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Sarapata K, Kania A. Revealing miRNAs patterns by employing matrix representations and energy analysis. J Mol Graph Model 2024; 132:108835. [PMID: 39106629 DOI: 10.1016/j.jmgm.2024.108835] [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: 06/24/2023] [Revised: 07/16/2024] [Accepted: 07/29/2024] [Indexed: 08/09/2024]
Abstract
MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression. Despite their relatively short length (about 21 nucleotides), they can regulate thousands of transcripts within a cell. Due to their low complementarity to targets, studying their activity and binding region preferences (3'UTR, 5'UTR, or CDS) is challenging. In this paper, we analyzed a set of human miRNAs to uncover their general patterns. We began with a sequence logo to verify conservation at specific positions. To discover long-range correlations, we employed chaos game representation (CGR) and genomatrix, methods that enable both graphical and analytical analysis of sequence sets and are well-established in bioinformatics. Our results showed that miRNAs exhibit strongly non-random and characteristic patterns. To incorporate physicochemical properties into the analysis, we applied the electron-ion interaction potential (EIIP) parameter. An important part of our study was to validate the division of miRNAs into two parts-seed and puzzle. The seed region is responsible for target binding, while the puzzle region likely interacts with the RISC complex. We estimated duplex binding energy within the 3'UTR, 5'UTR, and CDS regions using the miRanda tool. Based on the median energy distribution, we divided the miRNAs into two subsets, reflecting different patterns in chaos game representation. Interestingly, one subset displayed significant similarity to conserved and highly confidential miRNAs. Our results confirm the low complementarity of miRNA/mRNA interactions and support the functional division of miRNA structure. Additionally, we present findings related to the localization of transcript target sites, which form the basis for further analyses.
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Affiliation(s)
- Krzysztof Sarapata
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
| | - Adrian Kania
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland.
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2
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Zhang J, Liu L, Wei X, Zhao C, Luo Y, Li J, Le TD. Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data. BMC Biol 2024; 22:218. [PMID: 39334271 PMCID: PMC11438147 DOI: 10.1186/s12915-024-02020-x] [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: 01/15/2024] [Accepted: 09/24/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND RNA-sequencing technology provides an effective tool for understanding miRNA regulation in complex human diseases, including cancers. A large number of computational methods have been developed to make use of bulk and single-cell RNA-sequencing data to identify miRNA regulations at the resolution of multiple samples (i.e. group of cells or tissues). However, due to the heterogeneity of individual samples, there is a strong need to infer miRNA regulation specific to individual samples to uncover miRNA regulation at the single-sample resolution level. RESULTS Here, we develop a framework, Scan, for scanning sample-specific miRNA regulation. Since a single network inference method or strategy cannot perform well for all types of new data, Scan incorporates 27 network inference methods and two strategies to infer tissue-specific or cell-specific miRNA regulation from bulk or single-cell RNA-sequencing data. Results on bulk and single-cell RNA-sequencing data demonstrate the effectiveness of Scan in inferring sample-specific miRNA regulation. Moreover, we have found that incorporating the prior information of miRNA targets can generally improve the accuracy of miRNA target prediction. In addition, Scan can contribute to construct cell/tissue correlation networks and recover aggregate miRNA regulatory networks. Finally, the comparison results have shown that the performance of network inference methods is likely to be data-specific, and selecting optimal network inference methods is required for more accurate prediction of miRNA targets. CONCLUSIONS Scan provides a useful method to help infer sample-specific miRNA regulation for new data, benchmark new network inference methods and deepen the understanding of miRNA regulation at the resolution of individual samples.
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Affiliation(s)
- Junpeng Zhang
- School of Engineering, Dali University, Dali, 671003, Yunnan, China.
| | - Lin Liu
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Xuemei Wei
- School of Engineering, Dali University, Dali, 671003, Yunnan, China
| | - Chunwen Zhao
- School of Engineering, Dali University, Dali, 671003, Yunnan, China
| | - Yanbi Luo
- School of Engineering, Dali University, Dali, 671003, Yunnan, China
| | - Jiuyong Li
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Thuc Duy Le
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia.
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3
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Bereczki Z, Benczik B, Balogh OM, Marton S, Puhl E, Pétervári M, Váczy-Földi M, Papp ZT, Makkos A, Glass K, Locquet F, Euler G, Schulz R, Ferdinandy P, Ágg B. Mitigating off-target effects of small RNAs: conventional approaches, network theory and artificial intelligence. Br J Pharmacol 2024. [PMID: 39293936 DOI: 10.1111/bph.17302] [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: 11/30/2023] [Revised: 05/07/2024] [Accepted: 06/17/2024] [Indexed: 09/20/2024] Open
Abstract
Three types of highly promising small RNA therapeutics, namely, small interfering RNAs (siRNAs), microRNAs (miRNAs) and the RNA subtype of antisense oligonucleotides (ASOs), offer advantages over small-molecule drugs. These small RNAs can target any gene product, opening up new avenues of effective and safe therapeutic approaches for a wide range of diseases. In preclinical research, synthetic small RNAs play an essential role in the investigation of physiological and pathological pathways as silencers of specific genes, facilitating discovery and validation of drug targets in different conditions. Off-target effects of small RNAs, however, could make it difficult to interpret experimental results in the preclinical phase and may contribute to adverse events of small RNA therapeutics. Out of the two major types of off-target effects we focused on the hybridization-dependent, especially on the miRNA-like off-target effects. Our main aim was to discuss several approaches, including sequence design, chemical modifications and target prediction, to reduce hybridization-dependent off-target effects that should be considered even at the early development phase of small RNA therapy. Because there is no standard way of predicting hybridization-dependent off-target effects, this review provides an overview of all major state-of-the-art computational methods and proposes new approaches, such as the possible inclusion of network theory and artificial intelligence (AI) in the prediction workflows. Case studies and a concise survey of experimental methods for validating in silico predictions are also presented. These methods could contribute to interpret experimental results, to minimize off-target effects and hopefully to avoid off-target-related adverse events of small RNA therapeutics.
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Affiliation(s)
- Zoltán Bereczki
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
| | - Bettina Benczik
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Olivér M Balogh
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
| | - Szandra Marton
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
| | - Eszter Puhl
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
| | - Mátyás Pétervári
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Sanovigado Kft, Budapest, Hungary
| | - Máté Váczy-Földi
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
| | - Zsolt Tamás Papp
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
| | - András Makkos
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Kimberly Glass
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Fabian Locquet
- Physiologisches Institut, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Gerhild Euler
- Physiologisches Institut, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Rainer Schulz
- Physiologisches Institut, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Bence Ágg
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
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Tang L, Qiu H, Xu B, Su Y, Nyarige V, Li P, Chen H, Killham B, Liao J, Adam H, Yang A, Yu A, Jang M, Rubart M, Xie J, Zhu W. Microparticle Mediated Delivery of Apelin Improves Heart Function in Post Myocardial Infarction Mice. Circ Res 2024; 135:777-798. [PMID: 39145385 PMCID: PMC11392624 DOI: 10.1161/circresaha.124.324608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 07/31/2024] [Accepted: 08/06/2024] [Indexed: 08/16/2024]
Abstract
BACKGROUND Apelin is an endogenous prepropeptide that regulates cardiac homeostasis and various physiological processes. Intravenous injection has been shown to improve cardiac contractility in patients with heart failure. However, its short half-life prevents studying its impact on left ventricular remodeling in the long term. Here, we aim to study whether microparticle-mediated slow release of apelin improves heart function and left ventricular remodeling in mice with myocardial infarction (MI). METHODS A cardiac patch was fabricated by embedding apelin-containing microparticles in a fibrin gel scaffold. MI was induced via permanent ligation of the left anterior descending coronary artery in adult C57BL/6J mice followed by epicardial patch placement immediately after (acute MI) or 28 days (chronic MI) post-MI. Four groups were included in this study, namely sham, MI, MI plus empty microparticle-embedded patch treatment, and MI plus apelin-containing microparticle-embedded patch treatment. Cardiac function was assessed by transthoracic echocardiography. Cardiomyocyte morphology, apoptosis, and cardiac fibrosis were evaluated by histology. Cardioprotective pathways were determined by RNA sequencing, quantitative polymerase chain reaction, and Western blot. RESULTS The level of endogenous apelin was largely reduced in the first 7 days after MI induction and it was normalized by day 28. Apelin-13 encapsulated in poly(lactic-co-glycolic acid) microparticles displayed a sustained release pattern for up to 28 days. Treatment with apelin-containing microparticle-embedded patch inhibited cardiac hypertrophy and reduced scar size in both acute and chronic MI models, which is associated with improved cardiac function. Data from cellular and molecular analyses showed that apelin inhibits the activation and proliferation of cardiac fibroblasts by preventing transforming growth factor-β-mediated activation of Smad2/3 (supporessor of mothers against decapentaplegic 2/3) and downstream profibrotic gene expression. CONCLUSIONS Poly(lactic-co-glycolic acid) microparticles prolonged the apelin release time in the mouse hearts. Epicardial delivery of the apelin-containing microparticle-embedded patch protects mice from both acute and chronic MI-induced cardiac dysfunction, inhibits cardiac fibrosis, and improves left ventricular remodeling.
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Affiliation(s)
- Ling Tang
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center for Regenerative Medicine, Mayo Clinic Arizona, Scottsdale (L.T., H.Q., B.X., V.N., P.L., H.A., A. Yang, A. Yu, M.J., W.Z.)
| | - Huiliang Qiu
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center for Regenerative Medicine, Mayo Clinic Arizona, Scottsdale (L.T., H.Q., B.X., V.N., P.L., H.A., A. Yang, A. Yu, M.J., W.Z.)
| | - Bing Xu
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center for Regenerative Medicine, Mayo Clinic Arizona, Scottsdale (L.T., H.Q., B.X., V.N., P.L., H.A., A. Yang, A. Yu, M.J., W.Z.)
| | - Yajuan Su
- Department of Surgery-Transplant and Mary and Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha (Y.S., J.X.)
| | - Verah Nyarige
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center for Regenerative Medicine, Mayo Clinic Arizona, Scottsdale (L.T., H.Q., B.X., V.N., P.L., H.A., A. Yang, A. Yu, M.J., W.Z.)
| | - Pengsheng Li
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center for Regenerative Medicine, Mayo Clinic Arizona, Scottsdale (L.T., H.Q., B.X., V.N., P.L., H.A., A. Yang, A. Yu, M.J., W.Z.)
| | - Houjia Chen
- Department of Bioengineering, University of Texas at Arlington (H.C., B.K., J.L.)
| | - Brady Killham
- Department of Bioengineering, University of Texas at Arlington (H.C., B.K., J.L.)
| | - Jun Liao
- Department of Bioengineering, University of Texas at Arlington (H.C., B.K., J.L.)
| | - Henderson Adam
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center for Regenerative Medicine, Mayo Clinic Arizona, Scottsdale (L.T., H.Q., B.X., V.N., P.L., H.A., A. Yang, A. Yu, M.J., W.Z.)
| | - Aaron Yang
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center for Regenerative Medicine, Mayo Clinic Arizona, Scottsdale (L.T., H.Q., B.X., V.N., P.L., H.A., A. Yang, A. Yu, M.J., W.Z.)
| | - Alexander Yu
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center for Regenerative Medicine, Mayo Clinic Arizona, Scottsdale (L.T., H.Q., B.X., V.N., P.L., H.A., A. Yang, A. Yu, M.J., W.Z.)
| | - Michelle Jang
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center for Regenerative Medicine, Mayo Clinic Arizona, Scottsdale (L.T., H.Q., B.X., V.N., P.L., H.A., A. Yang, A. Yu, M.J., W.Z.)
| | - Michael Rubart
- Department of Pediatrics, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis (M.R.)
| | - Jingwei Xie
- Department of Surgery-Transplant and Mary and Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha (Y.S., J.X.)
| | - Wuqiang Zhu
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center for Regenerative Medicine, Mayo Clinic Arizona, Scottsdale (L.T., H.Q., B.X., V.N., P.L., H.A., A. Yang, A. Yu, M.J., W.Z.)
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Jusic A, Erpapazoglou Z, Dalgaard LT, Lakkisto P, de Gonzalo-Calvo D, Benczik B, Ágg B, Ferdinandy P, Fiedorowicz K, Schroen B, Lazou A, Devaux Y. Guidelines for mitochondrial RNA analysis. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102262. [PMID: 39091381 PMCID: PMC11292373 DOI: 10.1016/j.omtn.2024.102262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Mitochondria are the energy-producing organelles of mammalian cells with critical involvement in metabolism and signaling. Studying their regulation in pathological conditions may lead to the discovery of novel drugs to treat, for instance, cardiovascular or neurological diseases, which affect high-energy-consuming cells such as cardiomyocytes, hepatocytes, or neurons. Mitochondria possess both protein-coding and noncoding RNAs, such as microRNAs, long noncoding RNAs, circular RNAs, and piwi-interacting RNAs, encoded by the mitochondria or the nuclear genome. Mitochondrial RNAs are involved in anterograde-retrograde communication between the nucleus and mitochondria and play an important role in physiological and pathological conditions. Despite accumulating evidence on the presence and biogenesis of mitochondrial RNAs, their study continues to pose significant challenges. Currently, there are no standardized protocols and guidelines to conduct deep functional characterization and expression profiling of mitochondrial RNAs. To overcome major obstacles in this emerging field, the EU-CardioRNA and AtheroNET COST Action networks summarize currently available techniques and emphasize critical points that may constitute sources of variability and explain discrepancies between published results. Standardized methods and adherence to guidelines to quantify and study mitochondrial RNAs in normal and disease states will improve research outputs, their reproducibility, and translation potential to clinical application.
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Affiliation(s)
- Amela Jusic
- HAYA Therapeutics SA, Route De La Corniche 6, SuperLab Suisse - Batiment Serine, 1066 Epalinges, Switzerland
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
| | - Zoi Erpapazoglou
- Ιnstitute for Fundamental Biomedical Research, B.S.R.C. “Alexander Fleming”, Vari, 16672 Athens, Greece
| | - Louise Torp Dalgaard
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Päivi Lakkisto
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Bettina Benczik
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | - Bence Ágg
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | - Péter Ferdinandy
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | | | - Blanche Schroen
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, ER 6229 Maastricht, the Netherlands
| | - Antigone Lazou
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
| | - on behalf of EU-CardioRNA COST Action CA17129
- HAYA Therapeutics SA, Route De La Corniche 6, SuperLab Suisse - Batiment Serine, 1066 Epalinges, Switzerland
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
- Ιnstitute for Fundamental Biomedical Research, B.S.R.C. “Alexander Fleming”, Vari, 16672 Athens, Greece
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
- NanoBioMedical Centre, Adam Mickiewicz University in Poznan, 61614 Poznan, Poland
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, ER 6229 Maastricht, the Netherlands
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - AtheroNET COST Action CA21153
- HAYA Therapeutics SA, Route De La Corniche 6, SuperLab Suisse - Batiment Serine, 1066 Epalinges, Switzerland
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
- Ιnstitute for Fundamental Biomedical Research, B.S.R.C. “Alexander Fleming”, Vari, 16672 Athens, Greece
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
- NanoBioMedical Centre, Adam Mickiewicz University in Poznan, 61614 Poznan, Poland
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, ER 6229 Maastricht, the Netherlands
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Sharma A, Vikramdeo KS, Sudan SK, Anand S, Deshmukh SK, Singh AP, Singh S. Cortisol affects macrophage polarization by inducing miR-143/145 cluster to reprogram glucose metabolism and by promoting TCA cycle anaplerosis. J Biol Chem 2024; 300:107753. [PMID: 39260692 DOI: 10.1016/j.jbc.2024.107753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/22/2024] [Accepted: 08/29/2024] [Indexed: 09/13/2024] Open
Abstract
Chronic stress can have adverse consequences on human health by disrupting the hormonal balance in our body. Earlier, we observed elevated levels of cortisol, a primary stress hormone, and some exosomal microRNAs in the serum of patients with breast cancer. Here, we investigated the role of cortisol in microRNA induction and its functional consequences. We found that cortisol induced the expression of miR-143/145 cluster in human monocyte (THP1 and U937)-derived macrophages but not in breast cancer cells. In silico analysis identified glucocorticoid-response element in the upstream CARMN promoter utilized by the miR-143/145 cluster. Enhanced binding of glucocorticoid-receptor (GR) upon cortisol exposure and its regulatory significance was confirmed by chromatin-immunoprecipitation and promoter-reporter assays. Further, cortisol inhibited IFNγ-induced M1 polarization and promoted M2 polarization, and these effects were suppressed by miR-143-3p and miR-145-5p inhibitors pretreatment. Cortisol-treated macrophages exhibited increased oxygen-consumption rate (OCR) to extracellular-acidification rate (ECAR) ratio, and this change was neutralized by functional inhibition of miR-143-3p and miR-145-5p. HK2 and ADPGK were confirmed as the direct targets of miR-143-3p and miR-145-5p, respectively. Interestingly, silencing of HK2 and ADPGK inhibited IFNγ-induced M1 polarization but failed to induce M2 polarization, since it suppressed both ECAR and OCR, while OCR was largely sustained in cortisol-treated M2-polarized macrophages. We found that cortisol treatment sustained OCR by enhancing fatty acid and glutamine metabolism through upregulation of CPT2 and GLS, respectively, to support M2 polarization. Thus, our findings unfold a novel mechanism of immune suppression by cortisol and open avenues for preventive and therapeutic interventions.
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Affiliation(s)
- Amod Sharma
- Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, Mississippi, USA; Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Kunwar Somesh Vikramdeo
- Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, Mississippi, USA; Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Sarabjeet Kour Sudan
- Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, Mississippi, USA; Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Shashi Anand
- Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, Mississippi, USA; Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Sachin Kumar Deshmukh
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA; Department of Pathology, University of South Alabama, Mobile, Alabama, USA
| | - Ajay Pratap Singh
- Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, Mississippi, USA; Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Seema Singh
- Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, Mississippi, USA; Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA.
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7
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Ren Y, Wu C, Zhou H, Hu X, Miao Z. Dual-extraction modeling: A multi-modal deep-learning architecture for phenotypic prediction and functional gene mining of complex traits. PLANT COMMUNICATIONS 2024; 5:101002. [PMID: 38872306 DOI: 10.1016/j.xplc.2024.101002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/27/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024]
Abstract
Despite considerable advances in extracting crucial insights from bio-omics data to unravel the intricate mechanisms underlying complex traits, the absence of a universal multi-modal computational tool with robust interpretability for accurate phenotype prediction and identification of trait-associated genes remains a challenge. This study introduces the dual-extraction modeling (DEM) approach, a multi-modal deep-learning architecture designed to extract representative features from heterogeneous omics datasets, enabling the prediction of complex trait phenotypes. Through comprehensive benchmarking experiments, we demonstrate the efficacy of DEM in classification and regression prediction of complex traits. DEM consistently exhibits superior accuracy, robustness, generalizability, and flexibility. Notably, we establish its effectiveness in predicting pleiotropic genes that influence both flowering time and rosette leaf number, underscoring its commendable interpretability. In addition, we have developed user-friendly software to facilitate seamless utilization of DEM's functions. In summary, this study presents a state-of-the-art approach with the ability to effectively predict qualitative and quantitative traits and identify functional genes, confirming its potential as a valuable tool for exploring the genetic basis of complex traits.
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Affiliation(s)
- Yanlin Ren
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chenhua Wu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - He Zhou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaona Hu
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Zhenyan Miao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China.
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8
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Rodrigues P, Rizaev JA, Hjazi A, Altalbawy FMA, H M, Sharma K, Sharma SK, Mustafa YF, Jawad MA, Zwamel AH. Dual role of microRNA-31 in human cancers; focusing on cancer pathogenesis and signaling pathways. Exp Cell Res 2024; 442:114236. [PMID: 39245198 DOI: 10.1016/j.yexcr.2024.114236] [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: 08/16/2024] [Accepted: 09/04/2024] [Indexed: 09/10/2024]
Abstract
Widespread changes in the expression of microRNAs in cancer result in abnormal gene expression for the miRNAs that control those genes, which in turn causes changes to entire molecular networks and pathways. The frequently altered miR-31, which is found in a wide range of cancers, is one cancer-related miRNA that is particularly intriguing. MiR-31 has a very complicated set of biological functions, and depending on the type of tumor, it may act both as a tumor suppressor and an oncogene. The endogenous expression levels of miR-31 appear to be a key determinant of the phenotype brought on by aberrant expression. Varied expression levels of miR-31 could affect cell growth, metastasis, drug resistance, and other process by several mechanisms like targeting BRCA1-associated protein-1 (BAP1), large tumor suppressor kinase 1 (LATS1) and protein phosphatase 2 (PP2A). This review highlights the current understanding of the genes that miR-31 targets while summarizing the complex expression patterns of miR-31 in human cancers and the diverse phenotypes brought on by altered miR-31 expression.
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Affiliation(s)
- Paul Rodrigues
- Department of Computer Engineering, College of Computer Science, King Khalid University, Al-Faraa, Saudi Arabia.
| | - Jasur Alimdjanovich Rizaev
- Department of Public Health and Healthcare Management, Rector, Samarkand State Medical University, 18, Amir Temur Street, Samarkand, Uzbekistan.
| | - Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia.
| | - Farag M A Altalbawy
- Department of Chemistry, University College of Duba, University of Tabuk, Tabuk, Saudi Arabia.
| | - Malathi H
- Department of Biotechnology and Genetics, School of Sciences, JAIN (Deemed to Be University), Bangalore, Karnataka, India.
| | - Kirti Sharma
- Chandigarh Pharmacy College, Chandigarh Group of Colleges, Jhanjheri, Mohali, 140307, Punjab, India.
| | - Satish Kumar Sharma
- Vice Chancellor of Department of Pharmacy (Pharmacology), The Glocal University, Saharanpur, India.
| | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul, 41001, Iraq.
| | | | - Ahmed Hussein Zwamel
- Medical Laboratory Technique College, The Islamic University, Najaf, Iraq; Medical Laboratory Technique College, The Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq; Medical Laboratory Technique College, The Islamic University of Babylon, Babylon, Iraq.
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9
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Haas R, Frame G, Khan S, Neilsen BK, Hong BH, Yeo CPX, Yamaguchi TN, Ong EHW, Zhao W, Carlin B, Yeo ELL, Tan KM, Bugh YZ, Zhu C, Hugh-White R, Livingstone J, Poon DJJ, Chu PL, Patel Y, Tao S, Ignatchenko V, Kurganovs NJ, Higgins GS, Downes MR, Loblaw A, Vesprini D, Kishan AU, Chua MLK, Kislinger T, Boutros PC, Liu SK. The Proteogenomics of Prostate Cancer Radioresistance. CANCER RESEARCH COMMUNICATIONS 2024; 4:2463-2479. [PMID: 39166898 PMCID: PMC11411600 DOI: 10.1158/2767-9764.crc-24-0292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 07/23/2024] [Accepted: 08/15/2024] [Indexed: 08/23/2024]
Abstract
Prostate cancer is frequently treated with radiotherapy. Unfortunately, aggressive radioresistant relapses can arise, and the molecular underpinnings of radioresistance are unknown. Modern clinical radiotherapy is evolving to deliver higher doses of radiation in fewer fractions (hypofractionation). We therefore analyzed genomic, transcriptomic, and proteomic data to characterize prostate cancer radioresistance in cells treated with both conventionally fractionated and hypofractionated radiotherapy. Independent of fractionation schedule, resistance to radiotherapy involved massive genomic instability and abrogation of DNA mismatch repair. Specific prostate cancer driver genes were modulated at the RNA and protein levels, with distinct protein subcellular responses to radiotherapy. Conventional fractionation led to a far more aggressive biomolecular response than hypofractionation. Testing preclinical candidates identified in cell lines, we revealed POLQ (DNA Polymerase Theta) as a radiosensitizer. POLQ-modulated radioresistance in model systems and was predictive of it in large patient cohorts. The molecular response to radiation is highly multimodal and sheds light on prostate cancer lethality. SIGNIFICANCE Radiation is standard of care in prostate cancer. Yet, we have little understanding of its failure. We demonstrate a new paradigm that radioresistance is fractionation specific and identified POLQ as a radioresistance modulator.
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Affiliation(s)
- Roni Haas
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Gavin Frame
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Beth K Neilsen
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, California
| | - Boon Hao Hong
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Celestia P X Yeo
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Takafumi N Yamaguchi
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Enya H W Ong
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Wenyan Zhao
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Benjamin Carlin
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Eugenia L L Yeo
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Kah Min Tan
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Yuan Zhe Bugh
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Chenghao Zhu
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Rupert Hugh-White
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Julie Livingstone
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Dennis J J Poon
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Pek Lim Chu
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Yash Patel
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Shu Tao
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | | | | | - Geoff S Higgins
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Michelle R Downes
- Division of Anatomic Pathology, Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Andrew Loblaw
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Canada
| | - Danny Vesprini
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Canada
| | - Amar U Kishan
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, California
| | - Melvin L K Chua
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Stanley K Liu
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Canada
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10
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Naik D, Kalle AM. MicroRNA-mediated epigenetic regulation of HDAC8 and HDAC6: Functional significance in cervical cancer. Noncoding RNA Res 2024; 9:732-743. [PMID: 38577018 PMCID: PMC10990743 DOI: 10.1016/j.ncrna.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/25/2024] [Accepted: 02/17/2024] [Indexed: 04/06/2024] Open
Abstract
Cervical cancer, a leading global cause of female mortality, exhibits diverse molecular aberrations influencing gene expression and signaling pathways. Epigenetic factors, including histone deacetylases (HDACs) such as HDAC8 and HDAC6, along with microRNAs (miRNAs), play pivotal roles in cervical cancer progression. Recent investigations have unveiled miRNAs as potential regulators of HDACs, offering a promising therapeutic avenue. This study employed in-silico miRNA prediction, qRT-PCR co-expression studies, and Dual-Luciferase reporter assays to identify miRNAs governing HDAC8 and HDAC6 in HeLa, cervical cancer cells. Results pinpointed miR-497-3p and miR-324-3p as novel negative regulators of HDAC8 and HDAC6, respectively. Functional assays demonstrated that miR-497-3p overexpression in HeLa cells suppressed HDAC8, leading to increased acetylation of downstream targets p53 and α-tubulin. Similarly, miR-324-3p overexpression inhibited HDAC6 mRNA and protein expression, enhancing acetylation of Hsp90 and α-tubulin. Notably, inhibiting HDAC8 via miRNA overexpression correlated with reduced cell viability, diminished epithelial-to-mesenchymal transition (EMT), and increased microtubule bundle formation in HeLa cells. In conclusion, miR-497-3p and miR-324-3p emerge as novel negative regulators of HDAC8 and HDAC6, respectively, with potential therapeutic implications. Elevated expression of these miRNAs in cervical cancer cells holds promise for inhibiting metastasis, offering a targeted approach for intervention in cervical malignancy.
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Affiliation(s)
- Debasmita Naik
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana State, 500046, India
| | - Arunasree M. Kalle
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana State, 500046, India
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11
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Agrawal M, Mani A. Integrative in silico approaches to analyse microRNA-mediated responses in human diseases. J Gene Med 2024; 26:e3734. [PMID: 39197943 DOI: 10.1002/jgm.3734] [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: 04/24/2024] [Revised: 07/23/2024] [Accepted: 08/13/2024] [Indexed: 09/01/2024] Open
Abstract
Advancements in sequencing technologies have facilitated omics level information generation for various diseases in human. High-throughput technologies have become a powerful tool to understand differential expression studies and transcriptional network analysis. An understanding of complex transcriptional networks in human diseases requires integration of datasets representing different RNA species including microRNA (miRNA) and messenger RNA (mRNA). This review emphasises on conceptual explanation of generalized workflow and methodologies to the miRNA mediated responses in human diseases by using different in silico analysis. Although, there have been many prior explorations in miRNA-mediated responses in human diseases, the advantages, limitations and overcoming the limitation through different statistical techniques have not yet been discussed. This review focuses on miRNAs as important gene regulators in human diseases, methodologies for miRNA-target gene prediction and data driven methods for enrichment and network analysis for miRnome-targetome interactions. Additionally, it proposes an integrative workflow to analyse structural components of networks obtained from high-throughput data. This review explains how to apply the existing methods to analyse miRNA-mediated responses in human diseases. It addresses unique characteristics of different analysis, its limitations and its statistical solutions influencing the choice of methods for the analysis through a workflow. Moreover, it provides an overview of promising common integrative approaches to comprehend miRNA-mediated gene regulatory events in biological processes in humans. The proposed methodologies and workflow shall help in the analysis of multi-source data to identify molecular signatures of various human diseases.
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Affiliation(s)
- Meghna Agrawal
- Department of Biotechnology, Motilal Nehru Institute of Technology Allahabad, Prayagraj, India
| | - Ashutosh Mani
- Department of Biotechnology, Motilal Nehru Institute of Technology Allahabad, Prayagraj, India
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12
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Wang Y, Zhang J, Yang Y, Liu Z, Sun S, Li R, Zhu H, Li T, Zheng J, Li J, Ma L. Circular RNAs in human diseases. MedComm (Beijing) 2024; 5:e699. [PMID: 39239069 PMCID: PMC11374765 DOI: 10.1002/mco2.699] [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: 06/20/2023] [Revised: 07/25/2024] [Accepted: 07/30/2024] [Indexed: 09/07/2024] Open
Abstract
Circular RNAs (circRNAs) are a unique class of RNA molecules formed through back-splicing rather than linear splicing. As an emerging field in molecular biology, circRNAs have garnered significant attention due to their distinct structure and potential functional implications. A comprehensive understanding of circRNAs' functions and potential clinical applications remains elusive despite accumulating evidence of their involvement in disease pathogenesis. Recent research highlights their significant roles in various human diseases, but comprehensive reviews on their functions and applications remain scarce. This review provides an in-depth examination of circRNAs, focusing first on their involvement in non-neoplastic diseases such as respiratory, endocrine, metabolic, musculoskeletal, cardiovascular, and renal disorders. We then explore their roles in tumors, with particular emphasis on exosomal circular RNAs, which are crucial for cancer initiation, progression, and resistance to treatment. By detailing their biogenesis, functions, and impact on disease mechanisms, this review underscores the potential of circRNAs as diagnostic biomarkers and therapeutic targets. The review not only enhances our understanding of circRNAs' roles in specific diseases and tumor types but also highlights their potential as novel diagnostic and therapeutic tools, thereby paving the way for future clinical investigations and potential therapeutic interventions.
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Affiliation(s)
- Yuanyong Wang
- Department of Thoracic Surgery Tangdu Hospital Air Force Medical University Xi'an China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) The First Department of Thoracic Surgery Peking University Cancer Hospital and Institute Peking University School of Oncology Beijing China
| | - Jin Zhang
- Department of Traditional Chinese Medicine Tangdu Hospital Air Force Medical University Xi'an China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine Tumor Diagnosis and Treatment in Shaanxi Province Xi'an China
| | - Yuchen Yang
- Department of Traditional Chinese Medicine Tangdu Hospital Air Force Medical University Xi'an China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine Tumor Diagnosis and Treatment in Shaanxi Province Xi'an China
| | - Zhuofeng Liu
- Department of Traditional Chinese Medicine The Third Affiliated Hospital of Xi'an Medical University Xi'an China
| | - Sijia Sun
- Department of Traditional Chinese Medicine Tangdu Hospital Air Force Medical University Xi'an China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine Tumor Diagnosis and Treatment in Shaanxi Province Xi'an China
| | - Rui Li
- Department of Epidemiology School of Public Health Air Force Medical University Xi'an China
| | - Hui Zhu
- Department of Anatomy Medical College of Yan'an University Yan'an China
- Institute of Medical Research Northwestern Polytechnical University Xi'an China
| | - Tian Li
- School of Basic Medicine Fourth Military Medical University Xi'an China
| | - Jin Zheng
- Department of Traditional Chinese Medicine Tangdu Hospital Air Force Medical University Xi'an China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine Tumor Diagnosis and Treatment in Shaanxi Province Xi'an China
| | - Jie Li
- Department of Endocrine Xijing 986 Hospital Air Force Medical University Xi'an China
| | - Litian Ma
- Department of Thoracic Surgery Tangdu Hospital Air Force Medical University Xi'an China
- Department of Traditional Chinese Medicine Tangdu Hospital Air Force Medical University Xi'an China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine Tumor Diagnosis and Treatment in Shaanxi Province Xi'an China
- Department of Gastroenterology Tangdu Hospital Air Force Medical University Xi'an China
- School of Medicine Northwest University Xi'an China
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13
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He H, Hao D, Tian L, Zhu C, Guo L, Zhang K, Zhu S. Research on the expression of Mir-218-2 in the serum of patients with papillary thyroid cancer and its clinical significance. Eur J Transl Myol 2024; 34. [PMID: 39221591 DOI: 10.4081/ejtm.2024.12678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Accepted: 06/17/2024] [Indexed: 09/04/2024] Open
Abstract
Papillary thyroid carcinoma is an epithelial malignancy with follicular cell differentiation and sets of defined nuclear features and appearance of an irregular solid mass. The main objective of our study is to research on the expression of miR-218-2 in the serum of patients with papillary thyroid cancer and its clinical significance. Our study involved patients with thyroid nodules were divided into a capitate cancer group (N = 100) and a benign nodule group (N =100). Lastly, 50 cases of healthy individuals were used as controls. The total sample size was 250. All cases were clinically diagnosed and underwent histopathological examinations at the Tonglu County Hospital of Traditional Chinese Medicine between January 2023 and January 2024. Quantitative RT-PCR was used to assess the expression levels of miR-218-2 and its host gene SLIT3 in normal and cancer thyroid tissues. We found that 45% of tumour sizes were less than 1 cm with 90% of tumours did not infiltrate the glandular capsule, implying a favourable prognosis. Lastly, 85% of tumours were well differentiated with about 75% showing no metastasis while 60% of TNM stage were classified as stage I. Also, miR-218-2 and its host gene SLIT3 are significantly down-regulated in papillary thyroid carcinoma. The inhibitory effects of miR-218-2 act in synergy with its host gene SLIT3 to alter the rates of cell invasion, cell migration and cell proliferation. Our findings have clinical significance on the involvement of miR-218-2 and SLIT3. There exists a functional relationship between host genes and intronic miRNAs in the tumorigenesis of thyroid cancers.
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Affiliation(s)
- Haoting He
- Department of Oncology, Tonglu County Hospital of Traditional Chinese Medicine, Tonglu County, Hangzhou City, Zhejiang Province.
| | - Dingji Hao
- Department of Oncology, Tonglu County Hospital of Traditional Chinese Medicine, Tonglu County, Hangzhou City, Zhejiang Province.
| | - Linxiao Tian
- Department of Oncology, Tonglu County Hospital of Traditional Chinese Medicine, Tonglu County, Hangzhou City, Zhejiang Province.
| | - Congru Zhu
- Department of Oncology, Tonglu County Hospital of Traditional Chinese Medicine, Tonglu County, Hangzhou City, Zhejiang Province.
| | - Lili Guo
- Department of Oncology, Tonglu County Hospital of Traditional Chinese Medicine, Tonglu County, Hangzhou City, Zhejiang Province.
| | - Keao Zhang
- Department of Oncology, Tonglu County Hospital of Traditional Chinese Medicine, Tonglu County, Hangzhou City, Zhejiang Province.
| | - Siyao Zhu
- Department of Oncology, Tonglu County Hospital of Traditional Chinese Medicine, Tonglu County, Hangzhou City, Zhejiang Province.
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14
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Li Y, Wang Y, Chen S, Liu L. The landscape of miRNA-mRNA regulatory network and cellular sources in inflammatory bowel diseases: insights from text mining and single cell RNA sequencing analysis. Front Immunol 2024; 15:1454532. [PMID: 39238649 PMCID: PMC11374595 DOI: 10.3389/fimmu.2024.1454532] [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: 06/25/2024] [Accepted: 08/05/2024] [Indexed: 09/07/2024] Open
Abstract
Background Inflammatory Bowel Diseases (IBDs), encompassing Ulcerative Colitis (UC) and Crohn's Disease (CD), are chronic, recurrent inflammatory conditions of the gastrointestinal tract. The microRNA (miRNA) -mRNA regulatory network is pivotal in the initiation and progression of IBDs. Although individual studies provide valuable insights into miRNA mechanisms in IBDs, they often have limited scope due to constraints in population diversity, sample size, sequencing platform variability, batch effects, and potential researcher bias. Our study aimed to construct comprehensive miRNA-mRNA regulatory networks and determine the cellular sources and functions of key miRNAs in IBD pathogenesis. Methods To minimize potential bias from individual studies, we utilized a text mining-based approach on published scientific literature from PubMed and PMC databases to identify miRNAs and mRNAs associated with IBDs and their subtypes. We constructed miRNA-mRNA regulatory networks by integrating both predicted and experimentally validated results from DIANA, Targetscan, PicTar, Miranda, miRDB, and miRTarBase (all of which are databases for miRNA target annotation). The functions of miRNAs were determined through gene enrichment analysis of their target mRNAs. Additionally, we used two large-scale single-cell RNA sequencing datasets to identify the cellular sources of miRNAs and the association of their expression levels with clinical status, molecular and functional alternation in CD and UC. Results Our analysis systematically summarized IBD-related genes using text-mining methodologies. We constructed three comprehensive miRNA-mRNA regulatory networks specific to IBD, CD, and UC. Through cross-analysis with two large-scale scRNA-seq datasets, we determined the cellular sources of the identified miRNAs. Despite originating from different cell types, hsa-miR-142, hsa-miR-145, and hsa-miR-146a were common to both CD and UC. Notably, hsa-miR-145 was identified as myofibroblast-specific in both CD and UC. Furthermore, we found that higher tissue repair and enhanced glucose and lipid metabolism were associated with hsa-miR-145 in myofibroblasts in both CD and UC contexts. Conclusion This comprehensive approach revealed common and distinct miRNA-mRNA regulatory networks in CD and UC, identified cell-specific miRNA expressions (notably hsa-miR-145 in myofibroblasts), and linked miRNA expression to functional alterations in IBD. These findings not only enhance our understanding of IBD pathogenesis but also offer promising diagnostic biomarkers and therapeutic targets for clinical practice in managing IBDs.
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Affiliation(s)
- Yuan Li
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yao Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Simeng Chen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lijia Liu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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15
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Das S, Rai SN. Predicting the Effect of miRNA on Gene Regulation to Foster Translational Multi-Omics Research-A Review on the Role of Super-Enhancers. Noncoding RNA 2024; 10:45. [PMID: 39195574 DOI: 10.3390/ncrna10040045] [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: 06/13/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 08/29/2024] Open
Abstract
Gene regulation is crucial for cellular function and homeostasis. It involves diverse mechanisms controlling the production of specific gene products and contributing to tissue-specific variations in gene expression. The dysregulation of genes leads to disease, emphasizing the need to understand these mechanisms. Computational methods have jointly studied transcription factors (TFs), microRNA (miRNA), and messenger RNA (mRNA) to investigate gene regulatory networks. However, there remains a knowledge gap in comprehending gene regulatory networks. On the other hand, super-enhancers (SEs) have been implicated in miRNA biogenesis and function in recent experimental studies, in addition to their pivotal roles in cell identity and disease progression. However, statistical/computational methodologies harnessing the potential of SEs in deciphering gene regulation networks remain notably absent. However, to understand the effect of miRNA on mRNA, existing statistical/computational methods could be updated, or novel methods could be developed by accounting for SEs in the model. In this review, we categorize existing computational methods that utilize TF and miRNA data to understand gene regulatory networks into three broad areas and explore the challenges of integrating enhancers/SEs. The three areas include unraveling indirect regulatory networks, identifying network motifs, and enriching pathway identification by dissecting gene regulators. We hypothesize that addressing these challenges will enhance our understanding of gene regulation, aiding in the identification of therapeutic targets and disease biomarkers. We believe that constructing statistical/computational models that dissect the role of SEs in predicting the effect of miRNA on gene regulation is crucial for tackling these challenges.
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Affiliation(s)
- Sarmistha Das
- Biostatistics and Informatics Shared Resource, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Cancer Data Science Center, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Division of Biostatistics and Bioinformatics, Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Shesh N Rai
- Biostatistics and Informatics Shared Resource, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Cancer Data Science Center, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Division of Biostatistics and Bioinformatics, Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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16
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Przybyszewski O, Mik M, Nowicki M, Kusiński M, Mikołajczyk-Solińska M, Śliwińska A. Using microRNAs Networks to Understand Pancreatic Cancer-A Literature Review. Biomedicines 2024; 12:1713. [PMID: 39200178 PMCID: PMC11351910 DOI: 10.3390/biomedicines12081713] [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: 05/30/2024] [Revised: 07/26/2024] [Accepted: 07/28/2024] [Indexed: 09/02/2024] Open
Abstract
Pancreatic cancer is a severe disease, challenging to diagnose and treat, and thereby characterized by a poor prognosis and a high mortality rate. Pancreatic ductal adenocarcinoma (PDAC) represents approximately 90% of pancreatic cancer cases, while other cases include neuroendocrine carcinoma. Despite the growing knowledge of the pathophysiology of this cancer, the mortality rate caused by it has not been effectively reduced. Recently, microRNAs have aroused great interest among scientists and clinicians, as they are negative regulators of gene expression, which participate in many processes, including those related to the development of pancreatic cancer. The aim of this review is to show how microRNAs (miRNAs) affect key signaling pathways and related cellular processes in pancreatic cancer development, progression, diagnosis and treatment. We included the results of in vitro studies, animal model of pancreatic cancer and those performed on blood, saliva and tumor tissue isolated from patients suffering from PDAC. Our investigation identified numerous dysregulated miRNAs involved in KRAS, JAK/STAT, PI3/AKT, Wnt/β-catenin and TGF-β signaling pathways participating in cell cycle control, proliferation, differentiation, apoptosis and metastasis. Moreover, some miRNAs (miRNA-23a, miRNA-24, miRNA-29c, miRNA-216a) seem to be engaged in a crosstalk between signaling pathways. Evidence concerning the utility of microRNAs in the diagnosis and therapy of this cancer is poor. Therefore, despite growing knowledge of the involvement of miRNAs in several processes associated with pancreatic cancer, we are beginning to recognize and understand their role and usefulness in clinical practice.
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Affiliation(s)
- Oskar Przybyszewski
- Department of Nucleic Acid Biochemistry, Medical University of Lodz, 251 Pomorska St., 92-213 Lodz, Poland
| | - Michał Mik
- Department of General and Colorectal Surgery, Medical University of Lodz, 113 Stefana Żeromskiego St., 90-549 Lodz, Poland; (M.M.); (M.N.)
| | - Michał Nowicki
- Department of General and Colorectal Surgery, Medical University of Lodz, 113 Stefana Żeromskiego St., 90-549 Lodz, Poland; (M.M.); (M.N.)
| | - Michał Kusiński
- Department of Endocrinological, General and Oncological Surgery, Medical University of Lodz, 62 Pabianicka St., 93-513 Lodz, Poland;
| | - Melania Mikołajczyk-Solińska
- Department of Internal Medicine, Diabetology and Clinical Pharmacology, Medical University of Lodz, 251 Pomorska St., 92-213 Lodz, Poland;
| | - Agnieszka Śliwińska
- Department of Nucleic Acid Biochemistry, Medical University of Lodz, 251 Pomorska St., 92-213 Lodz, Poland
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17
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Alves LF, Marson LA, Sielski MS, Vicente CP, Kimura ET, Geraldo MV. DLK1-DIO3 region as a source of tumor suppressor miRNAs in papillary thyroid carcinoma. Transl Oncol 2024; 46:101849. [PMID: 38823258 PMCID: PMC11176784 DOI: 10.1016/j.tranon.2023.101849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/01/2023] [Accepted: 11/26/2023] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND In previous studies, we demonstrated the downregulation of several miRNAs from the DLK1-DIO3 genomic region in papillary thyroid carcinoma (PTC). Due to the large number of miRNAs within this region, the individual contribution of these molecules to PTC development and progression remains unclear. OBJECTIVE In this study, we aimed to clarify the contribution of DLK1-DIO3-derived miRNAs to PTC. METHODS We used different computational approaches and in vitro resources to assess the biological processes and signaling pathways potentially modulated by these miRNAs. RESULTS Our analysis suggests that, out of more than 100 mature miRNAs originated from the DLK1-DIO3 region, a set of 12 miRNAs accounts for most of the impact on PTC development and progression, cooperating to modulate distinct cancer-relevant biological processes, such as cell migration, extracellular matrix remodeling, and signal transduction. The restoration of the expression of one of these miRNAs (miR-485-5p) in a BRAFT199A-positive PTC cell line impaired proliferation and migration, suppressing the expression of GAB2 and RAC1, validated miR-485-5p targets. CONCLUSIONS Overall, our results shed light on the role of the DLK1-DIO3 region, which harbors promising tumor suppressor miRNAs in thyroid cancer, and open prospects for the functional exploration of these miRNAs as therapeutic targets for PTC.
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Affiliation(s)
- Letícia Ferreira Alves
- Department of Structural and Functional Biology, Institute of Biology, Universidade Estadual de Campinas, Brazil
| | - Leonardo Augusto Marson
- Department of Structural and Functional Biology, Institute of Biology, Universidade Estadual de Campinas, Brazil
| | - Micheli Severo Sielski
- Department of Structural and Functional Biology, Institute of Biology, Universidade Estadual de Campinas, Brazil
| | - Cristina Pontes Vicente
- Department of Structural and Functional Biology, Institute of Biology, Universidade Estadual de Campinas, Brazil
| | - Edna Teruko Kimura
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Murilo Vieira Geraldo
- Department of Structural and Functional Biology, Institute of Biology, Universidade Estadual de Campinas, Brazil.
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18
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Azzam M, Fahim S, ElMonier A, Maurice N. Functional analysis of a panel of molecular markers for diagnosis of systemic lupus erythematosus in rats. Biosci Rep 2024; 44:BSR20240318. [PMID: 38967046 PMCID: PMC11263041 DOI: 10.1042/bsr20240318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/04/2024] [Accepted: 06/12/2024] [Indexed: 07/06/2024] Open
Abstract
INTRODUCTION Systemic lupus erythematosus (SLE) is a diverse autoimmune disease that arises from a combination of complex genetic factors and environmental influences. While circRNAs and miRNAs have recently been identified as promising biomarkers for disease diagnosis, their specific expression patterns, and clinical implications in SLE are not yet fully understood. AIM OF THE WORK The aim of the present study was to determine the role of a panel of noncoding-RNAs specifically circRNAs (circ-TubD1, circ-CDC27, and circ-Med14), along with miRNA (rno-miR-146a-5p) and mRNA (TRAF6), as novel minimally invasive diagnostic biomarkers for experimentally induced SLE. Additionally, the study involved an insilico bioinformatics analysis to explore potential pathways involved in the pathogenesis of SLE, aiming to enhance our understanding of the disease, enable early diagnosis, and facilitate improved treatment strategies. MATERIALS AND METHODS SLE was induced in rats using single IP injection of incomplete Freund's adjuvant (IFA). The Induction was confirmed by assessing the ANA and anti-ds DNA levels using ELSA technique. qPCR analysis was conducted to assess the expression of selected RNAs in sera collected from a group of 10 rats with induced SLE and a control group of 10 rats. In addition, bioinformatics and functional analysis were used to construct a circRNA-miRNA-mRNA network and to determine the potential function of these differentially expressed circRNAs. RESULTS SLE rats demonstrated significantly higher expression levels of circ-CDC27, circ-Med14, and rno-miR-146a-5p as well as TRAF6, with lower expression level of circ-TubD1 in sera of SLE rats relative to controls. ROC curve analysis indicated that all the selected non-coding RNAs could serve as potential early diagnostic markers for SLE. In addition, the expression level of circ-TubD1 was negatively correlated with rno-miR-146a-5p, however, rno-miR-146a-5p was positively correlated with TRAF6. Bioinformatic analysis revealed the incorporation of the circRNAs targeted genes in various immune system and neurodegeneration pathways. CONCLUSIONS Therefore, circRNAs; circ-TubD1, circ-CDC27, and circ-Med14, in addition to the miRNA (rno-miR-146a-5p) and mRNA (TRAF6) may be involved in the development of SLE and may have promising roles for future diagnosis and targeted therapy.
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Affiliation(s)
- May A. Azzam
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, 11562, Cairo, Egypt
| | - Sally A. Fahim
- Department of Biochemistry, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, 12577, Giza, Egypt
| | - Asmaa A. ElMonier
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, 11562, Cairo, Egypt
| | - Nadine W. Maurice
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, 11562, Cairo, Egypt
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19
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Chen J, Liu K, Vadas MA, Gamble JR, McCaughan GW. The Role of the MiR-181 Family in Hepatocellular Carcinoma. Cells 2024; 13:1289. [PMID: 39120319 PMCID: PMC11311592 DOI: 10.3390/cells13151289] [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: 06/28/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the fourth-leading cause of cancer-related death worldwide. Due to the high mortality rate in HCC patients, discovering and developing novel systemic treatment options for HCC is a vital unmet medical need. Among the numerous molecular alterations in HCCs, microRNAs (miRNAs) have been increasingly recognised to play critical roles in hepatocarcinogenesis. We and others have recently revealed that members of the microRNA-181 (miR-181) family were up-regulated in some, though not all, human cirrhotic and HCC tissues-this up-regulation induced epithelial-mesenchymal transition (EMT) in hepatocytes and tumour cells, promoting HCC progression. MiR-181s play crucial roles in governing the fate and function of various cells, such as endothelial cells, immune cells, and tumour cells. Previous reviews have extensively covered these aspects in detail. This review aims to give some insights into miR-181s, their targets and roles in modulating signal transduction pathways, factors regulating miR-181 expression and function, and their roles in HCC.
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Affiliation(s)
- Jinbiao Chen
- Liver Injury and Cancer Program, Cancer Innovations Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Ken Liu
- Liver Injury and Cancer Program, Cancer Innovations Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia
| | - Mathew A. Vadas
- Vascular Biology Program, Healthy Ageing Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia; (M.A.V.); (J.R.G.)
| | - Jennifer R. Gamble
- Vascular Biology Program, Healthy Ageing Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia; (M.A.V.); (J.R.G.)
| | - Geoffrey W. McCaughan
- Liver Injury and Cancer Program, Cancer Innovations Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia
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20
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da Silva IIFG, Nascimento DDQ, Barbosa AD, Souto FO, Maia MDMD, Crovella S, de Souza PRE, Sandrin-Garcia P. miRNAs and NFKB1 and TRAF6 target genes: The initial functional study in CD14+ monocytes in rheumatoid arthritis patients. Genet Mol Biol 2024; 47:e20230235. [PMID: 39058384 PMCID: PMC11274900 DOI: 10.1590/1678-4685-gmb-2023-0235] [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: 10/06/2023] [Accepted: 05/10/2024] [Indexed: 07/28/2024] Open
Abstract
We predicted miRNAs with regulatory impact on NFKB1 and TRAF6 gene expression and selected the miR-194-5p, miR-124-3p, miR-9-5p, and miR-340-5p and their target genes for expression analyses on CD14+ monocytes from rheumatoid arthritis (RA) patients and healthy controls. Additionally, we evaluated the influence of genes and miRNA expression on RA patients' cytokine levels. No difference was observed in genes or miRNAs expression when compared to healthy controls and RA patients or clinical parameters. However, we found a significant difference between miR-194-5p and miR-9-5p levels (FC=-2.31; p=0.031; FC=-3.05;p=0.031, respectively) and non-prednisone users as compared to prednisone using patients. We conducted correlation analyses to identify the strength of the relationship between expression data and cytokine plasma levels. We observed a moderate positive correlation between miR-124-3p expression and IL-6 plasma levels (r=0.46; p=0.033). In addition, overexpression of miRNAs was concomitant to TRAF6 and NFKB1 genes as indicated by correlation analyses: TRAF6 and miR-194-5p (r=0.60;p<0.001) and miR-9-5p (r=0.63;p<0.001) and NFKB1 and miR-194-5p (r=0.72;p<0.001), miR-9-5p (r=0.72;p<0.001) and miR-340-5p (r=0.61;p<0.001). NFKB1 and TRAF6 genes and miRNAs monocyte expression do not appear to be related to RA but showed a significant difference in different groups of RA therapy. In addition, increased levels of miRNAs can be linked to concomitant overexpression of TRAF6 and NFKB1 in monocytes and act as its regulators.
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Affiliation(s)
- Isaura Isabelle Fonseca Gomes da Silva
- Universidade Federal de Pernambuco, Programa de Pós-Graduação em Genética e Biologia Molecular, Recife, PE, Brazil
- Instituto Keizo Asami, Recife, PE, Brazil
| | - Denise de Queiroga Nascimento
- Universidade Federal de Pernambuco, Programa de Pós-Graduação em Genética e Biologia Molecular, Recife, PE, Brazil
- Instituto Keizo Asami, Recife, PE, Brazil
| | - Alexandre Domingues Barbosa
- Policlínica Jamacy de Medeiros, Cabo de Santo Agostinho, PE, Brazil
- Universidade Federal de Pernambuco, Hospital das Clínicas, Recife, PE, Brazil
| | - Fabricio Oliveira Souto
- Instituto Keizo Asami, Recife, PE, Brazil
- Universidade Federal de Pernambuco, Centro Acadêmico do Agreste, Caruaru, PE, Brazil
| | | | - Sergio Crovella
- Universidade Federal de Pernambuco, Departamento de Genética, Recife, PE, Brazil
| | | | - Paula Sandrin-Garcia
- Universidade Federal de Pernambuco, Programa de Pós-Graduação em Genética e Biologia Molecular, Recife, PE, Brazil
- Universidade Federal de Pernambuco, Departamento de Genética, Recife, PE, Brazil
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21
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Gan L, Zheng L, Zou J, Luo P, Chen T, Zou J, Li W, Chen Q, Cheng L, Zhang F, Qian B. MicroRNA-21 in urologic cancers: from molecular mechanisms to clinical implications. Front Cell Dev Biol 2024; 12:1437951. [PMID: 39114567 PMCID: PMC11304453 DOI: 10.3389/fcell.2024.1437951] [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: 05/24/2024] [Accepted: 07/15/2024] [Indexed: 08/10/2024] Open
Abstract
The three most common kinds of urologic malignancies are prostate, bladder, and kidney cancer, which typically cause substantial morbidity and mortality. Early detection and effective treatment are essential due to their high fatality rates. As a result, there is an urgent need for innovative research to improve the clinical management of patients with urologic cancers. A type of small noncoding RNAs of 22 nucleotides, microRNAs (miRNAs) are well-known for their important roles in a variety of developmental processes. Among these, microRNA-21 (miR-21) stands out as a commonly studied miRNA with implications in tumorigenesis and cancer development, particularly in urological tumors. Recent research has shed light on the dysregulation of miR-21 in urological tumors, offering insights into its potential as a prognostic, diagnostic, and therapeutic tool. This review delves into the pathogenesis of miR-21 in prostate, bladder, and renal cancers, its utility as a cancer biomarker, and the therapeutic possibilities of targeting miR-21.
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Affiliation(s)
- Lifeng Gan
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Liying Zheng
- Department of Graduate, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Junrong Zou
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Peiyue Luo
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Tao Chen
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Jun Zou
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Wei Li
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Qi Chen
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Le Cheng
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Fangtao Zhang
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Biao Qian
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
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22
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Poggio P, Rocca S, Fusella F, Ferretti R, Ala U, D'Anna F, Giugliano E, Panuzzo C, Fontana D, Palumbo V, Carrà G, Taverna D, Gambacorti-Passerini C, Saglio G, Fava C, Piazza R, Morotti A, Orso F, Brancaccio M. miR-15a targets the HSP90 co-chaperone Morgana in chronic myeloid leukemia. Sci Rep 2024; 14:15089. [PMID: 38956394 PMCID: PMC11220062 DOI: 10.1038/s41598-024-65404-7] [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: 01/24/2024] [Accepted: 06/19/2024] [Indexed: 07/04/2024] Open
Abstract
Morgana is a ubiquitous HSP90 co-chaperone protein coded by the CHORDC1 gene. Morgana heterozygous mice develop with age a myeloid malignancy resembling human atypical myeloid leukemia (aCML), now renamed MDS/MPN with neutrophilia. Patients affected by this pathology exhibit low Morgana levels in the bone marrow (BM), suggesting that Morgana downregulation plays a causative role in the human malignancy. A decrease in Morgana expression levels is also evident in the BM of a subgroup of Philadelphia-positive (Ph+) chronic myeloid leukemia (CML) patients showing resistance or an incomplete response to imatinib. Despite the relevance of these data, the mechanism through which Morgana expression is downregulated in patients' bone marrow remains unclear. In this study, we investigated the possibility that Morgana expression is regulated by miRNAs and we demonstrated that Morgana is under the control of four miRNAs (miR-15a/b and miR-26a/b) and that miR-15a may account for Morgana downregulation in CML patients.
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MESH Headings
- Animals
- Humans
- Mice
- Bone Marrow/metabolism
- Bone Marrow/pathology
- Down-Regulation
- Gene Expression Regulation, Leukemic
- HSP90 Heat-Shock Proteins/metabolism
- HSP90 Heat-Shock Proteins/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Molecular Chaperones/metabolism
- Molecular Chaperones/genetics
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Affiliation(s)
- Pietro Poggio
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Stefania Rocca
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Federica Fusella
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Roberta Ferretti
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Ugo Ala
- Department of Veterinary Sciences, University of Turin, Grugliasco, TO, Italy
| | - Flora D'Anna
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Emilia Giugliano
- Division of Internal Medicine and Hematology, San Luigi Gonzaga Hospital, Orbassano, Italy
| | - Cristina Panuzzo
- Department of Clinical and Biological Science, University of Turin, Orbassano, Italy
| | - Diletta Fontana
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Valeria Palumbo
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Giovanna Carrà
- Department of Clinical and Biological Science, University of Turin, Orbassano, Italy
| | - Daniela Taverna
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Carlo Gambacorti-Passerini
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- Hematology Division and Bone Marrow Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Giuseppe Saglio
- Department of Clinical and Biological Science, University of Turin, Orbassano, Italy
| | - Carmen Fava
- Department of Clinical and Biological Science, University of Turin, Orbassano, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- Hematology Division and Bone Marrow Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Alessandro Morotti
- Department of Clinical and Biological Science, University of Turin, Orbassano, Italy
| | - Francesca Orso
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
- Department of Translational Medicine (DIMET), University of Piemonte Orientale, Novara, Italy
| | - Mara Brancaccio
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.
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23
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Evans LW, Durbin-Johnson B, Sutton KJ, Yam P, Bouzid YY, Cervantes E, Bonnel E, Stephenson CB, Bennett BJ. Specific circulating miRNAs are associated with plasma lipids in a healthy American cohort. Physiol Genomics 2024; 56:492-505. [PMID: 38557280 PMCID: PMC11368566 DOI: 10.1152/physiolgenomics.00087.2023] [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: 08/11/2023] [Revised: 02/20/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
Low-density lipoprotein cholesterol (LDL-c) is both a therapeutic target and a risk factor for cardiovascular disease (CVD). MicroRNA (miRNA) has been shown to regulate cholesterol homeostasis, and miRNA in blood circulation has been linked to hypercholesterolemia. However, few studies to date have associated miRNA with phenotypes like LDL-c in a healthy population. To this end, we analyzed circulating miRNA in relation to LDL-c in a healthy cohort of 353 participants using two separate bioinformatic approaches. The first approach found that miR-15b-5p and miR-16-5p were upregulated in individuals with at-risk levels of LDL-c. The second approach identified two miRNA clusters, one that positively and a second that negatively correlated with LDL-c. Included in the cluster that positively correlated with LDL-c were miR-15b-5p and miR-16-5p, as well as other miRNA from the miR-15/107, miR-30, and let-7 families. Cross-species analyses suggested that several miRNAs that associated with LDL-c are conserved between mice and humans. Finally, we examined the influence of diet on circulating miRNA. Our results robustly linked circulating miRNA with LDL-c, suggesting that miRNA could be used as biomarkers for hypercholesterolemia or targets for developing cholesterol-lowering drugs.NEW & NOTEWORTHY This study explored the association between circulating microRNA (miRNA) and low-density lipoprotein cholesterol (LDL-c) in a healthy population of 353 participants. Two miRNAs, miR-15b-5p and miR-16-5p, were upregulated in individuals with at-risk LDL-c levels. Several miRNA clusters were positively and negatively correlated with LDL-c and are known to target mRNA involved in lipid metabolism. The study also investigated the influence of diet on circulating miRNA, suggesting potential biomarkers for hypercholesterolemia.
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Affiliation(s)
- Levi W Evans
- USDA-ARS-Western Human Nutrition Research Center, Davis, California, United States
| | - Blythe Durbin-Johnson
- Division of Biostatistics, University of California, Davis, California, United States
| | - Kristen J Sutton
- Department of Nutrition, University of California, Davis, California, United States
| | - Phoebe Yam
- Department of Nutrition, University of California, Davis, California, United States
| | - Yasmine Y Bouzid
- Department of Nutrition, University of California, Davis, California, United States
| | - Eduardo Cervantes
- Department of Nutrition, University of California, Davis, California, United States
| | - Ellen Bonnel
- Department of Nutrition, University of California, Davis, California, United States
| | - Charles B Stephenson
- USDA-ARS-Western Human Nutrition Research Center, Davis, California, United States
- Department of Nutrition, University of California, Davis, California, United States
| | - Brian J Bennett
- USDA-ARS-Western Human Nutrition Research Center, Davis, California, United States
- Department of Nutrition, University of California, Davis, California, United States
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24
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Mun H, Lee S, Choi S, Jeong JH, Ko S, Chun YL, Deaton B, Yeager CT, Boyette A, Palmera J, Newman L, Zhou P, Shin S, Kim DC, Sagum CA, Bedford MT, Kim YK, Kwon J, Jung J, Chang JH, Yoon JH. Targeting of CYP2E1 by miRNAs in alcohol-induced intestine injury. Mol Cells 2024; 47:100074. [PMID: 38901530 PMCID: PMC11267015 DOI: 10.1016/j.mocell.2024.100074] [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: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/22/2024] Open
Abstract
Although binge alcohol-induced gut leakage has been studied extensively in the context of reactive oxygen species-mediated signaling, it was recently revealed that post-transcriptional regulation plays an essential role as well. Ethanol (EtOH)-inducible cytochrome P450-2E1 (CYP2E1), a key enzyme in EtOH metabolism, promotes alcohol-induced hepatic steatosis and inflammatory liver disease, at least in part by mediating changes in intestinal permeability. For instance, gut leakage and elevated intestinal permeability to endotoxins have been shown to be regulated by enhancing CYP2E1 mRNA and CYP2E1 protein levels. Although it is understood that EtOH promotes CYP2E1 induction and activation, the mechanisms that regulate CYP2E1 expression in the context of intestinal damage remain poorly defined. Specific miRNAs, including miR-132, miR-212, miR-378, and miR-552, have been shown to repress the expression of CYP2E1, suggesting that these miRNAs contribute to EtOH-induced intestinal injury. Here, we have shown that CYP2E1 expression is regulated post-transcriptionally through miRNA-mediated degradation, as follows: (1) the RNA-binding protein AU-binding factor 1 (AUF1) binds mature miRNAs, including CYP2E1-targeting miRNAs, and this binding modulates the degradation of corresponding target mRNAs upon EtOH treatment; (2) the serine/threonine kinase mammalian Ste20-like kinase 1 (MST1) mediates oxidative stress-induced phosphorylation of AUF1. Those findings suggest that reactive oxygen species-mediated signaling modulates AUF1/miRNA interaction through MST1-mediated phosphorylation. Thus, our study demonstrates the critical functions of AUF1 phosphorylation by MST1 in the decay of miRNAs targeting CYP2E1, the stabilization of CYP2E1 mRNA in the presence of EtOH, and the relationship of this pathway to subsequent intestinal injury.
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Affiliation(s)
- Hyejin Mun
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Department of Oncology Science, University of Oklahoma, Oklahoma City, OK 73104, USA
| | - Sungyul Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Suyoung Choi
- Department of Infection Biology, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea; Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea; Brain Korea 21 FOUR Project for Medical Science, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Ji-Hoon Jeong
- Department of Oncology Science, University of Oklahoma, Oklahoma City, OK 73104, USA
| | - Seungbeom Ko
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Yoo Lim Chun
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Benjamin Deaton
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Clay T Yeager
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Audrey Boyette
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Juliana Palmera
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - London Newman
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Ping Zhou
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Soona Shin
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Dong-Chan Kim
- Division of Medical Device R&D Center, NQ-Lab, Inc.,Yongin-si, Gyeonggi-do 16827, Republic of Korea
| | - Cari A Sagum
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD, Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD, Anderson Cancer Center, Houston, TX 77030, USA
| | - Young-Kook Kim
- Department of Biochemistry, Chonnam National University Medical School, Hwasun 58128, Republic of Korea
| | - Jaeyul Kwon
- Department of Infection Biology, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea; Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea; Brain Korea 21 FOUR Project for Medical Science, Chungnam National University, Daejeon 35015, Republic of Korea; Department of Medical Education, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea; Translational Immunology Institute, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Junyang Jung
- Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea.
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Department of Oncology Science, University of Oklahoma, Oklahoma City, OK 73104, USA.
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25
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Tang L, Nyarige V, Li P, Wang J, Zhu W. Identification of circular RNAs regulating cardiomyocyte proliferation in neonatal pig hearts. JCI Insight 2024; 9:e175625. [PMID: 38916964 PMCID: PMC11383601 DOI: 10.1172/jci.insight.175625] [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: 09/08/2023] [Accepted: 06/20/2024] [Indexed: 06/27/2024] Open
Abstract
Little is known about the expression patterns and functions of circular RNAs (circRNAs) in the heart of large mammals. In this study, we examined the expression profiles of circRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs) in neonatal pig hearts. Pig heart samples collected on postnatal days 1 (P1), 3 (P3), 7 (P7), and 28 (P28) were sent for total RNA sequencing. Our data revealed a total of 7,000 circRNAs in the 24 pig hearts. Pathway enrichment analysis of hallmark gene sets demonstrated that differentially expressed circRNAs were engaged in different pathways. The most significant difference was observed between P1 and the other 3 groups (P3, P7, and P28) in pathways related to cell cycle and muscle development. Out of the 10 circRNAs that were validated through real-time quantitative PCR to verify their expression, 6 exhibited significant effects on cell cycle activity in human induced pluripotent stem cell-derived cardiomyocytes following small interfering RNA-mediated knockdown. circRNA-miRNA-mRNA networks were constructed to understand the potential mechanisms of circRNAs in the heart. In conclusion, our study provided a data set for exploring the roles of circRNAs in pig hearts. In addition, we identified several circRNAs that regulate cardiomyocyte cell cycle.
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Affiliation(s)
- Ling Tang
- Departments of Cardiovascular Medicine and Physiology and Biomedical Engineering, Center for Regenerative Biotherapeutics, and
| | - Verah Nyarige
- Departments of Cardiovascular Medicine and Physiology and Biomedical Engineering, Center for Regenerative Biotherapeutics, and
- Department of Quantitative Health Sciences Research, Center for Individualized Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Pengsheng Li
- Departments of Cardiovascular Medicine and Physiology and Biomedical Engineering, Center for Regenerative Biotherapeutics, and
| | - Junwen Wang
- Department of Quantitative Health Sciences Research, Center for Individualized Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
- Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, the University of Hong Kong, Hong Kong SAR, China
| | - Wuqiang Zhu
- Departments of Cardiovascular Medicine and Physiology and Biomedical Engineering, Center for Regenerative Biotherapeutics, and
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26
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Paneru BD, Chini J, McCright SJ, DeMarco N, Miller J, Joannas LD, Henao-Mejia J, Titchenell PM, Merrick DM, Lim HW, Lazar MA, Hill DA. Myeloid-derived miR-6236 potentiates adipocyte insulin signaling and prevents hyperglycemia during obesity. Nat Commun 2024; 15:5394. [PMID: 38918428 PMCID: PMC11199588 DOI: 10.1038/s41467-024-49632-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
Adipose tissue macrophages (ATMs) influence obesity-associated metabolic dysfunction, but the mechanisms by which they do so are not well understood. We show that miR-6236 is a bona fide miRNA that is secreted by ATMs during obesity. Global or myeloid cell-specific deletion of miR-6236 aggravates obesity-associated adipose tissue insulin resistance, hyperglycemia, hyperinsulinemia, and hyperlipidemia. miR-6236 augments adipocyte insulin sensitivity by inhibiting translation of negative regulators of insulin signaling, including PTEN. The human genome harbors a miR-6236 homolog that is highly expressed in the serum and adipose tissue of obese people. hsa-MIR-6236 expression negatively correlates with hyperglycemia and glucose intolerance, and positively correlates with insulin sensitivity. Together, our findings establish miR-6236 as an ATM-secreted miRNA that potentiates adipocyte insulin signaling and protects against metabolic dysfunction during obesity.
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Affiliation(s)
- Bam D Paneru
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Julia Chini
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sam J McCright
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nicole DeMarco
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jessica Miller
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Leonel D Joannas
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jorge Henao-Mejia
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Paul M Titchenell
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - David M Merrick
- Department of Medicine, Division of Endocrinology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Endocrinology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - David A Hill
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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27
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Turk A, Čeh E, Calin GA, Kunej T. Multiple omics levels of chronic lymphocytic leukemia. Cell Death Discov 2024; 10:293. [PMID: 38906881 PMCID: PMC11192936 DOI: 10.1038/s41420-024-02068-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a lymphoproliferative malignancy characterized by the proliferation of functionally mature but incompetent B cells. It is the most prevalent type of leukemia in Western populations, accounting for approximately 25% of new leukemia cases. While recent advances, such as ibrutinib and venetoclax treatment have improved patient outlook, aggressive forms of CLL such as Richter transformation still pose a significant challenge. This discrepancy may be due to the heterogeneity of factors contributing to CLL development at multiple -omics levels. However, information on the omics of CLL is fragmented, hindering multi-omics-based research into potential treatment options. To address this, we aggregated and presented a selection of important aspects of various omics levels of the disease in this review. The purpose of the present literature analysis is to portray examples of CLL studies from different omics levels, including genomics, epigenomics, transcriptomics, epitranscriptomics, proteomics, epiproteomics, metabolomics, glycomics and lipidomics, as well as those identified by multi-omics approaches. The review includes the list of 102 CLL-associated genes with relevant genomics information. While single-omics studies yield substantial and useful data, they omit a significant level of complex biological interplay present in the disease. As multi-omics studies integrate several different layers of data, they may be better suited for complex diseases such as CLL and have thus far yielded promising results. Future multi-omics studies may assist clinicians in improved treatment choices based on CLL subtypes as well as allow the identification of novel biomarkers and targets for treatments.
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Grants
- P4-0220 Javna Agencija za Raziskovalno Dejavnost RS (Slovenian Research Agency)
- Dr. Calin is the Felix L. Haas Endowed Professor in Basic Science. Work in G.A.C.’s laboratory is supported by NCI grants 1R01 CA182905-01 and 1R01CA222007-01A1, NIGMS grant 1R01GM122775-01, DoD Idea Award W81XWH-21-1-0030, a Team DOD grant in Gastric Cancer W81XWH-21-1-0715, a Chronic Lymphocytic Leukemia Moonshot Flagship project, a CLL Global Research Foundation 2019 grant, a CLL Global Research Foundation 2020 grant, a CLL Global Research Foundation 2022 grant, The G. Harold & Leila Y. Mathers Foundation, two grants from Torrey Coast Foundation, an Institutional Research Grant and Development Grant associated with the Brain SPORE 2P50CA127001.
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Affiliation(s)
- Aleksander Turk
- Clinical Institute of Genomic Medicine, University Clinical Centre Ljubljana, Ljubljana, Slovenia
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Eva Čeh
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - George A Calin
- Department of Translational Molecular Pathology, Division of Pathology, MD Anderson Cancer Center, University of Texas, Houston, TX, 77030, USA.
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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28
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Hwang G, Kwon M, Seo D, Kim DH, Lee D, Lee K, Kim E, Kang M, Ryu JH. ASOptimizer: Optimizing antisense oligonucleotides through deep learning for IDO1 gene regulation. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102186. [PMID: 38706632 PMCID: PMC11066473 DOI: 10.1016/j.omtn.2024.102186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/03/2024] [Indexed: 05/07/2024]
Abstract
Recent studies have highlighted the effectiveness of using antisense oligonucleotides (ASOs) for cellular RNA regulation, including targets that are considered undruggable; however, manually designing optimal ASO sequences can be labor intensive and time consuming, which potentially limits their broader application. To address this challenge, we introduce a platform, the ASOptimizer, a deep-learning-based framework that efficiently designs ASOs at a low cost. This platform not only selects the most efficient mRNA target sites but also optimizes the chemical modifications for enhanced performance. Indoleamine 2,3-dioxygenase 1 (IDO1) promotes cancer survival by depleting tryptophan and producing kynurenine, leading to immunosuppression through the aryl-hydrocarbon receptor (Ahr) pathway within the tumor microenvironment. We used ASOptimizer to identify ASOs that target IDO1 mRNA as potential cancer therapeutics. Our methodology consists of two stages: sequence engineering and chemical engineering. During the sequence-engineering stage, we optimized and predicted ASO sequences that could target IDO1 mRNA efficiently. In the chemical-engineering stage, we further refined these ASOs to enhance their inhibitory activity while reducing their potential cytotoxicity. In conclusion, our research demonstrates the potential of ASOptimizer for identifying ASOs with improved efficacy and safety.
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Affiliation(s)
- Gyeongjo Hwang
- Spidercore Inc, 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Mincheol Kwon
- BIORCHESTRA Co., Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Dongjin Seo
- Spidercore Inc, 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Dae Hoon Kim
- BIORCHESTRA Co., Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Daehwan Lee
- Spidercore Inc, 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Kiwon Lee
- Spidercore Inc, 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Eunyoung Kim
- BIORCHESTRA Co., Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Mingeun Kang
- Spidercore Inc, 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
- Department of Electrical Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Jin-Hyeob Ryu
- BIORCHESTRA Co., Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
- BIORCHESTRA US., Inc., 1 Kendall Square, Building 200, Suite 2-103, Cambridge, MA 02139, USA
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29
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Chodur GM, Steinberg FM. Human MicroRNAs Modulated by Diet: A Scoping Review. Adv Nutr 2024; 15:100241. [PMID: 38734078 PMCID: PMC11150912 DOI: 10.1016/j.advnut.2024.100241] [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: 02/28/2024] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024] Open
Abstract
Because of their role in regulating and fine-tuning gene expression in the posttranscriptional period, microRNA (miRNA) may represent a mediating factor that connects diet and metabolic regulation. Given the vast number of miRNAs and that modulations in miRNA happen in response to a variety of stimuli, a comprehensive registry of miRNAs impacted by diet and the food items that modulate them, would have utility in the identification of miRNA complements for analysis of diet interventions and in helping to establish linkages between the specific impacts of diet components. A scoping literature search of online databases (PubMed, SCOPUS, EMBASE, and Web of Science) was performed. Only studies in human populations, those that used a diet intervention or meal challenge, and those that measured miRNA profiles in the same subject at multiple time points were included. Of the 6167 studies screened, only 25 met the study criteria and were included in the review. Seven studies examined miRNA following a meal challenge, whereas 18 investigated miRNA following a sustained diet intervention. The results demonstrated that miRNA are modulated following a variety of diet interventions and that intensity of miRNA response is greater in metabolically healthy subjects. Heterogeneity in the intensity and length of the diet intervention, the study populations being observed, and the methodology through which target miRNA are identified contribute to a lack of comparability across studies. The findings of this review highlight the need for more study of miRNA responsiveness to intake and provide recommendations for future research.
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Affiliation(s)
- Gwen M Chodur
- Department of Nutrition, University of California-Davis, Davis, CA, United States
| | - Francene M Steinberg
- Department of Nutrition, University of California-Davis, Davis, CA, United States.
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30
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Bayraktar R, Fontana B, Calin GA, Nemeth K. miRNA Biology in Chronic Lymphocytic Leukemia. Semin Hematol 2024; 61:181-193. [PMID: 38724414 DOI: 10.1053/j.seminhematol.2024.03.001] [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: 11/27/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 07/13/2024]
Abstract
microRNAs (miRNAs) are a class of small non-coding RNAs that play a crucial regulatory role in fundamental biological processes and have been implicated in various diseases, including cancer. The first evidence of the cancer-related function of miRNAs was discovered in chronic lymphocytic leukemia (CLL) in the early 2000s. Alterations in miRNA expression have since been shown to strongly influence the clinical course, prognosis, and response to treatment in patients with CLL. Therefore, the identification of specific miRNA alterations not only enhances our understanding of the molecular mechanisms underlying CLL but also holds promise for the development of novel diagnostic and therapeutic strategies. This review aims to provide a comprehensive summary of the current knowledge and recent insights into miRNA dysregulation in CLL, emphasizing its pivotal roles in disease progression, including the development of the lethal Richter syndrome, and to provide an update on the latest translational research in this field.
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Affiliation(s)
- Recep Bayraktar
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Beatrice Fontana
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - George A Calin
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX; The RNA Interference and Non-coding RNA Center, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kinga Nemeth
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX.
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31
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Su Y, Zhao L, Lei D, Yang X. Inhibition of circ_0073932 attenuates myocardial ischemia‒reperfusion injury via miR-493-3p/FAF1/JNK. In Vitro Cell Dev Biol Anim 2024; 60:628-643. [PMID: 38578382 DOI: 10.1007/s11626-024-00900-8] [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: 09/22/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
Oxidative stress and apoptosis play crucial roles in myocardial ischemia‒reperfusion injury (MIRI). In this study, we investigated the role of circ_0073932 in MIRI as well as its molecular mechanism. A hypoxia/reoxygenation (H/R) cardiomyocyte model was established with H9C2 cardiomyocytes, and RT-qPCR was used to measure gene expression. We observed that circ_0073932 expression was abnormally increased in the H/R cardiomyocyte model and in blood samples from MIRI patients. Inhibition of circ_0073932 suppressed H/R-induced cell apoptosis, oxidative stress (ROS, LDH and MDA), and p-JNK expression. Dual luciferase reporter assays showed that circ_0073932 targeted the downregulation of miR-493-3p, and miR-493-3p targeted the downregulation of FAF1. Furthermore, si-circ_0073932, an miR-493-3p inhibitor, oe-FAF1, or si-FAF1 were transfected into H9C2 cardiomyocytes to investigate the roles of these factors in MIRI. Our results showed that compared with the H/R group, si-circ_0073932 inhibited H/R-induced cell apoptosis, oxidative stress (ROS, LDH and MDA), and p-JNK expression. These results were reversed by the miR-493-3p inhibitor or oe-FAF1. Finally, a rat model of MIRI was established, and si-circ_0073932 was administered. Inhibition of circ_0073932 reduced the area of myocardial infarction and decreased the levels of apoptosis and oxidative stress by inhibiting the JNK signaling pathway. Our study indicated that circ_0073932 mediates MIRI via miR-493-3p/FAF1/JNK in vivo and in vitro, revealing novel insights into the pathogenesis of MIRI and providing a new target for the clinical treatment of MIRI.
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Affiliation(s)
- Yang Su
- The Outpatient Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, Yunnan, China
| | - Lili Zhao
- Radiology Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, Yunnan, China
| | - Dongli Lei
- Intensive Care Unit, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, Yunnan, China
| | - Xiaoming Yang
- Information Statistics Centre, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, Yunnan, China.
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32
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Yadav P, Tamilselvan R, Mani H, Singh KK. MicroRNA-mediated regulation of nonsense-mediated mRNA decay factors: Insights into microRNA prediction tools and profiling techniques. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195022. [PMID: 38437914 DOI: 10.1016/j.bbagrm.2024.195022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) stands out as a prominent RNA surveillance mechanism within eukaryotes, meticulously overseeing both RNA abundance and integrity by eliminating aberrant transcripts. These defective transcripts are discerned through the concerted efforts of translating ribosomes, eukaryotic release factors (eRFs), and trans-acting NMD factors, with Up-Frameshift 3 (UPF3) serving as a noteworthy component. Remarkably, in humans, UPF3 exists in two paralogous forms, UPF3A (UPF3) and UPF3B (UPF3X). Beyond its role in quality control, UPF3 wields significant influence over critical cellular processes, including neural development, synaptic plasticity, and axon guidance. However, the precise regulatory mechanisms governing UPF3 remain elusive. MicroRNAs (miRNAs) emerge as pivotal post-transcriptional gene regulators, exerting substantial impact on diverse pathological and physiological pathways. This comprehensive review encapsulates our current understanding of the intricate regulatory nexus between NMD and miRNAs, with particular emphasis on the essential role played by UPF3B in neurodevelopment. Additionally, we bring out the significance of the 3'-untranslated region (3'-UTR) as the molecular bridge connecting NMD and miRNA-mediated gene regulation. Furthermore, we provide an in-depth exploration of diverse computational tools tailored for the prediction of potential miRNA targets. To complement these computational approaches, we delineate experimental techniques designed to validate predicted miRNA-mRNA interactions, empowering readers with the knowledge necessary to select the most appropriate methodology for their specific research objectives.
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Affiliation(s)
- Priyanka Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Raja Tamilselvan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Harita Mani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Kusum Kumari Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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33
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Heidarzadehpilehrood R, Pirhoushiaran M. Biomarker potential of competing endogenous RNA networks in Polycystic Ovary Syndrome (PCOS). Noncoding RNA Res 2024; 9:624-640. [PMID: 38571815 PMCID: PMC10988127 DOI: 10.1016/j.ncrna.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/21/2023] [Accepted: 01/08/2024] [Indexed: 04/05/2024] Open
Abstract
Polycystic ovary syndrome (PCOS) is the most common condition affecting women of reproductive age globally. PCOS continues to be the largest contributing factor to female infertility despite significant progress in our knowledge of the molecular underpinnings and treatment of the condition. The fact that PCOS is a very diverse condition makes it one of the key reasons why we haven't been able to overcome it. Non-coding RNAs (ncRNAs) are implicated in the development of PCOS, according to growing evidence. However, it is unclear how the complex regulatory relationships between the many ncRNA types contribute to the growth of this malignancy. Competing endogenous RNA (ceRNA), a recently identified mechanism in the RNA world, suggests regulatory interactions between various RNAs, including long non-coding RNAs (lncRNAs), microRNAs (miRNAs), transcribed pseudogenes, and circular RNAs (circRNAs). Recent studies on PCOS have shown that dysregulation of multiple ceRNA networks (ceRNETs) between these ncRNAs plays crucial roles in developing the defining characteristics of PCOS development. And it is believed that such a finding may open a new door for a deeper comprehension of PCOS's unexplored facets. In addition, it may be able to provide fresh biomarkers and effective therapy targets for PCOS. This review will go over the body of information that exists about the primary roles of ceRNETs before highlighting the developing involvement of several newly found ceRNETs in a number of PCOS characteristics.
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Affiliation(s)
- Roozbeh Heidarzadehpilehrood
- Department of Obstetrics & Gynaecology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Maryam Pirhoushiaran
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, 1417613151, Iran
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Xu M, Li L, Yan J, Li D, Liu Y, Zhang W, Liu Y. Blocking miR396 activity by overexpression MIM396 improved switchgrass tiller number and biomass yield. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:69. [PMID: 38802880 PMCID: PMC11131217 DOI: 10.1186/s13068-024-02514-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND MicroRNA396 (miR396) plays an important role in the regulation of plant growth and development by repressing the expression level of its target growth-regulating factor (GRF) family genes. In our previous study, we found that overexpression of miR396 negatively regulated both tillering and biomass yield in switchgrass (Panicum virgatum L.). We, therefore, speculated that blocking the expression of miR396 could enhance switchgrass tillering and biomass yield. Here, we produced transgenic switchgrass plants overexpressing a target mimicry form of miR396 (MIM396) in wild type (WT) and Os-MIR319b overexpressing switchgrass plant (with higher enzymatic hydrolysis efficiency, but reduced tillering), in which the expression of miR396 was blocked. The phenotype and biological yields of these plants were analyzed. RESULTS Blocking miR396 to improve its target PvGRFs expression in switchgrass improved the tiller number and dry weight of transgenic plants. Further morphological analysis revealed that MIM396 plants increased the number of aerial branches and basal tillers compared to those of wild-type plants. The enzymatic efficiency of MIM396 plants was reduced; however, the total sugar production per plant was still significantly higher than that of wild-type plants due to the increase in biomass. In addition, blocking miR396 in a transgenic switchgrass plant overexpressing Os-MIR319b (TG21-Ms) significantly increased the PvGRF1/3/5 expression level and tiller number and biomass yield. The miR156-target gene PvSPL4, playing a negative role in aerial and basal buds outgrowth, showed significant downregulated in MIM396 and TG21-Ms. Those results indicate that miR396-PvGRFs, through disrupting the PvSPL4 expression, are involved in miR319-PvPCFs in regulating tiller number, at least partly. CONCLUSIONS MIM396 could be used as a molecular tool to improving tiller number and biomass yield in switchgrass wild type and miR319b transgenic plants. This finding may be applied to other graminaceous plants to regulate plant biological yield.
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Affiliation(s)
- Mingzhi Xu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lin Li
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianping Yan
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dayong Li
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, People's Republic of China
| | - Yaling Liu
- National Center of Pratacultural Technology Innovation (Under Preparation), Hohhot, 010010, China
| | - Wanjun Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yanrong Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
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Daniel Thomas S, Vijayakumar K, John L, Krishnan D, Rehman N, Revikumar A, Kandel Codi JA, Prasad TSK, S S V, Raju R. Machine Learning Strategies in MicroRNA Research: Bridging Genome to Phenome. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:213-233. [PMID: 38752932 DOI: 10.1089/omi.2024.0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
MicroRNAs (miRNAs) have emerged as a prominent layer of regulation of gene expression. This article offers the salient and current aspects of machine learning (ML) tools and approaches from genome to phenome in miRNA research. First, we underline that the complexity in the analysis of miRNA function ranges from their modes of biogenesis to the target diversity in diverse biological conditions. Therefore, it is imperative to first ascertain the miRNA coding potential of genomes and understand the regulatory mechanisms of their expression. This knowledge enables the efficient classification of miRNA precursors and the identification of their mature forms and respective target genes. Second, and because one miRNA can target multiple mRNAs and vice versa, another challenge is the assessment of the miRNA-mRNA target interaction network. Furthermore, long-noncoding RNA (lncRNA)and circular RNAs (circRNAs) also contribute to this complexity. ML has been used to tackle these challenges at the high-dimensional data level. The present expert review covers more than 100 tools adopting various ML approaches pertaining to, for example, (1) miRNA promoter prediction, (2) precursor classification, (3) mature miRNA prediction, (4) miRNA target prediction, (5) miRNA- lncRNA and miRNA-circRNA interactions, (6) miRNA-mRNA expression profiling, (7) miRNA regulatory module detection, (8) miRNA-disease association, and (9) miRNA essentiality prediction. Taken together, we unpack, critically examine, and highlight the cutting-edge synergy of ML approaches and miRNA research so as to develop a dynamic and microlevel understanding of human health and diseases.
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Affiliation(s)
- Sonet Daniel Thomas
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | - Krithika Vijayakumar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | - Levin John
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | - Deepak Krishnan
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | - Niyas Rehman
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | - Amjesh Revikumar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
- Kerala Genome Data Centre, Kerala Development and Innovation Strategic Council, Thiruvananthapuram, Kerala, India
| | - Jalaluddin Akbar Kandel Codi
- Department of Surgical Oncology, Yenepoya Medical College, Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | | | - Vinodchandra S S
- Department of Computer Science, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Rajesh Raju
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
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Song DH, Lee JS, Lee JH, Kim DC, Yang JW, Kim MH, Na JM, Cho HK, Yoo J, An HJ. Exosome-mediated secretion of miR-127-3p regulated by RAB27A accelerates metastasis in renal cell carcinoma. Cancer Cell Int 2024; 24:153. [PMID: 38685086 PMCID: PMC11057152 DOI: 10.1186/s12935-024-03334-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND The exosome-mediated extracellular secretion of miRNAs occurs in many cancers, and RAB27A is a potent regulator of exosome secretion. For metastatic renal cell carcinoma (RCC), this study examines the mechanisms of cancer metastasis via the RAB27A-regulated secretion of specific miRNAs. METHODS RAB27A knockdown (KD) and overexpressing (OE) RCC cells were used to examine cell migration and adhesion. The particle counts and sizes of exosomes in RAB27A OE cells were analyzed using Exoview, and those of intraluminal vesicles (ILV) and multivesicular bodies (MVB) were measured using an electron microscope. Analysis of RNA sequences, protein-protein interaction networks, and the competing endogenous RNA (ceRNA) network were used to identify representative downregulated miRNAs that are likely to undergo cargo-sorting into exosomes and subsequent secretion. A molecular beacon of miR-137-3p, one of the most representatively downregulated genes with a fold change of 339, was produced, and its secretion was analyzed using Exoview. RAB27A OE and control cells were incubated in an exosome-containing media to determine the uptake of tumor suppressor miRNAs that affect cancer cell metastasis. RESULTS Migration and cell adhesion were higher in RAB27A OE cells than in RAB27A KD cells. Electron microscopy revealed that the numbers of multivesicular bodies and intraluminal vesicles per cell were higher in RAB27A OE cells than in control cells, suggesting their secretion. The finding revealed that miR-127-3p was sorted into exosomes and disposed of extracellularly. Protein-protein interaction analysis revealed MYCN to be the most significant hub for RAB27A-OE RCC cells. ceRNA network analysis revealed that MAPK4 interacted strongly with miR-127-3p. CONCLUSION The disposal of miR-127-3p through exosome secretion in RAB27A overexpressing cells may not inhibit the MAPK pathway to gain metastatic potential by activating MYCN. The exosomes containing miRNAs are valuable therapeutic targets for cancer treatment.
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Affiliation(s)
- Dae Hyun Song
- Department of Pathology, Gyeongsang National University Changwon Hospital, Changwon, South Korea
- Institute of Medical Sciences, Gyeongsang National University, Jinju, South Korea
- Department of Pathology, Gyeongsang National University School of Medicine, Jinju, South Korea
| | - Jong Sil Lee
- Institute of Medical Sciences, Gyeongsang National University, Jinju, South Korea
- Department of Pathology, Gyeongsang National University School of Medicine, Jinju, South Korea
- Department of Pathology, Gyeongsang National University Hospital, Jinju, South Korea
| | - Jeong-Hee Lee
- Institute of Medical Sciences, Gyeongsang National University, Jinju, South Korea
- Department of Pathology, Gyeongsang National University School of Medicine, Jinju, South Korea
- Department of Pathology, Gyeongsang National University Hospital, Jinju, South Korea
| | - Dong Chul Kim
- Institute of Medical Sciences, Gyeongsang National University, Jinju, South Korea
- Department of Pathology, Gyeongsang National University School of Medicine, Jinju, South Korea
- Department of Pathology, Gyeongsang National University Hospital, Jinju, South Korea
| | - Jung Wook Yang
- Institute of Medical Sciences, Gyeongsang National University, Jinju, South Korea
- Department of Pathology, Gyeongsang National University School of Medicine, Jinju, South Korea
- Department of Pathology, Gyeongsang National University Hospital, Jinju, South Korea
| | - Min Hye Kim
- Department of Pathology, Gyeongsang National University Hospital, Jinju, South Korea
| | - Ji Min Na
- Department of Pathology, Gyeongsang National University Hospital, Jinju, South Korea
| | - Hyun-Kyung Cho
- Institute of Medical Sciences, Gyeongsang National University, Jinju, South Korea
- Department of Ophthalmology, Gyeongsang National University Changwon Hospital, Gyeongsang National University, School of Medicine, Changwon, South Korea
| | - Jiyun Yoo
- Division of Applied Life Science (BK21 Plus) and Research Institute of Life Sciences, Gyeongsang National University, Jinju, South Korea
| | - Hyo Jung An
- Department of Pathology, Gyeongsang National University Changwon Hospital, Changwon, South Korea.
- Institute of Medical Sciences, Gyeongsang National University, Jinju, South Korea.
- Department of Pathology, Gyeongsang National University School of Medicine, Jinju, South Korea.
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Lin CC, Law BF, Hettick JM. MicroRNA-mediated Krüppel-like factor 4 upregulation induces alternatively activated macrophage-associated marker and chemokine transcription in 4,4'-methylene diphenyl diisocyanate exposed macrophages. Xenobiotica 2024:1-19. [PMID: 38568505 DOI: 10.1080/00498254.2024.2334329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
1. Occupational exposure to 4,4'-methylene diphenyl diisocyanate (MDI) is associated with occupational asthma (OA) development. Alveolar macrophage-induced recruitment of immune cells to the lung microenvironment plays an important role during asthma pathogenesis. Previous studies identified that MDI/MDI-glutathione (GSH)-exposure downregulates endogenous hsa-miR-206-3p/hsa-miR-381-3p. Our prior report shows that alternatively activated (M2) macrophage-associated markers/chemokines are induced by MDI/MDI-GSH-mediated Krüppel-Like Factor 4 (KLF4) upregulation in macrophages and stimulates immune cell chemotaxis. However, the underlying molecular mechanism(s) by which MDI/MDI-GSH upregulates KLF4 remain unclear. 2. Following MDI-GSH exposure, microRNA(miR)-inhibitors/mimics or plasmid transfection, endogenous hsa-miR-206-3p/hsa-miR-381-3p, KLF4, or M2 macrophage-associated markers (CD206, TGM2), and chemokines (CCL17, CCL22, CCL24) were measured by either RT-qPCR, western blot, or luciferase assay. 3. MDI-GSH exposure downregulates hsa-miR-206-3p/hsa-miR-381-3p by 1.46- to 9.75-fold whereas upregulates KLF4 by 1.68- to 1.99-fold, respectively. In silico analysis predicts binding between hsa-miR-206-3p/hsa-miR-381-3p and KLF4. Gain- and loss-of-function, luciferase reporter assays and RNA-induced silencing complex-immunoprecipitation (RISC-IP) studies confirm the posttranscriptional regulatory roles of hsa-miR-206-3p/hsa-miR-381-3p and KLF4 in macrophages. Furthermore, hsa-miR-206-3p/hsa-miR-381-3p regulate the expression of M2 macrophage-associated markers and chemokines via KLF4. 4. In conclusion, hsa-miR-206-3p/hsa-miR-381-3p play a major role in regulation of MDI/MDI-GSH-induced M2 macrophage-associated markers and chemokines by targeting the KLF4 transcript, and KLF4-mediated regulation in macrophages.
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Affiliation(s)
- Chen-Chung Lin
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
| | - Brandon F Law
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
| | - Justin M Hettick
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
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McCarty KJ, DeCarlo AN, Ricks RE, Pratt SL, Long NM. Effects of maternal nutrient restriction during gestation on bovine serum microRNA abundance. Anim Reprod Sci 2024; 263:107435. [PMID: 38401394 DOI: 10.1016/j.anireprosci.2024.107435] [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: 05/11/2023] [Revised: 02/05/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024]
Abstract
The objective was to determine the effects of maternal nutrient restriction during gestation on serum microRNA (miRNA) abundance in cattle. Primiparous Angus-cross cows (n=22) were fed either control (CON; to gain 1 Kg/week) or nutrient restricted (NR; 0.55% NEm) diets based on National Research Council requirements. On day 30 of gestation, cows were blocked by body condition and randomly assigned to one of three diets: CON (n=8) days 30-190; NR (n=7) days 30-110 followed by CON days 110-190 (NR/C); or CON (n=7) days 30-110 followed by NR days 110-190 (C/NR). At 190 days of gestation, maternal serum was collected for RNA isolation and analyzed using a miRNA microarray of known Bos taurus sequences. Data were normalized using LOWESS and analyzed via ANOVA. At 190 days of gestation, 16 miRNAs exhibited differential abundance (P<0.05) between treatments. Cows that underwent NR, irrespective of when the insult occurred, had downregulated bta-miR-126-3p compared to CON cows. Bta-miR-16b was downregulated and three miRNAs upregulated in NR/C compared to C/NR and CON cows. Additionally, seven miRNAs were downregulated and four miRNAs upregulated in C/NR compared to NR/C and CON cows. Comparison of NR/C and C/NR cows revealed three differentially abundant (P<0.04) miRNAs (bta-miR-2487_L-2R-3_1ss15CT, bta-miR-215, and bta-miR-760-5p). Top KEGG pathway enrichment of target genes included: pathways in cancer, PI3K-Akt signaling, focal adhesion, Ras signaling, proteoglycans in cancer, and MAPK signaling. In summary, maternal nutrient restriction altered serum miRNA abundance profiles irrespective of the time at which the nutritional insult was induced.
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Affiliation(s)
- K J McCarty
- Department of Animal and Veterinary Sciences, Clemson University, Clemson, SC 29634, USA
| | - A N DeCarlo
- Department of Animal and Veterinary Sciences, Clemson University, Clemson, SC 29634, USA
| | - R E Ricks
- Department of Animal and Veterinary Sciences, Clemson University, Clemson, SC 29634, USA
| | - S L Pratt
- Department of Animal and Veterinary Sciences, Clemson University, Clemson, SC 29634, USA
| | - N M Long
- Department of Animal and Veterinary Sciences, Clemson University, Clemson, SC 29634, USA.
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Tong S, Zhu Y, Leng Y, Wu Y, Xiao X, Zhao W, Tan S. Restoration of miR-299-3p promotes macrophage phagocytosis and suppresses malignant phenotypes in breast cancer carcinogenesis via dual-targeting CD47 and ABCE1. Int Immunopharmacol 2024; 130:111708. [PMID: 38394889 DOI: 10.1016/j.intimp.2024.111708] [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: 12/11/2023] [Revised: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024]
Abstract
Immunoevasion has been a severe obstacle for the clinical treatment of breast cancer (BC). CD47, known as an anti-phagocytic molecule, plays a key role in governing the evasion of tumor cells from immune surveillance by interacting with signal-regulated protein α (SIRPα) on macrophages. Here, we report for the first time that miR-299-3p is a direct regulator of CD47 with tumor suppressive effects both in vitro and in vivo. miRNA expression profiles and overall survival of BC cohorts from the Cancer Genome Atlas, METABRIC, or GSE19783 datasets showed that miR-299-3p is downregulated in BC tissues and that BC patients with low levels of miR-299-3p have poorer prognoses. Using dual-luciferase reporter, qRT-PCR, Western blot, and phagocytosis assays, we proved that restoration of miR-299-3p can suppress CD47 expression by directly targeting the predicted seed sequence "CCCACAU" in its 3'-UTR, leading to phagocytosis of BC cells by macrophages, whereas miR-299-3p inhibition or deletion reversed this effect. Additionally, Gene Ontology (GO) analysis and a variety of confirmatory experiments revealed that miR-299-3p was inversely correlated with cell proliferation, migration, and the cell cycle process. Mechanistically, miR-299-3p can also directly target ABCE1, an essential ribosome recycling factor, alleviating these malignant phenotypes of BC cells. In vivo BC xenografts based on nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice further proved that restoration of miR-299-3p resulted in a significant suppression of tumorigenesis and a promotion of macrophage activation and infiltration. Overall, our study suggested that miR-299-3p is a potent inhibitor of CD47 and ABCE1 to exhibit bifunctional BC-suppressing effects through immune activation conjugated with malignant behavior inhibition in breast carcinogenesis and thus can potentially serve as a novel therapeutic target for BC.
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Affiliation(s)
- Shoufang Tong
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druhavggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, PR China.
| | - Yingli Zhu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druhavggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, PR China.
| | - Yeqing Leng
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druhavggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, PR China.
| | - Yunling Wu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druhavggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, PR China.
| | - Xingxing Xiao
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druhavggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, PR China.
| | - Wenfeng Zhao
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druhavggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, PR China.
| | - Shuhua Tan
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druhavggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, PR China.
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Andersen C, Walters M, Bundgaard L, Berg LC, Vonk LA, Lundgren-Åkerlund E, Henriksen BL, Lindegaard C, Skovgaard K, Jacobsen S. Intraarticular treatment with integrin α10β1-selected mesenchymal stem cells affects microRNA expression in experimental post-traumatic osteoarthritis in horses. Front Vet Sci 2024; 11:1374681. [PMID: 38596460 PMCID: PMC11002141 DOI: 10.3389/fvets.2024.1374681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/08/2024] [Indexed: 04/11/2024] Open
Abstract
Osteoarthritis (OA) remains a major cause of lameness in horses, which leads to lost days of training and early retirement. Still, the underlying pathological processes are poorly understood. MicroRNAs (miRNAs) are small non-coding RNAs that serve as regulators of many biological processes including OA. Analysis of miRNA expression in diseased joint tissues such as cartilage and synovial membrane may help to elucidate OA pathology. Since integrin α10β1-selected mesenchymal stem cell (integrin α10-MSC) have shown mitigating effect on equine OA we here investigated the effect of integrin α10-MSCs on miRNA expression. Cartilage and synovial membrane was harvested from the middle carpal joint of horses with experimentally induced, untreated OA, horses with experimentally induced OA treated with allogeneic adipose-derived MSCs selected for the marker integrin α10-MSCs, and from healthy control joints. miRNA expression in cartilage and synovial membrane was established by quantifying 70 pre-determined miRNAs by qPCR. Differential expression of the miRNAs was evaluated by comparing untreated OA and control, untreated OA and MSC-treated OA, and joints with high and low pathology score. A total of 60 miRNAs were successfully quantified in the cartilage samples and 55 miRNAs were quantified in the synovial membrane samples. In cartilage, miR-146a, miR-150 and miR-409 had significantly higher expression in untreated OA joints than in control joints. Expression of miR-125a-3p, miR-150, miR-200c, and miR-499-5p was significantly reduced in cartilage from MSC-treated OA joints compared to the untreated OA joints. Expression of miR-139-5p, miR-150, miR-182-5p, miR-200a, miR-378, miR-409-3p, and miR-7177b in articular cartilage reflected pathology score. Several of these miRNAs are known from research in human patients with OA and from murine OA models. Our study shows that these miRNAs are also differentially expressed in experimental equine OA, and that expression depends on OA severity. Moreover, MSC treatment, which resulted in less severe OA, also affected miRNA expression in cartilage.
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Affiliation(s)
- Camilla Andersen
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Taastrup, Denmark
| | - Marie Walters
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Taastrup, Denmark
| | - Louise Bundgaard
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Taastrup, Denmark
| | - Lise Charlotte Berg
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Taastrup, Denmark
| | | | | | | | - Casper Lindegaard
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Taastrup, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Stine Jacobsen
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Taastrup, Denmark
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Sun B, Meng XH, Li YM, Lin H, Xiao ZD. MicroRNA-18a prevents senescence of mesenchymal stem cells by targeting CTDSPL. Aging (Albany NY) 2024; 16:4904-4919. [PMID: 38460957 PMCID: PMC10968691 DOI: 10.18632/aging.205642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/26/2023] [Indexed: 03/11/2024]
Abstract
Stem cell therapy requires massive-scale homogeneous stem cells under strict qualification control. However, Prolonged ex vivo expansion impairs the biological functions and results in senescence of mesenchymal stem cells (MSCs). We investigated the function of CTDSPL in the premature senescence process of MSCs and clarified that miR-18a-5p played a prominent role in preventing senescence of long-term cultured MSCs and promoting the self-renewal ability of MSCs. Over-expression of CTDSPL resulted in an enlarged morphology, up-regulation of p16 and accumulation of SA-β-gal of MSCs. The reduced phosphorylated RB suggested cell cycle arrest of MSCs. All these results implied that CTDSPL induced premature senescence of MSCs. We further demonstrated that miR-18a-5p was a putative regulator of CTDSPL by luciferase reporter assay. Inhibition of miR-18a-5p promoted the expression of CTDSPL and induced premature senescence of MSCs. Continuous overexpression of miR-18a-5p improved self-renewal of MSCs by reducing ROS level, increased expression of Oct4 and Nanog, and promoted growth rate and differentiation capability. We reported for the first time that the dynamic interaction of miR-18a-5p and CTDSPL is crucial for stem cell senescence.
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Affiliation(s)
- Bo Sun
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xian-Hui Meng
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yu-Min Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Hao Lin
- Department of Clinical Science and Research, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Zhong-Dang Xiao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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Zhang J, Zhu H, Liu Y, Li X. miTDS: Uncovering miRNA-mRNA interactions with deep learning for functional target prediction. Methods 2024; 223:65-74. [PMID: 38280472 DOI: 10.1016/j.ymeth.2024.01.011] [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: 11/01/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 01/29/2024] Open
Abstract
MicroRNAs (miRNAs) are vital in regulating gene expression through binding to specific target sites on messenger RNAs (mRNAs), a process closely tied to cancer pathogenesis. Identifying miRNA functional targets is essential but challenging, due to incomplete genome annotation and an emphasis on known miRNA-mRNA interactions, restricting predictions of unknown ones. To address those challenges, we have developed a deep learning model based on miRNA functional target identification, named miTDS, to investigate miRNA-mRNA interactions. miTDS first employs a scoring mechanism to eliminate unstable sequence pairs and then utilizes a dynamic word embedding model based on the transformer architecture, enabling a comprehensive analysis of miRNA-mRNA interaction sites by harnessing the global contextual associations of each nucleotide. On this basis, miTDS fuses extended seed alignment representations learned in the multi-scale attention mechanism module with dynamic semantic representations extracted in the RNA-based dual-path module, which can further elucidate and predict miRNA and mRNA functions and interactions. To validate the effectiveness of miTDS, we conducted a thorough comparison with state-of-the-art miRNA-mRNA functional target prediction methods. The evaluation, performed on a dataset cross-referenced with entries from MirTarbase and Diana-TarBase, revealed that miTDS surpasses current methods in accurately predicting functional targets. In addition, our model exhibited proficiency in identifying A-to-I RNA editing sites, which represents an aberrant interaction that yields valuable insights into the suppression of cancerous processes.
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Affiliation(s)
- Jialin Zhang
- School of Artificial Intelligence, Jilin University, Changchun 130012, Jilin, China
| | - Haoran Zhu
- School of Artificial Intelligence, Jilin University, Changchun 130012, Jilin, China
| | - Yin Liu
- China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin, China
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Changchun 130012, Jilin, China.
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Vaswani CM, Simone J, Pavelick JL, Wu X, Tan GW, Ektesabi AM, Gupta S, Tsoporis JN, Dos Santos CC. Tiny Guides, Big Impact: Focus on the Opportunities and Challenges of miR-Based Treatments for ARDS. Int J Mol Sci 2024; 25:2812. [PMID: 38474059 DOI: 10.3390/ijms25052812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Acute Respiratory Distress Syndrome (ARDS) is characterized by lung inflammation and increased membrane permeability, which represents the leading cause of mortality in ICUs. Mechanical ventilation strategies are at the forefront of supportive approaches for ARDS. Recently, an increasing understanding of RNA biology, function, and regulation, as well as the success of RNA vaccines, has spurred enthusiasm for the emergence of novel RNA-based therapeutics. The most common types of RNA seen in development are silencing (si)RNAs, antisense oligonucleotide therapy (ASO), and messenger (m)RNAs that collectively account for 80% of the RNA therapeutics pipeline. These three RNA platforms are the most mature, with approved products and demonstrated commercial success. Most recently, miRNAs have emerged as pivotal regulators of gene expression. Their dysregulation in various clinical conditions offers insights into ARDS pathogenesis and offers the innovative possibility of using microRNAs as targeted therapy. This review synthesizes the current state of the literature to contextualize the therapeutic potential of miRNA modulation. It considers the potential for miR-based therapeutics as a nuanced approach that incorporates the complexity of ARDS pathophysiology and the multifaceted nature of miRNA interactions.
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Affiliation(s)
- Chirag M Vaswani
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
| | - Julia Simone
- Department of Medicine, McMaster University, Hamilton, ON L8V 5C2, Canada
| | - Jacqueline L Pavelick
- Institute of Medical Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Xiao Wu
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
| | - Greaton W Tan
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
| | - Amin M Ektesabi
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
- Institute of Medical Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sahil Gupta
- Faculty of Medicine, School of Medicine, The University of Queensland, Herston, QLD 4006, Australia
| | - James N Tsoporis
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
| | - Claudia C Dos Santos
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
- Institute of Medical Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Interdepartmental Division of Critical Care, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
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Fromm B, Sorger T. Rapid adaptation of cellular metabolic rate to the MicroRNA complements of mammals and its relevance to the evolution of endothermy. iScience 2024; 27:108740. [PMID: 38327773 PMCID: PMC10847693 DOI: 10.1016/j.isci.2023.108740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 09/13/2023] [Accepted: 12/12/2023] [Indexed: 02/09/2024] Open
Abstract
The metabolic efficiency of mammalian cells depends on the attenuation of intrinsic translation noise by microRNAs. We devised a metric of cellular metabolic rate (cMR), rMR/Mexp optimally fit to the number of microRNA families (mirFam), that is robust to variation in mass and sensitive to body temperature (Tb), consistent with the heat dissipation limit theory of Speakman and Król (2010). Using mirFam as predictor, an Ornstein-Uhlenbeck process of stabilizing selection, with an adaptive shift at the divergence of Boreoeutheria, accounted for 95% of the variation in cMR across mammals. Branchwise rates of evolution of cMR, mirFam and Tb concurrently increased 6- to 7-fold at the divergence of Boreoeutheria, independent of mass. Cellular MR variation across placental mammals was also predicted by the sum of model conserved microRNA-target interactions, revealing an unexpected degree of integration of the microRNA-target apparatus into the energy economy of the mammalian cell.
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Affiliation(s)
- Bastian Fromm
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Thomas Sorger
- Department of Biology, Roger Williams University, Bristol, RI 02809, USA
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Aljedaie MM, Alam P. In silico identification of human microRNAs pointing centrin genes in Leishmania donovani: Considering the RNAi-mediated gene control. Front Genet 2024; 14:1329339. [PMID: 38390455 PMCID: PMC10883313 DOI: 10.3389/fgene.2023.1329339] [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: 10/28/2023] [Accepted: 12/12/2023] [Indexed: 02/24/2024] Open
Abstract
Leishmaniasis, a parasitic disease caused by different species of the protozoa parasite Leishmania, is a neglected tropical human disease that is endemic in about a hundred countries worldwide. According to the World Health Organization (WHO), the annual incidence of cutaneous leishmaniasis (CL) is estimated to be 0.7-1.2 million cases globally, whereas the annual incidence of visceral leishmaniasis is estimated to be 0.2-0.4 million cases. In many eukaryotic organisms, including human beings and protozoan parasites, centrin genes encode proteins that play essential roles within the centrosome or basal body. Human microRNAs (miRNAs) have been linked to several infectious and non-infectious diseases associated with pathogen-host interactions, and they play the emphatic roles as gene expression regulators. In this study, we used the MirTarget bioinformatics tool, which is a machine learning-based approach implemented in miRDB, to predict the target of human miRNAs in Leishmania donovani centrin genes. For cross-validation, we utilized additional prediction algorithms, namely, RNA22 and RNAhybrid, targeting all five centrin isotypes. The centrin-3 (LDBPK_342160) and putative centrin-5 (NC_018236.1) genes in L. donovani were targeted by eight and twelve human miRNAs, respectively, among 2,635 known miRNAs (miRBase). hsa-miR-5193 consistently targeted both genes. Using TargetScan, TarBase, miRecords, and miRTarBase, we identified miRNA targets and off-targets in human homologs of centrin, inflammation, and immune-responsive genes. Significant targets were screened based on GO terminologies and KEGG pathway-enrichment analysis (Log10 p-value >0.0001). In silico tools that predict the biological roles of human miRNAs as primary gene regulators in pathogen-host interactions help unravel the regulatory patterns of these miRNAs, particularly in the early stages of inflammatory responses. It is also noted that these miRNAs played an important role in the late phase of adaptive immune response, inclusively their impacts on the immune system's response to L. donovani.
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Affiliation(s)
- Manei M Aljedaie
- Department of Biology, College of Sciences and Humanities, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Pravej Alam
- Department of Biology, College of Sciences and Humanities, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
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Lozano-Velasco E, Inácio JM, Sousa I, Guimarães AR, Franco D, Moura G, Belo JA. miRNAs in Heart Development and Disease. Int J Mol Sci 2024; 25:1673. [PMID: 38338950 PMCID: PMC10855082 DOI: 10.3390/ijms25031673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Cardiovascular diseases (CVD) are a group of disorders that affect the heart and blood vessels. They include conditions such as myocardial infarction, coronary artery disease, heart failure, arrhythmia, and congenital heart defects. CVDs are the leading cause of death worldwide. Therefore, new medical interventions that aim to prevent, treat, or manage CVDs are of prime importance. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the posttranscriptional level and play important roles in various biological processes, including cardiac development, function, and disease. Moreover, miRNAs can also act as biomarkers and therapeutic targets. In order to identify and characterize miRNAs and their target genes, scientists take advantage of computational tools such as bioinformatic algorithms, which can also assist in analyzing miRNA expression profiles, functions, and interactions in different cardiac conditions. Indeed, the combination of miRNA research and bioinformatic algorithms has opened new avenues for understanding and treating CVDs. In this review, we summarize the current knowledge on the roles of miRNAs in cardiac development and CVDs, discuss the challenges and opportunities, and provide some examples of recent bioinformatics for miRNA research in cardiovascular biology and medicine.
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Affiliation(s)
- Estefania Lozano-Velasco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (D.F.)
| | - José Manuel Inácio
- Stem Cells and Development Laboratory, iNOVA4Health, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1150-082 Lisbon, Portugal;
| | - Inês Sousa
- Genome Medicine Lab, Department of Medical Sciences, Institute for Biomedicine–iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (I.S.); (A.R.G.); (G.M.)
| | - Ana Rita Guimarães
- Genome Medicine Lab, Department of Medical Sciences, Institute for Biomedicine–iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (I.S.); (A.R.G.); (G.M.)
| | - Diego Franco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (D.F.)
| | - Gabriela Moura
- Genome Medicine Lab, Department of Medical Sciences, Institute for Biomedicine–iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (I.S.); (A.R.G.); (G.M.)
| | - José António Belo
- Stem Cells and Development Laboratory, iNOVA4Health, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1150-082 Lisbon, Portugal;
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Anuradha U, Mehra NK, Khatri DK. Understanding molecular mechanisms and miRNA-based targets in diabetes foot ulcers. Mol Biol Rep 2024; 51:82. [PMID: 38183502 DOI: 10.1007/s11033-023-09074-0] [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: 07/10/2023] [Accepted: 11/21/2023] [Indexed: 01/08/2024]
Abstract
In today's culture, obesity and overweight are serious issues that have an impact on how quickly diabetes develops and how it causes complications. For the development of more effective therapies, it is crucial to understand the molecular mechanisms underlying the chronic problems of diabetes. The most prominent effects of diabetes are microvascular abnormalities such as retinopathy, nephropathy, and neuropathy, especially diabetes foot ulcers, as well as macrovascular abnormalities such as heart disease and atherosclerosis. MicroRNAs (miRNAs), which are highly conserved endogenous short non-coding RNA molecules, have been implicated in several physiological functions recently, including the earliest stages of the disease. By binding to particular messenger RNAs (mRNAs), which cause mRNA degradation, translation inhibition, or even gene activation, it primarily regulates posttranscriptional gene expression. These molecules exhibit considerable potential as diagnostic biomarkers for disease and are interesting treatment targets. This review will provide an overview of the latest findings on the key functions that miRNAs role in diabetes and its complications, with an emphasis on the various stages of diabetic wound healing.
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Affiliation(s)
- Urati Anuradha
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Hyderabad, Telangana, 500037, India
| | - Neelesh Kumar Mehra
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Hyderabad, Telangana , 500037, India.
| | - Dharmendra Kumar Khatri
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Hyderabad, Telangana, 500037, India.
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Ahirwar SS, Rizwan R, Sethi S, Shahid Z, Malviya S, Khandia R, Agarwal A, Kotnis A. Comparative Analysis of Published Database Predicting MicroRNA Binding in 3'UTR of mRNA in Diverse Species. Microrna 2024; 13:2-13. [PMID: 37929739 DOI: 10.2174/0122115366261005231018070640] [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: 05/06/2023] [Revised: 09/03/2023] [Accepted: 09/15/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Micro-RNAs are endogenous non-coding RNA moieties of 22-27 nucleotides that play a crucial role in the regulation of various biological processes and make them useful prognostic and diagnostic biomarkers. Discovery and experimental validation of miRNA is a laborious and time-consuming process. For early prediction, multiple bioinformatics databases are available for miRNA target prediction; however, their utility can confuse amateur researchers in selecting the most appropriate tools for their study. OBJECTIVE This descriptive review aimed to analyse the usability of the existing database based on the following criteria: accessibility, efficiency, interpretability, updatability, and flexibility for miRNA target prediction of 3'UTR of mRNA in diverse species so that the researchers can utilize the database most appropriate to their research. METHODS A systematic literature search was performed in PubMed, Google Scholar and Scopus databases up to November 2022. ≥10,000 articles found online, including ⁓130 miRNA tools, which contain various information on miRNA. Out of them, 31 databases that provide information on validated 3'UTR miRNAs target databases were included and analysed in this review. RESULTS These miRNA database tools are being used in varied areas of biological research to select the most suitable miRNA for their experimental validation. These databases, updated until the year 2021, consist of miRNA-related data from humans, animals, mice, plants, viruses etc. They contain 525-29806351 data entries, and information from most databases is freely available on the online platform. CONCLUSION Reviewed databases provide significant information, but not all information is accurate or up-to-date. Therefore, Diana-TarBase and miRWalk are the most comprehensive and up-to-date databases.
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Affiliation(s)
- Sonu Singh Ahirwar
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Rehma Rizwan
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Samdish Sethi
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Zainab Shahid
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Shivani Malviya
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, Madhya Pradesh, 462026, India
| | - Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, Madhya Pradesh, 462026, India
| | - Amit Agarwal
- Department of Neurosurgery, All India Institute of Medical Sciences Bhopal, Bhopal MP, 462020, India
| | - Ashwin Kotnis
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
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Guo D, Wei Y, Li X, Bai Y, Liu Z, Li J, Chen Z, Shi B, Zhang X, Zhao Z, Hu J, Han X, Wang J, Liu X, Li S, Zhao F. Comprehensive Analysis of miRNA and mRNA Expression Profiles during Muscle Development of the Longissimus Dorsi Muscle in Gannan Yaks and Jeryaks. Genes (Basel) 2023; 14:2220. [PMID: 38137042 PMCID: PMC10742600 DOI: 10.3390/genes14122220] [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: 11/17/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
A hybrid offspring of Gannan yak and Jersey cattle, the Jeryak exhibits apparent hybrid advantages over the Gannan yak in terms of production performance and other factors. The small non-coding RNAs known as miRNAs post-transcriptionally exert a significant regulatory influence on gene expression. However, the regulatory mechanism of miRNA associated with muscle development in Jeryak remains elusive. To elucidate the regulatory role of miRNAs in orchestrating skeletal muscle development in Jeryak, we selected longissimus dorsi muscle tissues from Gannan yak and Jeryak for transcriptome sequencing analysis. A total of 230 (DE) miRNAs were identified in the longissimus dorsi muscle of Gannan yak and Jeryak. The functional enrichment analysis revealed a significant enrichment of target genes from differentially expressed (DE)miRNAs in signaling pathways associated with muscle growth, such as the Ras signaling pathway and the MAPK signaling pathway. The network of interactions between miRNA and mRNA suggest that some (DE)miRNAs, including miR-2478-z, miR-339-x, novel-m0036-3p, and novel-m0037-3p, played a pivotal role in facilitating muscle development. These findings help us to deepen our understanding of the hybrid dominance of Jeryaks and provide a theoretical basis for further research on the regulatory mechanisms of miRNAs associated with Jeryak muscle growth and development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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Wen J, Liu J, Wan L, Wang F. Long noncoding RNA/circular RNA regulates competitive endogenous RNA networks in rheumatoid arthritis: molecular mechanisms and traditional Chinese medicine therapeutic significances. Ann Med 2023; 55:973-989. [PMID: 36905646 PMCID: PMC10795602 DOI: 10.1080/07853890.2023.2172605] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/20/2023] [Indexed: 03/13/2023] Open
Abstract
Rheumatoid arthritis (RA) is a systemic and autoimmune disease that is mainly featured abnormal fibroblast-like synoviocyte (FLS) proliferation and inflammatory cell infiltration. Abnormal expression or function of long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are closely related to human diseases, including RA. There has been increasing evidence showing that in the competitive endogenous RNA (ceRNA) networks, both lncRNA and circRNA are vital in the biological functions of cells. Nevertheless, the exact mechanism of ceRNA in RA remains to be investigated. Herein, we summarized the molecular potencies of lncRNA/circRNA-mediated ceRNA networks in RA, with emphasis on the phenotypic regulation of ceRNA in the progression of RA, including regulation of proliferation, invasion, inflammation and apoptosis, as well as the role of ceRNA in traditional Chinese medicine (TCM) in the treatment of RA. In addition, we also discussed the future direction and potential clinical value of ceRNA in the treatment of RA, which may provide potential reference value for clinical trials of TCM therapy for the treatment of RA.Key messagesLong noncoding RNA/circular RNA can work as the competitive endogenous RNA sponge and participate in the pathogenesis of rheumatoid arthritis.Traditional Chinese medicine and its agents have shown potential roles in the prevention and treatment of rheumatoid arthritis via competitive endogenous RNA.
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Affiliation(s)
- Jianting Wen
- Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of Rheumatology, Anhui Academy of Chinese Medicine, Hefei, Anhui, China
- Key Laboratory of Xin’an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Jian Liu
- Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of Rheumatology, Anhui Academy of Chinese Medicine, Hefei, Anhui, China
- Department of Internal Medicine Application Foundation Research and Development, Anhui Province—Key Laboratory of Modern Chinese Medicine, Hefei, Anhui, China
| | - Lei Wan
- Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of Rheumatology, Anhui Academy of Chinese Medicine, Hefei, Anhui, China
- Department of Internal Medicine Application Foundation Research and Development, Anhui Province—Key Laboratory of Modern Chinese Medicine, Hefei, Anhui, China
| | - Fanfan Wang
- Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of Rheumatology, Anhui Academy of Chinese Medicine, Hefei, Anhui, China
- Department of Internal Medicine Application Foundation Research and Development, Anhui Province—Key Laboratory of Modern Chinese Medicine, Hefei, Anhui, China
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