao P, Yan B, Zeng Y, He Y, Chen D, Gale RP, Zhang Y, Zhang X. Human circulating small non-coding RNA signature as a non-invasive biomarker in clinical diagnosis of acute myeloid leukaemia. Theranostics 2023; 13:1289-1301. [PMID: 36923527 PMCID: PMC10008735 DOI: 10.7150/thno.80054] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Background: Acute myeloid leukaemia (AML) is the most common acute leukaemia in adults; AML is highly heterogeneous and involves abnormalities at multiple omics levels. Small non-coding RNAs (sncRNAs) present in body fluids are important regulatory molecules and considered promising non-invasive clinical diagnostic biomarkers for disease. However, the signature of sncRNA profile alteration in AML patient serum and bone marrow supernatant is still under exploration. Methods: We examined data for blood and bone marrow samples from 80 consecutive, newly-diagnosed patients with AML and 12 healthy controls for high throughput small RNA-sequencing. Differentially expressed sncRNAs were analysed to reveal distinct patterns between AML patients and controls. Machine learning methods were used to evaluate the efficiency of specific sncRNAs in discriminating individuals with AML from controls. The altered expression level of individual sncRNAs was evaluated by RT-PCR, Q-PCR, and northern blot. Correlation analysis was employed to assess sncRNA patterns between serum and bone marrow supernatant. Results: We identified over 20 types of sncRNA categories beyond miRNAs in both serum and bone marrow supernatant, with highly coordinated expression patterns between them. Non-classical sncRNAs, including rsRNA (62.86%), ysRNA (14.97%), and tsRNA (4.22%), dominated among serum sncRNAs and showed sensitive alteration patterns in AML patients. According to machine learning-based algorithms, the tsRNA-based signature robustly discriminated subjects with AML from controls and was more reliable than that comprising miRNAs. Our data also showed that serum tsRNAs to be closely associated with AML prognosis, suggesting the potential application of serum tsRNAs as biomarkers to assist in AML diagnosis. Conclusions: We comprehensively characterized the expression pattern of circulating sncRNAs in blood and bone marrow and their alteration signature between healthy controls and AML patients. This study enriches research of sncRNAs in the regulation of AML, and provides insights into the role of sncRNAs in AML.
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Affiliation(s)
- Lin Xia
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Huanping Guo
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Xiao Wu
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Yinying Xu
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Pan Zhao
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Bingbing Yan
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Yunjing Zeng
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Yundi He
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Dan Chen
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Robert Peter Gale
- Haematology Centre, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Yunfang Zhang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xi Zhang
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China.,Jinfeng Laboratory, Chongqing, China
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29
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Tong F, Tang G, Wang X. Characteristics of Human and Microbiome RNA Profiles in Saliva. RNA Biol 2023; 20:398-408. [PMID: 37401028 PMCID: PMC10321209 DOI: 10.1080/15476286.2023.2229596] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/08/2023] [Accepted: 06/17/2023] [Indexed: 07/05/2023] Open
Abstract
Saliva is a convenient non-invasive source of liquid biopsy to monitor human health and diagnose diseases. In particular, extracellular vesicles (EVs) in saliva can potentially reveal clinically relevant information for systemic health. Recent studies have shown that RNA in saliva EVs could be exploited as biomarkers for disease diagnosis. However, there is no standardized protocol for profiling RNA in saliva EV nor clear guideline on selecting saliva fractions for biomarker analysis. To address these issues, we established a robust protocol for small RNA profiling from fractionated saliva. With this method, we performed comprehensive small RNA sequencing of four saliva fractions, including cell-free saliva (CFS), EV-depleted saliva (EV-D), exosome (EXO), and microvesicle (MV) from ten healthy volunteers. By comparing the expression profiles of total RNA from these fractions, we found that MV was most enriched in microbiome RNA (76.2% of total reads on average), whereas EV-D was notably enriched in human RNA (70.3% of total reads on average). As for human RNA composition, CFS and EV-D were both enriched in snoRNA and tRNA compared with the two EV fractions (EXO and MV, P < 0.05). Interestingly, EXO and MV had highly correlated expression profiles for various noncoding RNAs such as miRNA, tRNA, and yRNA. Our study revealed unique characteristics of circulating RNAs in various saliva fractions, which provides a guideline on preparing saliva samples to study specific RNA biomarkers of interest.
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Affiliation(s)
- Fangjia Tong
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
- University of Illinois Cancer Center, Chicago, IL, USA
| | - Gongyu Tang
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
- University of Illinois Cancer Center, Chicago, IL, USA
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, MO, USA
| | - Xiaowei Wang
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
- University of Illinois Cancer Center, Chicago, IL, USA
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30
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Lima DDS, Amichi LJA, Fernandez MA, Constantino AA, Seixas FAV. NCYPred: A Bidirectional LSTM Network With Attention for Y RNA and Short Non-Coding RNA Classification. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:557-565. [PMID: 34826297 DOI: 10.1109/tcbb.2021.3131136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Short non-coding RNAs (sncRNAs) are involved in multiple cellular processes and can be divided into dozens of classes. Among such classes, Y RNAs have been gaining attention, being essential factors for the initiation of DNA replication on vertebrates, as well as potential tumor biomarkers. Homologs have also been described in nematodes and insects, as well as related sequences in bacteria. Methods capable of accurately predicting Y RNA transcripts are lacking. In this work, we developed an attention-based LSTM network and built a classification model able to classify sncRNAs (including Y RNA) directly from nucleotide sequences. A dataset consisting of 45,447 sncRNA sequences, from a wide range of organisms, obtained from Rfam 14.3 was built. Performance evaluation demonstrated that our proposed method, NCYPred (Non-Coding/Y RNA Prediction), can accurately predict Y RNA sequences and their homologs, as well as 11 additional classes, achieving results comparable with state-of-the-art methods. We also demonstrate that applying t-SNE on learned sequence representations could be useful for sequence analysis. Our model is freely available as a web-server (https://www.gpea.uem.br/ncypred/).
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31
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Estravís M, García-Sánchez A, Martin MJ, Pérez-Pazos J, Isidoro-García M, Dávila I, Sanz C. RNY3 modulates cell proliferation and IL13 mRNA levels in a T lymphocyte model: a possible new epigenetic mechanism of IL-13 regulation. J Physiol Biochem 2023; 79:59-69. [PMID: 36089628 PMCID: PMC9905197 DOI: 10.1007/s13105-022-00920-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022]
Abstract
Allergic asthma is the most common type of asthma. It is characterized by TH2 cell-driven inflammation in which interleukin-13 (IL-13) plays a pivotal role. Cytoplasmic RNAs (Y-RNAs), a variety of non-coding RNAs that are dysregulated in many cancer types, are also differentially expressed in patients with allergic asthma. Their function in the development of the disease is still unknown. We investigated the potential role of RNY3 RNA (hY3) in the TH2 cell inflammatory response using the Jurkat cell line as a model. hY3 expression levels were modulated to mimic the upregulation effect in allergic disease. We evaluated the effect of hY3 over cell stimulation and the expression of the TH2 cytokine IL13. Total RNA was isolated and retrotranscribed, and RNA levels were assessed by qPCR. In Jurkat cells, hY3 levels increased upon stimulation with phorbol 12-myristate 13-acetate (PMA) and ionomycin. When transfecting with high levels of hY3 mimic molecules, cell proliferation rate decreased while IL13 mRNA levels increased upon stimulation compared to stimulated control cells. Our results show the effect of increased hY3 levels on cell proliferation and the levels of IL13 mRNA in Jurkat cells. Also, we showed that hY3 could act over other cells via exosomes. This study opens up new ways to study the potential regulatory function of hY3 over IL-13 production and its implications for asthma development.
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Affiliation(s)
- Miguel Estravís
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Red Cooperativa de Investigación en Salud-RETICS ARADyAL, ISCIII, Madrid, Spain
| | - Asunción García-Sánchez
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain.
- Red Cooperativa de Investigación en Salud-RETICS ARADyAL, ISCIII, Madrid, Spain.
- Departamento de Ciencias Biomédicas y del Diagnóstico, Universidad de Salamanca, Salamanca, Spain.
| | - Maria J Martin
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Red Cooperativa de Investigación en Salud-RETICS ARADyAL, ISCIII, Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Salamanca, Spain
| | - Jacqueline Pérez-Pazos
- Unidad de Farmacogenética y Medicina de Precisión, Servicio de Bioquímica Clínica, Servicio de Alergología, Hospital Universitario de Salamanca, IBSAL, Salamanca, Spain
| | - María Isidoro-García
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Red Cooperativa de Investigación en Salud-RETICS ARADyAL, ISCIII, Madrid, Spain
- Servicio de Bioquímica Clínica, Complejo Asistencial Universitario de Salamanca, Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
| | - Ignacio Dávila
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Red Cooperativa de Investigación en Salud-RETICS ARADyAL, ISCIII, Madrid, Spain
- Departamento de Ciencias Biomédicas y del Diagnóstico, Universidad de Salamanca, Salamanca, Spain
- Servicio de Inmunoalergia, Complejo Asistencial Universitario de Salamanca, Salamanca, Spain
| | - Catalina Sanz
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Red Cooperativa de Investigación en Salud-RETICS ARADyAL, ISCIII, Madrid, Spain
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
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Kärkkäinen E, Heikkinen S, Tengström M, Kosma VM, Mannermaa A, Hartikainen JM. Expression profiles of small non-coding RNAs in breast cancer tumors characterize clinicopathological features and show prognostic and predictive potential. Sci Rep 2022; 12:22614. [PMID: 36585466 PMCID: PMC9803687 DOI: 10.1038/s41598-022-26954-w] [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: 12/17/2021] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
Precision medicine approaches are required for more effective therapies for cancer. As small non-coding RNAs (sncRNAs) have recently been suggested as intriguing candidates for cancer biomarkers and have shown potential also as novel therapeutic targets, we aimed at profiling the non-miRNA sncRNAs in a large sample set to evaluate their role in invasive breast cancer (BC). We used small RNA sequencing and 195 fresh-frozen invasive BC and 22 benign breast tissue samples to identify significant associations of small nucleolar RNAs, small nuclear RNAs, and miscellaneous RNAs with the clinicopathological features and patient outcome of BC. Ninety-six and five sncRNAs significantly distinguished (Padj < 0.01) invasive local BC from benign breast tissue and metastasized BC from invasive local BC, respectively. Furthermore, 69 sncRNAs significantly associated (Padj < 0.01) with the tumor grade, hormone receptor status, subtype, and/or tumor histology. Additionally, 42 sncRNAs were observed as candidates for prognostic markers and 29 for predictive markers for radiotherapy and/or tamoxifen response (P < 0.05). We discovered the clinical relevance of sncRNAs from each studied RNA type. By introducing new sncRNA biomarker candidates for invasive BC and validating the potential of previously described ones, we have guided the way for further research that is warranted for providing novel insights into BC biology.
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Affiliation(s)
- Emmi Kärkkäinen
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Yliopistonranta 1 C, 70210 Kuopio, Finland
| | - Sami Heikkinen
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland ,grid.9668.10000 0001 0726 2490School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Maria Tengström
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, Oncology, and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland ,grid.410705.70000 0004 0628 207XCancer Center, Kuopio University Hospital, Kuopio, Finland
| | - Veli-Matti Kosma
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Yliopistonranta 1 C, 70210 Kuopio, Finland ,grid.410705.70000 0004 0628 207XDepartment of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Arto Mannermaa
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Yliopistonranta 1 C, 70210 Kuopio, Finland ,grid.410705.70000 0004 0628 207XDepartment of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Jaana M. Hartikainen
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Yliopistonranta 1 C, 70210 Kuopio, Finland
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Midsize noncoding RNAs in cancers: a new division that clarifies the world of noncoding RNA or an unnecessary chaos? Rep Pract Oncol Radiother 2022; 27:1077-1093. [PMID: 36632289 PMCID: PMC9826665 DOI: 10.5603/rpor.a2022.0123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/18/2022] [Indexed: 12/31/2022] Open
Abstract
Most of the human genome is made out of noncoding RNAs (ncRNAs). These ncRNAs do not code for proteins but carry a vast number of important functions in human cells such as: modification and processing other RNAs (tRNAs, rRNAs, snRNAs, snoRNAs, miRNAs), help in the synthesis of ribosome proteins, initiation of DNA replication, regulation of transcription, processing of pre-messenger mRNA during its maturation and much more. The ncRNAs also have a significant impact on many events that occur during carcinogenesis in cancer cells, such as: regulation of cell survival, cellular signaling, apoptosis, proliferation or even influencing the metastasis process. The ncRNAs may be divided based on their length, into short and long, where 200 nucleotides is the "magic" border. However, a new division was proposed, suggesting the creation of the additional group called midsize noncoding RNAs, with the length ranging from 50-400 nucleotides. This new group may include: transfer RNA (tRNA), small nuclear RNAs (snRNAs) with 7SK and 7SL, small nucleolar RNAs (snoRNAs), small Cajal body-specific RNAs (scaRNAs) and YRNAs. In this review their structure, biogenesis, function and influence on carcinogenesis process will be evaluated. What is more, a question will be answered of whether this new division is a necessity that clears current knowledge or just creates an additional misunderstanding in the ncRNA world?
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Okamura A, Yoshioka Y, Saito Y, Ochiya T. Can Extracellular Vesicles as Drug Delivery Systems Be a Game Changer in Cardiac Disease? Pharm Res 2022; 40:889-908. [PMID: 36577860 PMCID: PMC10126064 DOI: 10.1007/s11095-022-03463-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/13/2022] [Indexed: 12/29/2022]
Abstract
Cardiac diseases such as myocardial infarction and heart failure have been the leading cause of death worldwide for more than 20 years, and new treatments continue to be investigated. Heart transplantation, a curative treatment for severe cardiac dysfunction, is available to only a small number of patients due to the rarity of donors and high costs. Cardiac regenerative medicine using embryonic stem cells and induced pluripotent stem cells is expected to be a new alternative to heart transplantation, but it has problems such as induction of immune response, tumor formation, and low survival rate of transplanted cells. On the other hand, there has been a focus on cell-free therapy using extracellular vesicles (EVs) due to their high biocompatibility and target specificity. Exosomes, one type of EV, play a role in the molecular transport system in vivo and can be considered a drug delivery system (DDS) innate to all living things. Exosomes contain nucleic acids and proteins, which are transported from secretory cells to recipient cells. Molecules in exosomes are encapsulated in a lipid bilayer, which allows them to exist stably in body fluids without being affected by nuclease degradation enzymes. Therefore, the therapeutic use of exosomes as DDSs has been widely explored and is being used in clinical trials and other clinical settings. This review summarizes the current topics of EVs as DDSs in cardiac disease.
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Affiliation(s)
- Akihiko Okamura
- Department of Molecular and Cellular Medicine, Institute of Medical Science, Tokyo Medical University, 6-7-1 Nishishinjuku, Shinjuku-Ku, Tokyo, 160-0023, Japan.,Department of Cardiovascular Medicine, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara, 634-8522, Japan
| | - Yusuke Yoshioka
- Department of Molecular and Cellular Medicine, Institute of Medical Science, Tokyo Medical University, 6-7-1 Nishishinjuku, Shinjuku-Ku, Tokyo, 160-0023, Japan
| | - Yoshihiko Saito
- Department of Cardiovascular Medicine, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara, 634-8522, Japan
| | - Takahiro Ochiya
- Department of Molecular and Cellular Medicine, Institute of Medical Science, Tokyo Medical University, 6-7-1 Nishishinjuku, Shinjuku-Ku, Tokyo, 160-0023, Japan.
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35
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Pantazi P, Clements T, Venø M, Abrahams VM, Holder B. Distinct non-coding RNA cargo of extracellular vesicles from M1 and M2 human primary macrophages. J Extracell Vesicles 2022; 11:e12293. [PMID: 36544271 PMCID: PMC9772496 DOI: 10.1002/jev2.12293] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/13/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Macrophages are important antigen presenting cells which can release extracellular vesicles (EVs) carrying functional cargo including non-coding RNAs. Macrophages can be broadly classified into M1 'classical' and M2 'alternatively-activated' macrophages. M1 macrophages have been linked with inflammation-associated pathologies, whereas a switch towards an M2 phenotype indicates resolution of inflammation and tissue regeneration. Here, we provide the first comprehensive analysis of the small RNA cargo of EVs from human M1 and M2 primary macrophages. Using small RNA sequencing, we identified several types of small non-coding RNAs in M1 and M2 macrophage EVs including miRNAs, isomiRs, tRNA fragments, piRNA, snRNA, snoRNA and Y-RNA fragments. Distinct differences were observed between M1 and M2 EVs, with higher relative abundance of miRNAs, and lower abundance of tRNA fragments in M1 compared to M2 EVs. MicroRNA-target enrichment analysis identified several gene targets involved in gene expression and inflammatory signalling pathways. EVs were also enriched in tRNA fragments, primarily originating from the 5' end or the internal region of the full length tRNAs, many of which were differentially abundant in M1 and M2 EVs. Similarly, several other small non-coding RNAs, namely snRNAs, snoRNAs and Y-RNA fragments, were differentially enriched in M1 and M2 EVs; we discuss their putative roles in macrophage EVs. In conclusion, we show that M1 and M2 macrophages release EVs with distinct RNA cargo, which has the potential to contribute to the unique effect of these cell subsets on their microenvironment.
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Affiliation(s)
- Paschalia Pantazi
- Institute of Reproductive and Developmental BiologyDepartment of Metabolism, Digestion, and ReproductionImperial College LondonLondonUK
| | - Toby Clements
- Institute of Reproductive and Developmental BiologyDepartment of Metabolism, Digestion, and ReproductionImperial College LondonLondonUK
| | | | - Vikki M. Abrahams
- Department of ObstetricsGynecology and Reproductive SciencesYale School of MedicineNew HavenConnecticutUSA
| | - Beth Holder
- Institute of Reproductive and Developmental BiologyDepartment of Metabolism, Digestion, and ReproductionImperial College LondonLondonUK
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Liu Q, Huang J, Xia J, Liang Y, Li G. Tracking tools of extracellular vesicles for biomedical research. Front Bioeng Biotechnol 2022; 10:943712. [PMID: 36466335 PMCID: PMC9716315 DOI: 10.3389/fbioe.2022.943712] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 11/03/2022] [Indexed: 08/02/2023] Open
Abstract
Imaging of extracellular vesicles (EVs) will facilitate a better understanding of their biological functions and their potential as therapeutics and drug delivery vehicles. In order to clarify EV-mediated cellular communication in vitro and to track the bio-distribution of EV in vivo, various strategies have been developed to label and image EVs. In this review, we summarized recent advances in the tracking of EVs, demonstrating the methods for labeling and imaging of EVs, in which the labeling methods include direct and indirect labeling and the imaging modalities include fluorescent imaging, bioluminescent imaging, nuclear imaging, and nanoparticle-assisted imaging. These techniques help us better understand the mechanism of uptake, the bio-distribution, and the function of EVs. More importantly, we can evaluate the pharmacokinetic properties of EVs, which will help promote their further clinical application.
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Affiliation(s)
- Qisong Liu
- Shenzhen Key Laboratory of Musculoskeletal Tissue Reconstruction and Function Restoration, Department of Orthopaedic Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen, China
| | - Jianghong Huang
- Department of Orthopedics, Shenzhen Second People’s Hospital (First Affiliated Hospital of Shenzhen University, Health Science Center), Shenzhen, China
- Tsinghua University Shenzhen International Graduate School, Shenzhen, China
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, China
| | - Yujie Liang
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, China
- Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
| | - Guangheng Li
- Shenzhen Key Laboratory of Musculoskeletal Tissue Reconstruction and Function Restoration, Department of Orthopaedic Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen, China
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37
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Sruthi KB, Menon A, P A, Vasudevan Soniya E. Pervasive translation of small open reading frames in plant long non-coding RNAs. FRONTIERS IN PLANT SCIENCE 2022; 13:975938. [PMID: 36352887 PMCID: PMC9638090 DOI: 10.3389/fpls.2022.975938] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) are primarily recognized as non-coding transcripts longer than 200 nucleotides with low coding potential and are present in both eukaryotes and prokaryotes. Recent findings reveal that lncRNAs can code for micropeptides in various species. Micropeptides are generated from small open reading frames (smORFs) and have been discovered frequently in short mRNAs and non-coding RNAs, such as lncRNAs, circular RNAs, and pri-miRNAs. The most accepted definition of a smORF is an ORF containing fewer than 100 codons, and ribosome profiling and mass spectrometry are the most prevalent experimental techniques used to identify them. Although the majority of micropeptides perform critical roles throughout plant developmental processes and stress conditions, only a handful of their functions have been verified to date. Even though more research is being directed toward identifying micropeptides, there is still a dearth of information regarding these peptides in plants. This review outlines the lncRNA-encoded peptides, the evolutionary roles of such peptides in plants, and the techniques used to identify them. It also describes the functions of the pri-miRNA and circRNA-encoded peptides that have been identified in plants.
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38
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Prangley E, Korennykh A. 2-5A-Mediated decay (2-5AMD): from antiviral defense to control of host RNA. Crit Rev Biochem Mol Biol 2022; 57:477-491. [PMID: 36939319 PMCID: PMC10576847 DOI: 10.1080/10409238.2023.2181308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 10/18/2022] [Accepted: 02/13/2023] [Indexed: 03/21/2023]
Abstract
Mammalian cells are exquisitely sensitive to the presence of double-stranded RNA (dsRNA), a molecule that they interpret as a signal of viral presence requiring immediate attention. Upon sensing dsRNA cells activate the innate immune response, which involves transcriptional mechanisms driving inflammation and secretion of interferons (IFNs) and interferon-stimulated genes (ISGs), as well as synthesis of RNA-like signaling molecules comprised of three or more 2'-5'-linked adenylates (2-5As). 2-5As were discovered some forty years ago and described as IFN-induced inhibitors of protein synthesis. The efforts of many laboratories, aimed at elucidating the molecular mechanism and function of these mysterious RNA-like signaling oligonucleotides, revealed that 2-5A is a specific ligand for the kinase-family endonuclease RNase L. RNase L decays single-stranded RNA (ssRNA) from viruses and mRNAs (as well as other RNAs) from hosts in a process we proposed to call 2-5A-mediated decay (2-5AMD). During recent years it has become increasingly recognized that 2-5AMD is more than a blunt tool of viral RNA destruction, but a pathway deeply integrated into sensing and regulation of endogenous RNAs. Here we present an overview of recently emerged roles of 2-5AMD in host RNA regulation.
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Affiliation(s)
- Eliza Prangley
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alexei Korennykh
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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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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Vabret N, Najburg V, Solovyov A, Gopal R, McClain C, Šulc P, Balan S, Rahou Y, Beauclair G, Chazal M, Varet H, Legendre R, Sismeiro O, Sanchez David RY, Chauveau L, Jouvenet N, Markowitz M, van der Werf S, Schwartz O, Tangy F, Bhardwaj N, Greenbaum BD, Komarova AV. Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1. iScience 2022; 25:104599. [PMID: 35789859 PMCID: PMC9250025 DOI: 10.1016/j.isci.2022.104599] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/01/2022] [Accepted: 06/07/2022] [Indexed: 11/18/2022] Open
Abstract
Pattern recognition receptors (PRRs) protect against microbial invasion by detecting specific molecular patterns found in pathogens and initiating an immune response. Although microbial-derived PRR ligands have been extensively characterized, the contribution and relevance of endogenous ligands to PRR activation remains overlooked. Here, we characterize the landscape of endogenous ligands that engage RIG-I-like receptors (RLRs) upon infection by different RNA viruses. In each infection, several RNAs transcribed by RNA polymerase III (Pol3) specifically engaged RLRs, particularly the family of Y RNAs. Sensing of Y RNAs was dependent on their mimicking of viral secondary structure and their 5'-triphosphate extremity. Further, we found that HIV-1 triggered a VPR-dependent downregulation of RNA triphosphatase DUSP11 in vitro and in vivo, inducing a transcriptome-wide change of cellular RNA 5'-triphosphorylation that licenses Y RNA immunogenicity. Overall, our work uncovers the contribution of endogenous RNAs to antiviral immunity and demonstrates the importance of this pathway in HIV-1 infection.
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Affiliation(s)
- Nicolas Vabret
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Valérie Najburg
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Alexander Solovyov
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ramya Gopal
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christopher McClain
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Petr Šulc
- Center for Molecular Design and Biomimetics at the Biodesign Institute and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Sreekumar Balan
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yannis Rahou
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Guillaume Beauclair
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Maxime Chazal
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Hugo Varet
- Transcriptome and EpiGenome Platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, Université de Paris, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Hub Informatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP-CNRS), Institut Pasteur, Université de Paris, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Rachel Legendre
- Transcriptome and EpiGenome Platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, Université de Paris, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Hub Informatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP-CNRS), Institut Pasteur, Université de Paris, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Odile Sismeiro
- Transcriptome and EpiGenome Platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, Université de Paris, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Raul Y. Sanchez David
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Lise Chauveau
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Nolwenn Jouvenet
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Martin Markowitz
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, NY, USA
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Frédéric Tangy
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Nina Bhardwaj
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Extra-mural Member, Parker Institute of Cancer Immunotherapy, USA
| | - Benjamin D. Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Physiology, Biophysics, & Systems Biology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Anastassia V. Komarova
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
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Van Bortle K, Marciano DP, Liu Q, Chou T, Lipchik AM, Gollapudi S, Geller BS, Monte E, Kamakaka RT, Snyder MP. A cancer-associated RNA polymerase III identity drives robust transcription and expression of snaR-A noncoding RNA. Nat Commun 2022; 13:3007. [PMID: 35637192 PMCID: PMC9151912 DOI: 10.1038/s41467-022-30323-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 04/13/2022] [Indexed: 11/09/2022] Open
Abstract
RNA polymerase III (Pol III) includes two alternate isoforms, defined by mutually exclusive incorporation of subunit POLR3G (RPC7α) or POLR3GL (RPC7β), in mammals. The contributions of POLR3G and POLR3GL to transcription potential has remained poorly defined. Here, we discover that loss of subunit POLR3G is accompanied by a restricted repertoire of genes transcribed by Pol III. Particularly sensitive is snaR-A, a small noncoding RNA implicated in cancer proliferation and metastasis. Analysis of Pol III isoform biases and downstream chromatin features identifies loss of POLR3G and snaR-A during differentiation, and conversely, re-establishment of POLR3G gene expression and SNAR-A gene features in cancer contexts. Our results support a model in which Pol III identity functions as an important transcriptional regulatory mechanism. Upregulation of POLR3G, which is driven by MYC, identifies a subgroup of patients with unfavorable survival outcomes in specific cancers, further implicating the POLR3G-enhanced transcription repertoire as a potential disease factor. RNA polymerase III changes its subunit composition during mammalian development. Here the authors report that loss of subunit POLR3G, which re-emerges in cancer, promotes expression of small NF90-associated RNA (snaR-A), a noncoding RNA implicated in cell proliferation and metastasis.
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An Expanded Landscape of Unusually Short RNAs in 11 Samples from Six Eukaryotic Organisms. Noncoding RNA 2022; 8:ncrna8030034. [PMID: 35645341 PMCID: PMC9149858 DOI: 10.3390/ncrna8030034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/09/2022] [Accepted: 05/16/2022] [Indexed: 11/30/2022] Open
Abstract
Small RNA sequencing (sRNA-Seq) approaches unveiled sequences derived from longer non-coding RNAs, such as transfer RNA (tRNA) and ribosomal RNA (rRNA) fragments, known as tRFs and rRFs, respectively. However, rRNAs and RNAs shorter than 16 nt are often depleted from library preparations/sequencing analyses, although they may be functional. Here, we sought to obtain a complete repertoire of small RNAs by sequencing the total RNA from 11 samples of 6 different eukaryotic organisms, from yeasts to human, in an extended 8- to 30-nt window of RNA length. The 8- to 15-nt window essentially contained fragments of longer non-coding RNAs, such as microRNAs, PIWI-associated RNAs (piRNAs), small nucleolar RNAs (snoRNAs), tRNAs and rRNAs. Notably, unusually short RNAs < 16 nt were more abundant than those >16 nt in bilaterian organisms. A new RT-qPCR method confirmed that two unusually short rRFs of 12 and 13 nt were more overly abundant (~3-log difference) than two microRNAs. We propose to not deplete rRNA and to reduce the lower threshold of RNA length to include unusually short RNAs in sRNA-Seq analyses and datasets, as their abundance and diversity support their potential role and importance as biomarkers of disease and/or mediators of cellular function.
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Li C, Wang W, Sun Y, Ni Y, Qin F, Li X, Wang T, Guo M, Sun G. Selective sorting and secretion of hY4 RNA fragments into extracellular vesicles mediated by methylated YBX1 to promote lung cancer progression. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:136. [PMID: 35410432 PMCID: PMC8996536 DOI: 10.1186/s13046-022-02346-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 03/25/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Extracellular vesicles (EVs) are emerging mediators of intercellular communication that have been shown to play important roles in tumor progression. YRNA fragments, a type of small non-coding RNA, are dysregulated in non-small cell lung cancer (NSCLC) cell-derived EVs, suggesting that they may be an effective biomarker for cancer diagnosis and treatment strategies. METHODS Differentially expressed YRNA hY4 fragments (hY4F) in EVs from NSCLC cells and normal lung fibroblasts were isolated by differential ultra-centrifugation. RNA-binding proteins that interacted with hY4F were identified by screening with an RNA pulldown assay and mass spectrometry. The molecular mechanism of hY4F and the RNA-binding protein Y box binding protein 1 (YBX1) was demonstrated by qRT-PCR, western blot, RNA pulldown, and rescue experiments. Transcriptome sequencing, qRT-PCR validation, bioinformatics analysis and NF-κB pathway inhibitor assays elucidate the mechanism of YBX1 and hY4F inhibiting lung cancer. A peptide pulldown assay was performed to screen and identify a potential methyltransferase for YBX1. The roles of hY4F, YBX1, and SET domain containing 3 in biological functions, such as proliferation, migration, invasion, and apoptosis, in lung cancer cells were also examined by EdU incorporation assay, Transwell assay, flow cytometry, and other methods. Lastly, a mouse xenograft assay was used to assess the clinical relevance of YBX1 and hY4F in vivo. RESULTS Our data demonstrate that hY4 RNA fragments were upregulated in lung cancer- derived EVs, hY4F inhibits tumor progression through downregulating MAPK/NF-κB signaling, and then the selective sorting and secretion of hY4F into lung cancer EVs is regulated by the RNA-binding protein YBX1. Furthermore, we identified lysine K264 within the YBX1 C-terminal domain as the necessary site for its interaction with hY4Fs. K264 is modified by methylation, which affects its binding to hY4F and subsequent selective sorting into EVs in lung cancer cells. CONCLUSION Our findings demonstrate that hY4F acts as a tumor suppressor and is selectively sorted into lung cancer cell-derived EVs by interacting with methylated YBX1, which in turn promotes lung cancer progression. hY4F is a promising circulating biomarker for non-small cell lung cancer diagnosis and prognosis and an exceptional candidate for further therapeutic exploration.
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Affiliation(s)
- Chuang Li
- School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, P. R. China.,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P. R. China
| | - Wei Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P. R. China
| | - Yuting Sun
- School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, P. R. China
| | - Yifan Ni
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P. R. China
| | - Fang Qin
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P. R. China
| | - Xiaolu Li
- Department of Radiation Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Tao Wang
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Mingxiong Guo
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P. R. China.
| | - Guihong Sun
- School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, P. R. China. .,Hubei Provincial Key Laboratory of Allergy and Immunology, Wuhan, Hubei, P. R. China.
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Structural and genome-wide analyses suggest that transposon-derived protein SETMAR alters transcription and splicing. J Biol Chem 2022; 298:101894. [PMID: 35378129 PMCID: PMC9062482 DOI: 10.1016/j.jbc.2022.101894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 11/22/2022] Open
Abstract
Extensive portions of the human genome have unknown function, including those derived from transposable elements. One such element, the DNA transposon Hsmar1, entered the primate lineage approximately 50 million years ago leaving behind terminal inverted repeat (TIR) sequences and a single intact copy of the Hsmar1 transposase, which retains its ancestral TIR-DNA-binding activity, and is fused with a lysine methyltransferase SET domain to constitute the chimeric SETMAR gene. Here, we provide a structural basis for recognition of TIRs by SETMAR and investigate the function of SETMAR through genome-wide approaches. As elucidated in our 2.37 Å crystal structure, SETMAR forms a dimeric complex with each DNA-binding domain bound specifically to TIR-DNA through the formation of 32 hydrogen bonds. We found that SETMAR recognizes primarily TIR sequences (∼5000 sites) within the human genome as assessed by chromatin immunoprecipitation sequencing analysis. In two SETMAR KO cell lines, we identified 163 shared differentially expressed genes and 233 shared alternative splicing events. Among these genes are several pre–mRNA-splicing factors, transcription factors, and genes associated with neuronal function, and one alternatively spliced primate-specific gene, TMEM14B, which has been identified as a marker for neocortex expansion associated with brain evolution. Taken together, our results suggest a model in which SETMAR impacts differential expression and alternative splicing of genes associated with transcription and neuronal function, potentially through both its TIR-specific DNA-binding and lysine methyltransferase activities, consistent with a role for SETMAR in simian primate development.
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45
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Emerging function and clinical significance of extracellular vesicle noncoding RNAs in lung cancer. Mol Ther Oncolytics 2022; 24:814-833. [PMID: 35317517 PMCID: PMC8908047 DOI: 10.1016/j.omto.2022.02.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Lung cancer (LC) is a commonly diagnosed cancer with an unsatisfactory prognosis. Extracellular vesicles (EVs) are lipid bilayer-delimited particles that mediate cell-cell communication by transporting various biomacromolecules, such as nucleic acids, proteins, and lipids. Noncoding RNAs (ncRNAs), including microRNAs, circular RNAs, and long noncoding RNAs, are important noncoding transcripts that play critical roles in a variety of physiological and pathological processes, especially in cancer. ncRNAs have been verified to be packaged into EVs and transported between LC cells and stromal cells, regulating multiple LC malignant phenotypes, such as proliferation, migration, invasion, epithelial-mesenchymal transition, metastasis, and treatment resistance. Additionally, EVs can be detected in various body fluids and are associated with the stage, grade, and metastasis of LC. Herein, we summarize the biological characteristics and functions of EV ncRNAs in the biological processes of LC, focusing on their potential to serve as diagnostic and prognostic biomarkers of LC as well as their probable role in the clinical treatment of LC. EV ncRNAs provide a new perspective for understanding the mechanism underlying LC pathogenesis and development, which might benefit numerous LC patients in the future.
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Mei H, Boom J, El Abdellaoui S, Abdelmohsen K, Munk R, Martindale JL, Kloet S, Kielbasa SM, Sharp TH, Gorospe M, Raz V. Alternative polyadenylation utilization results in ribosome assembly and mRNA translation deficiencies in a model for muscle aging. J Gerontol A Biol Sci Med Sci 2022; 77:1130-1140. [PMID: 35245938 PMCID: PMC9159670 DOI: 10.1093/gerona/glac058] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 11/15/2022] Open
Abstract
Aging-associated muscle wasting is regulated by multiple molecular processes, whereby aberrant mRNA processing regulation induces muscle wasting. The poly(A)-binding protein nuclear 1 (PABPN1) regulates polyadenylation site (PAS) utilization, in the absence of PABPN1 the alternative PAS (APA) is utilized. Reduced PABPN1 levels induce muscle wasting where the expression of cellular processes regulating protein homeostasis, the ubiquitin-proteasome system, and translation, are robustly dysregulated. Translation is impacted by mRNA levels, but PABPN1 impact on translation is not fully understood. Here we show that a persistent reduction in PABPN1 levels led to a significant loss of translation efficiency. RNA sequencing of rRNA-depleted libraries from polysome traces revealed reduced mRNA abundance across ribosomal fractions, as well as reduced levels of small RNAs. We show that the abundance of translated mRNAs in the polysomes correlated with PAS switches at the 3'-UTR. Those mRNAs are enriched in cellular processes that are essential for proper muscle function. This study suggests that the effect of PABPN1 on translation efficiency impacts protein homeostasis in aging-associated muscle atrophy.
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Affiliation(s)
- Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden, The Netherlands
| | - Jasper Boom
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden, The Netherlands
| | - Salma El Abdellaoui
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Susan Kloet
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Szymone M Kielbasa
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden The Netherlands
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Vered Raz
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
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Pediatric brain tumor cell lines exhibit miRNA-depleted, Y RNA-enriched extracellular vesicles. J Neurooncol 2022; 156:269-279. [PMID: 34984645 DOI: 10.1007/s11060-021-03914-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/25/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Medulloblastoma (MB) and diffuse infiltrative pontine glioma (DIPG) are malignant pediatric tumors. Extracellular vesicles (EVs) and their bioactive cargoes have been implicated in tumorigenesis. Most studies have focused on adult tumors, therefore the role of EVs and the noncoding RNA (ncRNA) landscape in pediatric brain tumors is not fully characterized. The overall aim of this pilot study was to isolate EVs from MB and DIPG patient-derived cell lines and to explore the small ncRNA transcriptome. METHODS EVs from 3 DIPG and 4 MB patient-derived cell lines were analyzed. High-throughput next generation sequencing interrogated the short non-coding RNA (ncRNA) transcriptome. Known and novel miRNAs were quantified. Differential expression analysis, in silico target prediction, and functional gene enrichment were performed. RESULTS EV secretomes from MB and DIPG patient-derived cell lines demonstrated discrete ncRNA biotypes. Notably, miRNAs were depleted and Y RNAs were enriched in EV samples. Hierarchical cluster analysis revealed high discrimination in miRNA expression between DIPG and MB cell lines and RNA-Seq identified novel miRNAs not previously implicated in MB or DIPG pathogenesis. Known and putative target genes of dysregulated miRNAs were identified. Functional annotation analysis of the target genes for differentially expressed EV-and parental-derived miRNAs revealed significant cancer-related pathway involvement. CONCLUSIONS This hypothesis-generating study demonstrated that pediatric brain tumor-derived cell lines secrete EVs comprised of various ncRNA cargoes. Validation of these findings in patient samples may provide new insights into the pediatric brain tumor microenvironment and identification of novel therapeutic candidates.
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Tesovnik T, Jenko Bizjan B, Šket R, Debeljak M, Battelino T, Kovač J. Technological Approaches in the Analysis of Extracellular Vesicle Nucleotide Sequences. Front Bioeng Biotechnol 2021; 9:787551. [PMID: 35004647 PMCID: PMC8733665 DOI: 10.3389/fbioe.2021.787551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
Together with metabolites, proteins, and lipid components, the EV cargo consists of DNA and RNA nucleotide sequence species, which are part of the intracellular communication network regulating specific cellular processes and provoking distinct target cell responses. The extracellular vesicle (EV) nucleotide sequence cargo molecules are often investigated in association with a particular pathology and may provide an insight into the physiological and pathological processes in hard-to-access organs and tissues. The diversity and biological function of EV nucleotide sequences are distinct regarding EV subgroups and differ in tissue- and cell-released EVs. EV DNA is present mainly in apoptotic bodies, while there are different species of EV RNAs in all subgroups of EVs. A limited sample volume of unique human liquid biopsy provides a small amount of EVs with limited isolated DNA and RNA, which can be a challenging factor for EV nucleotide sequence analysis, while the additional difficulty is technical variability of molecular nucleotide detection. Every EV study is challenged with its first step of the EV isolation procedure, which determines the EV's purity, yield, and diameter range and has an impact on the EV's downstream analysis with a significant impact on the final result. The gold standard EV isolation procedure with ultracentrifugation provides a low output and not highly pure isolated EVs, while modern techniques increase EV's yield and purity. Different EV DNA and RNA detection techniques include the PCR procedure for nucleotide sequence replication of the molecules of interest, which can undergo a small-input EV DNA or RNA material. The nucleotide sequence detection approaches with their advantages and disadvantages should be considered to appropriately address the study problem and to extract specific EV nucleotide sequence information with the detection using qPCR or next-generation sequencing. Advanced next-generation sequencing techniques allow the detection of total EV genomic or transcriptomic data even at the single-molecule resolution and thus, offering a sensitive and accurate EV DNA or RNA biomarker detection. Additionally, with the processes where the EV genomic or transcriptomic data profiles are compared to identify characteristic EV differences in specific conditions, novel biomarkers could be discovered. Therefore, a suitable differential expression analysis is crucial to define the EV DNA or RNA differences between conditions under investigation. Further bioinformatics analysis can predict molecular cell targets and identify targeted and affected cellular pathways. The prediction target tools with functional studies are essential to help specify the role of the investigated EV-targeted nucleotide sequences in health and disease and support further development of EV-related therapeutics. This review will discuss the biological diversity of human liquid biopsy-obtained EV nucleotide sequences DNA and RNA species reported as potential biomarkers in health and disease and methodological principles of their detection, from human liquid biopsy EV isolation, EV nucleotide sequence extraction, techniques for their detection, and their cell target prediction.
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Affiliation(s)
- Tine Tesovnik
- Institute for Special Laboratory Diagnostics, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
| | - Barbara Jenko Bizjan
- Institute for Special Laboratory Diagnostics, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
| | - Robert Šket
- Institute for Special Laboratory Diagnostics, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
| | - Maruša Debeljak
- Institute for Special Laboratory Diagnostics, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
| | - Tadej Battelino
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
- Faculty of Medicine, Chair of Paediatrics, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Kovač
- Institute for Special Laboratory Diagnostics, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
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Identification of Long Non-Coding RNAs Associated with Tomato Fruit Expansion and Ripening by Strand-Specific Paired-End RNA Sequencing. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7120522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As emerging essential regulators in plant development, long non-coding RNAs (lncRNAs) have been extensively investigated in multiple horticultural crops, as well as in different tissues of plants. Tomato fruits are an indispensable part of people’s diet and are consumed as fruits and vegetables. Meanwhile, tomato is widely used as a model to study the ripening mechanism in fleshy fruit. Although increasing evidence shows that lncRNAs are involved in lots of biological processes in tomato plants, the comprehensive identification of lncRNAs in tomato fruit during its expansion and ripening and their functions are partially known. Here, we performed strand-specific paired-end RNA sequencing (ssRNA-seq) of tomato Heinz1706 fruits at five different developmental stages, as well as flowers and leaves. We identified 17,674 putative lncRNAs by referencing the recently released SL4.0 and annotation ITAG4.0 in tomato plants. Many lncRNAs show different expression patterns in fleshy fruit at different developmental stages compared with leaves or flowers. Our results indicate that lncRNAs play an important role in the regulation of tomato fruit expansion and ripening, providing informative lncRNA candidates for further studies in tomato fruits. In addition, we also summarize the recent advanced progress in lncRNAs mediated regulation on horticultural fruits. Hence, our study updates the understanding of lncRNAs in horticultural plants and provides resources for future studies relating to the expansion and ripening of tomato fruits.
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50
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Mesquita-Ribeiro R, Fort RS, Rathbone A, Farias J, Lucci C, James V, Sotelo-Silveira J, Duhagon MA, Dajas-Bailador F. Distinct small non-coding RNA landscape in the axons and released extracellular vesicles of developing primary cortical neurons and the axoplasm of adult nerves. RNA Biol 2021; 18:832-855. [PMID: 34882524 PMCID: PMC8782166 DOI: 10.1080/15476286.2021.2000792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Neurons have highlighted the needs for decentralized gene expression and specific RNA function in somato-dendritic and axonal compartments, as well as in intercellular communication via extracellular vesicles (EVs). Despite advances in miRNA biology, the identity and regulatory capacity of other small non-coding RNAs (sncRNAs) in neuronal models and local subdomains has been largely unexplored.We identified a highly complex and differentially localized content of sncRNAs in axons and EVs during early neuronal development of cortical primary neurons and in adult axons in vivo. This content goes far beyond miRNAs and includes most known sncRNAs and precisely processed fragments from tRNAs, sno/snRNAs, Y RNAs and vtRNAs. Although miRNAs are the major sncRNA biotype in whole-cell samples, their relative abundance is significantly decreased in axons and neuronal EVs, where specific tRNA fragments (tRFs and tRHs/tiRNAs) mainly derived from tRNAs Gly-GCC, Val-CAC and Val-AAC predominate. Notably, although 5'-tRHs compose the great majority of tRNA-derived fragments observed in vitro, a shift to 3'-tRNAs is observed in mature axons in vivo.The existence of these complex sncRNA populations that are specific to distinct neuronal subdomains and selectively incorporated into EVs, equip neurons with key molecular tools for spatiotemporal functional control and cell-to-cell communication.
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Affiliation(s)
| | - Rafael Sebastián Fort
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Alex Rathbone
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Joaquina Farias
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.,Polo de Desarrollo Universitario "Espacio de Biología Vegetal del Noreste", Centro Universitario Regional Noreste, UdelaR, Uruguay
| | - Cristiano Lucci
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Victoria James
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Jose Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Maria Ana Duhagon
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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