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Confuorti C, Jaramillo M, Plante I. Hormonal regulation of miRNA during mammary gland development. Biol Open 2024; 13:bio060308. [PMID: 38712984 PMCID: PMC11190577 DOI: 10.1242/bio.060308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
The mammary gland is a unique organ as most of its development occurs after birth through stages of proliferation, differentiation and apoptosis that are tightly regulated by circulating hormones and growth factors. Throughout development, hormonal cues induce the regulation of different pathways, ultimately leading to differential transcription and expression of genes involved in this process, but also in the activation or inhibition of post-transcriptional mechanisms of regulation. However, the role of microRNAs (miRNAs) in the different phases of mammary gland remodeling is still poorly understood. The objectives of this study were to analyze the expression of miRNA in key stages of mammary gland development in mice and to determine whether it could be associated with hormonal variation between stages. To do so, miRNAs were isolated from mouse mammary glands at stages of adulthood, pregnancy, lactation and involution, and sequenced. Results showed that 490, 473, 419, and 460 miRNAs are detected in adult, pregnant, lactating and involuting mice, respectively, most of them being common to all four groups, and 58 unique to one stage. Most genes could be divided into six clusters of expression, including two encompassing the highest number of miRNA (clusters 1 and 3) and showing opposite profiles of expression, reaching a peak at adulthood and valley at lactation, or showing the lowest expression at adulthood and peaking at lactation. GO and KEGG analyses suggest that the miRNAs differentially expressed between stages influence the expression of targets associated with mammary gland homeostasis and hormone regulation. To further understand the links between miRNA expression and hormones involved in mammary gland development, miRNAs were then sequenced in breast cells exposed to estradiol, progesterone, prolactin and oxytocin. Four, 38, 24 and 66 miRNAs were associated with progesterone, estradiol, prolactin, and oxytocin exposure, respectively. Finally, when looking at miRNAs modulated by the hormones, differentially expressed during mammary gland development, and having a pattern of expression that could be correlated with the relative levels of hormones known to be found in vivo, 16 miRNAs were identified as likely regulated by circulating hormones. Overall, our study brings a better understanding of the regulation of miRNAs throughout mammary gland development and suggests that there is a relationship between their expression and the main hormones involved in mammary gland development. Future studies will examine this role more in detail.
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Affiliation(s)
- Cameron Confuorti
- INRS, Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Maritza Jaramillo
- INRS, Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Isabelle Plante
- INRS, Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
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Chen J, Wan H, Zhao H, Dai X, Wu W, Liu J, Xu J, Yang R, Xu B, Zeng C, Zhang X. Identification and expression analysis of the Xyloglucan transglycosylase/hydrolase (XTH) gene family under abiotic stress in oilseed (Brassica napus L.). BMC PLANT BIOLOGY 2024; 24:400. [PMID: 38745278 PMCID: PMC11095021 DOI: 10.1186/s12870-024-05121-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
XTH genes are key genes that regulate the hydrolysis and recombination of XG components and plays role in the structure and composition of plant cell walls. Therefore, clarifying the changes that occur in XTHs during plant defense against abiotic stresses is informative for the study of the plant stress regulatory mechanism mediated by plant cell wall signals. XTH proteins in Arabidopsis thaliana was selected as the seed sequences in combination with its protein structural domains, 80 members of the BnXTH gene family were jointly identified from the whole genome of the Brassica napus ZS11, and analyzed for their encoded protein physicochemical properties, phylogenetic relationships, covariance relationships, and interoperating miRNAs. Based on the transcriptome data, the expression patterns of BnXTHs were analyzed in response to different abiotic stress treatments. The relative expression levels of some BnXTH genes under Al, alkali, salt, and drought treatments after 0, 6, 12 and 24 h were analyzed by using qRT-PCR to explore their roles in abiotic stress tolerance in B. napus. BnXTHs showed different expression patterns in response to different abiotic stress signals, indicating that the response mechanisms of oilseed rape against different abiotic stresses are also different. This paper provides a theoretical basis for clarifying the function and molecular genetic mechanism of the BnXTH gene family in abiotic stress tolerance in rapeseed.
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Affiliation(s)
- Jingdong Chen
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Science, Jianghan University, Wuhan, 430056, Hubei, China
| | - Heping Wan
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Science, Jianghan University, Wuhan, 430056, Hubei, China
| | - Huixia Zhao
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Science, Jianghan University, Wuhan, 430056, Hubei, China
| | - Xigang Dai
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Science, Jianghan University, Wuhan, 430056, Hubei, China
| | - Wanjin Wu
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Science, Jianghan University, Wuhan, 430056, Hubei, China
| | - Jin Liu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Jinsong Xu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Rui Yang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Benbo Xu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Changli Zeng
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Science, Jianghan University, Wuhan, 430056, Hubei, China.
| | - Xuekun Zhang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China.
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Oste DJ, Pathmendra P, Richardson RAK, Johnson G, Ao Y, Arya MD, Enochs NR, Hussein M, Kang J, Lee A, Danon JJ, Cabanac G, Labbé C, Davis AC, Stoeger T, Byrne JA. Misspellings or "miscellings"-Non-verifiable and unknown cell lines in cancer research publications. Int J Cancer 2024. [PMID: 38751110 DOI: 10.1002/ijc.34995] [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: 02/29/2024] [Revised: 04/04/2024] [Accepted: 04/18/2024] [Indexed: 06/23/2024]
Abstract
Reproducible laboratory research relies on correctly identified reagents. We have previously described gene research papers with wrongly identified nucleotide sequence(s), including papers studying miR-145. Manually verifying reagent identities in 36 recent miR-145 papers found that 56% and 17% of papers described misidentified nucleotide sequences and cell lines, respectively. We also found 5 cell line identifiers in miR-145 papers with misidentified nucleotide sequences and cell lines, and 18 cell line identifiers published elsewhere, that did not represent indexed human cell lines. These 23 identifiers were described as non-verifiable (NV), as their identities were unclear. Studying 420 papers that mentioned 8 NV identifier(s) found 235 papers (56%) that referred to 7 identifiers (BGC-803, BSG-803, BSG-823, GSE-1, HGC-7901, HGC-803, and MGC-823) as independent cell lines. We could not find any publications describing how these cell lines were established. Six cell lines were sourced from cell line repositories with externally accessible online catalogs, but these cell lines were not indexed as claimed. Some papers also stated that short tandem repeat (STR) profiles had been generated for three cell lines, yet no STR profiles could be identified. In summary, as NV cell lines represent new challenges to research integrity and reproducibility, further investigations are required to clarify their status and identities.
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Affiliation(s)
- Danielle J Oste
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Pranujan Pathmendra
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Reese A K Richardson
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Gracen Johnson
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Yida Ao
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Maya D Arya
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Naomi R Enochs
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Muhammed Hussein
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Jinghan Kang
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Aaron Lee
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Jonathan J Danon
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Guillaume Cabanac
- IRIT UMR 5505 CNRS, University of Toulouse, Toulouse, France
- Institut Universitaire de France (IUF), Paris, France
| | - Cyril Labbé
- CNRS, Grenoble INP, Laboratoire d'Informatique de Grenoble, Université Grenoble Alpes, Grenoble, France
| | - Amanda Capes Davis
- CellBank Australia, Children's Medical Research Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Thomas Stoeger
- Feinberg School of Medicine in the Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
- The Potocsnak Longevity Institute, Northwestern University, Chicago, Illinois, USA
- Simpson Querrey Lung Institute for Translational Science, Chicago, Illinois, USA
| | - Jennifer A Byrne
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- NSW Health Statewide Biobank, NSW Health Pathology, Sydney, New South Wales, Australia
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Ayed A. The role of natural products versus miRNA in renal cell carcinoma: implications for disease mechanisms and diagnostic markers. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03121-8. [PMID: 38691151 DOI: 10.1007/s00210-024-03121-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Natural products are chemical compounds produced by living organisms. They are isolated and purified to determine their function and can potentially be used as therapeutic agents. The ability of some bioactive natural products to modify the course of cancer is fascinating and promising. In the past 50 years, there have been advancements in cancer therapy that have increased survival rates for localized tumors. However, there has been little progress in treating advanced renal cell carcinoma (RCC), which is resistant to radiation and chemotherapy. Oncogenes and tumor suppressors are two roles played by microRNAs (miRNAs). They are involved in important pathogenetic mechanisms like hypoxia and epithelial-mesenchymal transition (EMT); they control apoptosis, cell growth, migration, invasion, angiogenesis, and proliferation through target proteins involved in various signaling pathways. Depending on their expression pattern, miRNAs may identify certain subtypes of RCC or distinguish tumor tissue from healthy renal tissue. As diagnostic biomarkers of RCC, circulating miRNAs show promise. There is a correlation between the expression patterns of several miRNAs and the prognosis and diagnosis of patients with RCC. Potentially high-risk primary tumors may be identified by comparing original tumor tissue with metastases. Variations in miRNA expression between treatment-sensitive and therapy-resistant patients' tissues and serum allow for the estimation of responsiveness to target therapy. Our knowledge of miRNAs' function in RCC etiology has a tremendous uptick. Finding and validating their gene targets could have an immediate effect on creating anticancer treatments based on miRNAs. Several miRNAs have the potential to be used as biomarkers for diagnosis and prognosis. This review provides an in-depth analysis of the current knowledge regarding natural compounds and their modes of action in combating cancer. Also, this study aims to give information about the diagnostic and prognostic value of miRNAs as cancer biomarkers and their involvement in the pathogenesis of RCC.
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Affiliation(s)
- Abdullah Ayed
- Department of Surgery, College of Medicine, University of Bisha, P.O Box 551, 61922, Bisha, Saudi Arabia.
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Zhang M, Peng X, Liang X, Wang W, Yang Y, Xu F, Lu X, Geng D, Li M. MicroRNA-145-5p Regulates the Epithelial-Mesenchymal Transition in Nasal Polyps by Targeting Smad3. Clin Exp Otorhinolaryngol 2024; 17:122-136. [PMID: 38360523 DOI: 10.21053/ceo.2023.00025] [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: 10/27/2023] [Accepted: 02/15/2024] [Indexed: 02/17/2024] Open
Abstract
OBJECTIVES The annual prevalence of chronic rhinosinusitis (CRS) is increasing, and the lack of effective treatments imposes a substantial burden on both patients and society. The formation of nasal polyps in patients with CRS is closely related to tissue remodeling, which is largely driven by the epithelial-mesenchymal transition (EMT). MicroRNA (miRNA) plays a pivotal role in the pathogenesis of numerous diseases through the miRNA-mRNA regulatory network; however, the specific mechanism of the miRNAs involved in the formation of nasal polyps remains unclear. METHODS The expression of EMT markers and Smad3 were detected using western blots, quantitative real-time polymerase chain reaction, and immunohistochemical and immunofluorescence staining. Differentially expressed genes in nasal polyps and normal tissues were screened through the Gene Expression Omnibus database. To predict the target genes of miR-145-5p, three different miRNA target prediction databases were used. The migratory ability of cells was evaluated using cell migration assay and wound healing assays. RESULTS miR-145-5p was associated with the EMT process and was significantly downregulated in nasal polyp tissues. In vitro experiments revealed that the downregulation of miR-145-5p promoted EMT. Conversely, increasing miR-145-5p levels reversed the EMT induced by transforming growth factor-β1. Bioinformatics analysis suggested that miR-145-5p targets Smad3. Subsequent experiments confirmed that miR-145-5p inhibits Smad3 expression. CONCLUSION Overall, miR-145-5p is a promising target to inhibit nasal polyp formation, and the findings of this study provide a theoretical basis for nanoparticle-mediated miR-145-5p delivery for the treatment of nasal polyps.
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Affiliation(s)
- Mengyu Zhang
- Department of Otorhinolaryngology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaole Peng
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaolong Liang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Wentao Wang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuqing Yang
- Department of Otorhinolaryngology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fan Xu
- Department of Otorhinolaryngology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaomin Lu
- Department of Oncology, Affiliated Haian Hospital of Nantong University, Nantong, China
| | - Dechun Geng
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Manyi Li
- Department of Otorhinolaryngology, The First Affiliated Hospital of Soochow University, Suzhou, China
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Awan MJA, Farooq MA, Naqvi RZ, Karamat U, Bukhari SAR, Waqas MAB, Mahmood MA, Buzdar MI, Rasheed A, Amin I, Saeed NA, Mansoor S. Deciphering the differential expression patterns of yield-related negative regulators in hexaploid wheat cultivars and hybrids at different growth stages. Mol Biol Rep 2024; 51:537. [PMID: 38642174 DOI: 10.1007/s11033-024-09454-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/18/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Hexaploid bread wheat underwent a series of polyploidization events through interspecific hybridizations that conferred adaptive plasticity and resulted in duplication and neofunctionalization of major agronomic genes. The genetic architecture of polyploid wheat not only confers adaptive plasticity but also offers huge genetic diversity. However, the contribution of different gene copies (homeologs) encoded from different subgenomes (A, B, D) at different growth stages remained unexplored. METHODS In this study, hybrid of elite cultivars of wheat were developed via reciprocal crosses (cytoplasm swapping) and phenotypically evaluated. We assessed differential expression profiles of yield-related negative regulators in these cultivars and their F1 hybrids and identified various cis-regulatory signatures by employing bioinformatics tools. Furthermore, the preferential expression patterns of the syntenic triads encoded from A, B, and D subgenomes were assessed to decipher their functional redundancy at six different growth stages. RESULTS Hybrid progenies showed better heterosis such as up to 17% increase in the average number of grains and up to 50% increase in average thousand grains weight as compared to mid-parents. Based on the expression profiling, our results indicated significant dynamic transcriptional expression patterns, portraying the different homeolog-dominance at the same stage in the different cultivars and their hybrids. Albeit belonging to same syntenic triads, a dynamic trend was observed in the regulatory signatures of these genes that might be influencing their expression profiles. CONCLUSION These findings can substantially contribute and provide insights for the selective introduction of better cultivars into traditional and hybrid breeding programs which can be harnessed for the improvement of future wheat.
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Affiliation(s)
- Muhammad Jawad Akbar Awan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Awais Farooq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Umer Karamat
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sayyad Ali Raza Bukhari
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Abu Bakar Waqas
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Arslan Mahmood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Ismail Buzdar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS) & CIMMYT-China office, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Nasir A Saeed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan.
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
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Garreau M, Weidner J, Hamilton R, Kolosionek E, Toki N, Stavenhagen K, Paris C, Bonetti A, Czechtizky W, Gnerlich F, Rydzik A. Chemical modification patterns for microRNA therapeutic mimics: a structure-activity relationship (SAR) case-study on miR-200c. Nucleic Acids Res 2024; 52:2792-2807. [PMID: 38421619 PMCID: PMC11014349 DOI: 10.1093/nar/gkae141] [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: 12/21/2022] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
microRNA (miRNA) mimics are an emerging class of oligonucleotide therapeutics, with a few compounds already in clinical stages. Synthetic miRNAs are able to restore downregulated levels of intrinsic miRNAs, allowing for parallel regulation of multiple genes involved in a particular disease. In this work, we examined the influence of chemical modifications patterns in miR-200c mimics, assessing the regulation of a selection of target messenger RNAs (mRNA) and, subsequently, of the whole transcriptome in A549 cells. We have probed 37 mimics and provided an initial set of instructions for designing miRNA mimics with potency and selectivity similar to an unmodified miRNA duplex. Additionally, we have examined the stability of selected mimics in serum. Finally, the selected two modification patterns were translated to two other miRNAs, miR-34a and miR-155. To differing degrees, these designs acted on target mRNAs in a similar manner to the unmodified mimic. Here, for the first time, we describe a structured overview of 'miRNA mimics modification templates' that are chemically stabilised and optimised for use in an in vitro set up and highlight the need of further sequence specific optimization when mimics are to be used beyond in vitro tool experiments.
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Affiliation(s)
- Marion Garreau
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Julie Weidner
- Translational Science Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Russell Hamilton
- Translational Science Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Cambridge, UK
| | - Ewa Kolosionek
- Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Naoko Toki
- Translational Genomics, Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Kathrin Stavenhagen
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Clément Paris
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Alessandro Bonetti
- Translational Genomics, Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Felix Gnerlich
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Anna Rydzik
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
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8
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Zhu Y, Li M, Li Z, Song J, Zhao W. Study on the mechanism of miRNAs on liver injury in the condition of Protoscocephalus alveolarus transhepatic portal vein infection. Immun Inflamm Dis 2024; 12:e1236. [PMID: 38652009 PMCID: PMC11037255 DOI: 10.1002/iid3.1236] [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: 10/17/2023] [Revised: 02/29/2024] [Accepted: 03/17/2024] [Indexed: 04/25/2024] Open
Abstract
OBJECTIVE To explore the role of miRNA in liver damage caused by Echinococcus multilocularis infection. METHODS Six female C57BL mice were randomly divided into two groups, the control group and the infection group. Mice in the control group were injected with 100 μL PBS through the hepatic portal vein, and mice in the infection group were infected with E. multilocularis via the hepatic portal vein to establish a mouse model of infection. Small RNA sequencing was performed for detecting the expression of miRNAs in the liver of mice infected with 2000 E. multilocularis after 3 months of infection, screen out miRNAs related to liver damage, and verify by RT-PCR. RESULTS Seventy-one differentially expressed miRNAs were found in the liver in comparison with control, and a total of 36 mouse miRNAs with |FC| >0.585 were screened out, respectively. In addition, Targetscan (V5.0) and miRanda (v3.3a) software were used to predict differential miRNAs target genes and functional enrichment of target genes. Functional annotation showed that "cytokine-cytokine interaction," "positive regulation of cytokine production," "inflammatory response," and "leukocyte activation" were enriched in the liver of E. multilocularis-infected mice. Moreover, the pathways "human cytomegalovirus infection," "cysteine and methionine metabolism," "Notch signaling pathway," and "ferroptosis" were involved in liver disease. Furthermore, four miRNAs (mmu-miR-30e-3p, mmu-miR-203-3p, mmu-miR-125b-5p, and mmu-miR-30c-2-3p) related to liver injury were screened and verified. CONCLUSION This study revealed that the expression profiling of miRNAs in the livers was changed after E. multilocularis infection, and improved our understanding of the transcriptomic landscape of hepatic echinococcosis in mice.
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Affiliation(s)
- Yazhou Zhu
- Department of Pathogen Biology, School of Basic MedicineNingxia Medical UniversityYinchuanChina
- Ningxia Key Laboratory of Prevention and Control of Common Infectious DiseasesYinchuanChina
| | - Ming Li
- General Hospital of Ningxia Medical UniversityYinchuanChina
| | - Zihua Li
- Ningxia Key Laboratory of Prevention and Control of Common Infectious DiseasesYinchuanChina
- Department of Cell Biology and GeneticsNingxia Medical UniversityYinchuanChina
| | - Jiahui Song
- Ningxia Key Laboratory of Prevention and Control of Common Infectious DiseasesYinchuanChina
| | - Wei Zhao
- Department of Pathogen Biology, School of Basic MedicineNingxia Medical UniversityYinchuanChina
- Ningxia Key Laboratory of Prevention and Control of Common Infectious DiseasesYinchuanChina
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9
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Hart M, Kern F, Fecher-Trost C, Krammes L, Aparicio E, Engel A, Hirsch P, Wagner V, Keller V, Schmartz GP, Rheinheimer S, Diener C, Fischer U, Mayer J, Meyer MR, Flockerzi V, Keller A, Meese E. Experimental capture of miRNA targetomes: disease-specific 3'UTR library-based miRNA targetomics for Parkinson's disease. Exp Mol Med 2024; 56:935-945. [PMID: 38556547 PMCID: PMC11059366 DOI: 10.1038/s12276-024-01202-5] [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: 08/21/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 04/02/2024] Open
Abstract
The identification of targetomes remains a challenge given the pleiotropic effect of miRNAs, the limited effects of miRNAs on individual targets, and the sheer number of estimated miRNA-target gene interactions (MTIs), which is around 44,571,700. Currently, targetome identification for single miRNAs relies on computational evidence and functional studies covering smaller numbers of targets. To ensure that the targetome analysis could be experimentally verified by functional assays, we employed a systematic approach and explored the targetomes of four miRNAs (miR-129-5p, miR-129-1-3p, miR-133b, and miR-873-5p) by analyzing 410 predicted target genes, both of which were previously associated with Parkinson's disease (PD). After performing 13,536 transfections, we validated 442 of the 705 putative MTIs (62,7%) through dual luciferase reporter assays. These analyses increased the number of validated MTIs by at least 2.1-fold for miR-133b and by a maximum of 24.3-fold for miR-873-5p. Our study contributes to the experimental capture of miRNA targetomes by addressing i) the ratio of experimentally verified MTIs to predicted MTIs, ii) the sizes of disease-related miRNA targetomes, and iii) the density of MTI networks. A web service to support the analyses on the MTI level is available online ( https://ccb-web.cs.uni-saarland.de/utr-seremato ), and all the data have been added to the miRATBase database ( https://ccb-web.cs.uni-saarland.de/miratbase ).
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Affiliation(s)
- Martin Hart
- Human Genetics, Saarland University, 66421, Homburg, Germany.
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany
| | - Claudia Fecher-Trost
- Department of Experimental and Clinical Pharmacology & Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Lena Krammes
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Ernesto Aparicio
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Annika Engel
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Pascal Hirsch
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Viktoria Wagner
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Verena Keller
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Department for Internal Medicine II, Saarland University Hospital, 66421, Homburg, Germany
| | | | | | - Caroline Diener
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Ulrike Fischer
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Jens Mayer
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Markus R Meyer
- Department of Experimental and Clinical Pharmacology & Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Veit Flockerzi
- Department of Experimental and Clinical Pharmacology & Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany
| | - Eckart Meese
- Human Genetics, Saarland University, 66421, Homburg, Germany
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10
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Nappi F. Non-Coding RNA-Targeted Therapy: A State-of-the-Art Review. Int J Mol Sci 2024; 25:3630. [PMID: 38612441 PMCID: PMC11011542 DOI: 10.3390/ijms25073630] [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: 01/23/2024] [Revised: 03/11/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
The use of non-coding RNAs (ncRNAs) as drug targets is being researched due to their discovery and their role in disease. Targeting ncRNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), is an attractive approach for treating various diseases, such as cardiovascular disease and cancer. This seminar discusses the current status of ncRNAs as therapeutic targets in different pathological conditions. Regarding miRNA-based drugs, this approach has made significant progress in preclinical and clinical testing for cardiovascular diseases, where the limitations of conventional pharmacotherapy are evident. The challenges of miRNA-based drugs, including specificity, delivery, and tolerability, will be discussed. New approaches to improve their success will be explored. Furthermore, it extensively discusses the potential development of targeted therapies for cardiovascular disease. Finally, this document reports on the recent advances in identifying and characterizing microRNAs, manipulating them, and translating them into clinical applications. It also addresses the challenges and perspectives towards clinical application.
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Affiliation(s)
- Francesco Nappi
- Department of Cardiac Surgery, Centre Cardiologique du Nord, 93200 Saint-Denis, France
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11
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兰 元, 余 丽, 胡 芝, 邹 淑. [Research Progress in the Regulatory Role of circRNA-miRNA Network in Bone Remodeling]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2024; 55:263-272. [PMID: 38645873 PMCID: PMC11026875 DOI: 10.12182/20240360301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Indexed: 04/23/2024]
Abstract
The dynamic balance between bone formation and bone resorption is a critical process of bone remodeling. The imbalance of bone formation and bone resorption is closely associated with the occurrence and development of various bone-related diseases. Under both physiological and pathological conditions, non-coding RNAs (ncRNAs) play a crucial regulatory role in protein expression through either inhibiting mRNAs translation or promoting mRNAs degradation. Circular RNAs (circRNAs) are a type of non-linear ncRNAs that can resist the degradation of RNA exonucleases. There is accumulating evidence suggesting that circRNAs and microRNAs (miRNAs) serve as critical regulators of bone remodeling through their direct or indirect regulation of the expression of osteogenesis-related genes. Additionally, recent studies have revealed the involvement of the circRNAs-miRNAs regulatory network in the process by which mesenchymal stem cells (MSCs) differentiate towards the osteoblasts (OB) lineage and the process by which bone marrow-derived macrophages (BMDM) differentiate towards osteoclasts (OC). The circRNA-miRNA network plays an important regulatory role in the osteoblastic-osteoclastic balance of bone remodeling. Therefore, a thorough understanding of the circRNA-miRNA regulatory mechanisms will contribute to a better understanding of the regulatory mechanisms of the balance between osteoblastic and osteoclastic activities in the process of bone remodeling and the diagnosis and treatment of related diseases. Herein, we reviewed the functions of circRNA and microRNA. We also reviewed their roles in and the mechanisms of the circRNA-miRNA regulatory network in the process of bone remodeling. This review provides references and ideas for further research on the regulation of bone remodeling and the prevention and treatment of bone-related diseases.
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Affiliation(s)
- 元辰 兰
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 正畸科 (成都 610041)State Key Laboratory of Oral Disease and National Clinical Research Center for Oral Diseases and Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 丽媛 余
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 正畸科 (成都 610041)State Key Laboratory of Oral Disease and National Clinical Research Center for Oral Diseases and Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 芝爱 胡
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 正畸科 (成都 610041)State Key Laboratory of Oral Disease and National Clinical Research Center for Oral Diseases and Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 淑娟 邹
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 正畸科 (成都 610041)State Key Laboratory of Oral Disease and National Clinical Research Center for Oral Diseases and Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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12
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Du R, Flynn MJ, Honsa M, Jungmann R, Elowitz MB. miRNA circuit modules for precise, tunable control of gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.583048. [PMID: 38559239 PMCID: PMC10979901 DOI: 10.1101/2024.03.12.583048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The ability to express transgenes at specified levels is critical for understanding cellular behaviors, and for applications in gene and cell therapy. Transfection, viral vectors, and other gene delivery methods produce varying protein expression levels, with limited quantitative control, while targeted knock-in and stable selection are inefficient and slow. Active compensation mechanisms can improve precision, but the need for additional proteins or lack of tunability have prevented their widespread use. Here, we introduce a toolkit of compact, synthetic miRNA-based circuit modules that provide precise, tunable control of transgenes across diverse cell types. These circuits, termed DIMMERs (Dosage-Invariant miRNA-Mediated Expression Regulators) use multivalent miRNA regulatory interactions within an incoherent feed-forward loop architecture to achieve nearly uniform protein expression over more than two orders of magnitude variation in underlying gene dosages or transcription rates. They also allow coarse and fine control of expression, and are portable, functioning across diverse cell types. In addition, a heuristic miRNA design algorithm enables the creation of orthogonal circuit variants that independently control multiple genes in the same cell. These circuits allowed dramatically improved CRISPR imaging, and super-resolution imaging of EGFR receptors with transient transfections. The toolbox provided here should allow precise, tunable, dosage-invariant expression for research, gene therapy, and other biotechnology applications.
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Affiliation(s)
- Rongrong Du
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael J. Flynn
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Monique Honsa
- Max Planck Institute of Biochemistry, Martinsried, Germany; Faculty of Physics, Ludwig Maximilian University, Munich, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Martinsried, Germany; Faculty of Physics, Ludwig Maximilian University, Munich, Germany
| | - Michael B. Elowitz
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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13
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Qin B, Peng Q, Dong H, Lei L, Wu S. Non-coding RNAs in diabetic foot ulcer- a focus on infected wounds. Diabetes Metab Res Rev 2024; 40:e3740. [PMID: 37839046 DOI: 10.1002/dmrr.3740] [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: 11/29/2022] [Revised: 07/19/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023]
Abstract
Diabetes mellitus is associated with a wide range of neuropathies, vasculopathies, and immunopathies, resulting in many complications. More than 30% of diabetic patients risk developing diabetic foot ulcers (DFUs). Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), play essential roles in various biological functions in the hyperglycaemic environment that determines the development of DFU. Ulceration results in tissue breakdown and skin barrier scavenging, thereby facilitating bacterial infection and biofilm formation. Many bacteria contribute to diabetic foot infection (DFI), including Staphylococcus aureus (S. aureus) et al. A heterogeneous group of "ncRNAs," termed small RNAs (sRNAs), powerfully regulates biofilm formation and DFI healing. Multidisciplinary foot care interventions have been identified for nonhealing ulcers. With an appreciation of the link between disease processes and ncRNAs, a novel therapeutic model of bioactive materials loaded with ncRNAs has been developed to prevent and manage diabetic foot complications.
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Affiliation(s)
- Boquan Qin
- Department of Orthopedic Surgery and Orthopedic Research Institute, Laboratory of Stem Cell and Tissue Engineering, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Qi Peng
- Department of Orthopedic Surgery and Orthopedic Research Institute, Laboratory of Stem Cell and Tissue Engineering, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hongxian Dong
- Department of Orthopedic Surgery and Orthopedic Research Institute, Laboratory of Stem Cell and Tissue Engineering, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Lei Lei
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shizhou Wu
- Department of Orthopedic Surgery and Orthopedic Research Institute, Laboratory of Stem Cell and Tissue Engineering, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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14
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Yang JH, Tsitsipatis D, Gorospe M. Stoichiometry of long noncoding RNA interactions with other RNAs: Insights from OIP5-AS1. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1841. [PMID: 38576135 DOI: 10.1002/wrna.1841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/27/2024] [Accepted: 03/07/2024] [Indexed: 04/06/2024]
Abstract
Long noncoding (lnc)RNAs modulate gene expression programs in a range of developmental processes in different organs. In skeletal muscle, lncRNAs have been implicated in myogenesis, the process whereby muscle precursor cells form muscle fibers during embryonic development and regenerate muscle fibers in the adult. Here, we discuss OIP5-AS1, a lncRNA that is highly expressed in skeletal muscle and is capable of coordinating protein expression programs during myogenesis. Given that several myogenic functions of OIP5-AS1 involve interactions with MEF2C mRNA and with the microRNA miR-7, it was critical to carefully evaluate the precise levels of OIP5-AS1 during myogenesis. We discuss the approaches used to examine lncRNA copy number using OIP5-AS1 as an example, focusing on quantification by quantitative PCR analysis with reference to nucleic acids of known abundance, by droplet digital (dd)PCR measurement, and by microscopic visualization of individual lncRNAs in cells. We discuss considerations of RNA stoichiometry in light of developmental processes in which lncRNAs are implicated. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Jen-Hao Yang
- Institute of Biomedical Sciences, National Sun Yat-set University, Kaohsiung, Taiwan
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - Dimitrios Tsitsipatis
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
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15
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Dzau VJ, Hodgkinson CP. RNA Therapeutics for the Cardiovascular System. Circulation 2024; 149:707-716. [PMID: 38408142 DOI: 10.1161/circulationaha.123.067373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
RNA therapeutics hold significant promise in the treatment of cardiovascular diseases. RNAs are biologically diverse and functionally specific and can be used for gain- or loss-of-function purposes. The effectiveness of mRNA-based vaccines in the recent COVID-19 pandemic has undoubtedly proven the benefits of an RNA-based approach. RNA-based therapies are becoming more common as a treatment modality for cardiovascular disease. This is most evident in hypertension where several small interfering RNA-based drugs have proven to be effective in managing high blood pressure in several clinical trials. As befits a rapidly burgeoning field, there is significant interest in other classes of RNA. Revascularization of the infarcted heart through an mRNA drug is under clinical investigation. mRNA technology may provide the platform for the expression of paracrine factors for myocardial protection and regeneration. Emergent technologies on the basis of microRNAs and gene editing are tackling complex diseases in a novel fashion. RNA-based gene editing offers hope of permanent cures for monogenic cardiovascular diseases, and long-term control of complex diseases such as essential hypertension, as well. Likewise, microRNAs are proving effective in regenerating cardiac muscle. The aim of this review is to provide an overview of the current landscape of RNA-based therapies for the treatment of cardiovascular disease. The review describes the large number of RNA molecules that exist with a discussion of the clinical development of each RNA type. In addition, the review also presents a number of avenues for future development.
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Affiliation(s)
- Victor J Dzau
- Mandel Center for Hypertension and Atherosclerosis, and the Duke Cardiovascular Research Center, Duke University Medical Center, Durham, NC (V.J.D., C.P.H.)
- National Academy of Medicine, Washington, DC (V.J.D.)
| | - Conrad P Hodgkinson
- Mandel Center for Hypertension and Atherosclerosis, and the Duke Cardiovascular Research Center, Duke University Medical Center, Durham, NC (V.J.D., C.P.H.)
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16
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Ishikawa T, Sugawara K, Zhang J, Funatsu T, Okabe K. Direct observation of cytoskeleton-dependent trafficking of miRNA visualized by the introduction of pre-miRNA. iScience 2024; 27:108811. [PMID: 38303695 PMCID: PMC10831896 DOI: 10.1016/j.isci.2024.108811] [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: 04/06/2023] [Revised: 10/08/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
MicroRNA (miRNA) plays physiologically and pathologically important roles in post-transcriptional regulation. Although miRNA has been suggested to dynamically interact with cellular organelles, the dynamicity of intracellular miRNA behavior has remained unclear. Here, by introducing fluorescently labeled pre-miRNA into living cells, we improved the miRNA visualization method using exogenous miRNA precursors. Through the combination of our miRNA visualization method and single-molecule sensitive fluorescence microscopy, we quantitatively analyzed the process of miRNA maturation. Furthermore, single-particle tracking of fluorescent miRNA in cells revealed the directed movements of miRNA on cytoskeletal components (i.e., microtubules and actin filaments). Our results also suggest that cytoskeleton-dependent miRNA trafficking is associated with the interaction of miRNAs with the nucleus and the endoplasmic reticulum/Golgi apparatus. Our method should facilitate the elucidation of the mechanism and physiological significance of the subcellular localization and organelle interaction of miRNA.
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Affiliation(s)
- Toshinari Ishikawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ko Sugawara
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Junwei Zhang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kohki Okabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- JST, PRESTO, 4-8-1 Honcho, Kawaguchi, Saitama 332-0012, Japan
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17
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Shi Y, Zhen X, Zhang Y, Li Y, Koo S, Saiding Q, Kong N, Liu G, Chen W, Tao W. Chemically Modified Platforms for Better RNA Therapeutics. Chem Rev 2024; 124:929-1033. [PMID: 38284616 DOI: 10.1021/acs.chemrev.3c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
RNA-based therapies have catalyzed a revolutionary transformation in the biomedical landscape, offering unprecedented potential in disease prevention and treatment. However, despite their remarkable achievements, these therapies encounter substantial challenges including low stability, susceptibility to degradation by nucleases, and a prominent negative charge, thereby hindering further development. Chemically modified platforms have emerged as a strategic innovation, focusing on precise alterations either on the RNA moieties or their associated delivery vectors. This comprehensive review delves into these platforms, underscoring their significance in augmenting the performance and translational prospects of RNA-based therapeutics. It encompasses an in-depth analysis of various chemically modified delivery platforms that have been instrumental in propelling RNA therapeutics toward clinical utility. Moreover, the review scrutinizes the rationale behind diverse chemical modification techniques aiming at optimizing the therapeutic efficacy of RNA molecules, thereby facilitating robust disease management. Recent empirical studies corroborating the efficacy enhancement of RNA therapeutics through chemical modifications are highlighted. Conclusively, we offer profound insights into the transformative impact of chemical modifications on RNA drugs and delineates prospective trajectories for their future development and clinical integration.
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Affiliation(s)
- Yesi Shi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Xueyan Zhen
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yiming Zhang
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yongjiang Li
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Seyoung Koo
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Qimanguli Saiding
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Na Kong
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Gang Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Wei Chen
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
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18
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Yang S, Zhang Y, Zhang Y, Yin L, Han X, Zhao X, Wang N, Xu L. LncRNA Gm28382 promotes lipogenesis by interacting with miR-326-3p to regulate ChREBP signaling pathway in NAFLD. Int Immunopharmacol 2024; 127:111444. [PMID: 38157698 DOI: 10.1016/j.intimp.2023.111444] [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: 10/20/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Long non-coding RNAs (lncRNAs) have been demonstrated to play vital roles in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). However, their biological roles and function mechanisms in NAFLD remain largely unknown. In this study, we found that Gm28382 may be a potential pathogenic lncRNA of NAFLD and highly expressed in NAFLD through RNA-seq. Overexpression of Gm28382 significantly enhanced the lipid accumulation in AML12 cells, whereas Gm28382 silencing reduced lipogenesis both in palmitic acid (PA)-induced AML12 cells and high fat diet (HFD)-induced mice. Then, bioinformatics were employed to speculate the potential interacting genes of Gm28382, and found that Gm28382 may regulate ChREBP expression through binding with miR-326-3p. Fluorescence in situ hybridization (FISH), dual luciferase reporter assay, immunofluorescence RNA pull-down and RNA immunoprecipitation (RIP) assays were used to validate the binding and targeting relationship of these genes, and we confirmed that Gm28382 competitively binds to miR-326-3p to increase ChREBP expression as a ceRNA. Mechanistically, overexpression of Gm28382 upregulated the ChREBP-mediated lipid synthesis signaling pathway, but the function was sabotaged by miR-326-3p deletion or ChREBP overexpression. Furthermore, in PA-challenged AML12 cells or HFD-induced mice, silencing of Gm28382 reversed the aberrant ChREBP signaling pathway and lipid accumulation, whereas ChREBP overexpression or liver-specific silencing of miR-326-3p blocked this function of Gm28382. Collectively, these findings reveal a critical role of Gm28382 in the promotion of lipogenesis in NAFLD by regulating the ChREBP signaling pathway through interaction with miR-326-3p, which could serve as a potential therapeutic target for NAFLD treatment.
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Affiliation(s)
- Sen Yang
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Yang Zhang
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Yan Zhang
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Lianhong Yin
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Xu Han
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Xuerong Zhao
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Ning Wang
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Lina Xu
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China.
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19
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Li J, Chen Z, Li Q, Liu R, Zheng J, Gu Q, Xiang F, Li X, Zhang M, Kang X, Wu R. Study of miRNA and lymphocyte subsets as potential biomarkers for the diagnosis and prognosis of gastric cancer. PeerJ 2024; 12:e16660. [PMID: 38259671 PMCID: PMC10802158 DOI: 10.7717/peerj.16660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/21/2023] [Indexed: 01/24/2024] Open
Abstract
Objective The aim of this study was to identify the expression of miRNA and lymphocyte subsets in the blood of gastric cancer (GC) patients, elucidate their clinical significance in GC, and establish novel biomarkers for the early diagnosis and prognosis of GC. Methods The expression of miRNAs in the serum of GC patients was screened using second-generation sequencing and detected using qRT-PCR. The correlation between miRNA expression and clinicopathological characteristics of GC patients was analyzed, and molecular markers for predicting cancer were identified. Additionally, flow cytometry was used to detect the proportion of lymphocyte subsets in GC patients compared to healthy individuals. The correlations between differential lymphocyte subsets, clinicopathological features of GC patients, and their prognosis were analyzed statistically. Results The study revealed that hsa-miR-1306-5p, hsa-miR-3173-5p, and hsa-miR-296-5p were expressed at lower levels in the blood of GC patients, which is consistent with miRNA-seq findings. The AUC values of hsa-miR-1306-5p, hsa-miR-3173-5p, and hsa-miR-296-5p were found to be effective predictors of GC occurrence. Additionally, hsa-miR-296-5p was found to be negatively correlated with CA724. Furthermore, hsa-miR-1306-5p, hsa-miR-3173-5p, and hsa-miR-296-5p were found to be associated with the stage of the disease and were closely linked to the clinical pathology of GC. The lower the levels of these miRNAs, the greater the clinical stage of the tumor and the worse the prognosis of gastric cancer patients. Finally, the study found that patients with GC had lower absolute numbers of CD3+ T cells, CD4+ T cells, CD8+ T cells, CD19+ B cells, and lymphocytes compared to healthy individuals. The quantity of CD4+ T lymphocytes and the level of the tumor marker CEA were shown to be negatively correlated. The ROC curve and multivariate logistic regression analysis demonstrated that lymphocyte subsets can effectively predict gastric carcinogenesis and prognosis. Conclusion These miRNAs such as hsa-miR-1306-5p, hsa-miR-3173-5p, hsa-miR-296-5p and lymphocyte subsets such as the absolute numbers of CD3+ T cells, CD4+ T cells, CD8+ T cells, CD19+ B cells, lymphocytes are down-regulated in GC and are closely related to the clinicopathological characteristics and prognosis of GC patients. They may serve as new molecular markers for predicting the early diagnosis and prognosis of GC patients.
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Affiliation(s)
- Jinpeng Li
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zixi Chen
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qian Li
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rongrong Liu
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jin Zheng
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qing Gu
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fenfen Xiang
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoxiao Li
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Mengzhe Zhang
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiangdong Kang
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rong Wu
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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20
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Hofman CR, Corey DR. Targeting RNA with synthetic oligonucleotides: Clinical success invites new challenges. Cell Chem Biol 2024; 31:125-138. [PMID: 37804835 PMCID: PMC10841528 DOI: 10.1016/j.chembiol.2023.09.005] [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: 07/05/2023] [Revised: 08/27/2023] [Accepted: 09/15/2023] [Indexed: 10/09/2023]
Abstract
Synthetic antisense oligonucleotides (ASOs) and duplex RNAs (dsRNAs) are an increasingly successful strategy for drug development. After a slow start, the pace of success has accelerated since the approval of Spinraza (nusinersen) in 2016 with several drug approvals. These accomplishments have been achieved even though oligonucleotides are large, negatively charged, and have little resemblance to traditional small-molecule drugs-a remarkable achievement of basic and applied science. The goal of this review is to summarize the foundation underlying recent progress and describe ongoing research programs that may increase the scope and impact of oligonucleotide therapeutics.
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Affiliation(s)
- Cristina R Hofman
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - David R Corey
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA.
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21
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Kondoh H. The Significance of Repressive Processes in Developmental Regulation. Results Probl Cell Differ 2024; 72:127-142. [PMID: 38509256 DOI: 10.1007/978-3-031-39027-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Encountering a developmental process confined to a limited time window or a restricted embryonic area, one may deem that the mechanism to activate the process occurs with such precision in temporal and spatial terms. However, in many instances, the activation mechanism is initiated in a broad time and space, but the mechanism is actuated only when repressive mechanisms are lifted. Thus, the operation of repressive processes is essential for precise developmental regulation. Repressive regulations occur at various levels. The following representative repressive regulations and their consequences at various levels will be discussed: intercellular signaling, epigenetic regulation, transcriptional regulation, and posttranscriptional regulation.
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Affiliation(s)
- Hisato Kondoh
- Osaka University, Suita, Osaka, Japan
- Biohistory Research Hall, Takatsuki, Osaka, Japan
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22
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Qi W, Guan W. A Comprehensive Review on the Importance of MiRNA-206 in the Animal Model and Human Diseases. Curr Neuropharmacol 2024; 22:1064-1079. [PMID: 37032500 DOI: 10.2174/1570159x21666230407124146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 04/11/2023] Open
Abstract
MicroRNA-206 (miR-206) is a microRNA that is involved in many human diseases, such as myasthenia gravis, osteoarthritis, depression, cancers, etc. Both inhibition effects and progression roles of miR-206 have been reported for the past few years. High expression of miR-206 was observed in patients with osteoarthritis, gastric cancer and epithelial ovarian cancer compared to normal people. The study also showed that miR-206 promotes cancer progression in breast cancer patients and avascular necrosis of the femoral head. Meanwhile, several studies have shown that expression levels of miR-206 were down-regulated in laryngeal carcinoma cell multiplication, as well as in hepatocellular carcinoma, non-small lung cancer and infantile hemangioma. Moreover, miR-206 was up-regulated in the mild stage of amyotrophic lateral sclerosis patients and then down-regulated in the moderate and severe stages, indicating that miR-206 has the double effects of starting and aggravating the disease. In neuropsychiatric disorders, such as depression, miR-206 also plays an important role in the progression of the disease; the level of miR-206 is most highly expressed in the brains of patients with depression. In the current review, we summarize the role of miR-206 in various diseases, and miR-206 may be developed as a new biomarker for diagnosing diseases in the near future.
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Affiliation(s)
- Wang Qi
- Department of Pharmacology, The First People's Hospital of Yancheng, Yancheng, 224000, Jiangsu, China
| | - Wei Guan
- Department of Pharmacology, Pharmacy College, Nantong University, Nantong, 226001, Jiangsu, China
- School of Medicine, Nantong University, Nantong, China
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23
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Engel A, Ludwig N, Grandke F, Wagner V, Kern F, Fehlmann T, Schmartz GP, Aparicio-Puerta E, Henn D, Walch-Rückheim B, Hannig M, Rupf S, Meese E, Laschke MW, Keller A. Skin treatment with non-thermal plasma modulates the immune system through miR-223-3p and its target genes. RNA Biol 2024; 21:31-44. [PMID: 38828710 PMCID: PMC11152102 DOI: 10.1080/15476286.2024.2361571] [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] [Accepted: 05/24/2024] [Indexed: 06/05/2024] Open
Abstract
Non-thermal plasma, a partially ionized gas, holds significant potential for clinical applications, including wound-healing support, oral therapies, and anti-tumour treatments. While its applications showed promising outcomes, the underlying molecular mechanisms remain incompletely understood. We thus apply non-thermal plasma to mouse auricular skin and conducted non-coding RNA sequencing, as well as single-cell blood sequencing. In a time-series analysis (five timepoints spanning 2 hours), we compare the expression of microRNAs in the plasma-treated left ears to the unexposed right ears of the same mice as well as to the ears of unexposed control mice. Our findings indicate specific effects in the treated ears for a set of five miRNAs: mmu-miR-144-5p, mmu-miR-144-3p, mmu-miR-142a-5p, mmu-miR-223-3p, and mmu-miR-451a. Interestingly, mmu-miR-223-3p also exhibits an increase over time in the right non-treated ear of the exposed mice, suggesting systemic effects. Notably, this miRNA, along with mmu-miR-142a-5p and mmu-miR-144-3p, regulates genes and pathways associated with wound healing and tissue regeneration (namely ErbB, FoxO, Hippo, and PI3K-Akt signalling). This co-regulation is particularly remarkable considering the significant seed dissimilarities among the miRNAs. Finally, single-cell sequencing of PBMCs reveals the downregulation of 12 from 15 target genes in B-cells, Cd4+ and Cd8+ T-cells. Collectively, our data provide evidence for a systemic effect of non-thermal plasma.
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Affiliation(s)
- Annika Engel
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg/Saar, Germany
- Center for Human and Molecular Biology, Saarland University, Homburg/Saar, Germany
| | - Friederike Grandke
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Viktoria Wagner
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
- Department of Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Georges P. Schmartz
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | | | - Dominic Henn
- Department of Plastic Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Barbara Walch-Rückheim
- Center of Human und Molecular Biology (ZHMB), Virology & Immunology, Saarland University, Homburg/Saar, Germany
| | - Matthias Hannig
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, Homburg/Saar, Germany
| | - Stefan Rupf
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, Homburg/Saar, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg/Saar, Germany
| | - Matthias W. Laschke
- Institute for Clinical and Experimental Surgery, Saarland University, Homburg/Saar, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
- Department of Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarbrücken, Germany
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24
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Li Y. Non-Coding RNA Performs Its Biological Function by Interacting with Macromolecules. Int J Mol Sci 2023; 24:16246. [PMID: 38003435 PMCID: PMC10671565 DOI: 10.3390/ijms242216246] [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: 10/30/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
One of the most significant discoveries resulting from the sequencing of the human genome is the realization that a large portion (over 85%) of the genome is transcribed into RNA, yet less than 2% of it encodes protein-coding genes [...].
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Affiliation(s)
- Yao Li
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai 200433, China
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25
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Kosek DM, Banijamali E, Becker W, Petzold K, Andersson E. Efficient 3'-pairing renders microRNA targeting less sensitive to mRNA seed accessibility. Nucleic Acids Res 2023; 51:11162-11177. [PMID: 37819016 PMCID: PMC10639062 DOI: 10.1093/nar/gkad795] [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: 07/21/2022] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate gene expression by binding to specific sites in mRNAs. Site recognition is primarily mediated by the seed region (nucleotides g2-g8 in the miRNA), but pairing beyond the seed (3'-pairing) is important for some miRNA:target interactions. Here, we use SHAPE, luciferase reporter assays and transcriptomics analyses to study the combined effect of 3'-pairing and secondary structures in mRNAs on repression efficiency. Using the interaction between miR-34a and its SIRT1 binding site as a model, we provide structural and functional evidence that 3'-pairing can compensate for low seed-binding site accessibility, enabling repression of sites that would otherwise be ineffective. We show that miRNA 3'-pairing regions can productively base-pair with nucleotides far upstream of the seed-binding site and that both hairpins and unstructured bulges within the target site are tolerated. We use SHAPE to show that sequences that overcome inaccessible seed-binding sites by strong 3'-pairing adopt the predicted structures and corroborate the model using luciferase assays and high-throughput modelling of 8177 3'-UTR targets for six miRNAs. Finally, we demonstrate that PHB2, a target of miR-141, is an inaccessible target rescued by efficient 3'-pairing. We propose that these results could refine predictions of effective target sites.
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Affiliation(s)
- David M Kosek
- Department of Cell and Molecular Biology, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177Stockholm, Sweden
| | - Elnaz Banijamali
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177Stockholm, Sweden
| | - Walter Becker
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177Stockholm, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177Stockholm, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Centre D9:3, Husargatan 3, 752 37 Uppsala, Sweden
| | - Emma R Andersson
- Department of Cell and Molecular Biology, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177Stockholm, Sweden
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26
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Ranjan P, Colin K, Dutta RK, Verma SK. Challenges and future scope of exosomes in the treatment of cardiovascular diseases. J Physiol 2023; 601:4873-4893. [PMID: 36398654 PMCID: PMC10192497 DOI: 10.1113/jp282053] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/21/2022] [Indexed: 07/28/2023] Open
Abstract
Exosomes are nanosized vesicles that carry biologically diverse molecules for intercellular communication. Researchers have been trying to engineer exosomes for therapeutic purposes by using different approaches to deliver biologically active molecules to the various target cells efficiently. Recent technological advances may allow the biodistribution and pharmacokinetics of exosomes to be modified to meet scientific needs with respect to specific diseases. However, it is essential to determine an exosome's optimal dosage and potential side effects before its clinical use. Significant breakthroughs have been made in recent decades concerning exosome labelling and imaging techniques. These tools provide in situ monitoring of exosome biodistribution and pharmacokinetics and pinpoint targetability. However, because exosomes are nanometres in size and vary significantly in contents, a deeper understanding is required to ensure accurate monitoring before they can be applied in clinical settings. Different research groups have established different approaches to elucidate the roles of exosomes and visualize their spatial properties. This review covers current and emerging strategies for in vivo and in vitro exosome imaging and tracking for potential studies.
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Affiliation(s)
- Prabhat Ranjan
- Department of Medicine, Division of Cardiovascular Disease, The University of Alabama at Birmingham, Birmingham, AL-35233
| | - Karen Colin
- Department of Medicine, Division of Cardiovascular Disease, The University of Alabama at Birmingham, Birmingham, AL-35233
- UAB School of Health Professions, The University of Alabama at Birmingham, Birmingham, AL
| | - Roshan Kumar Dutta
- Department of Medicine, Division of Cardiovascular Disease, The University of Alabama at Birmingham, Birmingham, AL-35233
| | - Suresh Kumar Verma
- Department of Medicine, Division of Cardiovascular Disease, The University of Alabama at Birmingham, Birmingham, AL-35233
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, Alabama
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27
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Yang J, Chen Z, He J, Zhao Y, Zhou C, Zhao X, Meng X. A circRNA-based ceRNA network shows its diagnostic value in non-small-cell lung cancer. Clin Biochem 2023; 121-122:110657. [PMID: 37793583 DOI: 10.1016/j.clinbiochem.2023.110657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/28/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023]
Abstract
BACKGROUND Numerous studies have reported the vital roles of circular RNA (circRNA)-based competitive endogenous RNA (ceRNA) regulatory networks in cancers. Here, we established a non-small-cell lung cancer (NSCLC)-related circRNA-miRNA-mRNA axis and estimated its diagnostic value in NSCLC. METHODS The circ_0061235-miR-3180-5p-PPM1L axis was constructed by small RNA deep sequencing, bioinformatics databases, and preliminary testing. The serum levels of the selected circ_0061235, miR-3180-5p, and PPM1L were quantified using quantitative polymerase chain reaction. Receiver operating characteristic analyses were conducted to evaluate the diagnostic power. RESULTS The levels of circ_0061235, miR-3180-5p, and PPM1L showed close correlations according to the ceRNA regulation rule. They were significantly dysregulated in NSCLC and showed the diagnostic ability to discriminate between healthy and NSCLC, and remarkably, between benign lung tumors and NSCLC. Additionally, the down-regulated levels of hsa_circ_0061235, the up-regulated levels of miR-3180-5p, and the decreased levels of PPM1L were correlated to more aggressive features of NSCLC, such as lymph node metastasis, distant metastasis, and higher stages. Intriguingly, compared to the single circ_0061235, miR-3180-5p, PPM1L, and traditional tumor markers, the diverse combinations of circ_0061235, miR-3180-5p, and PPM1L showed much higher sensitivity and specificity to differentiate greater or lesser severity of NSCLC. GO annotation and KEGG pathway analyses revealed the underlying role of the circ_0061235-miR-3180-5p-PPM1L axis in NSCLC. CONCLUSIONS We established a specific circRNA-miRNA-mRNA network with higher sensitivity and specificity to diagnose NSCLC, particularly more aggressive NSCLC, providing a new strategy for further developing tumor biomarkers.
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Affiliation(s)
- Jianuo Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China; Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Zhenhua Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China; Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jinxian He
- Department of Thoracic Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo 315048, China
| | - Yikai Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China; Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Chengwei Zhou
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315020, China
| | - Xiaodong Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315020, China
| | - Xiaodan Meng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China; Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China.
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28
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Larivera S, Neumeier J, Meister G. Post-transcriptional gene silencing in a dynamic RNP world. Biol Chem 2023; 404:1051-1067. [PMID: 37739934 DOI: 10.1515/hsz-2023-0203] [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: 05/05/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
MicroRNA (miRNA)-guided gene silencing is a key regulatory process in various organisms and linked to many human diseases. MiRNAs are processed from precursor molecules and associate with Argonaute proteins to repress the expression of complementary target mRNAs. Excellent work by numerous labs has contributed to a detailed understanding of the mechanisms of miRNA function. However, miRNA effects have mostly been analyzed and viewed as isolated events and their natural environment as part of complex RNA-protein particles (RNPs) is often neglected. RNA binding proteins (RBPs) regulate key enzymes of the miRNA processing machinery and furthermore RBPs or readers of RNA modifications may modulate miRNA activity on mRNAs. Such proteins may function similarly to miRNAs and add their own contributions to the overall expression level of a particular gene. Therefore, post-transcriptional gene regulation might be more the sum of individual regulatory events and should be viewed as part of a dynamic and complex RNP world.
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Affiliation(s)
- Simone Larivera
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Julia Neumeier
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
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29
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Wang N, Yao Y, Qian Y, Qiu D, Cao H, Xiang H, Wang J. Cargoes of exosomes function as potential biomarkers for Mycobacterium tuberculosis infection. Front Immunol 2023; 14:1254347. [PMID: 37928531 PMCID: PMC10622749 DOI: 10.3389/fimmu.2023.1254347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
Exosomes as double-membrane vesicles contain various contents of lipids, proteins, mRNAs and non-coding RNAs, and involve in multiple physiological processes, for instance intercellular communication and immunomodulation. Currently, numerous studies found that the components of exosomal proteins, nucleic acids or lipids released from host cells are altered following infection with Mycobacterium tuberculosis. Exosomal contents provide excellent biomarkers for the auxiliary diagnosis, efficacy evaluation, and prognosis of tuberculosis. This study aimed to review the current literatures detailing the functions of exosomes in the procedure of M. tuberculosis infection, and determine the potential values of exosomes as biomarkers to assist in the diagnosis and monitoring of tuberculosis.
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Affiliation(s)
- Nan Wang
- Department of Clinical Laboratory, Kunshan Hospital Affiliated to Jiangsu University, Suzhou, Jiangsu, China
| | - Yongliang Yao
- Department of Clinical Laboratory, Kunshan Hospital Affiliated to Jiangsu University, Suzhou, Jiangsu, China
| | - Yingfen Qian
- Department of Clinical Laboratory, Kunshan Fourth People’s Hospital, Suzhou, Jiangsu, China
| | - Dewen Qiu
- Department of Clinical Laboratory, Jiangxi Maternal and Child Health Hospital Maternal and Child Heath Hospital of Nanchang College, Nanchang, China
| | - Hui Cao
- Department of Food and Nutrition Safety, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Huayuan Xiang
- Department of Clinical Laboratory, Kunshan Hospital Affiliated to Jiangsu University, Suzhou, Jiangsu, China
| | - Jianjun Wang
- Department of Clinical Laboratory, Kunshan Hospital Affiliated to Jiangsu University, Suzhou, Jiangsu, China
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30
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Schreiber S, Daum P, Danzer H, Hauke M, Jäck HM, Wittmann J. Identification of miR-128 Target mRNAs That Are Expressed in B Cells Using a Modified Dual Luciferase Vector. Biomolecules 2023; 13:1517. [PMID: 37892199 PMCID: PMC10605364 DOI: 10.3390/biom13101517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
MicroRNAs (miRNAs) are 21-25 nucleotide long non-coding ribonucleic acids that modulate gene expression by degrading transcripts or inhibiting translation. The miRNA miR-128, originally thought to be brain-specific, was later also found in immune cells. To identify a valuable immune cell model system to modulate endogenous miR-128 amounts and to validate predicted miR-128 target mRNAs in B cells, we first investigated miR-128 expression using Northern blot analysis in several cell lines representing different stages of B cell development. The results showed that only primary brain cells showed significant levels of mature miR-128. To study the function of miR-128 in immune cells, we modified dual luciferase vectors to allow easy transfer of 3' UTR fragments with predicted miR-128 binding sites from widely used single to dual luciferase vectors. Comparison of in silico predicted miR-128-regulated mRNAs in single and dual luciferase constructs yielded similar results, validating the dual luciferase vector for miRNA target analysis. Furthermore, we confirmed miR-128-regulated mRNAs identified in silico and in vivo using the Ago HITS-CLIP technique and known to be expressed in B cells using the dual luciferase assay. In conclusion, this study provides new insights into the expression and function of miR-128 by validating novel target mRNAs expressed in B cells and identifying additional pathways likely controlled by this miRNA in the immune system.
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Affiliation(s)
| | | | | | | | | | - Jürgen Wittmann
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus-Fiebiger-Center of Molecular Medicine (NFZ), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Glückstraße 6, D-91054 Erlangen, Germany
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31
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Terriaca S, Scioli MG, Pisano C, Ruvolo G, Ferlosio A, Orlandi A. miR-632 Induces DNAJB6 Inhibition Stimulating Endothelial-to-Mesenchymal Transition and Fibrosis in Marfan Syndrome Aortopathy. Int J Mol Sci 2023; 24:15133. [PMID: 37894814 PMCID: PMC10607153 DOI: 10.3390/ijms242015133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/19/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Marfan syndrome (MFS) is a connective tissue disorder caused by FBN1 gene mutations leading to TGF-β signaling hyperactivation, vascular wall weakness, and thoracic aortic aneurysms (TAAs). The pathogenetic mechanisms are not completely understood and patients undergo early vascular surgery to prevent TAA ruptures. We previously reported miR-632 upregulation in MFS TAA tissues compared with non-genetic TAA tissues. DNAJB6 is a gene target of miR-632 in cancer and plays a critical role in blocking epithelial-to-mesenchymal transition by inhibiting the Wnt/β catenin pathway. TGF-β signaling also activates Wnt/β catenin signaling and induces endothelial-to-mesenchymal transition (End-Mt) and fibrosis. We documented that miR-632 upregulation correlated with DNAJB6 expression in both the endothelium and the tunica media of MFS TAA (p < 0.01). Wnt/β catenin signaling, End-Mt, and fibrosis markers were also upregulated in MFS TAA tissues (p < 0.05, p < 0.01 and p < 0.001). Moreover, miR-632 overexpression inhibited DNAJB6, inducing Wnt/β catenin signaling, as well as End-Mt and fibrosis exacerbation (p < 0.05 and p < 0.01). TGF-β1 treatment also determined miR-632 upregulation (p < 0.01 and p < 0.001), with the consequent activation of the aforementioned processes. Our study provides new insights about the pathogenetic mechanisms in MFS aortopathy. Moreover, the high disease specificity of miR-632 and DNAJB6 suggests new potential prognostic factors and/or therapeutic targets in the progression of MFS aortopathy.
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Affiliation(s)
- Sonia Terriaca
- Anatomic Pathology, Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (A.F.); (A.O.)
| | - Maria Giovanna Scioli
- Anatomic Pathology, Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (A.F.); (A.O.)
| | - Calogera Pisano
- Cardiac Surgery, Department of Surgical Sciences, Tor Vergata University, 00133 Rome, Italy; (C.P.); (G.R.)
| | - Giovanni Ruvolo
- Cardiac Surgery, Department of Surgical Sciences, Tor Vergata University, 00133 Rome, Italy; (C.P.); (G.R.)
| | - Amedeo Ferlosio
- Anatomic Pathology, Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (A.F.); (A.O.)
| | - Augusto Orlandi
- Anatomic Pathology, Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (A.F.); (A.O.)
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32
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Chen Q, Zhou T. Emerging functional principles of tRNA-derived small RNAs and other regulatory small RNAs. J Biol Chem 2023; 299:105225. [PMID: 37673341 PMCID: PMC10562873 DOI: 10.1016/j.jbc.2023.105225] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Recent advancements in small RNA sequencing have unveiled a previously hidden world of regulatory small noncoding RNAs (sncRNAs) that extend beyond the well-studied small interfering RNAs, microRNAs, and piwi-interacting RNAs. This exploration, starting with tRNA-derived small RNAs, has led to the discovery of a diverse universe of sncRNAs derived from various longer structured RNAs such as rRNAs, small nucleolar RNAs, small nuclear RNAs, Y RNAs, and vault RNAs, with exciting uncharted functional possibilities. In this perspective, we discuss the emerging functional principles of sncRNAs beyond the well-known RNAi-like mechanisms, focusing on those that operate independent of linear sequence complementarity but rather function in an aptamer-like fashion. Aptamers use 3D structure for specific interactions with ligands and are modulated by RNA modifications and subcellular environments. Given that aptamer-like sncRNA functions are widespread and present in species lacking RNAi, they may represent an ancient functional principle that predates RNAi. We propose a rethinking of the origin of RNAi and its relationship with these aptamer-like functions in sncRNAs and how these complementary mechanisms shape biological processes. Lastly, the aptamer-like function of sncRNAs highlights the need for caution in using small RNA mimics in research and therapeutics, as their specificity is not restricted solely to linear sequence.
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Affiliation(s)
- Qi Chen
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah, USA; Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA.
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA.
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Liao T, Gan M, Qiu Y, Lei Y, Chen Q, Wang X, Yang Y, Chen L, Zhao Y, Niu L, Wang Y, Zhang S, Zhu L, Shen L. miRNAs derived from cobra venom exosomes contribute to the cobra envenomation. J Nanobiotechnology 2023; 21:356. [PMID: 37777744 PMCID: PMC10544165 DOI: 10.1186/s12951-023-02131-7] [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: 04/19/2023] [Accepted: 09/26/2023] [Indexed: 10/02/2023] Open
Abstract
Currently, there is an increasing amount of evidence indicating that exosomes and the miRNAs they contain are crucial players in various biological processes. However, the role of exosomes and miRNAs in snake venom during the envenomation process remains largely unknown. In this study, fresh venom from Naja atra of different ages (2-month-old, 1-year-old, and 5-year-old) was collected, and exosomes were isolated through ultracentrifugation. The study found that exosomes with inactivated proteins and enzymes can still cause symptoms similar to cobra envenomation, indicating that substances other than proteins and enzymes in exosomes may also play an essential role in cobra envenomation. Furthermore, the expression profiles of isolated exosome miRNAs were analyzed. The study showed that a large number of miRNAs were co-expressed and abundant in cobra venom exosomes (CV-exosomes) of different ages, including miR-2904, which had high expression abundance and specific sequences. The specific miR-2094 derived from CV-exosomes (CV-exo-miR-2904) was overexpressed both in vitro and in vivo. As a result, CV-exo-miR-2904 induced symptoms similar to cobra envenomation in mice and caused liver damage, demonstrating that it plays a crucial role in cobra envenomation. These results reveal that CV-exosomes and the miRNAs they contain play a significant regulatory role in cobra envenomation. Our findings provide new insights for the treatment of cobra bites and the development of snake venom-based medicines.
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Affiliation(s)
- Tianci Liao
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Mailin Gan
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yanhao Qiu
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yuhang Lei
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Qiuyang Chen
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xingyu Wang
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yiting Yang
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Lei Chen
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Ye Zhao
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Lili Niu
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yan Wang
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Shunhua Zhang
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Li Zhu
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Linyuan Shen
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130 China
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Jiang Q, Zhao J, Jia Q, Wang H, Xue W, Ning F, Wang J, Wang Y, Zhu Z, Tian L. MiR-148a-3p within HucMSC-Derived Extracellular Vesicles Suppresses Hsp90b1 to Prevent Fibroblast Collagen Synthesis and Secretion in Silica-Induced Pulmonary Fibrosis. Int J Mol Sci 2023; 24:14477. [PMID: 37833927 PMCID: PMC10572270 DOI: 10.3390/ijms241914477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023] Open
Abstract
Silicosis is a fatal occupational respiratory disease caused by the prolonged inhalation of respirable silica. The core event of silicosis is the heightened activity of fibroblasts, which excessively synthesize extracellular matrix (ECM) proteins. Our previous studies have highlighted that human umbilical cord mesenchymal stem cell-derived extracellular vesicles (hucMSC-EVs) hold promise in mitigating silicosis and the significant role played by microRNAs (miRNAs) in this process. Delving deeper into this mechanism, we found that miR-148a-3p was the most abundant miRNA of the differential miRNAs in hucMSC-EVs, with the gene heat shock protein 90 beta family member 1 (Hsp90b1) as a potential target. Notably, miR-148a-3p's expression was downregulated during the progression of silica-induced pulmonary fibrosis both in vitro and in vivo, but was restored after hucMSC-EVs treatment (p < 0.05). Introducing miR-148a-3p mimics effectively hindered the collagen synthesis and secretion of fibroblasts induced by transforming growth factor-β1 (TGF-β1) (p < 0.05). Confirming our hypothesis, Hsp90b1 was indeed targeted by miR-148a-3p, with significantly reduced collagen activity in TGF-β1-treated fibroblasts upon Hsp90b1 inhibition (p < 0.05). Collectively, our findings provide compelling evidence that links miR-148a-3p present in hucMSC-EVs with the amelioration of silicosis, suggesting its therapeutic potential by specifically targeting Hsp90b1, thereby inhibiting fibroblast collagen activities. This study sheds light on the role of miR-148a-3p in hucMSC-EVs, opening avenues for innovative therapeutic interventions targeting molecular pathways in pulmonary fibrosis.
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Affiliation(s)
- Qiyue Jiang
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Jing Zhao
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Qiyue Jia
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Hongwei Wang
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Wenming Xue
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Fuao Ning
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Jiaxin Wang
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Yan Wang
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Zhonghui Zhu
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Lin Tian
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
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35
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Nappi F, Avtaar Singh SS, Jitendra V, Alzamil A, Schoell T. The Roles of microRNAs in the Cardiovascular System. Int J Mol Sci 2023; 24:14277. [PMID: 37762578 PMCID: PMC10531750 DOI: 10.3390/ijms241814277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The discovery of miRNAs and their role in disease represent a significant breakthrough that has stimulated and propelled research on miRNAs as targets for diagnosis and therapy. Cardiovascular disease is an area where the restrictions of early diagnosis and conventional pharmacotherapy are evident and deserve attention. Therefore, miRNA-based drugs have significant potential for development. Research and its application can make considerable progress, as seen in preclinical and clinical trials. The use of miRNAs is still experimental but has a promising role in diagnosing and predicting a variety of acute coronary syndrome presentations. Its use, either alone or in combination with currently available biomarkers, might be adopted soon, particularly if there is diagnostic ambiguity. In this review, we examine the current understanding of miRNAs as possible targets for diagnosis and treatment in the cardiovascular system. We report on recent advances in recognising and characterising miRNAs with a focus on clinical translation. The latest challenges and perspectives towards clinical application are discussed.
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Affiliation(s)
- Francesco Nappi
- Department of Cardiac Surgery, Centre Cardiologique du Nord, 93200 Saint-Denis, France; (A.A.); (T.S.)
| | | | - Vikram Jitendra
- Department of Cardiothoracic Surgery, Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK;
| | - Almothana Alzamil
- Department of Cardiac Surgery, Centre Cardiologique du Nord, 93200 Saint-Denis, France; (A.A.); (T.S.)
| | - Thibaut Schoell
- Department of Cardiac Surgery, Centre Cardiologique du Nord, 93200 Saint-Denis, France; (A.A.); (T.S.)
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36
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Zheng MH, Shan SK, Lin X, Xu F, Wu F, Guo B, Li FXZ, Zhou ZA, Wang Y, Lei LM, Tang KX, Duan JY, Wu YY, Cao YC, Liao XB, Yuan LQ. Vascular wall microenvironment: exosomes secreted by adventitial fibroblasts induced vascular calcification. J Nanobiotechnology 2023; 21:315. [PMID: 37667298 PMCID: PMC10478424 DOI: 10.1186/s12951-023-02000-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/12/2023] [Indexed: 09/06/2023] Open
Abstract
Vascular calcification often occurs in patients with chronic renal failure (CRF), which significantly increases the incidence of cardiovascular events in CRF patients. Our previous studies identified the crosstalk between the endothelial cells (ECs) and vascular smooth muscle cells (VSMCs), and the paracrine effect of VSMCs, which regulate the calcification of VSMCs. Herein, we aim to investigate the effects of exosomes secreted by high phosphorus (HPi) -induced adventitial fibroblasts (AFs) on the calcification of VSMCs and the underlying mechanism, which will further elucidate the important role of AFs in high phosphorus vascular wall microenvironment. The conditioned medium of HPi-induced AFs promotes the calcification of VSMCs, which is partially abrogated by GW4869, a blocker of exosomes biogenesis or release. Exosomes secreted by high phosphorus-induced AFs (AFsHPi-Exos) show similar effects on VSMCs. miR-21-5p is enriched in AFsHPi-Exos, and miR-21-5p enhances osteoblast-like differentiation of VSMCs by downregulating cysteine-rich motor neuron 1 (Crim1) expression. AFsHPi-Exos and exosomes secreted by AFs with overexpression of miR-21-5p (AFsmiR21M-Exos) significantly accelerate vascular calcification in CRF mice. In general, AFsHPi-Exos promote the calcification of VSMCs and vascular calcification by delivering miR-21-5p to VSMCs and subsequently inhibiting the expression of Crim1. Combined with our previous studies, the present experiment supports the theory of vascular wall microenvironment.
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Grants
- 81770881, 81870623, 82100494, 82100944 and 82070910 National Natural Science Foundation of China
- 81770881, 81870623, 82100494, 82100944 and 82070910 National Natural Science Foundation of China
- 81770881, 81870623, 82100494, 82100944 and 82070910 National Natural Science Foundation of China
- 81770881, 81870623, 82100494, 82100944 and 82070910 National Natural Science Foundation of China
- 2020SK2078 Key R&D Plan of Hunan Province
- 2021JJ40842 Natural Science Foundation of Hunan Province
- Key R&D Plan of Hunan Province
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Affiliation(s)
- Ming-Hui Zheng
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, the Second Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Su-Kang Shan
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, the Second Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Xiao Lin
- Department of Radiology, the Second Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Feng Xu
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, the Second Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Feng Wu
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Bei Guo
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, the Second Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Fu-Xing-Zi Li
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, the Second Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Zhi-Ang Zhou
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Yi Wang
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, the Second Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Li-Min Lei
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, the Second Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Ke-Xin Tang
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, the Second Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Jia-Yue Duan
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, the Second Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Yun-Yun Wu
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, the Second Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Ye-Chi Cao
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, the Second Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Xiao-Bo Liao
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, 410000, China.
| | - Ling-Qing Yuan
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, the Second Xiangya Hospital, Central South University, Changsha, 410000, China.
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Du S, Qu H, Zhang Y, Zhu S, Wang Y, Zhang S, Wang Z, Yang Q, Fu S, Dong K. MiR-375 promotes cisplatin sensitivity of lung adenocarcinoma. Pathol Res Pract 2023; 249:154765. [PMID: 37625279 DOI: 10.1016/j.prp.2023.154765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/30/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023]
Abstract
BACKGROUND Cisplatin-based chemotherapy has been widely used in the treatment of lung adenocarcinoma (LUAD). However, the development of cisplatin resistance becomes a major obstacle impeding the curative effect. It remains necessary to uncover the molecular mechanism of cisplatin resistance. METHODS Based on the CCLE database, lung cancer cell lines were divided into cisplatin-resistant and cisplatin-sensitive groups. The differentially expressed miRNAs were filtered and further identified by survival prognosis analysis. After transfection with miR-375 inhibitor or mimic, cell cytotoxicity assay, flow cytometry and western blot were conducted to validate the role of miR-375. The transcription factor (TF)-miRNA network was constructed based on TransmiR. The target genes of miR-375 were predicted by Starbase and further verified by RT-qPCR and immunohistochemistry results in the Human Protein Atlas. Functional enrichment analysis was performed with GO terms and KEGG. RESULTS In this study, miR-375 showed the ability to promote cisplatin sensitivity and apoptosis of LUAD. Genes correlated with miR-375 in LUAD were analyzed and ABCC8 showed the strongest positive correlation. Moreover, transcription factors that regulate miR-375 expression were predicted. MBNL1, PTPN3, PRKD1 and RPN1 were identified as the target genes of miR-375. Enrichment analysis demonstrated that miR-375-related genes associated with promoting cell proliferation and anti-apoptosis were involved in the MAPK signaling pathway. CONCLUSION Overall, this study provides new insights into the role of miR-375 in the cisplatin sensitivity of LUAD. Our present findings may serve as a theoretical basis for new therapeutic strategies and predictive models of cisplatin resistance in LUAD.
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Affiliation(s)
- Shuomeng Du
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Han Qu
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Ying Zhang
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Shihao Zhu
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Yang Wang
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Shuopeng Zhang
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Zhao Wang
- Department of Gynecological Radiotherapy, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Qian Yang
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Songbin Fu
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Kexian Dong
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.
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38
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Luo HL, Lee YC, Chang YL, Hsu WC, Wu YT, Jhan JH, Lin HH, Wu YR, Ke HL, Liu HY. MicroRNA-145-5p suppresses cell proliferation, migration, and invasion in upper tract urothelial carcinoma by targeting 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase. J Cell Biochem 2023; 124:1324-1345. [PMID: 37475541 DOI: 10.1002/jcb.30449] [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: 04/26/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 07/22/2023]
Abstract
Upper tract urothelial carcinoma (UTUC), including renal, pelvic, and ureteral carcinoma, has a high incidence rate in Taiwan, which is different from that in Western countries. Therefore, it is imperative to elucidate the mechanisms underlying UTUC growth and metastasis. To explore the function of miR-145-5p in UTUC, we transfected the BFTC909 cell line with miR-145-5p mimics and analyzed the differences in protein levels by performing two-dimensional polyacrylamide gel electrophoresis. Real-time polymerase chain reaction and Western blot analysis were used to analyze 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/inositol monophosphate cyclohydrolase (ATIC) messenger RNA and protein levels. A dual-luciferase assay was performed to identify the target of miR-145-5p in ATIC. The effects of miR-145-5p and ATIC expression by cell transfection on cell proliferation, migration, and invasion were also assessed. miR-145-5p downregulated ATIC protein expression. High ATIC expression is associated with tumor stage, metastasis, recurrence, and a poor prognosis in patients with UTUC. Cell function assays revealed that ATIC knockdown inhibited the proliferation, migration, and invasive abilities of UTUC cells. In contrast, miR-145-5p affected the proliferation, migration, and invasive abilities of UTUC cells by directly targeting the 3'-untranslated regions of ATIC. Furthermore, we used RNA sequencing and Ingenuity Pathway Analysis to identify possible downstream genes regulated by ATIC and found that miR-145-5p regulated the protein levels of fibronectin 1, Slug, cyclin A2, cyclin B1, P57, and interferon-induced transmembrane 1 via ATIC. ATIC may be a valuable predictor of prognosis and a potential therapeutic target for UTUC.
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Affiliation(s)
- Hao-Lun Luo
- Department of Urology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University and College of Medicine, Kaohsiung, Taiwan
- Center for Shockwave Medicine and Tissue Engineering, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yi-Chen Lee
- Department of Anatomy, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yin-Lun Chang
- Department of Urology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University and College of Medicine, Kaohsiung, Taiwan
| | - Wei-Chi Hsu
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yen-Ting Wu
- Department of Urology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University and College of Medicine, Kaohsiung, Taiwan
| | - Jhen-Hao Jhan
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Urology, Kaohsiung Municipal Siaogang Hospital, Kaohsiung, Taiwan
| | - Hui-Hui Lin
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yi-Ru Wu
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hung-Lung Ke
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Urology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
| | - Hui-Ying Liu
- Department of Urology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University and College of Medicine, Kaohsiung, Taiwan
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Jia T, Yuan F, Tao J, Wang G, Zhang X, Zhang B, Li H. CRISPR/Cas13d targeting GZMA in PARs pathway regulates the function of osteoclasts in chronic apical periodontitis. Cell Mol Biol Lett 2023; 28:70. [PMID: 37626297 PMCID: PMC10464397 DOI: 10.1186/s11658-023-00477-2] [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: 05/05/2023] [Accepted: 07/17/2023] [Indexed: 08/27/2023] Open
Abstract
Chronic apical periodontitis is a prevalent oral disease characterized by bone loss, and its underlying mechanisms remain unclear. This study aimed to investigate the role and mechanism of the serine protease GZMA in osteoclasts during chronic apical periodontitis. To address this, we employed crRNA/Cas13d to inhibit GZMA expression and examined its impact on osteoclast behavior. Our findings revealed that GZMA plays a significant role in promoting osteoclast cell proliferation while inhibiting cell apoptosis. Additionally, the inhibition of GZMA led to a notable increase in miR-25-3p expression, which, in turn, downregulated the expression of TGF-β. Consequently, the reduction in TGF-β expression led to a decrease in PAR1 expression within the PARs pathway. These results suggest that GZMA might serve as a promising therapeutic target for the treatment of chronic apical periodontitis. Furthermore, our study highlights the potential of targeting GZMA using crRNA/Cas13d as a valuable approach for future therapeutic interventions.
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Affiliation(s)
- Tingting Jia
- Department of Stomatology, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Fang Yuan
- Department of Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Jingqiao Tao
- Department of Stomatology, Southern Medical Branch of PLA General Hospital, Beijing, China
| | - Gang Wang
- Medical School of Chinese PLA, Beijing, China
| | - Xianhua Zhang
- Department of Stomatology, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Bin Zhang
- Department of Stomatology, The First Medical Centre, Chinese PLA General Hospital, Beijing, China.
| | - Hongbo Li
- Department of Stomatology, The First Medical Centre, Chinese PLA General Hospital, Beijing, China.
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40
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Johnson KC, Johnson ST, Liu J, Chu Y, Arana C, Han Y, Wang T, Corey DR. Consequences of depleting TNRC6, AGO, and DROSHA proteins on expression of microRNAs. RNA (NEW YORK, N.Y.) 2023; 29:1166-1184. [PMID: 37169394 PMCID: PMC10351893 DOI: 10.1261/rna.079647.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/21/2023] [Indexed: 05/13/2023]
Abstract
The potential for microRNAs (miRNAs) to regulate gene expression remains incompletely understood. DROSHA initiates the biogenesis of miRNAs while variants of Argonaute (AGO) and trinucleotide repeat containing six (TNRC6) family proteins form complexes with miRNAs to facilitate RNA recognition and gene regulation. Here we investigate the fate of miRNAs in the absence of these critical RNAi protein factors. Knockout of DROSHA expression reduces levels of some miRNAs annotated in miRBase but not others. The identity of miRNAs with reduced expression matches the identity of miRNAs previously identified by experimental approaches. The MirGeneDB resource offers the closest alignment with experimental results. In contrast, the loss of TNRC6 proteins had much smaller effects on miRNA levels. Knocking out AGO proteins, which directly contact the mature miRNA, decreased expression of the miRNAs most strongly associated with AGO2 as determined from enhanced crosslinking immunoprecipitation (AGO2-eCLIP). Evaluation of miRNA binding to endogenously expressed AGO proteins revealed that miRNA:AGO association was similar for AGO1, AGO2, AGO3, and AGO4. Our data emphasize the need to evaluate annotated miRNAs based on approximate cellular abundance, DROSHA-dependence, and physical association with AGO when forming hypotheses related to their function.
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Affiliation(s)
- Krystal C Johnson
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75205, USA
| | | | - Jing Liu
- Iris Medicine, Palo Alto, California 94304, USA
| | | | - Carlos Arana
- Genomics Core, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yi Han
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - David R Corey
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75205, USA
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41
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Bracken CP. "Crowd-control" by RNA: a pervasive theme in biology. RNA (NEW YORK, N.Y.) 2023; 29:885-888. [PMID: 37055151 DOI: 10.1261/rna.079644.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
As we continue to find new regulatory roles for RNAs, a theme is emerging in which regulation may not be mediated through the actions of a specific RNA, as one typically thinks of a regulator and target, but rather through the collective nature of many RNAs, each contributing a small degree of the regulatory load. This mechanism has been termed "crowd-control" and may apply broadly to miRNAs and to RNAs that bind and regulate protein activity. This provides an alternative way of thinking about how RNAs can act as biological regulators and has repercussions, both for the understanding of biological systems, and for the interpretation of results in which individual members of the "crowd" can replicate the effects of the crowd when overexpressed, but are not individually significant biological regulators.
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Affiliation(s)
- Cameron P Bracken
- Centre for Cancer Biology, an Alliance of SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
- Department of Medicine, University of Adelaide, Adelaide, SA 5005, Australia
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42
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Chen YH, Xu YC, Lin TT, Chen H, Dong RN, Cai FP, Ke ZB, Chen JY, Wei Y, Zheng QS, Xue XY, Xu N. Exosomal MiR-381 from M2-polarized macrophages attenuates urethral fibroblasts activation through YAP/GLS1-regulated glutaminolysis. Inflamm Res 2023:10.1007/s00011-023-01735-x. [PMID: 37340070 DOI: 10.1007/s00011-023-01735-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/01/2023] [Accepted: 04/13/2023] [Indexed: 06/22/2023] Open
Abstract
OBJECTIVE AND DESIGN Post-traumatic urethral stricture is a clinical challenge for both patients and clinicians. Targeting glutamine metabolism to suppress excessive activation of urethral fibroblasts (UFBs) is assumed to be a potent and attractive strategy for preventing urethral scarring and stricture. MATERIAL OR SUBJECTS In cellular experiments, we explored whether glutaminolysis meets the bioenergetic and biosynthetic demands of quiescent UFBs converted into myofibroblasts. At the same time, we examined the specific effects of M2-polarized macrophages on glutaminolysis and activation of UFBs, as well as the mechanism of intercellular signaling. In addition, findings were further verified in vivo in New Zealand rabbits. RESULTS It revealed that glutamine deprivation or knockdown of glutaminase 1 (GLS1) significantly inhibited UFB activation, proliferation, biosynthesis, and energy metabolism; however, these effects were rescued by cell-permeable dimethyl α-ketoglutarate. Moreover, we found that exosomal miR-381 derived from M2-polarized macrophages could be ingested by UFBs and inhibited GLS1-dependent glutaminolysis, thereby preventing excessive activation of UFBs. Mechanistically, miR-381 directly targets the 3'UTR of Yes-associated protein (YAP) mRNA to reduce its stability at the transcriptional level, ultimately downregulating expression of YAP, and GLS1. In vivo experiments revealed that treatment with either verteporfin or exosomes derived from M2-polarized macrophages significantly reduced urethral stricture in New Zealand rabbits after urethral trauma. CONCLUSION Collectively, this study demonstrates that exosomal miR-381 from M2-polarized macrophages reduces myofibroblast formation of UFBs and urethral scarring and stricture by inhibiting YAP/GLS1-dependent glutaminolysis.
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Affiliation(s)
- Ye-Hui Chen
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Yi-Cheng Xu
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Ting-Ting Lin
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Hang Chen
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Ru-Nan Dong
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Feng-Ping Cai
- Department of Ultrasonography, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Zhi-Bin Ke
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Jia-Yin Chen
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Yong Wei
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Qing-Shui Zheng
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Xue-Yi Xue
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China.
| | - Ning Xu
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China.
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43
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Liu Y, Zhang H, Fang Y, Tang D, Luo Z. Non-coding RNAs in renal cell carcinoma: Implications for drug resistance. Biomed Pharmacother 2023; 164:115001. [PMID: 37315433 DOI: 10.1016/j.biopha.2023.115001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/16/2023] Open
Abstract
Renal cell carcinoma (RCC) represents a malignant tumor of the urinary system. Individuals with early-stage RCC could be cured by surgical treatment, but a considerable number of cases of advanced RCC progress to drug resistance. Recently, numerous reports have demonstrated that a variety of non-coding RNAs (ncRNAs) contribute to tumor occurrence and development. ncRNAs can act as oncogenic or tumor suppressor genes to regulate proliferation, migration, drug resistance and other processes in RCC cells through a variety of signaling pathways. Considering the lack of treatment options for advanced RCC after drug resistance, ncRNAs may be a good choice as biomarkers of drug resistance in RCC and targets to overcome drug resistance. In this review, we discussed the effects of ncRNAs on drug resistance in RCC and the great potential of ncRNAs as a biomarker of or a new therapeutic method in RCC.
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Affiliation(s)
- Yiqi Liu
- Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China
| | - Hu Zhang
- The First Affiliated Hospital, Department of Urology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China
| | - Yuan Fang
- Organ Transplantation Center, The First Affiliated Hospital, Kunming Medical University, Kunming, Yunnan, 650032, PR China
| | - Dongshan Tang
- School of Resources & Environment and Safety Engineering, University of South China, Hengyang, Hunan 421001, PR China.
| | - Zhigang Luo
- The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China.
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44
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Knockdown of lncRNA FOXD1-AS1 promotes the radiosensitivity of lung squamous cell carcinoma cells by regulating the miR-4801/PUM1 axis. JOURNAL OF RADIATION RESEARCH AND APPLIED SCIENCES 2023. [DOI: 10.1016/j.jrras.2023.100548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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45
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Le MN, Nguyen TD, Nguyen TA. SRSF7 and SRSF3 depend on RNA sequencing motifs and secondary structures to regulate Microprocessor. Life Sci Alliance 2023; 6:e202201779. [PMID: 36750366 PMCID: PMC9905709 DOI: 10.26508/lsa.202201779] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
Human Microprocessor cleaves pri-miRNAs to initiate miRNA biogenesis. The accuracy and efficiency of Microprocessor cleavage ensure appropriate miRNA sequence and expression and thus its proper gene regulation. However, Microprocessor cleaves many pri-miRNAs incorrectly, so it requires assistance from many cofactors. For example, SRSF3 enhances Microprocessor cleavage by interacting with the CNNC motif in pri-miRNAs. However, whether SRSF3 can function with other motifs and/or requires the motifs in a certain secondary structure is unknown. In addition, the function of SRSF7 (a paralog of SRSF3) in miRNA biogenesis still needs to be discovered. Here, we demonstrated that SRSF7 could stimulate Microprocessor cleavage. In addition, by conducting high-throughput pri-miRNA cleavage assays for Microprocessor and SRSF7 or SRSF3, we demonstrated that SRSF7 and SRSF3 function with the CRC and CNNC motifs, adopting certain secondary structures. In addition, SRSF7 and SRSF3 affect the Microprocessor cleavage sites in human cells. Our findings demonstrate the roles of SRSF7 in miRNA biogenesis and provide a comprehensive view of the molecular mechanism of SRSF7 and SRSF3 in enhancing Microprocessor cleavage.
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Affiliation(s)
- Minh Ngoc Le
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Trung Duc Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Tuan Anh Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
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46
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Johnson KC, Corey DR. RNAi in cell nuclei: potential for a new layer of biological regulation and a new strategy for therapeutic discovery. RNA (NEW YORK, N.Y.) 2023; 29:415-422. [PMID: 36657971 PMCID: PMC10019369 DOI: 10.1261/rna.079500.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
RNA interference is almost always associated with post-transcriptional silencing in the cytoplasm. MicroRNAs (miRNAs) and critical RNAi protein factors like argonaute (AGO) and trinucleotide repeat binding containing 6 protein (TNRC6), however, are also found in cell nuclei, suggesting that nuclear miRNAs may be targets for gene regulation. Designed small duplex RNAs (dsRNAs) can modulate nuclear processes such as transcription and splicing, suggesting that they can also provide leads for therapeutic discovery. The goal of this Perspective is to provide the background on nuclear RNAi necessary to guide discussions on whether nuclear RNAi can play a role in therapeutic development programs.
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Affiliation(s)
- Krystal C Johnson
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - David R Corey
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
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47
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Chen LY, Kao TW, Chen CC, Niaz N, Lee HL, Chen YH, Kuo CC, Shen YA. Frontier Review of the Molecular Mechanisms and Current Approaches of Stem Cell-Derived Exosomes. Cells 2023; 12:cells12071018. [PMID: 37048091 PMCID: PMC10093591 DOI: 10.3390/cells12071018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Exosomes are effective therapeutic vehicles that may transport their substances across cells. They are shown to possess the capacity to affect cell proliferation, migration, anti-apoptosis, anti-scarring, and angiogenesis, via the action of transporting molecular components. Possessing immense potential in regenerative medicine, exosomes, especially stem cell-derived exosomes, have the advantages of low immunogenicity, minimal invasiveness, and broad clinical applicability. Exosome biodistribution and pharmacokinetics may be altered, in response to recent advancements in technology, for the purpose of treating particular illnesses. Yet, prior to clinical application, it is crucial to ascertain the ideal dose and any potential negative consequences of an exosome. This review focuses on the therapeutic potential of stem cell-derived exosomes and further illustrates the molecular mechanisms that underpin their potential in musculoskeletal regeneration, wound healing, female infertility, cardiac recovery, immunomodulation, neurological disease, and metabolic regulation. In addition, we provide a summary of the currently effective techniques for isolating exosomes, and describe the innovations in biomaterials that improve the efficacy of exosome-based treatments. Overall, this paper provides an updated overview of the biological factors found in stem cell-derived exosomes, as well as potential targets for future cell-free therapeutic applications.
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48
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Banijamali E, Baronti L, Becker W, Sajkowska-Kozielewicz JJ, Huang T, Palka C, Kosek D, Sweetapple L, Müller J, Stone MD, Andersson ER, Petzold K. RNA:RNA interaction in ternary complexes resolved by chemical probing. RNA (NEW YORK, N.Y.) 2023; 29:317-329. [PMID: 36617673 PMCID: PMC9945442 DOI: 10.1261/rna.079190.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
RNA regulation can be performed by a second targeting RNA molecule, such as in the microRNA regulation mechanism. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) probes the structure of RNA molecules and can resolve RNA:protein interactions, but RNA:RNA interactions have not yet been addressed with this technique. Here, we apply SHAPE to investigate RNA-mediated binding processes in RNA:RNA and RNA:RNA-RBP complexes. We use RNA:RNA binding by SHAPE (RABS) to investigate microRNA-34a (miR-34a) binding its mRNA target, the silent information regulator 1 (mSIRT1), both with and without the Argonaute protein, constituting the RNA-induced silencing complex (RISC). We show that the seed of the mRNA target must be bound to the microRNA loaded into RISC to enable further binding of the compensatory region by RISC, while the naked miR-34a is able to bind the compensatory region without seed interaction. The method presented here provides complementary structural evidence for the commonly performed luciferase-assay-based evaluation of microRNA binding-site efficiency and specificity on the mRNA target site and could therefore be used in conjunction with it. The method can be applied to any nucleic acid-mediated RNA- or RBP-binding process, such as splicing, antisense RNA binding, or regulation by RISC, providing important insight into the targeted RNA structure.
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Affiliation(s)
- Elnaz Banijamali
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Lorenzo Baronti
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Walter Becker
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | | | - Ting Huang
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Christina Palka
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | - David Kosek
- Department of Cell and Molecular Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Lara Sweetapple
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Juliane Müller
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | - Emma R Andersson
- Department of Cell and Molecular Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa
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49
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The Role of MicroRNAs in Pancreatitis Development and Progression. Int J Mol Sci 2023; 24:ijms24021057. [PMID: 36674571 PMCID: PMC9862468 DOI: 10.3390/ijms24021057] [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: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Pancreatitis (acute and chronic) is an inflammatory disease associated with significant morbidity, including a high rate of hospitalization and mortality. MicroRNAs (miRs) are essential post-transcriptional modulators of gene expression. They are crucial in many diseases' development and progression. Recent studies have demonstrated aberrant miRs expression patterns in pancreatic tissues obtained from patients experiencing acute and chronic pancreatitis compared to tissues from unaffected individuals. Increasing evidence showed that miRs regulate multiple aspects of pancreatic acinar biology, such as autophagy, mitophagy, and migration, impact local and systemic inflammation and, thus, are involved in the disease development and progression. Notably, multiple miRs act on pancreatic acinar cells and regulate the transduction of signals between pancreatic acinar cells, pancreatic stellate cells, and immune cells, and provide a complex interaction network between these cells. Importantly, recent studies from various animal models and patients' data combined with advanced detection techniques support their importance in diagnosing and treating pancreatitis. In this review, we plan to provide an up-to-date summary of the role of miRs in the development and progression of pancreatitis.
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50
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Samad AFA, Kamaroddin MF. Innovative approaches in transforming microRNAs into therapeutic tools. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1768. [PMID: 36437633 DOI: 10.1002/wrna.1768] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/06/2022] [Accepted: 11/08/2022] [Indexed: 11/29/2022]
Abstract
MicroRNA (miRNA) is regarded as a prominent genetic regulator, as it can fine-tune an entire biological pathway by targeting multiple target genes. This characteristic makes miRNAs promising therapeutic tools to reinstate cell functions that are disrupted as a consequence of diseases. Currently, miRNA replacement by miRNA mimics and miRNA inhibition by anti-miRNA oligonucleotides are the main approaches to utilizing miRNA molecules for therapeutic purposes. Nevertheless, miRNA-based therapeutics are hampered by major issues such as off-target effects, immunogenicity, and uncertain delivery platforms. Over the past few decades, several innovative approaches have been established to minimize off-target effects, reduce immunostimulation, and provide efficient transfer to the target cells in which these molecules exert their function. Recent achievements have led to the testing of miRNA-based drugs in clinical trials, and these molecules may become next-generation therapeutics for medical intervention. Despite the achievement of exciting milestones, the dosage of miRNA administration remains unclear, and ways to address this issue are proposed. Elucidating the current status of the main factors of therapeutic miRNA would allow further developments and innovations to achieve safe therapeutic tools. This article is categorized under: RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action.
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Affiliation(s)
- Abdul Fatah A Samad
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Mohd Farizal Kamaroddin
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
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