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Zirak B, Naghipourfar M, Saberi A, Pouyabahar D, Zarezadeh A, Luo L, Fish L, Huh D, Navickas A, Sharifi-Zarchi A, Goodarzi H. Revealing the grammar of small RNA secretion using interpretable machine learning. CELL GENOMICS 2024; 4:100522. [PMID: 38460515 PMCID: PMC11019361 DOI: 10.1016/j.xgen.2024.100522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 11/02/2023] [Accepted: 02/12/2024] [Indexed: 03/11/2024]
Abstract
Small non-coding RNAs can be secreted through a variety of mechanisms, including exosomal sorting, in small extracellular vesicles, and within lipoprotein complexes. However, the mechanisms that govern their sorting and secretion are not well understood. Here, we present ExoGRU, a machine learning model that predicts small RNA secretion probabilities from primary RNA sequences. We experimentally validated the performance of this model through ExoGRU-guided mutagenesis and synthetic RNA sequence analysis. Additionally, we used ExoGRU to reveal cis and trans factors that underlie small RNA secretion, including known and novel RNA-binding proteins (RBPs), e.g., YBX1, HNRNPA2B1, and RBM24. We also developed a novel technique called exoCLIP, which reveals the RNA interactome of RBPs within the cell-free space. Together, our results demonstrate the power of machine learning in revealing novel biological mechanisms. In addition to providing deeper insight into small RNA secretion, this knowledge can be leveraged in therapeutic and synthetic biology applications.
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Affiliation(s)
- Bahar Zirak
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US
| | - Mohsen Naghipourfar
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Ali Saberi
- Department of Electrical and Computer Engineering, McGill University, Montreal, QC H3A 0E9, Canada; McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, 740 Dr Penfield Avenue, Montreal, QC H3A 0G1, Canada
| | - Delaram Pouyabahar
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Amirhossein Zarezadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Lixi Luo
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US; Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lisa Fish
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US
| | - Doowon Huh
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Albertas Navickas
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US; Institut Curie, CNRS UMR3348, INSERM U1278, Orsay, France.
| | - Ali Sharifi-Zarchi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran.
| | - Hani Goodarzi
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US.
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2
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Li J, Kang X, Guidi I, Lu L, Fernández-Millán P, Prats-Ejarque G, Boix E. Structural determinants for tRNA selective cleavage by RNase 2/EDN. Structure 2024; 32:328-341.e4. [PMID: 38228145 DOI: 10.1016/j.str.2023.12.012] [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: 08/22/2023] [Revised: 11/03/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024]
Abstract
tRNA-derived fragments (tRFs) have emerged as key players of immunoregulation. Some RNase A superfamily members participate in the shaping of the tRFs population. By comparing wild-type and knockout macrophage cell lines, our previous work revealed that RNase 2 can selectively cleave tRNAs. Here, we confirm the in vitro protein cleavage pattern by screening of synthetic tRNAs, single-mutant variants, and anticodon-loop DNA/RNA hairpins. By sequencing of tRF products, we identified the cleavage selectivity of recombinant RNase 2 with base specificity at B1 (U/C) and B2 (A) sites, consistent with a previous cellular study. Lastly, protein-hairpin complexes were predicted by MD simulations. Results reveal the contribution of the α1, loop 3 and loop 4, and β6 RNase 2 regions, where residues Arg36/Asn39/Gln40/Asn65/Arg68/Arg132 provide interactions, spanning from P-1 to P2 sites that are essential for anticodon loop recognition. Knowledge of RNase 2-specific tRFs generation might guide new therapeutic approaches for infectious and immune-related diseases.
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Affiliation(s)
- Jiarui Li
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain.
| | - Xincheng Kang
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Irene Guidi
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Lu Lu
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Pablo Fernández-Millán
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Guillem Prats-Ejarque
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain.
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3
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Yadav A, Mathan J, Dubey AK, Singh A. The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling. Noncoding RNA 2024; 10:13. [PMID: 38392968 PMCID: PMC10893181 DOI: 10.3390/ncrna10010013] [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: 12/11/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research.
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Affiliation(s)
- Amit Yadav
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
| | - Jyotirmaya Mathan
- Sashi Bhusan Rath Government Autonomous Women’s College, Brahmapur 760001, India;
| | - Arvind Kumar Dubey
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Anuradha Singh
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, USA
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Drozdov A, Lebedev E, Adonin L. Comparative Analysis of Bivalve and Sea Urchin Genetics and Development: Investigating the Dichotomy in Bilateria. Int J Mol Sci 2023; 24:17163. [PMID: 38138992 PMCID: PMC10742642 DOI: 10.3390/ijms242417163] [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: 10/31/2023] [Revised: 11/19/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
This comprehensive review presents a comparative analysis of early embryogenesis in Protostomia and Deuterostomia, the first of which exhibit a mosaic pattern of development, where cells are fated deterministically, while Deuterostomia display a regulatory pattern of development, where the fate of cells is indeterminate. Despite these fundamental differences, there are common transcriptional mechanisms that underline their evolutionary linkages, particularly in the field of functional genomics. By elucidating both conserved and unique regulatory strategies, this review provides essential insights into the comparative embryology and developmental dynamics of these groups. The objective of this review is to clarify the shared and distinctive characteristics of transcriptional regulatory mechanisms. This will contribute to the extensive areas of functional genomics, evolutionary biology and developmental biology, and possibly lay the foundation for future research and discussion on this seminal topic.
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Affiliation(s)
- Anatoliy Drozdov
- Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Egor Lebedev
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia;
| | - Leonid Adonin
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia;
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
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Harvey J, Pishva E, Chouliaras L, Lunnon K. Elucidating distinct molecular signatures of Lewy body dementias. Neurobiol Dis 2023; 188:106337. [PMID: 37918758 DOI: 10.1016/j.nbd.2023.106337] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/15/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023] Open
Abstract
Dementia with Lewy bodies and Parkinson's disease dementia are common neurodegenerative diseases that share similar neuropathological profiles and spectra of clinical symptoms but are primarily differentiated by the order in which symptoms manifest. The question of whether a distinct molecular pathological profile could distinguish these disorders is yet to be answered. However, in recent years, studies have begun to investigate genomic, epigenomic, transcriptomic and proteomic differences that may differentiate these disorders, providing novel insights in to disease etiology. In this review, we present an overview of the clinical and pathological hallmarks of Lewy body dementias before summarizing relevant research into genetic, epigenetic, transcriptional and protein signatures in these diseases, with a particular interest in those resolving "omic" level changes. We conclude by suggesting future research directions to address current gaps and questions present within the field.
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Affiliation(s)
- Joshua Harvey
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, the Netherlands
| | - Leonidas Chouliaras
- Department of Psychiatry, School of Clinical Medicine, University of Cambridge, Cambridge, UK; Specialist Dementia and Frailty Service, Essex Partnership University NHS Foundation Trust, Epping, UK
| | - Katie Lunnon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
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Jiang Z, Han K, Min D, Kong W, Wang S, Gao M. Identification of the methotrexate resistance-related diagnostic markers in osteosarcoma via adaptive total variation netNMF and multi-omics datasets. Front Genet 2023; 14:1288073. [PMID: 37937197 PMCID: PMC10625916 DOI: 10.3389/fgene.2023.1288073] [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: 09/03/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023] Open
Abstract
Osteosarcoma is one of the most common malignant bone tumors with high chemoresistance and poor prognosis, exhibiting abnormal gene regulation and epigenetic events. Methotrexate (MTX) is often used as a primary agent in neoadjuvant chemotherapy for osteosarcoma; However, the high dosage of methotrexate and strong drug resistance limit its therapeutic efficacy and application prospects. Studies have shown that abnormal expression and dysfunction of some coding or non-coding RNAs (e.g., DNA methylation and microRNA) affect key features of osteosarcoma progression, such as proliferation, migration, invasion, and drug resistance. Comprehensive multi-omics analysis is critical to understand its chemoresistant and pathogenic mechanisms. Currently, the network analysis-based non-negative matrix factorization (netNMF) method is widely used for multi-omics data fusion analysis. However, the effects of data noise and inflexible settings of regularization parameters affect its performance, while integrating and processing different types of genetic data is also a challenge. In this study, we introduced a novel adaptive total variation netNMF (ATV-netNMF) method to identify feature modules and characteristic genes by integrating methylation and gene expression data, which can adaptively choose an anisotropic smoothing scheme to denoise or preserve feature details based on the gradient information of the data by introducing an adaptive total variation constraint in netNMF. By comparing with other similar methods, the results showed that the proposed method could extract multi-omics fusion features more effectively. Furthermore, by combining the mRNA and miRNA data of methotrexate (MTX) resistance with the extracted feature genes, four genes, Carboxypeptidase E (CPE), LIM, SH3 protein 1 (LASP1), Pyruvate Dehydrogenase Kinase 1 (PDK1) and Serine beta-lactamase-like protein (LACTB) were finally identified. The results showed that the gene signature could reliably predict the prognostic status and immune status of osteosarcoma patients.
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Affiliation(s)
- Zhihan Jiang
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Kun Han
- Department of Medical Oncology, The Sixth People’s Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Daliu Min
- Department of Medical Oncology, The Sixth People’s Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wei Kong
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Shuaiqun Wang
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Min Gao
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
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7
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Fattahi M, Shahrabi S, Saadatpour F, Rezaee D, Beyglu Z, Delavari S, Amrolahi A, Ahmadi S, Bagheri-Mohammadi S, Noori E, Majidpoor J, Nouri S, Aghaei-Zarch SM, Falahi S, Najafi S, Le BN. microRNA-382 as a tumor suppressor? Roles in tumorigenesis and clinical significance. Int J Biol Macromol 2023; 250:125863. [PMID: 37467828 DOI: 10.1016/j.ijbiomac.2023.125863] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/30/2023] [Accepted: 07/15/2023] [Indexed: 07/21/2023]
Abstract
MicroRNAs (miRNAs) are small single-stranded RNAs belonging to a class of non-coding RNAs with an average length of 18-22 nucleotides. Although not able to encode any protein, miRNAs are vastly studied and found to play role in various human physiologic as well as pathological conditions. A huge number of miRNAs have been identified in human cells whose expression is straightly regulated with crucial biological functions, while this number is constantly increasing. miRNAs are particularly studied in cancers, where they either can act with oncogenic function (oncomiRs) or tumor-suppressors role (referred as tumor-suppressor/oncorepressor miRNAs). miR-382 is a well-studied miRNA, which is revealed to play regulatory roles in physiological processes like osteogenic differentiation, hematopoietic stem cell differentiation and normal hematopoiesis, and liver progenitor cell differentiation. Notably, miR-382 deregulation is reported in pathologic conditions, such as renal fibrosis, muscular dystrophies, Rett syndrome, epidural fibrosis, atrial fibrillation, amelogenesis imperfecta, oxidative stress, human immunodeficiency virus (HIV) replication, and various types of cancers. The majority of oncogenesis studies have claimed miR-382 downregulation in cancers and suppressor impact on malignant phenotype of cancer cells in vitro and in vivo, while a few studies suggest opposite findings. Given the putative role of this miRNA in regulation of oncogenesis, assessment of miR-382 expression is suggested in a several clinical investigations as a prognostic/diagnostic biomarker for cancer patients. In this review, we have an overview to recent studies evaluated the role of miR-382 in oncogenesis as well as its clinical potential.
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Affiliation(s)
- Mehdi Fattahi
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam; School of Engineering & Technology, Duy Tan University, Da Nang, Vietnam
| | - Saeid Shahrabi
- Department of Biochemistry and Hematology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Fatemeh Saadatpour
- Pharmaceutical Biotechnology Lab, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Delsuz Rezaee
- School of Allied Medical Sciences, Ilam University of Medical Sciences, Ilam, Iran
| | - Zahra Beyglu
- Department of Genetics, Qom Branch, Islamic Azad University, Qom, Iran
| | - Sana Delavari
- Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Anita Amrolahi
- Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shirin Ahmadi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeid Bagheri-Mohammadi
- Department of Physiology and Neurophysiology Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Effat Noori
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jamal Majidpoor
- Department of Anatomy, Faculty of Medicine, Infectious Disease Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Shadi Nouri
- Department of Radiology, School of Medicine, Arak University of Medical Sciences, Arak, Iran.
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Shahab Falahi
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran.
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Binh Nguyen Le
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam; School of Engineering & Technology, Duy Tan University, Da Nang, Vietnam
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8
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Zeng X, Zheng Q, Wang L, Chen T, Lin W, Lin Q. Sevoflurane suppresses the malignant progression of breast cancer via the hsa_circ_0000129/miR-578/EPSTI1 axis. Thorac Cancer 2023; 14:2665-2677. [PMID: 37533139 PMCID: PMC10493489 DOI: 10.1111/1759-7714.15053] [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: 05/25/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Sevoflurane (Sev) is a commonly used volatile anesthetic that might suppress the process of breast cancer. Also, circular RNAs (circRNAs) have been reported to partake in the pathogenesis of breast cancer. Accordingly, this research was designed to investigate the mechanism of hsa_circ_0005962 on Sev-mediated breast cancer development. METHODS Sev was applied to treat breast cancer cells. Cell proliferation ability, migration, invasion, and apoptosis were detected using Cell Counting Kit-8 (CCK-8), 5-ethynyl-2'-deoxyuridine (EdU), Transwell, and flow cytometry assay. Proliferating cell nuclear antigen (PCNA), Matrix metallopeptidase 9 (MMP9), B-cell lymphoma-2 (Bcl-2)-associated X protein (Bax), and Epithelial stromal interaction 1 (EPSTI1) were assessed using western blot assay. circ_0000129, microRNA-578 (miR-578), and EPSTI1 levels were determined using real-time quantitative polymerase chain reaction (RT-qPCR). Using bioinformatics software (Circinteractome and Targetscan), the binding between miR-578 and circ_0000129 or EPSTI1 were predicted, and proved using dual-luciferase reporter and RNA pull-down assay. The biological roles of circ_0000129 and Sevoflurane on tumor growth were analyzed using a xenograft tumor model in vivo. RESULTS Sevoflurane blocked tumor cell proliferation, migration, invasion, and promoted apoptosis. Circ_0000129 and EPSTI1 expression were increased, and miR-578 was decreased in breast cancer cells. Also, they presented an opposite trend in Sev-treated tumor cells. Circ_0000129 upregulation might abolish Sev-mediated tumor progression in vitro. Mechanically, circ_0000129 can affect EPSTI1 expression by sponging miR-578. Sev might inhibit tumor growth by regulating circ_0000129 in vivo. CONCLUSION Circ_0000129 relieved Sev-triggered suppression impacts on breast cancer development partly via the miR-578/EPSTI1 axis, which provides a new mechanism for studying mediated therapy of breast cancer treatment.
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Affiliation(s)
- Xuehui Zeng
- Department of AnesthesiologyZhongshan Hospital Xiamen UniversityXiamen CityChina
| | - Qingqi Zheng
- Department of AnesthesiologyZhongshan Hospital Xiamen UniversityXiamen CityChina
| | - Lang Wang
- Department of AnesthesiologyZhongshan Hospital Xiamen UniversityXiamen CityChina
| | - Tao Chen
- Department of AnesthesiologyZhongshan Hospital Xiamen UniversityXiamen CityChina
| | - Wenxin Lin
- Department of AnesthesiologyZhongshan Hospital Xiamen UniversityXiamen CityChina
| | - Quanyang Lin
- Department of AnesthesiologyZhongshan Hospital Xiamen UniversityXiamen CityChina
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9
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Niderla-Bielińska J, Jankowska-Steifer E, Włodarski P. Non-Coding RNAs and Human Diseases: Current Status and Future Perspectives. Int J Mol Sci 2023; 24:11679. [PMID: 37511438 PMCID: PMC10380467 DOI: 10.3390/ijms241411679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are a family of RNA molecules that, unlike messenger RNAs, are not templates for protein synthesis but have an essential or regulatory role in this process [...].
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Affiliation(s)
| | - Ewa Jankowska-Steifer
- Histology and Embryology Department, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Paweł Włodarski
- Department of Methodology, Center for Preclinical Research, Medical University of Warsaw, 1B Banacha Street, 02-097 Warsaw, Poland
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10
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Khan S, Rehman U, Parveen N, Kumar S, Baboota S, Ali J. siRNA therapeutics: insights, challenges, remedies and future prospects. Expert Opin Drug Deliv 2023; 20:1167-1187. [PMID: 37642354 DOI: 10.1080/17425247.2023.2251890] [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: 10/01/2022] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
INTRODUCTION Among conventional and novel therapeutic approaches, the siRNA strategy stands out for treating disease by silencing the gene responsible for the corresponding disorder. Gene silencing is supposedly intended to target any disease-causing gene, and therefore, several attempts and investments were made to exploit siRNA gene therapy and advance it into clinical settings. Despite the remarkable beneficial prospects, the applicability of siRNA therapeutics is very challenging due to various pathophysiological barriers that hamper its target reach, which is the cytosol, and execution of gene silencing action. AREAS COVERED The present review provides insights into the field of siRNA therapeutics, significant in vivo hurdles that mitigate the target accessibility of siRNA, and remedies to overcome these siRNA delivery challenges. Nonetheless, the current review also highlights the on-going clinical trials and the regulatory aspects of siRNA modalities. EXPERT OPINION The siRNAs have the potential to reach previously untreated target sites and silence the concerned gene owing to their modification as polymeric or lipidic nanoparticles, conjugates, and the application of advanced drug delivery strategies. With such mounting research attempts to improve the delivery of siRNA to target tissue, we might shortly witness revolutionary therapeutic outcomes, new approvals, and clinical implications.
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Affiliation(s)
- Saba Khan
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Urushi Rehman
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Neha Parveen
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Shobhit Kumar
- Department of Pharmaceutical Technology, Meerut Institute of Engineering and Technology, Meerut, Uttar Pradesh, India
| | - Sanjula Baboota
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Javed Ali
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
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11
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Soheilifar MH, Nobari S, Hakimi M, Adel B, Masoudi-Khoram N, Reyhani E, Neghab HK. Current concepts of microRNA-mediated regulatory mechanisms in human pulp tissue-derived stem cells: a snapshot in the regenerative dentistry. Cell Tissue Res 2023:10.1007/s00441-023-03792-4. [PMID: 37247032 DOI: 10.1007/s00441-023-03792-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/12/2023] [Indexed: 05/30/2023]
Abstract
One of the most studied class of non-coding RNAs is microRNAs (miRNAs) which regulate more than 60% of human genes. A network of miRNA gene interactions participates in stem cell self-renewal, proliferation, migration, apoptosis, immunomodulation, and differentiation. Human pulp tissue-derived stem cells (PSCs) are an attractive source of dental mesenchymal stem cells (MSCs) which comprise human dental pulp stem cells (hDPSCs) obtained from the dental pulp of permanent teeth and stem cells isolated from exfoliated deciduous teeth (SHEDs) that would be a therapeutic opportunity in stomatognathic system reconstruction and repair of other damaged tissues. The regenerative capacity of hDPSCs and SHEDs is mediated by osteogenic, odontogenic, myogenic, neurogenic, angiogenic differentiation, and immunomodulatory function. Multi-lineage differentiation of PSCs can be induced or inhibited by the interaction of miRNAs with their target genes. Manipulating the expression of functional miRNAs in PSCs by mimicking miRNAs or inhibiting miRNAs emerged as a therapeutic tool in the clinical translation. However, the effectiveness and safety of miRNA-based therapeutics, besides higher stability, biocompatibility, less off-target effects, and immunologic reactions, have received particular attention. This review aimed to comprehensively overview the molecular mechanisms underlying miRNA-modified PSCs as a futuristic therapeutic option in regenerative dentistry.
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Affiliation(s)
| | - Sima Nobari
- Research Center for Molecular Medicine, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Maryam Hakimi
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bashir Adel
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Nastaran Masoudi-Khoram
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Elahe Reyhani
- Faculty of Dentistry, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Hoda Keshmiri Neghab
- Department of Photo Healing and Regeneration, Medical Laser Research Center, Yara Institute, ACECR, Tehran, Iran
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12
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Morales C, Arias-Carrasco R, Maracaja-Coutinho V, Seron P, Lanas F, Salazar LA, Saavedra N. Differences in Bacterial Small RNAs in Stool Samples from Hypercholesterolemic and Normocholesterolemic Subjects. Int J Mol Sci 2023; 24:ijms24087213. [PMID: 37108373 PMCID: PMC10138442 DOI: 10.3390/ijms24087213] [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: 01/27/2023] [Revised: 03/13/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Cholesterol metabolism is important at the physiological level as well as in several diseases, with small RNA being an element to consider in terms of its epigenetic control. Thus, the aim of this study was to identify differences between bacterial small RNAs present at the gut level in hypercholesterolemic and normocholesterolemic individuals. Twenty stool samples were collected from hypercholesterolemic and normocholesterolemic subjects. RNA extraction and small RNA sequencing were performed, followed by bioinformatics analyses with BrumiR, Bowtie 2, BLASTn, DESeq2, and IntaRNA, after the filtering of the reads with fastp. In addition, the prediction of secondary structures was obtained with RNAfold WebServer. Most of the small RNAs were of bacterial origin and presented a greater number of readings in normocholesterolemic participants. The upregulation of small RNA ID 2909606 associated with Coprococcus eutactus (family Lachnospiraceae) was presented in hypercholesterolemic subjects. In addition, a positive correlation was established between small RNA ID 2149569 from the species Blautia wexlerae and hypercholesterolemic subjects. Other bacterial and archaeal small RNAs that interacted with the LDL receptor (LDLR) were identified. For these sequences, the prediction of secondary structures was also obtained. There were significant differences in bacterial small RNAs associated with cholesterol metabolism in hypercholesterolemic and normocholesterolemic participants.
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Affiliation(s)
- Cristian Morales
- Centro de Biología Molecular y Farmacogenética, Núcleo Científico-Tecnológico en Biorecursos BIOREN, Universidad de La Frontera, Temuco 4811230, Chile
- Tecnología Médica, Facultad de Salud, Universidad Santo Tomás, Temuco 4801076, Chile
| | - Raul Arias-Carrasco
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago 8330378, Chile
| | - Vinicius Maracaja-Coutinho
- Advanced Center for Chronic Diseases-ACCDiS, Facultad de Química y Ciencias Farmacéuticas, Universidad de Chile, Santiago 8380494, Chile
| | - Pamela Seron
- Departamento de Ciencias de La Rehabilitación, Facultad de Medicina, Universidad de La Frontera, Temuco 4781151, Chile
| | - Fernando Lanas
- Departamento de Medicina Interna, Facultad de Medicina, Universidad de La Frontera, Temuco 4781151, Chile
| | - Luis A Salazar
- Centro de Biología Molecular y Farmacogenética, Núcleo Científico-Tecnológico en Biorecursos BIOREN, Universidad de La Frontera, Temuco 4811230, Chile
- Departamento de Ciencias Básicas, Facultad de Medicina, Universidad de La Frontera, Temuco 4811230, Chile
| | - Nicolás Saavedra
- Centro de Biología Molecular y Farmacogenética, Núcleo Científico-Tecnológico en Biorecursos BIOREN, Universidad de La Frontera, Temuco 4811230, Chile
- Departamento de Ciencias Básicas, Facultad de Medicina, Universidad de La Frontera, Temuco 4811230, Chile
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13
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Kohestani H, Wereszczynski J. The effects of RNA.DNA-DNA triple helices on nucleosome structures and dynamics. Biophys J 2023; 122:1229-1239. [PMID: 36798026 PMCID: PMC10111275 DOI: 10.1016/j.bpj.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 01/22/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Noncoding RNAs (ncRNAs) are an emerging epigenetic factor and have been recognized as playing a key role in many gene expression pathways. Structurally, binding of ncRNAs to isolated DNA is strongly dependent on sequence complementary and results in the formation of an RNA.DNA-DNA (RDD) triple helix. However, in vivo DNA is not isolated but is rather packed in chromatin fibers, the fundamental unit of which is the nucleosome. Biochemical experiments have shown that ncRNA binding to nucleosomal DNA is elevated at DNA entry and exit sites and is dependent on the presence of the H3 N-terminal tails. However, the structural and dynamical bases for these mechanisms remain unknown. Here, we have examined the mechanisms and effects of RDD formation in the context of the nucleosome using a series of all-atom molecular dynamics simulations. Results highlight the importance of DNA sequence on complex stability, elucidate the effects of the H3 tails on RDD structures, show how RDD formation impacts the structure and dynamics of the H3 tails, and show how RNA alters the local and global DNA double-helical structure. Together, our results suggest ncRNAs can modify nucleosome, and potentially higher-order chromatin, structures and dynamics as a means of exerting epigenetic control.
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Affiliation(s)
- Havva Kohestani
- Department of Biology, Illinois Institute of Technology, Chicago, Illinois
| | - Jeff Wereszczynski
- Departments of Physics & Biology, Illinois Institute of Technology, Chicago, Illinois.
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14
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Rbbani G, Nedoluzhko A, Siriyappagouder P, Sharko F, Galindo-Villegas J, Raeymaekers JAM, Joshi R, Fernandes JMO. The novel circular RNA CircMef2c is positively associated with muscle growth in Nile tilapia. Genomics 2023; 115:110598. [PMID: 36906188 PMCID: PMC7614353 DOI: 10.1016/j.ygeno.2023.110598] [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: 09/20/2022] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023]
Abstract
Muscle growth in teleosts is a complex biological process orchestrated by numerous protein-coding genes and non-coding RNAs. A few recent studies suggest that circRNAs are involved in teleost myogenesis, but the molecular networks involved remain poorly understood. In this study, an integrative omics approach was used to determine myogenic circRNAs in Nile tilapia by quantifying and comparing the expression profile of mRNAs, miRNAs, and circRNAs in fast muscle from full-sib fish with distinct growth rates. There were 1947 mRNAs, 9 miRNAs, and 4 circRNAs differentially expressed between fast- and slow-growing individuals. These miRNAs can regulate myogenic genes and have binding sites for the novel circRNA circMef2c. Our data indicate that circMef2c may interact with three miRNAs and 65 differentially expressed mRNAs to form multiple competing endogenous RNA networks that regulate growth, thus providing novel insights into the role of circRNAs in the regulation of muscle growth in teleosts.
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Affiliation(s)
- Golam Rbbani
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Artem Nedoluzhko
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway; Paleogenomics laboratory, European University at Saint Petersburg, 191187 Saint-Petersburg, Russia
| | | | | | - Jorge Galindo-Villegas
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Joost A M Raeymaekers
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | | | - Jorge M O Fernandes
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway.
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15
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Identification of Appropriate Endogenous Controls for Circulating miRNA Quantification in Working Dogs under Physiological Stress Conditions. Animals (Basel) 2023; 13:ani13040576. [PMID: 36830363 PMCID: PMC9951723 DOI: 10.3390/ani13040576] [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: 11/17/2022] [Revised: 01/31/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
Cell-free miRNAs, called circulating miRNAs (cmiRNAs), can act in a paracrine manner by facilitating a diversity of signaling mechanisms between cells. Real-time qPCR is the most accepted method for quantifying miRNA expression levels. The use of stable miRNA endogenous control (EC) for qPCR data normalization allows an accurate cross-sample gene expression comparison. The appropriate selection of EC is a crucial step because qPCR data can change drastically when normalization is performed using an unstable versus a stable EC. To find EC cmiRNA with stable expression in search and rescue (SAR) working dogs, we explored the serum miRNome by Next-Generation Sequencing (NGS) at T0 (resting state) and T1 immediately after SAR performance (state of physiologically recovered stress). The cmiRNAs selected in the NGS circulating miRNome as probable ECs were validated by qPCR, and miRNA stability was evaluated using the Delta Ct, BestKeeper, NormFinder, and GeNorm algorithms. Finally, RefFinder was used to rank the stability orders at both T0 and T1 by establishing miR-320 and miR-191 as the best-circulating ECs. We are confident that this study not only provides a helpful result in itself but also an experimental design for selecting the best endogenous controls to normalize gene expression for genes beyond circulating miRNAs.
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16
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Macvanin MT, Gluvic Z, Radovanovic J, Essack M, Gao X, Isenovic ER. Diabetic cardiomyopathy: The role of microRNAs and long non-coding RNAs. Front Endocrinol (Lausanne) 2023; 14:1124613. [PMID: 36950696 PMCID: PMC10025540 DOI: 10.3389/fendo.2023.1124613] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Diabetes mellitus (DM) is on the rise, necessitating the development of novel therapeutic and preventive strategies to mitigate the disease's debilitating effects. Diabetic cardiomyopathy (DCMP) is among the leading causes of morbidity and mortality in diabetic patients globally. DCMP manifests as cardiomyocyte hypertrophy, apoptosis, and myocardial interstitial fibrosis before progressing to heart failure. Evidence suggests that non-coding RNAs, such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), regulate diabetic cardiomyopathy-related processes such as insulin resistance, cardiomyocyte apoptosis and inflammation, emphasizing their heart-protective effects. This paper reviewed the literature data from animal and human studies on the non-trivial roles of miRNAs and lncRNAs in the context of DCMP in diabetes and demonstrated their future potential in DCMP treatment in diabetic patients.
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Affiliation(s)
- Mirjana T. Macvanin
- Department of Radiobiology and Molecular Genetics, VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
- *Correspondence: Mirjana T. Macvanin,
| | - Zoran Gluvic
- University Clinical-Hospital Centre Zemun-Belgrade, Clinic of Internal Medicine, Department of Endocrinology and Diabetes, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jelena Radovanovic
- Department of Radiobiology and Molecular Genetics, VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Magbubah Essack
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Esma R. Isenovic
- Department of Radiobiology and Molecular Genetics, VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
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17
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Zhang Y, Zhang T, Xu L, Zhu Y, Zhao LL, Li XD, Yang WW, Chen J, Gu M, Gu XS, Yang J. Evolution of the ErbB gene family and analysis of regulators of Egfr expression during development of the rat spinal cord. Neural Regen Res 2022; 17:2484-2490. [PMID: 35535900 PMCID: PMC9120683 DOI: 10.4103/1673-5374.339010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Egfr, a member of the ErbB gene family, plays a critical role in tissue development and homeostasis, wound healing, and disease. However, expression and regulators of Egfr during spinal cord development remain poorly understood. In this study, we investigated ErbB evolution and analyzed co-expression modules, miRNAs, and transcription factors that may regulate Egfr expression in rats. We found that ErbB family members formed via Egfr duplication in the ancient vertebrates but diverged after speciation of gnathostomes. We identified a module that was co-expressed with Egfr, which involved cell proliferation and blood vessel development. We predicted 25 miRNAs and nine transcription factors that may regulate Egfr expression. Dual-luciferase reporter assays showed six out of nine transcription factors significantly affected Egfr promoter reporter activity. Two of these transcription factors (KLF1 and STAT3) inhibited the Egfr promoter reporter, whereas four transcription factors (including FOXA2) activated the Egfr promoter reporter. Real-time PCR and immunofluorescence experiments showed high expression of FOXA2 during the embryonic period and FOXA2 was expressed in the floor plate of the spinal cord, suggesting the importance of FOXA2 during embryonic spinal cord development. Considering the importance of Egfr in embryonic spinal cord development, wound healing, and disease (specifically in cancer), regulatory elements identified in this study may provide candidate targets for nerve regeneration and disease treatment in the future.
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Affiliation(s)
- Yu Zhang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Tao Zhang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Lian Xu
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Ye Zhu
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Li-Li Zhao
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Xiao-Di Li
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Wei-Wei Yang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Jing Chen
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Miao Gu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Xiao-Song Gu
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Jian Yang
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
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18
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Majumder R, Ghosh S, Das A, Singh MK, Samanta S, Saha A, Saha RP. Prokaryotic ncRNAs: Master regulators of gene expression. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2022; 3:100136. [PMID: 36568271 PMCID: PMC9780080 DOI: 10.1016/j.crphar.2022.100136] [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: 06/30/2022] [Revised: 09/11/2022] [Accepted: 10/14/2022] [Indexed: 12/14/2022] Open
Abstract
ncRNA plays a very pivotal role in various biological activities ranging from gene regulation to controlling important developmental networks. It is imperative to note that this small molecule is not only present in all three domains of cellular life, but is an important modulator of gene regulation too in all these domains. In this review, we discussed various aspects of ncRNA biology, especially their role in bacteria. The last two decades of scientific research have proved that this molecule plays an important role in the modulation of various regulatory pathways in bacteria including the adaptive immune system and gene regulation. It is also very surprising to note that this small molecule is also employed in various processes related to the pathogenicity of virulent microorganisms.
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Affiliation(s)
- Rajib Majumder
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Sanmitra Ghosh
- Department of Biological Sciences, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Arpita Das
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Manoj Kumar Singh
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Saikat Samanta
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Abinit Saha
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India,Corresponding authors.
| | - Rudra P. Saha
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India,Corresponding authors.
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19
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Liu XX, Wang MJ, Kan QN, Li C, Xiao Z, Jiang YH, Li W, Li X, Jiang ZY. Kukoamine A Improves Mycoplasma pneumoniae Pneumonia by Regulating miR-222-3p/Superoxide Dismutase 2. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2064013. [PMID: 35774277 PMCID: PMC9239828 DOI: 10.1155/2022/2064013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/13/2022] [Accepted: 06/02/2022] [Indexed: 11/21/2022]
Abstract
Mycoplasma pneumoniae pneumonia (MPP) represents a common respiratory disease in children patients. Kukoamine A (KuA) is a spermine alkaloid found in the Chinese herb Cortex Lycii radices, which has a variety of pharmacological properties. However, no study has been reported on the role of KuA in MPP. Exosomes, a type of lipid bilayer-enclosed extracellular vesicles, can be delivered to the target cells, where they regulate function and physiology. With the use of human alveolar basal epithelial cells (HABECs) as an in vitro model, in this study, we sought to characterize the changes in levels of superoxide dismutase 2 (SOD2) and proinflammatory cytokines including IL-6 and TNF-α in HABECs in response to exosomes, which were isolated from peripheral blood serum of MPP patients. We found that, compared to normal, MPP patients exhibited a significant up-regulated miR-222-3p. Further, exosomal miR-222-3p downregulated SOD2 activity but promoted nuclear NF-κB activity and expression of IL-6 and TNF-α in HABECs, ultimately leading to an oxidative stress condition. Interestingly, such stimulating effects were attenuated by the pretreatment of KuA. This study suggests a critical role possessed by KuA in MPP by regulating the miR-222-3p/SOD2 axis, which represents a promising strategy for the treatment of MPP.
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Affiliation(s)
- Xiu-Xiu Liu
- Department of Pediatrics, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Ming-Jing Wang
- Department of Pediatrics, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Qian-Na Kan
- Department of Pediatrics, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Cui Li
- Institute of Respiratory Diseases, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Zhen Xiao
- Department of Pediatrics, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Yong-Hong Jiang
- Department of Pediatrics, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Wen Li
- Department of Pediatrics, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Xiao Li
- Department of Pediatrics, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Zhi-Yan Jiang
- Department of Pediatrics, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
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20
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Rojas-Pirela M, Andrade-Alviárez D, Medina L, Castillo C, Liempi A, Guerrero-Muñoz J, Ortega Y, Maya JD, Rojas V, Quiñones W, Michels PA, Kemmerling U. MicroRNAs: master regulators in host-parasitic protist interactions. Open Biol 2022; 12:210395. [PMID: 35702995 PMCID: PMC9198802 DOI: 10.1098/rsob.210395] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
MicroRNAs (miRNAs) are a group of small non-coding RNAs present in a wide diversity of organisms. MiRNAs regulate gene expression at a post-transcriptional level through their interaction with the 3' untranslated regions of target mRNAs, inducing translational inhibition or mRNA destabilization and degradation. Thus, miRNAs regulate key biological processes, such as cell death, signal transduction, development, cellular proliferation and differentiation. The dysregulation of miRNAs biogenesis and function is related to the pathogenesis of diseases, including parasite infection. Moreover, during host-parasite interactions, parasites and host miRNAs determine the probability of infection and progression of the disease. The present review is focused on the possible role of miRNAs in the pathogenesis of diseases of clinical interest caused by parasitic protists. In addition, the potential role of miRNAs as targets for the design of drugs and diagnostic and prognostic markers of parasitic diseases is also discussed.
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Affiliation(s)
- Maura Rojas-Pirela
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile,Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile,Facultad de Farmacia y Bioanálisis, Universidad de Los Andes, Mérida, Venezuela
| | - Diego Andrade-Alviárez
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Lisvaneth Medina
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Christian Castillo
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile,Núcleo de Investigación Aplicada en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Chile
| | - Ana Liempi
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Jesús Guerrero-Muñoz
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Yessica Ortega
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile,Facultad de Farmacia y Bioanálisis, Universidad de Los Andes, Mérida, Venezuela
| | - Juan Diego Maya
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Verónica Rojas
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Paul A. Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Ulrike Kemmerling
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
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21
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Zhang Y, Tian Z, Ye H, Sun X, Zhang H, Sun Y, Mao Y, Yang Z, Li M. Emerging functions of circular RNA in the regulation of adipocyte metabolism and obesity. Cell Death Dis 2022; 8:268. [PMID: 35595755 PMCID: PMC9122900 DOI: 10.1038/s41420-022-01062-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 02/08/2023]
Abstract
As noncoding RNAs, circular RNAs (circRNAs) are covalently enclosed endogenous biomolecules in eukaryotes that have tissue specificity and cell specificity. circRNAs were once considered a rare splicing byproduct. With the development of high-throughput sequencing, it has been confirmed that they are expressed in thousands of mammalian genes. To date, only a few circRNA functions and regulatory mechanisms have been verified. Adipose is the main tissue for body energy storage and energy supply. Adipocyte metabolism is a physiological process involving a series of genes and affects biological activities in the body, such as energy metabolism, immunity, and signal transmission. When adipocyte formation is dysregulated, it will cause a series of diseases, such as atherosclerosis, obesity, fatty liver, and diabetes. In recent years, many noncoding RNAs involved in adipocyte metabolism have been revealed. This review provides a comprehensive overview of the basic structure and biosynthetic mechanism of circRNAs, and further discusses the circRNAs related to adipocyte formation in adipose tissue and liver. Our review will provide a reference for further elucidating the genetic regulation mechanism of circRNAs involved in adipocyte metabolism.
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Affiliation(s)
- Yuanyuan Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China.,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Zhichen Tian
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China.,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Haibo Ye
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China.,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Xiaomei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China.,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Huiming Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China.,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Yujia Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China.,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Yongjiang Mao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China.,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Zhangping Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China. .,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China.
| | - Mingxun Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China. .,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China.
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22
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Gong W, Li Y, Xian J, Yang L, Wang Y, Zhang X, Zhou Y, Wang X, Qiao G, Chen C, Datta S, Gao X, Lu J, Qiu F. Long non-coding RNA LSAMP-1 is down-regulated in non-small cell lung cancer and predicts a poor prognosis. Cancer Cell Int 2022; 22:181. [PMID: 35524253 PMCID: PMC9074231 DOI: 10.1186/s12935-022-02592-0] [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: 09/13/2021] [Accepted: 04/18/2022] [Indexed: 12/05/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) are emerging as master regulators for gene expression and thus play a vital role in human tumorigenesis and progression. But the involvement of novel lncRNAs in non-small cell lung cancer (NSCLC) remains largely unelucidated. Methods A total of 170 NSCLC and their adjacent non-tumor tissues were enrolled to detect the expression of Lnc-LSAMP-1 by RT-qPCR. The effects of Lnc-LSAMP-1 on cell proliferation, migration, invasion and drug-sensitivity were determined by in vitro and in vivo experiments. The proteins that interact with Lnc-LSAMP-1were confirmed by RNA pull-down assay. RNA-sequencing were used to identify the potential targets of Lnc-LSAMP-1 in NSCLC. Results We found that Lnc-LSAMP-1 was significantly down-regulated in 170 cases of NSCLC tissues when compared to their adjacent non-cancerous tissues. Loss expression of Lnc-LSAMP-1 was notably correlated with unfavorable prognosis of NSCLC patients. The ectopic expression of Lnc-LSAMP-1 drastically inhibited lung cancer cell proliferation, viability, invasion and migration ability, arrested cell cycle and facilitated apoptosis. Chemotherapy sensitization experiments showed that over-expressed Lnc-LSAMP-1 enhanced the inhibition of cell proliferation induced by TKI. Mechanistically, Lnc-LSAMP-1-LSAMP formed a complex which could protect the degradation of LSAMP gene, and thus exerted crucial roles in NSCLC progression and TKI targeted treatment. Conclusions Consequently, our findings highlight the function and prognostic value of Lnc-LSAMP-1 in NSCLC and provide potential novel therapeutic targets and prognostic biomarkers for patients with NSCLC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02592-0.
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Affiliation(s)
- Wei Gong
- The State Key Lab of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, 151 Yanjiangxi Road, Guangzhou, 510120, China.,The School of Public Health, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, 511436, China.,Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, and Guangdong Key Laboratory of Urology, Guangzhou, Guangdong, China
| | - Yinyan Li
- The School of Public Health, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, 511436, China
| | - Jianfeng Xian
- The School of Public Health, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, 511436, China
| | - Lei Yang
- The State Key Lab of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, 151 Yanjiangxi Road, Guangzhou, 510120, China.,The School of Public Health, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, 511436, China
| | - Yuanyuan Wang
- The School of Public Health, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, 511436, China
| | - Xin Zhang
- The State Key Lab of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, 151 Yanjiangxi Road, Guangzhou, 510120, China
| | - Yifeng Zhou
- Department of Genetics, Medical College of Soochow University, 1 Shizi Road, Suzhou, 215123, China
| | - Xinhua Wang
- School of Public Health, Heping Development Zone, Gansu University of Chinese Medicine. No.1, Chinese Medicine Road, Lanzhou, 730101, Gansu Province, China
| | - Guibin Qiao
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Cuiyi Chen
- Third People's Hospital of Dongguan City, Dongguan, 523326, China
| | - Soham Datta
- The School of Public Health, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, 511436, China
| | - Xincheng Gao
- The State Key Lab of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, 151 Yanjiangxi Road, Guangzhou, 510120, China.,Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, and Guangdong Key Laboratory of Urology, Guangzhou, Guangdong, China
| | - Jiachun Lu
- The State Key Lab of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, 151 Yanjiangxi Road, Guangzhou, 510120, China. .,The School of Public Health, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, 511436, China.
| | - Fuman Qiu
- The State Key Lab of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, 151 Yanjiangxi Road, Guangzhou, 510120, China. .,The School of Public Health, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, 511436, China.
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Shen Q, Xie B, Galaj E, Yu H, Li X, Lu Y, Zhang M, Wen D, Ma C. CircTmeff-1 in the nucleus accumbens regulates the reconsolidation of cocaine-associated memory. Brain Res Bull 2022; 185:64-73. [PMID: 35489671 DOI: 10.1016/j.brainresbull.2022.04.010] [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: 03/22/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 12/27/2022]
Abstract
Reconsolidation of drug memories is the process of restoring unstable memories after unconditioned (UCS; e.g., drugs) or conditioned stimulus (CS; e.g., drug-paired contexts), and provides promise for prevention of drug relapse. Circular RNAs (circRNAs) have important effects on the transcription and post-transcriptional regulation of gene expression. However, the role of circRNAs in the reconsolidation of drug memories is unclear. Here, we observed that cocaine-induced memory retrieval significantly increased circTmeff-1 level in the nucleus accumbens (NAc) core but not shell. Importantly, the disrupted expression of circTmeff-1 using virus in the NAc core damaged the reconsolidation of cocaine-associated memories. The knockdown of circTmeff-1 in the NAc shell or without UCS retrieval or 9 h after UCS retrieval had no such effects. Mechanistically, using bioinformatic analysis and loss- or gain- of function assays, we revealed that antagomiR-206 reversed the inhibitory effect of circTmeff-1 knockdown on the expression of brain-derived neurotrophic factor (BDNF) during the reconsolidation of cocaine-associated memories. Taken together, these results demonstrate the role of circTmeff-1 in the reconsolidation of cocaine-associated memory and that circTmeff-1 may function as a decoy for miR-206 to regulate the expression of BDNF.
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Affiliation(s)
- Qianchao Shen
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Bing Xie
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Ewa Galaj
- Department of Psychological and Brain Sciences, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - Hailei Yu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Xiaojie Li
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Yun Lu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Minglong Zhang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Di Wen
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China.
| | - Chunling Ma
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China.
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24
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Chen C, Chang X, Zhang S, Zhao Q, Lei C. CircRNA CTNNB1 (circCTNNB1) ameliorates cerebral ischemia/reperfusion injury by sponging miR-96-5p to up-regulate scavenger receptor class B type 1 (SRB1) expression. Bioengineered 2022; 13:10258-10273. [PMID: 35435123 PMCID: PMC9162012 DOI: 10.1080/21655979.2022.2061304] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Emerging studies show that circRNA catenin beta 1 (circCTNNB1) plays a critical role in cancer. However, the expression and function of circCTNNB1 in cerebral ischemia/reperfusion injury (IRI) have not been reported. The present study discovered that circCTNNB1 and scavenger receptor class B type 1 (SRB1) expression levels were significantly down-regulated in mouse astrocytes (mAS) treated with oxygen glucose deprivation and reperfusion (OGD/R), and similar results were observed in a mouse middle cerebral artery occlusion model. Overexpression of circCTNNB1 alleviated cell apoptosis, oxidative stress and the inflammatory response induced by OGD/R in vitro. Up-regulation of circCTNNB1 increased SRB1 expression levels to protect mAS cells from OGD/R-induced damage. CircCTNNB1 and SRB1 interacted with miR-96-5p, and the overexpression of miR-96-5p efficiently reversed the function of circCTNNB1 in OGD/R-treated mAS cells. CircCTNNB1 protected against cerebral ischemia-reperfusion injury by up-regulating SRB1 in vivo. In conclusion, our findings suggest that circCTNNB1 acts as a competitive endogenous RNA for miR-96-5p to alleviate cerebral IRI, which provides novel evidence that circCTNNB1 and SRB1 may be biomarkers and therapeutic targets for cerebral IRI.
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Affiliation(s)
- Chun Chen
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiaolong Chang
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shifei Zhang
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Qi Zhao
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chunyan Lei
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
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25
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Ribosome-Associated ncRNAs (rancRNAs) Adjust Translation and Shape Proteomes. Noncoding RNA 2022; 8:ncrna8020022. [PMID: 35314615 PMCID: PMC8938821 DOI: 10.3390/ncrna8020022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 12/02/2022] Open
Abstract
The regulation of protein synthesis is of extreme importance for cell survival in challenging environmental conditions. Modulating gene expression at the level of translation allows a swift and low-energy-cost response to external stimuli. In the last decade, an emerging class of regulatory ncRNAs, namely ribosome-associated non-coding RNAs (rancRNAs), has been discovered. These rancRNAs have proven to be efficient players in the regulation of translation as a first wave of stress adaptation by directly targeting the ribosome, the central enzyme of protein production. This underlying principle appears to be highly conserved, since rancRNAs are present in all three domains of life. Here, we review the major findings and mechanistic peculiarities of rancRNAs, a class of transcripts that is providing new and broader perspectives on the complexity of the ribosome and translation regulation.
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26
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Abstract
Finding out predisposition and makeup alterations in cancer cells has prompted the exploration of exogenous small interference RNA (siRNA) as a therapeutic agent to deal with cancer. siRNA is subjected to many limitations that hinders its cellular uptake. Various nanocarriers have been loaded with siRNA to improve their cellular transportation and have moved to clinical trials. However, many restrictions as low encapsulation efficiency, nanocarrier cytotoxicity and premature release of siRNA have impeded the single nanocarrier use. The realm of nanohybrid systems has emerged to overcome these limitations and to synergize the criteria of two or more nanocarriers. Different nanohybrid systems that were developed as cellular pathfinders for the exogenous siRNA to target cancer will be illustrated in this review.
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27
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Role of MicroRNAs and Long Non-Coding RNAs in Sarcopenia. Cells 2022; 11:cells11020187. [PMID: 35053303 PMCID: PMC8773898 DOI: 10.3390/cells11020187] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/23/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Sarcopenia is an age-related pathological process characterized by loss of muscle mass and function, which consequently affects the quality of life of the elderly. There is growing evidence that non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), play a key role in skeletal muscle physiology. Alterations in the expression levels of miRNAs and lncRNAs contribute to muscle atrophy and sarcopenia by regulating various signaling pathways. This review summarizes the recent findings regarding non-coding RNAs associated with sarcopenia and provides an overview of sarcopenia pathogenesis promoted by multiple non-coding RNA-mediated signaling pathways. In addition, we discuss the impact of exercise on the expression patterns of non-coding RNAs involved in sarcopenia. Identifying non-coding RNAs associated with sarcopenia and understanding the molecular mechanisms that regulate skeletal muscle dysfunction during aging will provide new insights to develop potential treatment strategies.
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28
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Yang Y, Yue W, Wang N, Wang Z, Li B, Zeng J, Yoshida S, Ding C, Zhou Y. Altered Expressions of Transfer RNA-Derived Small RNAs and microRNAs in the Vitreous Humor of Proliferative Diabetic Retinopathy. Front Endocrinol (Lausanne) 2022; 13:913370. [PMID: 35903272 PMCID: PMC9315217 DOI: 10.3389/fendo.2022.913370] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/23/2022] [Indexed: 11/28/2022] Open
Abstract
PURPOSE We sought to reveal the expression profiles of transfer RNA-derived small RNAs (tsRNAs) and microRNAs (miRNAs) in the vitreous humor of patients with proliferative diabetic retinopathy (PDR). METHODS Vitreous humor samples were obtained from PDR patients and a control group for this study. Sequencing of small RNAs was conducted to assess the expression profiles of tsRNAs and miRNAs in both groups, which was followed by validation using reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR). Bioinformatics analyses were conducted to predict the target genes and their potential biological functions and signaling pathways. RESULTS A total of 37 tsRNAs and 70 miRNAs with significant differences were screened out from the vitreous humor samples of PDR patients compared to controls. Following validation by RT-qPCR, the target genes of the validated tsRNAs and miRNAs were predicted, and Gene Ontology analysis indicated that the target genes of the tsRNAs were most enriched in the cellular macromolecule metabolic process, cytoplasm, and ion-binding, while those of the miRNAs were most abundant in the regulation of major metabolic process, cytoplasm, and protein-binding. In addition, Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the target genes of said tsRNAs and miRNAs were most enriched in the adenosine monophosphate-activated protein kinase signaling pathway and Th17 cell differentiation, respectively. CONCLUSIONS The present study identified altered tsRNAs and miRNAs in vitreous humor samples of PDR patients, which may play important roles in the pathogenesis of PDR and could be considered potential therapeutic targets in the treatment of PDR.
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Affiliation(s)
- Yan Yang
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
| | - Wenyun Yue
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
| | - Nan Wang
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
| | - Zicong Wang
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
| | - Bingyan Li
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
| | - Jun Zeng
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
| | - Shigeo Yoshida
- Department of Ophthalmology, Kurume University School of Medicine, Kurume, Japan
| | - Chun Ding
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
- *Correspondence: Yedi Zhou, ; Chun Ding,
| | - Yedi Zhou
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
- *Correspondence: Yedi Zhou, ; Chun Ding,
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RKIP Pleiotropic Activities in Cancer and Inflammatory Diseases: Role in Immunity. Cancers (Basel) 2021; 13:cancers13246247. [PMID: 34944867 PMCID: PMC8699197 DOI: 10.3390/cancers13246247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary The human body consists of tissues and organs formed by cells. In each cell there is a switch that allows the cell to divide or not. In contrast, cancer cells have their switch on which allow them to divide and invade other sites leading to death. Over two decades ago, Doctor Kam Yeung, University of Toledo, Ohio, has identified a factor (RKIP) that is responsible for the on/off switch which functions normally in healthy tissues but is inactive or absent in cancers. Since this early discovery, many additional properties have been ascribed to RKIP including its role in inhibiting cancer metastasis and resistance to therapeutics and its role in modulating the normal immune response. This review describes all of the above functions of RKIP and suggesting therapeutics to induce RKIP in cancers to inhibit their growth and metastases as well as inhibit its activity to treat non-cancerous inflammatory diseases. Abstract Several gene products play pivotal roles in the induction of inflammation and the progression of cancer. The Raf kinase inhibitory protein (RKIP) is a cytosolic protein that exerts pleiotropic activities in such conditions, and thus regulates oncogenesis and immune-mediated diseases through its deregulation. Herein, we review the general properties of RKIP, including its: (i) molecular structure; (ii) involvement in various cell signaling pathways (i.e., inhibition of the Raf/MEK/ERK pathway; the NF-kB pathway; GRK-2 or the STAT-3 pathway; as well as regulation of the GSK3Beta signaling; and the spindle checkpoints); (iii) regulation of RKIP expression; (iv) expression’s effects on oncogenesis; (v) role in the regulation of the immune system to diseases (i.e., RKIP regulation of T cell functions; the secretion of cytokines and immune mediators, apoptosis, immune check point inhibitors and RKIP involvement in inflammatory diseases); and (vi) bioinformatic analysis between normal and malignant tissues, as well as across various immune-related cells. Overall, the regulation of RKIP in different cancers and inflammatory diseases suggest that it can be used as a potential therapeutic target in the treatment of these diseases.
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Correia CCM, Rodrigues LF, de Avila Pelozin BR, Oliveira EM, Fernandes T. Long Non-Coding RNAs in Cardiovascular Diseases: Potential Function as Biomarkers and Therapeutic Targets of Exercise Training. Noncoding RNA 2021; 7:ncrna7040065. [PMID: 34698215 PMCID: PMC8544698 DOI: 10.3390/ncrna7040065] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022] Open
Abstract
Despite advances in treatments and therapies, cardiovascular diseases (CVDs) remain one of the leading causes of death worldwide. The discovery that most of the human genome, although transcribed, does not encode proteins was crucial for focusing on the potential of long non-coding RNAs (lncRNAs) as essential regulators of cell function at the epigenetic, transcriptional, and post-transcriptional levels. This class of non-coding RNAs is related to the pathophysiology of the cardiovascular system. The different expression profiles of lncRNAs, in different contexts of CVDs, change a great potential in their use as a biomarker and targets of therapeutic intervention. Furthermore, regular physical exercise plays a protective role against CVDs; on the other hand, little is known about its underlying molecular mechanisms. In this review, we look at the accumulated knowledge on lncRNAs and their functions in the cardiovascular system, focusing on the cardiovascular pathology of arterial hypertension, coronary heart disease, acute myocardial infarction, and heart failure. We discuss the potential of these molecules as biomarkers for clinical use, their limitations, and how the manipulation of the expression profile of these transcripts through physical exercise can begin to be suggested as a strategy for the treatment of CVDs.
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Affiliation(s)
- Camila Caldas Martins Correia
- Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-030, Brazil;
- Laboratory of Biochemistry and Molecular Biology of Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil; (L.F.R.); (B.R.d.A.P.); (E.M.O.)
| | - Luis Felipe Rodrigues
- Laboratory of Biochemistry and Molecular Biology of Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil; (L.F.R.); (B.R.d.A.P.); (E.M.O.)
| | - Bruno Rocha de Avila Pelozin
- Laboratory of Biochemistry and Molecular Biology of Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil; (L.F.R.); (B.R.d.A.P.); (E.M.O.)
| | - Edilamar Menezes Oliveira
- Laboratory of Biochemistry and Molecular Biology of Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil; (L.F.R.); (B.R.d.A.P.); (E.M.O.)
| | - Tiago Fernandes
- Laboratory of Biochemistry and Molecular Biology of Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil; (L.F.R.); (B.R.d.A.P.); (E.M.O.)
- Correspondence: ; Tel.: + 55-11-2648-1566 (ext. 05508-030)
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Loh D, Reiter RJ. Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders. Antioxidants (Basel) 2021; 10:1483. [PMID: 34573116 PMCID: PMC8465482 DOI: 10.3390/antiox10091483] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that form dynamic, chemically distinct subcellular compartments organizing macromolecules such as proteins, RNA, and DNA in unicellular prokaryotic bacteria and complex eukaryotic cells. Separated from surrounding environments, MLOs in the nucleoplasm, cytoplasm, and mitochondria assemble by liquid-liquid phase separation (LLPS) into transient, non-static, liquid-like droplets that regulate essential molecular functions. LLPS is primarily controlled by post-translational modifications (PTMs) that fine-tune the balance between attractive and repulsive charge states and/or binding motifs of proteins. Aberrant phase separation due to dysregulated membrane lipid rafts and/or PTMs, as well as the absence of adequate hydrotropic small molecules such as ATP, or the presence of specific RNA proteins can cause pathological protein aggregation in neurodegenerative disorders. Melatonin may exert a dominant influence over phase separation in biomolecular condensates by optimizing membrane and MLO interdependent reactions through stabilizing lipid raft domains, reducing line tension, and maintaining negative membrane curvature and fluidity. As a potent antioxidant, melatonin protects cardiolipin and other membrane lipids from peroxidation cascades, supporting protein trafficking, signaling, ion channel activities, and ATPase functionality during condensate coacervation or dissolution. Melatonin may even control condensate LLPS through PTM and balance mRNA- and RNA-binding protein composition by regulating N6-methyladenosine (m6A) modifications. There is currently a lack of pharmaceuticals targeting neurodegenerative disorders via the regulation of phase separation. The potential of melatonin in the modulation of biomolecular condensate in the attenuation of aberrant condensate aggregation in neurodegenerative disorders is discussed in this review.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX 78229, USA
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Aung LHH, Chen X, Cueva Jumbo JC, Li Z, Wang SY, Zhao C, Liu Z, Wang Y, Li P. Cardiomyocyte mitochondrial dynamic-related lncRNA 1 (CMDL-1) may serve as a potential therapeutic target in doxorubicin cardiotoxicity. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:638-651. [PMID: 34589283 PMCID: PMC8463323 DOI: 10.1016/j.omtn.2021.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/13/2021] [Indexed: 11/19/2022]
Abstract
Doxorubicin (DOX)-induced cardiotoxicity has been one of the major limitations for its clinical use. Although extensive studies have been conducted to decipher the molecular mechanisms underlying DOX cardiotoxicity, no effective preventive or therapeutic measures have yet been identified. Microarray analysis showed that multiple long non-coding RNAs (lncRNAs) are differentially expressed between control- and DOX-treated cardiomyocytes. Functional enrichment analysis indicated that the differentially expressed genes are annotated to cardiac hypertrophic pathways. Among differentially expressed lncRNAs, cardiomyocyte mitochondrial dynamic-related lncRNA 1 (CMDL-1) is the most significantly downregulated lncRNA in cardiomyocytes after DOX exposure. The protein-RNA interaction analysis showed that CMDL-1 may target dynamin-related protein 1 (Drp1). Mechanistic analysis shows that lentiviral overexpression of CMDL-1 prevents DOX-induced mitochondrial fission and apoptosis in cardiomyocytes. However, overexpression of CMDL-1 cannot effectively reduce mitochondrial fission when Drp1 is minimally expressed by small interfering RNA Drp1 (siDrp1). Overexpression of CMDL-1 promotes the association between CMDL-1 and Drp1, as well as with phosphorylated (p-)Drp1, as evidenced by RNA immunoprecipitation analysis. These data indicate the role of CMDL-1 in posttranslational modification of a target protein via regulating its phosphorylation. Collectively, our data indicate that CMDL-1 may play an anti-apoptotic role in DOX cardiotoxicity by regulating Drp1 S637 phosphorylation. Thus, CMDL-1 may serve as a potential therapeutic target in DOX cardiotoxicity.
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Affiliation(s)
- Lynn Htet Htet Aung
- Center for Molecular Genetics, Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266000, Shandong, China
- Center for Bioinformatics, Institute of Translational Medicine, College of Medicine, Qingdao University, Qingdao 266000, Shandong, China
- Corresponding author: Lynn Htet Htet Aung, Center for Molecular Genetics, Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266000, Shandong, China.
| | - Xiatian Chen
- Center for Molecular Genetics, Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266000, Shandong, China
| | - Juan Carlos Cueva Jumbo
- School of Preclinical Medicine, Nanobody Research Center, Guangxi Medical University, Nanning 530021, China
| | - Zhe Li
- Center for Molecular Genetics, Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266000, Shandong, China
| | - Shao-ying Wang
- Center for Molecular Genetics, Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266000, Shandong, China
| | - Cheng Zhao
- Center for Molecular Genetics, Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266000, Shandong, China
| | - Ziqian Liu
- Center for Molecular Genetics, Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266000, Shandong, China
| | - Yin Wang
- Center for Molecular Genetics, Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266000, Shandong, China
| | - Peifeng Li
- Center for Molecular Genetics, Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266000, Shandong, China
- Center for Bioinformatics, Institute of Translational Medicine, College of Medicine, Qingdao University, Qingdao 266000, Shandong, China
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Yan Q, Wang K, Han X, Tan Z. The Regulatory Mechanism of Feeding a Diet High in Rice Grain on the Growth and microRNA Expression Profiles of the Spleen, Taking Goats as an Artiodactyl Model. BIOLOGY 2021; 10:biology10090832. [PMID: 34571708 PMCID: PMC8467863 DOI: 10.3390/biology10090832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/22/2021] [Accepted: 08/24/2021] [Indexed: 12/28/2022]
Abstract
Several researchers have testified that feeding with diets high in rice grain induces subacute ruminal acidosis and increases the risk of gastrointestinal inflammation. However, whether diets high in rice grain affect spleen growth and related molecular events remains unknown. Therefore, the present study was conducted to investigate the effects of feeding a high-concentrate (HC) diet based on rice on the growth and microRNA expression profiles in goat spleen. Sixteen Liuyang black goats were used as an artiodactyl model and fed an HC diet for five weeks. Visceral organ weight, LPS (lipopolysaccharide) concentration in the liver and spleen, and microRNA expression were analyzed. The results showed that feeding an HC diet increased the heart and spleen indexes and decreased the liver LPS concentration (p < 0.05). In total, 596 microRNAs were identified, and twenty-one of them were differentially expressed in the spleens of goats fed with the HC diet. Specifically, several microRNAs (miR-107, miR-512, miR-51b, miR-191, miR-296, miR-326, miR-6123 and miR-433) were upregulated. Meanwhile, miR-30b, miR-30d, miR-1468, miR-502a, miR-145, miR-139, miR-2284f, miR-101 and miR-92a were downregulated. Additionally, their target gene CPPED1, CDK6, CCNT1 and CASP7 expressions were inhibited (p < 0.05). These results indicated that the HC diet promoted the growth of the heart and spleen. The HC diet also regulated the expression of miR-326, miR-512-3p, miR-30b, miR-30d, miR-502a and their target genes (CPPED1, CDK6 and CCNT1) related to the enhancement of splenocyte proliferation. The HC diet also modulated the expression of miR-15b-5p, miR-1468 and miR-92a, related to the suppression of splenocyte apoptosis.
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Affiliation(s)
- Qiongxian Yan
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Q.Y.); (K.W.); (X.H.)
| | - Kaijun Wang
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Q.Y.); (K.W.); (X.H.)
| | - Xuefeng Han
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Q.Y.); (K.W.); (X.H.)
| | - Zhiliang Tan
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Q.Y.); (K.W.); (X.H.)
- Hunan Co-Innovation Center of Animal Production Safety—CICAPS, Changsha 410128, China
- Correspondence:
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Ahmadi S, Zobeiri M, Mohammadi Talvar S, Masoudi K, Khanizad A, Fotouhi S, Bradburn S. Differential expression of H19, BC1, MIAT1, and MALAT1 long non-coding RNAs within key brain reward regions after repeated morphine treatment. Behav Brain Res 2021; 414:113478. [PMID: 34302875 DOI: 10.1016/j.bbr.2021.113478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/22/2021] [Accepted: 07/19/2021] [Indexed: 12/14/2022]
Abstract
Morphine-induced analgesic tolerance and dependence are significant limits of pain control; however, the exact molecular mechanisms underlying morphine tolerance and dependence have remained unclear. The role of long non-coding RNAs (lncRNAs) in morphine tolerance and dependence is yet to be determined. We aimed to explore the association of specific lncRNAs expression in key brain reward regions after repeated injection of morphine. Male Wistar rats received subcutaneous injections of twice-daily morphine (10 mg/kg) or saline (1 mL/kg) for eight days. On day 8 of the repeated injections, induction of morphine analgesic tolerance and dependence was confirmed through a hotplate test and a naloxone-precipitated withdrawal analysis, respectively. Expression of H19, BC1, MIAT1, and MALAT1 lncRNAs was determined from the midbrain, striatum, hypothalamus, prefrontal cortex (PFC), and hippocampus by real-time PCR on day 8 of the repeated injections. The H19 expression was significantly different between morphine-treated and control saline-treated rats in all investigated areas except for the hippocampus. The BC1 expression significantly altered in the midbrain, hypothalamus, and hippocampus, but not in the striatum and PFC after repeated morphine treatment. The MIAT1 and MALAT1 expression site-specifically altered in the midbrain, hypothalamus, and striatum; however, no significant changes were detected in their expression in the PFC and hippocampus after repeated morphine treatment. We conclude that alterations in the expression of these lncRNAs in the brain reward regions especially in the midbrain, striatum and hypothalamus may have critical roles in the development of morphine dependence and tolerance, which need to be considered in future researches.
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Affiliation(s)
- Shamseddin Ahmadi
- Department of Biological Science, Faculty of Science, University of Kurdistan, Sanandaj, Iran.
| | - Mohammad Zobeiri
- Department of Biological Science, Faculty of Science, University of Kurdistan, Sanandaj, Iran
| | - Shiva Mohammadi Talvar
- Department of Biological Science, Faculty of Science, University of Kurdistan, Sanandaj, Iran
| | - Kayvan Masoudi
- Department of Biological Science, Faculty of Science, University of Kurdistan, Sanandaj, Iran
| | - Amir Khanizad
- Department of Biological Science, Faculty of Science, University of Kurdistan, Sanandaj, Iran
| | - Shima Fotouhi
- Department of Biological Science, Faculty of Science, University of Kurdistan, Sanandaj, Iran
| | - Steven Bradburn
- Department of Life Sciences, Bioscience Research Centre, Manchester Metropolitan University, Manchester, UK
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Formichi C, Nigi L, Grieco GE, Maccora C, Fignani D, Brusco N, Licata G, Sebastiani G, Dotta F. Non-Coding RNAs: Novel Players in Insulin Resistance and Related Diseases. Int J Mol Sci 2021; 22:7716. [PMID: 34299336 PMCID: PMC8306942 DOI: 10.3390/ijms22147716] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
The rising prevalence of metabolic diseases related to insulin resistance (IR) have stressed the urgent need of accurate and applicable tools for early diagnosis and treatment. In the last decade, non-coding RNAs (ncRNAs) have gained growing interest because of their potential role in IR modulation. NcRNAs are variable-length transcripts which are not translated into proteins but are involved in gene expression regulation. Thanks to their stability and easy detection in biological fluids, ncRNAs have been investigated as promising diagnostic and therapeutic markers in metabolic diseases, such as type 2 diabetes mellitus (T2D), obesity and non-alcoholic fatty liver disease (NAFLD). Here we review the emerging role of ncRNAs in the development of IR and related diseases such as obesity, T2D and NAFLD, and summarize current evidence concerning their potential clinical application.
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Affiliation(s)
- Caterina Formichi
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (C.F.); (L.N.); (G.E.G.); (D.F.); (N.B.); (G.L.); (G.S.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Laura Nigi
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (C.F.); (L.N.); (G.E.G.); (D.F.); (N.B.); (G.L.); (G.S.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Giuseppina Emanuela Grieco
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (C.F.); (L.N.); (G.E.G.); (D.F.); (N.B.); (G.L.); (G.S.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Carla Maccora
- Section of Medical Pathophysiology, Food Science and Endocrinology, Department of Experimental Medicine, Sapienza University, 00185 Rome, Italy;
| | - Daniela Fignani
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (C.F.); (L.N.); (G.E.G.); (D.F.); (N.B.); (G.L.); (G.S.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Noemi Brusco
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (C.F.); (L.N.); (G.E.G.); (D.F.); (N.B.); (G.L.); (G.S.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Giada Licata
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (C.F.); (L.N.); (G.E.G.); (D.F.); (N.B.); (G.L.); (G.S.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Guido Sebastiani
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (C.F.); (L.N.); (G.E.G.); (D.F.); (N.B.); (G.L.); (G.S.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Francesco Dotta
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (C.F.); (L.N.); (G.E.G.); (D.F.); (N.B.); (G.L.); (G.S.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
- Tuscany Centre for Precision Medicine (CReMeP), 53100 Siena, Italy
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36
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Reuther J, Schneider L, Iacovache I, Pircher A, Gharib WH, Zuber B, Polacek N. A small ribosome-associated ncRNA globally inhibits translation by restricting ribosome dynamics. RNA Biol 2021; 18:2617-2632. [PMID: 34121604 PMCID: PMC8632108 DOI: 10.1080/15476286.2021.1935573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Ribosome-associated non-coding RNAs (rancRNAs) have been recognized as an emerging class of regulatory molecules capable of fine-tuning translation in all domains of life. RancRNAs are ideally suited for allowing a swift response to changing environments and are therefore considered pivotal during the first wave of stress adaptation. Previously, we identified an mRNA-derived 18 nucleotides long rancRNA (rancRNA_18) in Saccharomyces cerevisiae that rapidly downregulates protein synthesis during hyperosmotic stress. However, the molecular mechanism of action remained enigmatic. Here, we combine biochemical, genetic, transcriptome-wide and structural evidence, thus revealing rancRNA_18 as global translation inhibitor by targeting the E-site region of the large ribosomal subunit. Ribosomes carrying rancRNA_18 possess decreased affinity for A-site tRNA and impaired structural dynamics. Cumulatively, these discoveries reveal the mode of action of a rancRNA involved in modulating protein biosynthesis at a thus far unequalled precision.
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Affiliation(s)
- Julia Reuther
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Lukas Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Ioan Iacovache
- Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Andreas Pircher
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Walid H Gharib
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Benoît Zuber
- Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Norbert Polacek
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
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Pourshahian S. THERAPEUTIC OLIGONUCLEOTIDES, IMPURITIES, DEGRADANTS, AND THEIR CHARACTERIZATION BY MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:75-109. [PMID: 31840864 DOI: 10.1002/mas.21615] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Oligonucleotides are an emerging class of drugs that are manufactured by solid-phase synthesis. As a chemical class, they have unique product-related impurities and degradants, characterization of which is an essential step in drug development. The synthesis cycle, impurities produced during the synthesis and degradation products are presented and discussed. The use of liquid chromatography combined with mass spectrometry for characterization and quantification of product-related impurities and degradants is reviewed. In addition, sequence determination of oligonucleotides by gas-phase fragmentation and indirect mass spectrometric methods is discussed. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Soheil Pourshahian
- Janssen Pharmaceutical Companies of Johnson & Johnson, South San Francisco, CA, 94080
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38
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Vierbuchen T, Fitzgerald KA. Long non-coding RNAs in antiviral immunity. Semin Cell Dev Biol 2021; 111:126-134. [DOI: 10.1016/j.semcdb.2020.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/07/2020] [Accepted: 06/12/2020] [Indexed: 12/15/2022]
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Khelghati N, Soleimanpour Mokhtarvand J, Mir M, Alemi F, Asemi Z, Sadeghpour A, Maleki M, Samadi Kafil H, Jadidi-Niaragh F, Majidinia M, Yousefi B. The importance of co-delivery of nanoparticle-siRNA and anticancer agents in cancer therapy. Chem Biol Drug Des 2021; 97:997-1015. [PMID: 33458952 DOI: 10.1111/cbdd.13824] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/10/2021] [Indexed: 01/12/2023]
Abstract
According to global statistics, cancer is the second leading cause of death worldwide. Because of the heterogeneity of cancer, single-drug therapy has many limitations due to low efficacy. Therefore, combination therapy with two or more therapeutic agents is being arisen. One of the most important approaches in cancer therapy is the shot down of key genes involved in apoptotic processes and cell cycle. In this regard, siRNA is a good candidate, a highly attractive method to suppressing tumor growth and invasion. Combination therapy with siRNAs and chemotherapeutic agents can overcome the multidrug resistance and increase apoptosis. The efficient delivery of siRNA to the target cell/tissue/organ has been a challenge. To overcome these challenges, the presence of suitable delivery systems by using nanoparticles is interesting. In this review, we discuss the current challenges for successful RNA interference. Also, we suggested proper a strategy for delivering siRNA that can be useful in targeting therapy. Finally, the combination of a variety of anticancer drugs and siRNA through acceptable delivery systems and their effects on cell cycle and apoptosis will be evaluated.
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Affiliation(s)
- Nafiseh Khelghati
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mostafa Mir
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Forough Alemi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Science, Tabriz, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | - Alireza Sadeghpour
- Department of Orthopedic Surgery, School of Medicine and Shohada Educational Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masomeh Maleki
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Science, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Maryam Majidinia
- Solid Tumor Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Bahman Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Gallardo-Escárate C, Valenzuela-Muñoz V, Nuñez-Acuña G, Valenzuela-Miranda D, Gonçalves AT, Escobar-Sepulveda H, Liachko I, Nelson B, Roberts S, Warren W. Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis. Sci Data 2021; 8:60. [PMID: 33574331 PMCID: PMC7878743 DOI: 10.1038/s41597-021-00842-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 01/25/2021] [Indexed: 12/19/2022] Open
Abstract
Caligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. In this study, we report a chromosome-scale assembly of the sea louse (C. rogercresseyi) genome based on single-molecule real-time sequencing (SMRT) and proximity ligation (Hi-C) analysis. Coding RNAs and non-coding RNAs, and specifically long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were identified through whole transcriptome sequencing from different life stages. A total of 23,686 protein-coding genes and 12,558 non-coding RNAs were annotated. In addition, 6,308 lncRNAs and 5,774 miRNAs were found to be transcriptionally active from larvae to adult stages. Taken together, this genomic resource for C. rogercresseyi represents a valuable tool to develop sustainable control strategies in the salmon aquaculture industry.
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Affiliation(s)
- Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile.
- Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile.
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile
| | - Gustavo Nuñez-Acuña
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile
| | - Diego Valenzuela-Miranda
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile
| | - Ana Teresa Gonçalves
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile
| | - Hugo Escobar-Sepulveda
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile
| | | | | | - Steven Roberts
- School of Aquatic and Fishery Sciences (SAFS), University of Washington, Seattle, USA
| | - Wesley Warren
- Bond Life Sciences Center, University of Missouri, Columbia, USA
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van den Berg AIS, Yun CO, Schiffelers RM, Hennink WE. Polymeric delivery systems for nucleic acid therapeutics: Approaching the clinic. J Control Release 2021; 331:121-141. [PMID: 33453339 DOI: 10.1016/j.jconrel.2021.01.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/26/2020] [Accepted: 01/08/2021] [Indexed: 12/20/2022]
Abstract
Gene therapy using nucleic acids has many clinical applications for the treatment of diseases with a genetic origin as well as for the development of innovative vaccine formulations. Since nucleic acids in their free form are rapidly degraded by nucleases present in extracellular matrices, have poor pharmacokinetics and hardly pass cellular membranes, carrier systems are required. Suitable carriers that protect the nucleic acid payload against enzymatic attack, prolong circulation time after systemic administration and assist in cellular binding and internalization are needed to develop nucleic acid based drug products. Viral vectors have been investigated and are also clinically used as delivery vehicles. However, some major drawbacks are associated with their use. Therefore there has been substantial attention on the use of non-viral carrier systems based on cationic lipids and polymers. This review focuses on the properties of polymer-based nucleic acid formulations, also referred as polyplexes. Different polymeric systems are summarized, and the cellular barriers polyplexes encounter and ways to tackle these are discussed. Finally attention is given to the clinical status of non-viral nucleic acid formulations.
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Affiliation(s)
- Annette I S van den Berg
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Heidelberglaan 100, 3584, CX, Utrecht, the Netherlands
| | - Chae-Ok Yun
- Institute of Nano Science and Technology, Department of Bioengineering, College of Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Raymond M Schiffelers
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Heidelberglaan 100, 3584, CX, Utrecht, the Netherlands
| | - Wim E Hennink
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584, CG, Utrecht, the Netherlands.
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Yang C, Cheng X, Shen P. Silencing of BCSG1 with specific siRNA via nanocarriers for breast cancer treatment. Bull Cancer 2021; 108:323-332. [PMID: 33423781 DOI: 10.1016/j.bulcan.2020.10.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 10/15/2020] [Accepted: 10/29/2020] [Indexed: 01/22/2023]
Abstract
Breast cancer is the most common cancer diagnosed in women worldwide. The current treatments for breast cancer, including surgery, radiotherapy and chemotherapy aim to destroy cancer cells, whereas they also cause damage to normal tissues and cells. Thus, an effective, safe and specific breast cancer treatment is urgently needed. The breast cancer-specific gene 1 (BCSG1) has been shown to be specific for the development of breast cancer and is a target for breast cancer diagnosis and treatment. It is expected to silence the expression of BCSG1 at the gene level for the purpose of treating breast cancer. The effect of RNAi technology on silencing target genes is comparable to gene knockout and has been widely used in animal experiments and plant genetic research. In the field of cancer therapy, numerous investigators have used siRNAs to specifically inhibit target genes, demonstrating that siRNAs can treat cancers at the molecular level. However, the delivery of siRNAs into humans needs to overcome multiple physiological barriers, limiting the clinical applications of siRNAs. This review focuses on the application of BCSG1 gene, siRNAs in cancer treatments, and the nanocarrier delivery system of siRNAs. The potential application and research value of BCSG1-specific siRNA in the treatment of breast cancer are discussed.
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Affiliation(s)
- Chenbo Yang
- Zhengzhou University, School of Basic Medical Sciences, Zhengzhou, Henan Province 450001, China
| | - Xiaoman Cheng
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Peihong Shen
- The Cancer Hospital Affiliated of Zhengzhou University, Zhengzhou, Henan Province 450008, China.
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Role of DNA Methyl-CpG-Binding Protein MeCP2 in Rett Syndrome Pathobiology and Mechanism of Disease. Biomolecules 2021; 11:biom11010075. [PMID: 33429932 PMCID: PMC7827577 DOI: 10.3390/biom11010075] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 12/16/2022] Open
Abstract
Rett Syndrome (RTT) is a severe, rare, and progressive developmental disorder with patients displaying neurological regression and autism spectrum features. The affected individuals are primarily young females, and more than 95% of patients carry de novo mutation(s) in the Methyl-CpG-Binding Protein 2 (MECP2) gene. While the majority of RTT patients have MECP2 mutations (classical RTT), a small fraction of the patients (atypical RTT) may carry genetic mutations in other genes such as the cyclin-dependent kinase-like 5 (CDKL5) and FOXG1. Due to the neurological basis of RTT symptoms, MeCP2 function was originally studied in nerve cells (neurons). However, later research highlighted its importance in other cell types of the brain including glia. In this regard, scientists benefitted from modeling the disease using many different cellular systems and transgenic mice with loss- or gain-of-function mutations. Additionally, limited research in human postmortem brain tissues provided invaluable findings in RTT pathobiology and disease mechanism. MeCP2 expression in the brain is tightly regulated, and its altered expression leads to abnormal brain function, implicating MeCP2 in some cases of autism spectrum disorders. In certain disease conditions, MeCP2 homeostasis control is impaired, the regulation of which in rodents involves a regulatory microRNA (miR132) and brain-derived neurotrophic factor (BDNF). Here, we will provide an overview of recent advances in understanding the underlying mechanism of disease in RTT and the associated genetic mutations in the MECP2 gene along with the pathobiology of the disease, the role of the two most studied protein variants (MeCP2E1 and MeCP2E2 isoforms), and the regulatory mechanisms that control MeCP2 homeostasis network in the brain, including BDNF and miR132.
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Li T, Xu Y, Wang Y, Jiang Y. Differential expression profiles of long noncoding RNAs and mRNAs in human bone marrow mesenchymal stem cells after exposure to a high dosage of dexamethasone. Stem Cell Res Ther 2021; 12:9. [PMID: 33407832 PMCID: PMC7788840 DOI: 10.1186/s13287-020-02040-8] [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: 06/14/2020] [Accepted: 11/19/2020] [Indexed: 12/28/2022] Open
Abstract
Background Abnormalities in apoptosis, cell cycle, proliferation, and differentiation of human bone marrow mesenchymal stem cells (hBMSCs) significantly impact bone metabolism and remodeling, resulting in various skeletal disorders. Long-term exposure to a high dosage of dexamethasone (Dex) induces apoptosis and inhibits the proliferation of mesenchymal stromal cells (MSCs), which are probable primary causes of various skeletal disorders. However, to date, the exact mechanisms of action of Dex on hBMSCs have not been fully elucidated. Methods To explore the effects of Dex on apoptosis, cell cycle, proliferation, senescence, osteogenic and adipogenic differentiation of hBMSCs at the various exposure times and concentrations, Hoechst 33342/PI staining, flow cytometry, crystal violet assay, β-galactosidase (β-GAL) activity assay, alizarin red S (ARS) staining assay, and Oil Red O (ORO) staining assay were performed. A microarray assay was used to identify differentially expressed lncRNAs and mRNAs in 10− 6 mol/L Dex-treated hBMSCs, and a bioinformatics analysis was conducted to further explore the role of these differentially expressed lncRNAs and mRNAs in the coding and noncoding (CNC) network. Furthermore, the microarray results were validated using quantitative real-time PCR (qRT-PCR) analysis. Results Over the range of 10−8, 10−7, and 10−6 mol/L, Dex induced apoptosis, arrest of the cell cycle, inhibition of osteogenic differentiation, and promotion adipogenic differentiation of the hBMSCs in a dose-dependent manner. In addition, 10−6 mol/L Dex significantly induced apoptosis, suppressed proliferation, and increased the senescence of hBMSCs in a time-dependent manner. Interestingly, this time-dependent effect of Dex on the apoptosis of hBMSCs plateaued at the 7th day and decreased from the 8th day to the 10th day, while Dex treatment increased senescence of the hBMSCs on the 6th day. Furthermore, the microarray analysis identified a total of 137 differentially expressed mRNAs (90 upregulated and 47 downregulated) and 90 differentially expressed lncRNAs (61 upregulated and 29 downregulated) in hBMSCs after exposure to 10−6 mol/L Dex. The differentially expressed mRNAs and lncRNAs were associated with the regulation of cell apoptosis, proliferation, and cell cycle. Meanwhile, several signaling pathways involved in these processes, including the mTOR signaling pathway, Ras signaling pathway, HIF-1 signaling pathway, NF-kappa B signaling pathway, and TGF-beta signaling pathway, also were identified through the interaction net in the significant pathways (Path-Net) analysis. Furthermore, the CNC network further identified 78 core regulatory genes involved in the regulation of apoptosis. Additionally, qRT-PCR was used to confirm the identity of the key differentially expressed mRNAs and lncRNAs found to be closely associated with cell apoptosis to confirm the reliability of the microarray dataset. Conclusions In summary, the effect of Dex on apoptosis, cell cycle, proliferation, and osteogenic differentiation and adipogenic differentiation of the hBMSCs depended on exposure time and concentration. Continuous exposure to 10−6 mol/L of Dex for 7 days may be a suitable protocol for inducing the apoptosis of hBMSCs. Under this protocol, differentially expressed lncRNAs and mRNAs associated with apoptosis, cell cycle, and proliferation were identified, providing a new research direction for further studies. Supplementary information The online version contains supplementary material available at 10.1186/s13287-020-02040-8.
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Affiliation(s)
- Tao Li
- Department of Joint Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Yingxing Xu
- Department of Joint Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China.,Qingdao University, Qingdao, 266071, Shandong, China.,Medical Department of Qingdao University, Qingdao, 266071, Shandong, China
| | - Yingzhen Wang
- Department of Joint Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Yaping Jiang
- Department of Oral Implantology, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China.
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Dang H, Polineni D, Pace RG, Stonebraker JR, Corvol H, Cutting GR, Drumm ML, Strug LJ, O’Neal WK, Knowles MR. Mining GWAS and eQTL data for CF lung disease modifiers by gene expression imputation. PLoS One 2020; 15:e0239189. [PMID: 33253230 PMCID: PMC7703903 DOI: 10.1371/journal.pone.0239189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/02/2020] [Indexed: 12/18/2022] Open
Abstract
Genome wide association studies (GWAS) have identified several genomic loci with candidate modifiers of cystic fibrosis (CF) lung disease, but only a small proportion of the expected genetic contribution is accounted for at these loci. We leveraged expression data from CF cohorts, and Genotype-Tissue Expression (GTEx) reference data sets from multiple human tissues to generate predictive models, which were used to impute transcriptional regulation from genetic variance in our GWAS population. The imputed gene expression was tested for association with CF lung disease severity. By comparing and combining results from alternative approaches, we identified 379 candidate modifier genes. We delved into 52 modifier candidates that showed consensus between approaches, and 28 of them were near known GWAS loci. A number of these genes are implicated in the pathophysiology of CF lung disease (e.g., immunity, infection, inflammation, HLA pathways, glycosylation, and mucociliary clearance) and the CFTR protein biology (e.g., cytoskeleton, microtubule, mitochondrial function, lipid metabolism, endoplasmic reticulum/Golgi, and ubiquitination). Gene set enrichment results are consistent with current knowledge of CF lung disease pathogenesis. HLA Class II genes on chr6, and CEP72, EXOC3, and TPPP near the GWAS peak on chr5 are most consistently associated with CF lung disease severity across the tissues tested. The results help to prioritize genes in the GWAS regions, predict direction of gene expression regulation, and identify new candidate modifiers throughout the genome for potential therapeutic development.
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Affiliation(s)
- Hong Dang
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine Cystic Fibrosis/Pulmonary Research & Treatment Center, Chapel Hill, North Carolina, United States of America
| | - Deepika Polineni
- University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Rhonda G. Pace
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine Cystic Fibrosis/Pulmonary Research & Treatment Center, Chapel Hill, North Carolina, United States of America
| | - Jaclyn R. Stonebraker
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine Cystic Fibrosis/Pulmonary Research & Treatment Center, Chapel Hill, North Carolina, United States of America
| | - Harriet Corvol
- Pediatric Pulmonary Department, Assistance Publique-Hôpitaux sde Paris (AP-HP), Hôpital Trousseau, Institut National de la Santé et la Recherche Médicale (INSERM) U938, Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC), Paris 6, Paris, France
| | - Garry R. Cutting
- McKusick-Nathans Institute of Genetic Medicine, Baltimore, Maryland, United States of America
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Mitchell L. Drumm
- Department of Pediatrics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Lisa J. Strug
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Wanda K. O’Neal
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine Cystic Fibrosis/Pulmonary Research & Treatment Center, Chapel Hill, North Carolina, United States of America
| | - Michael R. Knowles
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine Cystic Fibrosis/Pulmonary Research & Treatment Center, Chapel Hill, North Carolina, United States of America
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LINC00473 regulated apoptosis, proliferation and migration but could not reverse cell cycle arrest of human bone marrow mesenchymal stem cells induced by a high-dosage of dexamethasone. Stem Cell Res 2020; 48:101954. [DOI: 10.1016/j.scr.2020.101954] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 12/14/2022] Open
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Witte K, de Andrés MC, Wells J, Dalby MJ, Salmeron-Sanchez M, Oreffo ROC. Chondrobags: A high throughput alginate-fibronectin micromass platform for in vitro human cartilage formation. Biofabrication 2020; 12:045034. [DOI: 10.1088/1758-5090/abb653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Exploration of space to achieve scientific breakthroughs. Biotechnol Adv 2020; 43:107572. [PMID: 32540473 DOI: 10.1016/j.biotechadv.2020.107572] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/05/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.
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Ampofo E, Nalbach L, Menger MD, Laschke MW. Regulatory Mechanisms of Somatostatin Expression. Int J Mol Sci 2020; 21:ijms21114170. [PMID: 32545257 PMCID: PMC7312888 DOI: 10.3390/ijms21114170] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 12/17/2022] Open
Abstract
Somatostatin is a peptide hormone, which most commonly is produced by endocrine cells and the central nervous system. In mammals, somatostatin originates from pre-prosomatostatin and is processed to a shorter form, i.e., somatostatin-14, and a longer form, i.e., somatostatin-28. The two peptides repress growth hormone secretion and are involved in the regulation of glucagon and insulin synthesis in the pancreas. In recent years, the processing and secretion of somatostatin have been studied intensively. However, little attention has been paid to the regulatory mechanisms that control its expression. This review provides an up-to-date overview of these mechanisms. In particular, it focuses on the role of enhancers and silencers within the promoter region as well as on the binding of modulatory transcription factors to these elements. Moreover, it addresses extracellular factors, which trigger key signaling pathways, leading to an enhanced somatostatin expression in health and disease.
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Affiliation(s)
- Emmanuel Ampofo
- Correspondence: ; Tel.: +49-6841-162-6561; Fax: +49-6841-162-6553
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The Underlying Mechanisms of Noncoding RNAs in the Chemoresistance of Hepatocellular Carcinoma. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 21:13-27. [PMID: 32505000 PMCID: PMC7270498 DOI: 10.1016/j.omtn.2020.05.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/15/2020] [Accepted: 05/11/2020] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most lethal human malignancies. Chemotherapeutic agents, such as sorafenib and lenvatinib, can improve the outcomes of HCC patients. Nevertheless, chemoresistance has become a major hurdle in the effective treatment of HCC. Noncoding RNAs (ncRNAs), including mircoRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs), have been demonstrated to participate in the onset and progression of HCC. Moreover, multiple lines of evidence have indicated that ncRNAs also play a pivotal role in HCC drug resistance. ncRNAs can regulate drug efflux and metabolism, glucose metabolism, cellular death pathways, and malignant characteristics in HCC. A deeper understanding of the molecular mechanisms responsible for ncRNA-mediated drug resistance in HCC will provide new opportunities for improving the treatment of HCC. In this review, we summarize recent findings on the molecular mechanisms by which ncRNAs regulate HCC chemoresistance, as well as their potential clinical implications in overcoming HCC chemoresistance.
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