1
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Gao C, Nie H. Exploring the Heat-Responsive miRNAs and their Target Gene Regulation in Ruditapes philippinarum Under Acute Heat Stress. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:810-826. [PMID: 39046591 DOI: 10.1007/s10126-024-10348-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/13/2024] [Indexed: 07/25/2024]
Abstract
This study aimed to investigate the inherent molecular regulatory mechanisms of Ruditapes philippinarum in response to extremely high-temperature environments and to enhance the sustainable development of the R. philippinarum aquaculture industry. In this study, we established a differential expression profile of miRNA under acute heat stress and identified a total of 46 known miRNAs and 80 novel miRNAs, three of which were detected to be significantly differentially expressed. We analyzed the functions of target genes regulated by differentially expressed miRNAs (DEMs) of R. philippinarum. The findings of the KEGG enrichment analysis revealed that 29 enriched pathways in the group were subjected to acute heat stress. Notably, fatty acid metabolism, FoxO signaling pathway, TGF-β signaling pathway, and ubiquitin-mediated proteolysis were found to play significant roles in response to acute heat stress. We established a regulatory map of DEMs and their target genes in response to heat stress and constructed the miRNA-mRNA regulation network. This study provides valuable insights into the response of R. philippinarum to high temperature, helping to understand its underlying molecular regulatory mechanisms under high-temperature stress.
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Affiliation(s)
- Changsheng Gao
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China.
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, China.
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2
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Aghajani Mir M. Illuminating the pathogenic role of SARS-CoV-2: Insights into competing endogenous RNAs (ceRNAs) regulatory networks. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105613. [PMID: 38844190 DOI: 10.1016/j.meegid.2024.105613] [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: 03/07/2024] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
The appearance of SARS-CoV-2 in 2019 triggered a significant economic and health crisis worldwide, with heterogeneous molecular mechanisms that contribute to its development are not yet fully understood. Although substantial progress has been made in elucidating the mechanisms behind SARS-CoV-2 infection and therapy, it continues to rank among the top three global causes of mortality due to infectious illnesses. Non-coding RNAs (ncRNAs), being integral components across nearly all biological processes, demonstrate effective importance in viral pathogenesis. Regarding viral infections, ncRNAs have demonstrated their ability to modulate host reactions, viral replication, and host-pathogen interactions. However, the complex interactions of different types of ncRNAs in the progression of COVID-19 remains understudied. In recent years, a novel mechanism of post-transcriptional gene regulation known as "competing endogenous RNA (ceRNA)" has been proposed. Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and viral ncRNAs function as ceRNAs, influencing the expression of associated genes by sequestering shared microRNAs. Recent research on SARS-CoV-2 has revealed that disruptions in specific ceRNA regulatory networks (ceRNETs) contribute to the abnormal expression of key infection-related genes and the establishment of distinctive infection characteristics. These findings present new opportunities to delve deeper into the underlying mechanisms of SARS-CoV-2 pathogenesis, offering potential biomarkers and therapeutic targets. This progress paves the way for a more comprehensive understanding of ceRNETs, shedding light on the intricate mechanisms involved. Further exploration of these mechanisms holds promise for enhancing our ability to prevent viral infections and develop effective antiviral treatments.
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Affiliation(s)
- Mahsa Aghajani Mir
- Deputy of Research and Technology, Babol University of Medical Sciences, Babol, Iran.
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3
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Tang Y, Zhang S, Yang X, Chen Y, Chen S, Xi Q, Chao L, Huang Z, Nie L. In situ imaging of intracellular miRNAs in tumour cells by branched hybridisation chain reaction. Cell Prolif 2024:e13721. [PMID: 39034809 DOI: 10.1111/cpr.13721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 06/28/2024] [Accepted: 07/10/2024] [Indexed: 07/23/2024] Open
Abstract
The ability to visualise microRNA in situ is crucial for studying microRNAs, their microRNA-associated biological functions and disease diagnosis. Traditional fluorescence in situ hybridisation methods based on paraformaldehyde fixation of microRNAs suffer from release of microRNAs from cells, which limits the sensitivity of in situ hybridisation, making them unsuitable for the detection of small, low-abundance microRNAs. To reduce the loss, microRNAs were covalently cross-linked to proteins within cells by combining EDC and paraformaldehyde, and the target microRNA was used as the initiator chain for a branched hybridisation chain reaction to detect microRNA expression levels in situ. A simplified branched hybridisation chain reaction can be realised by coupling two hybridisation chain reaction circuits with a hairpin linker. Upon forming the primary hybridisation chain reaction product with extended sequence, this sequence reacts with the linker hairpin H3 to release the initiator sequence, resulting in the formation of numerous dendritic branched hybridisation chain reaction products. Imaging results show that this technique can detect microRNAs with high sensitivity and selectivity at both the single-cell and single-molecule levels. Compared with the traditional fluorescence in situ hybridisation technique, this method greatly improves the sensitivity and image resolution of in situ imaging detection. Therefore, we believe that the target-initiated branched hybridisation chain reaction based in situ detection method provides a reliable assay platform for analysing disease-related microRNA expression.
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Affiliation(s)
- Ying Tang
- Hunan Key Lab of Biomedical Materials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
| | - Siwei Zhang
- Hunan Key Lab of Biomedical Materials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
| | - Xinyu Yang
- Hunan Key Lab of Biomedical Materials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
| | - Yao Chen
- Hunan Key Lab of Biomedical Materials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
| | - Sha Chen
- Hunan Key Lab of Biomedical Materials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
- Zhuzhou City Joint Laboratory of Environmental Microbiology and Plant Resources Utilization, Zhuzhou, China
| | - Qiang Xi
- Hunan Prevention and Treatment Institute for Occupational Diseases, Changsha, China
| | - Long Chao
- Hunan Key Lab of Biomedical Materials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
| | - Zhao Huang
- Hunan Key Lab of Biomedical Materials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
| | - Libo Nie
- Hunan Key Lab of Biomedical Materials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
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4
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Chowdhury D, Nayeem M, Vanderven HA, Sarker S. Role of miRNA in Highly Pathogenic H5 Avian Influenza Virus Infection: An Emphasis on Cellular and Chicken Models. Viruses 2024; 16:1102. [PMID: 39066264 PMCID: PMC11281567 DOI: 10.3390/v16071102] [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: 06/19/2024] [Revised: 07/01/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
The avian influenza virus, particularly the H5N1 strain, poses a significant and ongoing threat to both human and animal health. Recent outbreaks have affected domestic and wild birds on a massive scale, raising concerns about the virus' spread to mammals. This review focuses on the critical role of microRNAs (miRNAs) in modulating pro-inflammatory signaling pathways during the pathogenesis of influenza A virus (IAV), with an emphasis on highly pathogenic avian influenza (HPAI) H5 viral infections. Current research indicates that miRNAs play a significant role in HPAI H5 infections, influencing various aspects of the disease process. This review aims to synthesize recent findings on the impact of different miRNAs on immune function, viral cytopathogenicity, and respiratory viral replication. Understanding these mechanisms is essential for developing new therapeutic strategies to combat avian influenza and mitigate its effects on both human and animal populations.
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Affiliation(s)
- Dibakar Chowdhury
- Laboratory of Influenza Research, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea;
| | - Md. Nayeem
- One Health Institute, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram 4225, Bangladesh;
| | - Hillary A. Vanderven
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia;
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC 3010, Australia
| | - Subir Sarker
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia;
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
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Satake E, Krolewski B, Kobayashi H, Md Dom ZI, Ricca J, Wilson JM, Hoon DS, Duffin KL, Pezzolesi MG, Krolewski AS. Preanalytical considerations in quantifying circulating miRNAs that predict end-stage kidney disease in diabetes. JCI Insight 2024; 9:e174153. [PMID: 38912578 DOI: 10.1172/jci.insight.174153] [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: 07/26/2023] [Accepted: 05/08/2024] [Indexed: 06/25/2024] Open
Abstract
Our previous study identified 8 risk and 9 protective plasma miRNAs associated with progression to end-stage kidney disease (ESKD) in diabetes. This study aimed to elucidate preanalytical factors that influence the quantification of circulating miRNAs. Using the EdgeSeq platform, which quantifies 2,002 miRNAs in plasma, including ESKD-associated miRNAs, we compared miRNA profiles in whole plasma versus miRNA profiles in RNA extracted from the same plasma specimens. Less than half of the miRNAs were detected in standard RNA extraction from plasma. Detection of individual and concentrations of miRNAs were much lower when RNA extracted from plasma was quantified by RNA sequencing (RNA-Seq) or quantitative reverse transcription PCR (qRT-PCR) platforms compared with EdgeSeq. Plasma profiles of miRNAs determined by the EdgeSeq platform had excellent reproducibility in assessment and had no variation with age, sex, hemoglobin A1c, BMI, and cryostorage time. The risk ESKD-associated miRNAs were detected and measured accurately only in whole plasma and using the EdgeSeq platform. Protective ESKD-associated miRNAs were detected by all platforms except qRT-PCR; however, correlations among concentrations obtained with different platforms were weak or nonexistent. In conclusion, preanalytical factors have a profound effect on detection and quantification of circulating miRNAs in ESKD in diabetes. Quantification of miRNAs in whole plasma and using the EdgeSeq platform may be the preferable method to study profiles of circulating cell-free miRNAs associated with ESKD and possibly other diseases.
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Affiliation(s)
- Eiichiro Satake
- Research Division, Joslin Diabetes Center, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Bozena Krolewski
- Research Division, Joslin Diabetes Center, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Hiroki Kobayashi
- Research Division, Joslin Diabetes Center, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Division of Nephrology, Hypertension, and Endocrinology, Nihon University School of Medicine, Tokyo, Japan
| | - Zaipul I Md Dom
- Research Division, Joslin Diabetes Center, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph Ricca
- Research Division, Joslin Diabetes Center, Boston, Massachusetts, USA
| | | | - Dave Sb Hoon
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Providence Health and Service, Santa Monica, California, USA
| | | | - Marcus G Pezzolesi
- Department of Internal Medicine, Division of Nephrology and Hypertension, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Andrzej S Krolewski
- Research Division, Joslin Diabetes Center, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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6
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Tsai YC, Chang CH, Chong YB, Wu CH, Tsai HP, Cheng TL, Lin CL. MicroRNA-195-5p Attenuates Intracerebral-Hemorrhage-Induced Brain Damage by Inhibiting MMP-9/MMP-2 Expression. Biomedicines 2024; 12:1373. [PMID: 38927580 PMCID: PMC11201846 DOI: 10.3390/biomedicines12061373] [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: 05/14/2024] [Revised: 06/14/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Intracerebral hemorrhage (ICH) remains a devastating disease with high mortality, and there is a lack of effective strategies to improve functional outcomes. The primary injury of ICH is mechanical damage to brain tissue caused by the hematoma. Secondary injury, resulting from inflammation, red cell lysis, and thrombin production, presents a potential target for therapeutic intervention. Inflammation, crucial in secondary brain injury, involves both cellular and molecular components. MicroRNAs (miRNAs) are vital regulators of cell growth, differentiation, and apoptosis. Their deregulation may lead to diseases, and modulating miRNA expression has shown therapeutic potential, especially in cancer. Recent studies have implicated miRNAs in the pathogenesis of stroke, affecting endothelial dysfunction, neurovascular integrity, edema, apoptosis, inflammation, and extracellular matrix remodeling. Preclinical and human studies support the use of miRNA-directed gene modulation as a therapeutic strategy for ICH. Our study focused on the effects of miR-195 in ICH models. Neurological tests, including the corner turn and grip tests, indicated that miR-195 treatment led to improvements in motor function impairments caused by ICH. Furthermore, miR-195-5p significantly reduced brain edema in the ipsilateral hemisphere and restored blood-brain barrier (BBB) integrity, as shown by reduced Evans blue dye extravasation. These results suggest miR-195-5p's potential in attenuating ICH-induced apoptosis, possibly related to its influence on MMP-9 and MMP-2 expression, enzymes associated with secondary brain injury. The anti-apoptotic effects of miR-195-5p, demonstrated through TUNEL assays, further underscore its therapeutic promise in addressing the secondary brain injury and apoptosis associated with ICH. In conclusion, miR-195-5p demonstrates a significant neuroprotective effect against ICH-induced neural damage, brain edema, and BBB disruption, primarily through the downregulation of MMP-9 and MMP-2. Our findings indicate that miR-195-5p holds therapeutic potential in managing cerebral cell death following ICH.
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Affiliation(s)
- Yi-Cheng Tsai
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (Y.-C.T.); (C.-H.C.); (Y.B.C.)
- Division of Neurosurgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan; (C.-H.W.); (H.-P.T.)
| | - Chih-Hui Chang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (Y.-C.T.); (C.-H.C.); (Y.B.C.)
- Division of Neurosurgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan; (C.-H.W.); (H.-P.T.)
| | - Yoon Bin Chong
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (Y.-C.T.); (C.-H.C.); (Y.B.C.)
- Division of Neurosurgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan; (C.-H.W.); (H.-P.T.)
| | - Chieh-Hsin Wu
- Division of Neurosurgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan; (C.-H.W.); (H.-P.T.)
- Department of Surgery, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Hung-Pei Tsai
- Division of Neurosurgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan; (C.-H.W.); (H.-P.T.)
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Tian-Lu Cheng
- Department of Biochemistry, School of Post Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chih-Lung Lin
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (Y.-C.T.); (C.-H.C.); (Y.B.C.)
- Division of Neurosurgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan; (C.-H.W.); (H.-P.T.)
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7
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Schoettler FI, Fatehi Hassanabad A, Jadli AS, Patel VB, Fedak PWM. Exploring the role of pericardial miRNAs and exosomes in modulating cardiac fibrosis. Cardiovasc Pathol 2024; 73:107671. [PMID: 38906439 DOI: 10.1016/j.carpath.2024.107671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/26/2024] [Accepted: 06/15/2024] [Indexed: 06/23/2024] Open
Abstract
The potential of the pericardial space as a therapeutic delivery tool for cardiac fibrosis and heart failure (HF) treatment has yet to be elucidated. Recently, miRNAs and exosomes have been discovered to be present in human pericardial fluid (PF). Novel studies have shown characteristic human PF miRNA compositions associated with cardiac diseases and higher miRNA expressions in PF compared to peripheral blood. Five key studies found differentially expressed miRNAs in HF, angina pectoris, aortic stenosis, ventricular tachycardia, and congenital heart diseases with either atrial fibrillation or sinus rhythm. As miRNA-based therapeutics for cardiac fibrosis and HF showed promising results in several in vivo studies for multiple miRNAs, we hypothesize a potential role of miRNA-based therapeutics delivered through the pericardial cavity. This is underlined by the favorable results of the first phase 1b clinical trial in this emerging field. Presenting the first human miRNA antisense drug trial, inhibition of miR-132 by intravenous administration of a novel antisense oligonucleotide, CDR132L, established efficacy in reducing miR-132 in plasma samples in a dose-dependent manner. We screened the literature, provided an overview of the miRNAs and exosomes present in PF, and drew a connection to those miRNAs previously elucidated in cardiac fibrosis and HF. Further, we speculate about clinical implications and potential delivery methods.
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Affiliation(s)
- Friederike I Schoettler
- Department of Cardiac Sciences, Libin Cardiovascular Institute, University of Calgary, Calgary, Alberta, Canada; Department of Cardiac Surgery, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-University, Düsseldorf, Germany
| | - Ali Fatehi Hassanabad
- Department of Cardiac Sciences, Libin Cardiovascular Institute, University of Calgary, Calgary, Alberta, Canada; Department of Cardiac Sciences, Section of Cardiac Surgery, Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Anshul S Jadli
- Department of Cardiac Sciences, Libin Cardiovascular Institute, University of Calgary, Calgary, Alberta, Canada; Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Vaibhav B Patel
- Department of Cardiac Sciences, Libin Cardiovascular Institute, University of Calgary, Calgary, Alberta, Canada; Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Paul W M Fedak
- Department of Cardiac Sciences, Libin Cardiovascular Institute, University of Calgary, Calgary, Alberta, Canada; Department of Cardiac Sciences, Section of Cardiac Surgery, Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
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8
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Doyle C, Callaghan B, Roodnat AW, Armstrong L, Lester K, Simpson DA, Atkinson SD, Sheridan C, McKenna DJ, Willoughby CE. The TGFβ Induced MicroRNAome of the Trabecular Meshwork. Cells 2024; 13:1060. [PMID: 38920689 PMCID: PMC11201560 DOI: 10.3390/cells13121060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/08/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
Primary open-angle glaucoma (POAG) is a progressive optic neuropathy with a complex, multifactorial aetiology. Raised intraocular pressure (IOP) is the most important clinically modifiable risk factor for POAG. All current pharmacological agents target aqueous humour dynamics to lower IOP. Newer therapeutic agents are required as some patients with POAG show a limited therapeutic response or develop ocular and systemic side effects to topical medication. Elevated IOP in POAG results from cellular and molecular changes in the trabecular meshwork driven by increased levels of transforming growth factor β (TGFβ) in the anterior segment of the eye. Understanding how TGFβ affects both the structural and functional changes in the outflow pathway and IOP is required to develop new glaucoma therapies that target the molecular pathology in the trabecular meshwork. In this study, we evaluated the effects of TGF-β1 and -β2 treatment on miRNA expression in cultured human primary trabecular meshwork cells. Our findings are presented in terms of specific miRNAs (miRNA-centric), but given miRNAs work in networks to control cellular pathways and processes, a pathway-centric view of miRNA action is also reported. Evaluating TGFβ-responsive miRNA expression in trabecular meshwork cells will further our understanding of the important pathways and changes involved in the pathogenesis of glaucoma and could lead to the development of miRNAs as new therapeutic modalities in glaucoma.
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Affiliation(s)
- Chelsey Doyle
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Breedge Callaghan
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Anton W. Roodnat
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Lee Armstrong
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Karen Lester
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - David A. Simpson
- Wellcome Wolfson Institute for Experimental Medicine, Queens’ University, Belfast BT9 7BL, UK;
| | - Sarah D. Atkinson
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Carl Sheridan
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK;
| | - Declan J. McKenna
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Colin E. Willoughby
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
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9
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Nivedha M, Harish S, Angappan K, Karthikeyan G, Kumar KK, Murugan M, Infant Richard J. Profiling of Groundnut bud necrosis orthotospovirus-responsive microRNA and their targets in tomato based on deep sequencing. J Virol Methods 2024; 327:114924. [PMID: 38574773 DOI: 10.1016/j.jviromet.2024.114924] [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: 12/13/2023] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Tomato, an extensively cultivated vegetable crop produces miRNAs in response to infection with Groundnut bud necrosis orthotospovirus, a viral pathogen causing significant economic losses. High-throughput miRNA sequencing was performed on tomato leaves inoculated with GBNV and mock-inoculated leaves as controls. Analysis revealed 73 known miRNAs belonging to 24 miRNA families, with variable expression levels. Interestingly, 39 miRNAs were upregulated, and 34 were downregulated in response to GBNV infection. Stem-loop quantitative reverse transcription PCR validated the differential expression of selected miRNAs. Additionally, 30 miRNA encoded proteins were identified to be involved in disease resistance and susceptibility. The miRNA-target interactions were found to play significant roles in cellular and metabolic activities, as well as modulating signaling pathways during the plant-virus interaction. The findings shed light on the intricate regulatory network of miRNAs in tomato response to viral infection and may contribute to developing strategies for improving crop protection against viral diseases.
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Affiliation(s)
- M Nivedha
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - S Harish
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India.
| | - K Angappan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - G Karthikeyan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - K K Kumar
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - M Murugan
- Department of Agricultural Entomology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - J Infant Richard
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
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10
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Lee S. Cardiovascular Disease and miRNAs: Possible Oxidative Stress-Regulating Roles of miRNAs. Antioxidants (Basel) 2024; 13:656. [PMID: 38929095 PMCID: PMC11200533 DOI: 10.3390/antiox13060656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
MicroRNAs (miRNAs) have been highlighted as key players in numerous diseases, and accumulating evidence indicates that pathological expressions of miRNAs contribute to both the development and progression of cardiovascular diseases (CVD), as well. Another important factor affecting the development and progression of CVD is reactive oxygen species (ROS), as well as the oxidative stress they may impose on the cells. Considering miRNAs are involved in virtually every biological process, it is not unreasonable to assume that miRNAs also play critical roles in the regulation of oxidative stress. This narrative review aims to provide mechanistic insights on possible oxidative stress-regulating roles of miRNAs in cardiovascular diseases based on differentially expressed miRNAs reported in various cardiovascular diseases and their empirically validated targets that have been implicated in the regulation of oxidative stress.
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Affiliation(s)
- Seahyoung Lee
- Department of Convergence Science, College of Medicine, Catholic Kwandong University, Gangneung-si 25601, Republic of Korea
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11
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Wu L, Wei G, Yan Y, Zhou X, Zhu X, Zhang Y, Li X. Effects of miR-306 Perturbation on Life Parameters in the English Grain Aphid, Sitobion avenae (Homoptera: Aphididae). Int J Mol Sci 2024; 25:5680. [PMID: 38891867 PMCID: PMC11171923 DOI: 10.3390/ijms25115680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
MicroRNAs (miRNA) play a vital role in insects' growth and development and have significant potential value in pest control. Previously, we identified miR-306 from small RNA libraries within the English grain aphid, Sitobion avenae, a devasting insect pest for wheat. miR-306 not only involves in wing morphogenesis, but also is critically important for aphid survival. Its specific impacts on the life history traits, however, remain unclear. Here, we evaluate the impact of miR-306 perturbation on S. avenae populations using a two-sex life table approach. This comprehensive analysis revealed that miR-306 perturbation significantly prolongs the developmental stages (9.64% and 8.20%) and adult longevity of S. avenae, while decreasing pre-adult survival rate (41.45% and 38.74%) and slightly reducing average fecundity (5.80% and 13.05%). Overall, miR-306 perturbation negatively affects the life table parameters of the aphid population. The population prediction models show a significant decline in the aphid population 60 days post interference, compared to the control groups (98.14% and 97.76%). Our findings highlight the detrimental effects of miR-306 perturbation on S. avenae population growth and suggest potential candidate genes for the development of RNAi-based biopesticides targeted specifically at this pest species.
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Affiliation(s)
- Linyuan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.W.); (G.W.); (Y.Y.); (X.Z.)
| | - Guohua Wei
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.W.); (G.W.); (Y.Y.); (X.Z.)
| | - Yi Yan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.W.); (G.W.); (Y.Y.); (X.Z.)
| | - Xuguo Zhou
- Department of Entomology, School of Integrative Biology, College of Liberal Arts & Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA;
| | - Xun Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.W.); (G.W.); (Y.Y.); (X.Z.)
| | - Yunhui Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.W.); (G.W.); (Y.Y.); (X.Z.)
| | - Xiangrui Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.W.); (G.W.); (Y.Y.); (X.Z.)
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12
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Xue JD, Xiang WF, Cai MQ, Lv XY. Biological functions and therapeutic potential of SRY related high mobility group box 5 in human cancer. Front Oncol 2024; 14:1332148. [PMID: 38835366 PMCID: PMC11148273 DOI: 10.3389/fonc.2024.1332148] [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: 11/02/2023] [Accepted: 04/26/2024] [Indexed: 06/06/2024] Open
Abstract
Cancer is a heavy human burden worldwide, with high morbidity and mortality. Identification of novel cancer diagnostic and prognostic biomarkers is important for developing cancer treatment strategies and reducing mortality. Transcription factors, including SRY associated high mobility group box (SOX) proteins, are thought to be involved in the regulation of specific biological processes. There is growing evidence that SOX transcription factors play an important role in cancer progression, including tumorigenesis, changes in the tumor microenvironment, and metastasis. SOX5 is a member of SOX Group D of Sox family. SOX5 is expressed in various tissues of human body and participates in various physiological and pathological processes and various cellular processes. However, the abnormal expression of SOX5 is associated with cancer of various systems, and the abnormal expression of SOX5 acts as a tumor promoter to promote cancer cell viability, proliferation, invasion, migration and EMT through multiple mechanisms. In addition, the expression pattern of SOX5 is closely related to cancer type, stage and adverse clinical outcome. Therefore, SOX5 is considered as a potential biomarker for cancer diagnosis and prognosis. In this review, the expression of SOX5 in various human cancers, the mechanism of action and potential clinical significance of SOX5 in tumor, and the therapeutic significance of Sox5 targeting in cancer were reviewed. In order to provide a new theoretical basis for cancer clinical molecular diagnosis, molecular targeted therapy and scientific research.
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Affiliation(s)
- Juan-di Xue
- The School of Basic Medicine Sciences of Lanzhou University, Lanzhou, China
| | - Wan-Fang Xiang
- School/Hospital of Stomatology of Lanzhou University, Lanzhou, China
| | - Ming-Qin Cai
- School/Hospital of Stomatology of Lanzhou University, Lanzhou, China
| | - Xiao-Yun Lv
- The School of Basic Medicine Sciences of Lanzhou University, Lanzhou, China
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13
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Dorrity TJ, Shin H, Gertie JA, Chung H. The Sixth Sense: Self-nucleic acid sensing in the brain. Adv Immunol 2024; 161:53-83. [PMID: 38763702 PMCID: PMC11186578 DOI: 10.1016/bs.ai.2024.03.001] [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] [Indexed: 05/21/2024]
Abstract
Our innate immune system uses pattern recognition receptors (PRRs) as a first line of defense to detect microbial ligands and initiate an immune response. Viral nucleic acids are key ligands for the activation of many PRRs and the induction of downstream inflammatory and antiviral effects. Initially it was thought that endogenous (self) nucleic acids rarely activated these PRRs, however emerging evidence indicates that endogenous nucleic acids are able to activate host PRRs in homeostasis and disease. In fact, many regulatory mechanisms are in place to finely control and regulate sensing of self-nucleic acids by PRRs. Sensing of self-nucleic acids is particularly important in the brain, as perturbations to nucleic acid sensing commonly leads to neuropathology. This review will highlight the role of nucleic acid sensors in the brain, both in disease and homeostasis. We also indicate the source of endogenous stimulatory nucleic acids where known and summarize future directions for the study of this growing field.
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Key Words
- Brain
- DNA sensing PRRs: cGAS, AIM2, TLR9
- Neurodegeneration: Aicardi-Goutieres syndrome (AGS), Alzheimer's disease, Amyotrophic lateral sclerosis, Stroke, Traumatic brain injury
- Neurodevelopment
- Neuroinflammation
- Nuecleic acid immunity
- Pattern recognition receptors (PRRs)
- RNA sensing PRRs: MDA5, RIG-I, PKR, TLR3, TLR7/8
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Affiliation(s)
- Tyler J Dorrity
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, United States
| | - Heegwon Shin
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, United States
| | - Jake A Gertie
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, United States; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States; Medical Scientist Training Program, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Hachung Chung
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, United States.
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14
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Di Carlo D, Falasca F, Mazzuti L, Guerrizio G, Migliara G, Santori M, Lazzaro A, Mezzaroma I, D'Ettorre G, Fimiani C, Iaiani G, Antonelli G, Turriziani O. MicroRNA Expression Levels in Peripheral Blood Mononuclear Cells from Human Immunodeficiency Virus Type 1 Positive Individuals and Relationship with Different Levels of Viral Suppression. AIDS Res Hum Retroviruses 2024; 40:321-329. [PMID: 37523231 DOI: 10.1089/aid.2022.0165] [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] [Indexed: 08/01/2023] Open
Abstract
The persistence of low human immunodeficiency virus type 1 (HIV-1) replication in individuals undergoing antiretroviral therapy (ART) still threatens their health. Previous findings have shown that microRNAs (miRNAs) could interfere with several steps of the viral life cycle. Herein, we set out to investigate the expression of miR-150, miR-223, miR-382, miR-324-5p, miR-33a-5p, miR-34a, and miR-132 in the whole peripheral blood mononuclear cell (PBMC) population from people living with HIV-1 showing different levels of viral suppression. Levels of PBMC-associated miRNAs were analyzed in 30 individuals with undetectable viremia (target not detected) and 30 individuals with detectable low-level viremia (1-200 copies/mL). In addition, 30 samples from treatment-naive (NAIVE) individuals were investigated. Results were compared to a control group of 28 HIV-negative donors. All miRNAs analyzed were strongly downregulated in the NAIVE population, either compared to the treated group or to controls. Stratification of ART-treated donors according to the therapeutic regimen showed the downregulation of miR-33a-5p in subjects treated with non-nucleoside reverse transcriptase inhibitors compared with those treated with protease inhibitors. Collectively, the present study shows that uncontrolled viral replication leads to profound miRNA deregulation while treated individuals, irrespective of the degree of viral suppression, and even the types of antiviral drugs seem to be specifically associated with miRNA expression profiles. These evidences suggest that virological suppression could be favored by miRNA modulation.
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Affiliation(s)
- Daniele Di Carlo
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
- Pasteur Laboratories, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Francesca Falasca
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
- Transfusion Medicine Unit, "F. Veneziale" Hospital, Isernia, Italy
| | - Laura Mazzuti
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
- Department of Clinical and Molecular Medicine, Sapienza University, Sant'Andrea Hospital, Rome, Italy
| | - Giuliana Guerrizio
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Giuseppe Migliara
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Marta Santori
- Department Internal Medicine, Endocrine-Metabolic Sciences and Infectious Diseases, Policlinico Umberto I, Rome, Italy
| | - Alessandro Lazzaro
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Ivano Mezzaroma
- Department of Translational and Precision Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Gabriella D'Ettorre
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Caterina Fimiani
- Department Internal Medicine, Endocrine-Metabolic Sciences and Infectious Diseases, Policlinico Umberto I, Rome, Italy
| | - Giancarlo Iaiani
- Department Internal Medicine, Endocrine-Metabolic Sciences and Infectious Diseases, Policlinico Umberto I, Rome, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Ombretta Turriziani
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
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15
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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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16
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Bhadra M, Sachan M, Nara S. Current strategies for early epithelial ovarian cancer detection using miRNA as a potential tool. Front Mol Biosci 2024; 11:1361601. [PMID: 38690293 PMCID: PMC11058280 DOI: 10.3389/fmolb.2024.1361601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/20/2024] [Indexed: 05/02/2024] Open
Abstract
Ovarian cancer is one of the most aggressive and significant malignant tumor forms in the female reproductive system. It is the leading cause of death among gynecological cancers owing to its metastasis. Since its preliminary disease symptoms are lacking, it is imperative to develop early diagnostic biomarkers to aid in treatment optimization and personalization. In this vein, microRNAs, which are short sequence non-coding molecules, displayed great potential as highly specific and sensitive biomarker. miRNAs have been extensively advocated and proven to serve an instrumental part in the clinical management of cancer, especially ovarian cancer, by promoting the cancer cell progression, invasion, delayed apoptosis, epithelial-mesenchymal transition, metastasis of cancer cells, chemosensitivity and resistance and disease therapy. Here, we cover our present comprehension of the most up-to-date microRNA-based approaches to detect ovarian cancer, as well as current diagnostic and treatment strategies, the role of microRNAs as oncogenes or tumor suppressor genes, and their significance in ovarian cancer progression, prognosis, and therapy.
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17
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He J, Li M, Qiu J, Pu X, Guo Y. HOPEXGB: A Consensual Model for Predicting miRNA/lncRNA-Disease Associations Using a Heterogeneous Disease-miRNA-lncRNA Information Network. J Chem Inf Model 2024; 64:2863-2877. [PMID: 37604142 DOI: 10.1021/acs.jcim.3c00856] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Predicting disease-related microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) is crucial to find new biomarkers for the prevention, diagnosis, and treatment of complex human diseases. Computational predictions for miRNA/lncRNA-disease associations are of great practical significance, since traditional experimental detection is expensive and time-consuming. In this paper, we proposed a consensual machine-learning technique-based prediction approach to identify disease-related miRNAs and lncRNAs by high-order proximity preserved embedding (HOPE) and eXtreme Gradient Boosting (XGB), named HOPEXGB. By connecting lncRNA, miRNA, and disease nodes based on their correlations and relationships, we first created a heterogeneous disease-miRNA-lncRNA (DML) information network to achieve an effective fusion of information on similarities, correlations, and interactions among miRNAs, lncRNAs, and diseases. In addition, a more rational negative data set was generated based on the similarities of unknown associations with the known ones, so as to effectively reduce the false negative rate in the data set for model construction. By 10-fold cross-validation, HOPE shows better performance than other graph embedding methods. The final consensual HOPEXGB model yields robust performance with a mean prediction accuracy of 0.9569 and also demonstrates high sensitivity and specificity advantages compared to lncRNA/miRNA-specific predictions. Moreover, it is superior to other existing methods and gives promising performance on the external testing data, indicating that integrating the information on lncRNA-miRNA interactions and the similarities of lncRNAs/miRNAs is beneficial for improving the prediction performance of the model. Finally, case studies on lung, stomach, and breast cancers indicate that HOPEXGB could be a powerful tool for preclinical biomarker detection and bioexperiment preliminary screening for the diagnosis and prognosis of cancers. HOPEXGB is publicly available at https://github.com/airpamper/HOPEXGB.
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Affiliation(s)
- Jian He
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Jiangguo Qiu
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu 610064, China
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18
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Kiel K, Król SK, Bronisz A, Godlewski J. MiR-128-3p - a gray eminence of the human central nervous system. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102141. [PMID: 38419943 PMCID: PMC10899074 DOI: 10.1016/j.omtn.2024.102141] [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] [Indexed: 03/02/2024]
Abstract
MicroRNA-128-3p (miR-128-3p) is a versatile molecule with multiple functions in the physiopathology of the human central nervous system. Perturbations of miR-128-3p, which is enriched in the brain, contribute to a plethora of neurodegenerative disorders, brain injuries, and malignancies, as this miRNA is a crucial regulator of gene expression in the brain, playing an essential role in the maintenance and function of cells stemming from neuronal lineage. However, the differential expression of miR-128-3p in pathologies underscores the importance of the balance between its high and low levels. Significantly, numerous reports pointed to miR-128-3p as one of the most depleted in glioblastoma, implying it is a critical player in the disease's pathogenesis and thus may serve as a therapeutic agent for this most aggressive form of brain tumor. In this review, we summarize the current knowledge of the diverse roles of miR-128-3p. We focus on its involvement in the neurogenesis and pathophysiology of malignant and neurodegenerative diseases. We also highlight the promising potential of miR-128-3p as an antitumor agent for the future therapy of human cancers, including glioblastoma, and as the linchpin of brain development and function, potentially leading to the development of new therapies for neurological conditions.
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Affiliation(s)
- Klaudia Kiel
- Tumor Microenvironment Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
| | - Sylwia Katarzyna Król
- Department of Neurooncology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
| | - Agnieszka Bronisz
- Tumor Microenvironment Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
| | - Jakub Godlewski
- Department of Neurooncology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
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19
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Raghubeer S. The influence of epigenetics and inflammation on cardiometabolic risks. Semin Cell Dev Biol 2024; 154:175-184. [PMID: 36804178 DOI: 10.1016/j.semcdb.2023.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
Cardiometabolic diseases include metabolic syndrome, obesity, type 2 diabetes mellitus, and hypertension. Epigenetic modifications participate in cardiometabolic diseases through several pathways, including inflammation, vascular dysfunction, and insulin resistance. Epigenetic modifications, which encompass alterations to gene expression without mutating the DNA sequence, have gained much attention in recent years, since they have been correlated with cardiometabolic diseases and may be targeted for therapeutic interventions. Epigenetic modifications are greatly influenced by environmental factors, such as diet, physical activity, cigarette smoking, and pollution. Some modifications are heritable, indicating that the biological expression of epigenetic alterations may be observed across generations. Moreover, many patients with cardiometabolic diseases present with chronic inflammation, which can be influenced by environmental and genetic factors. The inflammatory environment worsens the prognosis of cardiometabolic diseases and further induces epigenetic modifications, predisposing patients to the development of other metabolism-associated diseases and complications. A deeper understanding of inflammatory processes and epigenetic modifications in cardiometabolic diseases is necessary to improve our diagnostic capabilities, personalized medicine approaches, and the development of targeted therapeutic interventions. Further understanding may also assist in predicting disease outcomes, especially in children and young adults. This review describes epigenetic modifications and inflammatory processes underlying cardiometabolic diseases, and further discusses advances in the research field with a focus on specific points for interventional therapy.
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Affiliation(s)
- Shanel Raghubeer
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health & Wellness Sciences, Cape Peninsula University of Technology, South Africa.
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20
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Reddy S, Hu D, Zhao M, Ichimura S, Barnes EA, Cornfield DN, Alejandre Alcázar MA, Spiekerkoetter E, Fajardo G, Bernstein D. MicroRNA-34a-Dependent Attenuation of Angiogenesis in Right Ventricular Failure. J Am Heart Assoc 2024; 13:e029427. [PMID: 38293915 PMCID: PMC11056115 DOI: 10.1161/jaha.123.029427] [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: 01/06/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024]
Abstract
BACKGROUND The right ventricle (RV) is at risk in patients with complex congenital heart disease involving right-sided obstructive lesions. We have shown that capillary rarefaction occurs early in the pressure-loaded RV. Here we test the hypothesis that microRNA (miR)-34a, which is induced in RV hypertrophy and RV failure (RVF), blocks the hypoxia-inducible factor-1α-vascular endothelial growth factor (VEGF) axis, leading to the attenuated angiogenic response and increased susceptibility to RV failure. METHODS AND RESULTS Mice underwent pulmonary artery banding to induce RV hypertrophy and RVF. Capillary rarefaction occurred immediately. Although hypoxia-inducible factor-1α expression increased (0.12±0.01 versus 0.22±0.03, P=0.05), VEGF expression decreased (0.61±0.03 versus 0.22±0.05, P=0.01). miR-34a expression was most upregulated in fibroblasts (4-fold), but also in cardiomyocytes and endothelial cells (2-fold). Overexpression of miR-34a in endothelial cells increased cell senescence (10±3% versus 22±2%, P<0.05) by suppressing sirtulin 1 expression, and decreased tube formation by 50% via suppression of hypoxia-inducible factor-1α, VEGF A, VEGF B, and VEGF receptor 2. miR-34a was induced by stretch, transforming growth factor-β1, adrenergic stimulation, and hypoxia in cardiac fibroblasts and cardiomyocytes. In mice with RVF, locked nucleic acid-antimiR-34a improved RV shortening fraction and survival half-time and restored capillarity and VEGF expression. In children with congenital heart disease-related RVF, RV capillarity was decreased and miR-34a increased 5-fold. CONCLUSIONS In summary, miR-34a from fibroblasts, cardiomyocytes, and endothelial cells mediates capillary rarefaction by suppressing the hypoxia-inducible factor-1α-VEGF axis in RV hypertrophy/RVF, raising the potential for anti-miR-34a therapeutics in patients with at-risk RVs.
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Affiliation(s)
- Sushma Reddy
- Department of Pediatrics (Cardiology) and Cardiovascular InstituteStanford UniversityStanfordCA
| | - Dong‐Qing Hu
- Department of Pediatrics (Cardiology) and Cardiovascular InstituteStanford UniversityStanfordCA
| | - Mingming Zhao
- Department of Pediatrics (Cardiology) and Cardiovascular InstituteStanford UniversityStanfordCA
| | - Shoko Ichimura
- Department of Pediatrics (Cardiology) and Cardiovascular InstituteStanford UniversityStanfordCA
| | | | | | | | | | - Giovanni Fajardo
- Department of Pediatrics (Cardiology) and Cardiovascular InstituteStanford UniversityStanfordCA
| | - Daniel Bernstein
- Department of Pediatrics (Cardiology) and Cardiovascular InstituteStanford UniversityStanfordCA
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21
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Takamizawa S, Kojima J, Umezu T, Kuroda M, Hayashi S, Maruta T, Okamoto A, Nishi H. miR‑146a‑5p and miR‑191‑5p as novel diagnostic marker candidates for ovarian clear cell carcinoma. Mol Clin Oncol 2024; 20:14. [PMID: 38264014 PMCID: PMC10804375 DOI: 10.3892/mco.2023.2712] [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: 03/13/2023] [Accepted: 08/11/2023] [Indexed: 01/25/2024] Open
Abstract
Ovarian cancer is a malignant gynecologic disease rarely diagnosed in the early stages. Among the various types of ovarian cancer, clear cell carcinoma has a poor prognosis due to its malignant potential. MicroRNAs (miRNAs/miRs) regulate gene expression in cells by suppressing the translation of target genes or by degrading the target mRNA. miRNAs are also secreted from the cells in the blood, binding to proteins or lipids and assisting in cell-cell communication. Therefore, serum miRNAs may be considered potential diagnostic biomarkers for ovarian cancer. The present study investigated and identified specific miRNAs associated with ovarian clear cell carcinoma and compared them to those in ovarian endometrioma samples and healthy controls. CA125, an ovarian tumor marker, did not differ between patients with ovarian clear cell carcinoma, endometriosis or healthy controls. Subsequently, four miRNAs (miR-146a-5p, miR-191-5p, miR-484 and miR-574-3p) were analyzed. The expression levels of miR-146a-5p and miR-191-5p were significantly increased in the serum samples from patients with ovarian clear cell carcinoma compared with those in the healthy controls, but there was no significant difference compared with in patients with endometriosis. Furthermore, the bioinformatics analysis showed that CCND2 and NOTCH2 were the candidate target genes of miR-146a-5p and miR-191-5p. In conclusion, the results of the present study demonstrated that miR-146a-5p and miR-191-5p may be useful as early and non-invasive diagnostic tools in ovarian clear cell carcinoma. These miRNAs can help in distinguishing between ovarian clear cell carcinoma and ovarian endometrioma. To the best of our knowledge, no previous studies have screened any candidates specifically for ovarian clear cell carcinoma.
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Affiliation(s)
- Shigeatsu Takamizawa
- Department of Obstetrics and Gynecology, Tokyo Medical University, Tokyo 160-0023, Japan
| | - Junya Kojima
- Department of Obstetrics and Gynecology, Tokyo Medical University, Tokyo 160-0023, Japan
| | - Tomohiro Umezu
- Department of Molecular Pathology, Tokyo Medical University, Tokyo 160-8402, Japan
| | - Masahiko Kuroda
- Department of Molecular Pathology, Tokyo Medical University, Tokyo 160-8402, Japan
| | - Shigehiro Hayashi
- Department of Obstetrics and Gynecology, Tokyo Medical University, Tokyo 160-0023, Japan
| | - Takenori Maruta
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Hirotaka Nishi
- Department of Obstetrics and Gynecology, Tokyo Medical University, Tokyo 160-0023, Japan
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22
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Chamanara S, Hozouri V, Irandoost E. Inhibition of NLRP3 inflammasome-A potential mechanistic therapeutic for treatment of polycystic ovary syndrome? J Biochem Mol Toxicol 2024; 38:e23592. [PMID: 38054794 DOI: 10.1002/jbt.23592] [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: 05/02/2023] [Revised: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023]
Abstract
This review article explores the relationship between the NOD-like receptor protein 3 (NLRP3) inflammasome and the risk of developing polycystic ovary syndrome (PCOS). The NLRP3 inflammasome, a fundamental element of the innate immune system, plays a crucial role in the production of proinflammatory mediators and pyroptosis, a type inflammatory cell death. We conducted a thorough search on scientific databases to gather relevant information on this topic, utilizing relevant keywords. The reviewed studies indicated a correlation between PCOS and a higher incidence of granulosa cell (GC) death and the presence of ovarian tissue fibrosis. NLRP3 inflammasome stimulation and subsequent pyroptosis in GCs play a significant role in the pathophysiology of PCOS. Active NLRP3 inflammasome is involved in the production of inflammatory mediators like interleukin-1β (IL-1β) and IL-18, contributing to the development of PCOS, particularly in overweight patients. Therefore, inhibiting NLRP3 activation and pyroptosis could potentially offer novel therapeutic strategies for PCOS. Some limited studies have explored the use of agents with antioxidant and anti-inflammatory properties, as well as gene therapy approaches, to target the NLRP3 and pyroptosis signaling pathways. This study overview the understanding of the relationship between NLRP3 inflammasome activation, pyroptosis, and PCOS. It highlights the potential of targeting the NLRP3 inflammasome as an approach for treating PCOS. Nonetheless, further research and clinical trials are imperative to validate these results and explore the effectiveness of NLRP3 inflammasome inhibition in the management of PCOS.
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Affiliation(s)
- Solmaz Chamanara
- Department of Gynecology and Obstetrics, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Vahid Hozouri
- Internal Medicine Department, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Elnaz Irandoost
- Department of Gynecology and Obstetrics, Tehran University of Medical Sciences, Tehran, Iran
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23
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Weng S, Yang X, Yu N, Wang PC, Xiong S, Ruan H. Harnessing ADAR-Mediated Site-Specific RNA Editing in Immune-Related Disease: Prediction and Therapeutic Implications. Int J Mol Sci 2023; 25:351. [PMID: 38203521 PMCID: PMC10779106 DOI: 10.3390/ijms25010351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/15/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
ADAR (Adenosine Deaminases Acting on RNA) proteins are a group of enzymes that play a vital role in RNA editing by converting adenosine to inosine in RNAs. This process is a frequent post-transcriptional event observed in metazoan transcripts. Recent studies indicate widespread dysregulation of ADAR-mediated RNA editing across many immune-related diseases, such as human cancer. We comprehensively review ADARs' function as pattern recognizers and their capability to contribute to mediating immune-related pathways. We also highlight the potential role of site-specific RNA editing in maintaining homeostasis and its relationship to various diseases, such as human cancers. More importantly, we summarize the latest cutting-edge computational approaches and data resources for predicting and analyzing RNA editing sites. Lastly, we cover the recent advancement in site-directed ADAR editing tool development. This review presents an up-to-date overview of ADAR-mediated RNA editing, how site-specific RNA editing could potentially impact disease pathology, and how they could be harnessed for therapeutic applications.
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Affiliation(s)
- Shenghui Weng
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Xinyi Yang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Nannan Yu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Peng-Cheng Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Sidong Xiong
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Hang Ruan
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou 215123, China
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24
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Bagheri R, Ghorbian M, Ghorbian S. Tumor circulating biomarkers in colorectal cancer. Cancer Treat Res Commun 2023; 38:100787. [PMID: 38194840 DOI: 10.1016/j.ctarc.2023.100787] [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: 11/03/2023] [Revised: 12/11/2023] [Accepted: 12/21/2023] [Indexed: 01/11/2024]
Abstract
CRC is a major global health concern and is responsible for a significant number of cancer-related deaths each year. The successful treatment of CRC becomes more difficult when it goes undetected until it has advanced to a later stage. Diagnostic biomarkers can play a critical role in the early detection of CRC, which leads to improved patient outcomes and increased survival rates. It is important to develop reliable biomarkers for the early detection of CRC to enable timely diagnosis and treatment. To date, CRC detection methods such as endoscopy, blood, and stool tests are imperfect and often only identify cases in the later stages of the disease. To overcome these limitations, researchers are turning to molecular biomarkers as a promising avenue for improving CRC detection. Diagnostic information can be provided more reliably through a noninvasive approach using biomarkers such as mRNA, circulating cell-free DNA, micro-RNA, long non-coding RNA, and proteins. These biomarkers can be found in blood, tissue, feces, and volatile organic compounds. The identification of molecular biomarkers with high sensitivity and specificity for early detection of CRC that are safe, cost-effective, and easily measurable remains a significant challenge for researchers. In this article, we will explore the latest advancements in blood-based diagnostic biomarkers for CRC and their potential impact on improving patient survival rates.
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Affiliation(s)
- Raana Bagheri
- Department of Molecular Genetics, Ahar Branch, Islamic Azad University, Ahar, Iran
| | - Mohsen Ghorbian
- Department of Computer Engineering, Qom Branch, Islamic Azad University, Qom, Iran
| | - Saeid Ghorbian
- Department of Molecular Genetics, Ahar Branch, Islamic Azad University, Ahar, Iran.
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25
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Kumari R, Roy U, Desai S, Mondal AS, Nair RR, Nilavar N, Choudhary B, Raghavan SC. MicroRNA, miR-501 regulate the V(D)J recombination in B cells. Biochem J 2023; 480:2061-2077. [PMID: 38084601 DOI: 10.1042/bcj20230250] [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: 06/26/2023] [Revised: 11/13/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
The stringent regulation of RAGs (Recombination activating genes), the site-specific endonuclease responsible for V(D)J recombination, is important to prevent genomic rearrangements and chromosomal translocations in lymphoid cells. In the present study, we identify a microRNA, miR-501, which can regulate the expression of RAG1 in lymphoid cells. Overexpression of the pre-miRNA construct led to the generation of mature miRNAs and a concomitant reduction in RAG1 expression, whereas inhibition using anti-miRs resulted in its enhanced expression. The direct interaction of the 3'UTR of miR-501 with RAG1 was confirmed by the reporter assay. Importantly, overexpression of miRNAs led to inhibition of V(D)J recombination in B cells, revealing their impact on the physiological function of RAGs. Of interest is the inverse correlation observed for miR-501 with RAG1 in various leukemia patients and lymphoid cell lines, suggesting its possible use in cancer therapy. Thus, our results reveal the regulation of RAG1 by miR-501-3p in B cells and thus V(D)J recombination and its possible implications on immunoglobulin leukemogenesis.
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Affiliation(s)
- Rupa Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Urbi Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sagar Desai
- Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India
| | - Arannya S Mondal
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Rajshree R Nair
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Namrata Nilavar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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26
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Khan MM, Sharma V, Serajuddin M. Emerging role of miRNA in prostate cancer: A future era of diagnostic and therapeutics. Gene 2023; 888:147761. [PMID: 37666374 DOI: 10.1016/j.gene.2023.147761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/17/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Prostate cancer (PCa) is the most common cancer in men (20%) and is responsible for 6.8% (1/5) of all cancer-related deaths in men around the world. The development and spread of prostate cancer are driven by a wide variety of genomic changes and extensive epigenetic events. Because of this, the MicroRNA (miRNA) and associated molecular mechanisms involved in PCa genesis and aggressive were only partially identified until today. The miRNAs are a newly discovered category of regulatorsthat have recently been recognized to have a significant role in regulating numerous elements of cancer mechanisms, such as proliferation, differentiation, metabolism, and apoptosis. The miRNAs are a type of small (22-24 nucleotides), non-coding, endogenous, single-stranded RNA and work as potent gene regulators. Various types of cancer, including PCa, have found evidence that miRNA genes, which are often located in cancer-related genetic regions or fragile locations, have a role in the primary steps of tumorigenesis, either as oncogenes or tumorsuppressors. To explain the link between miRNAs and their function in the initiation and advancement of PCa, we conducted a preliminary assessment. The purpose of this research was to enhance our understanding of the connection between miRNA expression profiles and PCa by elucidating the fundamental processes of miRNA expression and the target genes.
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Affiliation(s)
- Mohd Mabood Khan
- Department of Zoology, University of Lucknow, Lucknow 226007, Uttar Pradesh, India.
| | - Vineeta Sharma
- Department of Medicine, Vanderbilt University Medical Center, Nashville 37232, TN, USA
| | - Mohammad Serajuddin
- Department of Zoology, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
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27
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Kim JH, Lee CH, Lee SW. Adenovirus VA RNAs impair maturation of primary microRNA. J Gene Med 2023; 25:e3564. [PMID: 37434327 DOI: 10.1002/jgm.3564] [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: 01/02/2023] [Revised: 05/12/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Adenovirus expresses two non-coding virus-associated (VA) RNAs: VA I RNA and VA II RNA. Adenovirus-expressed VA RNAs interfere with the microRNA (miRNA) pathway by competing with precursor miRNAs. The processing pattern of primary miRNA (pri-miRNA) and factors to affect its processing are not exactly known when using adenovirus for the delivery of pri-miRNA. METHODS To observe pri-miRNA processing, plasmid construct encoding pri-miRNA was co-transfected with VA I/II RNA expression plasmid, or recombinant adenovirus encoding pri-miRNA was generated and infected. Levels of miRNAs, VA I RNA and VA II RNA were analyzed by a quantitative real-time PCR (RT-PCR). VA I-II full-length RNA was analyzed by a RT-PCR. RNA immunoprecipitation analysis to pull-down the VA I-II full-length RNA binding with Drosha was conducted with Drosha antibody. RESULTS pri-miRNA was normally processed into mature miRNA when it was expressed in cells using plasmid. However, miRNA maturation was impaired when pri-miRNA was delivered and expressed using adenovirus. Of note, pri-miRNA processing was observed to be blocked by VA RNA expression. Such blocked processing could be recovered by introducing antisense RNA of VA RNA, anti-3'VA RNA. In addition, VA RNAs were transcribed into VA I-II full-length RNA, which was found to bind and sequester Drosha. CONCLUSIONS Adenovirus infection downregulated the processing of pri-miRNAs in cells, and such downregulation could be derived from VA I-II full-length RNAs in pri-miRNA-like form through competitively binding to Drosha protein. These results indicated that the expression of adenovirus VA RNAs should be inhibited for successful delivery and expression of pri-miRNA or shRNA in cells using adenovirus.
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Affiliation(s)
- Ji Hyun Kim
- R&D Center, Rznomics Inc., Seongnam, Republic of Korea
| | - Chang Ho Lee
- Department of Bioconvergence Engineering, Research Institute of Advanced Omics, Dankook University, Yongin, Republic of Korea
| | - Seong-Wook Lee
- R&D Center, Rznomics Inc., Seongnam, Republic of Korea
- Department of Bioconvergence Engineering, Research Institute of Advanced Omics, Dankook University, Yongin, Republic of Korea
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28
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Chen J, Ma Y, Guan Z, Liu Q, Shi Q, Qi G, Chen T, Lyu L. Labor division of worker ants can be controlled by insulin synthesis targeted through miR-279c-5p in Solenopsis invicta (Hymenoptera: Formicidae). PEST MANAGEMENT SCIENCE 2023; 79:5029-5043. [PMID: 37552557 DOI: 10.1002/ps.7704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/24/2023] [Accepted: 08/08/2023] [Indexed: 08/10/2023]
Abstract
BACKGROUND In social insects, the labor division of workers is ubiquitous and controlled by genetic and environmental factors. However, how they modulate this coordinately remains poorly understood. RESULTS We report miR-279c-5p participation in insulin synthesis and behavioral transition by negatively regulating Rab8A in Solenopsis invicta. Eusocial specific miR-279c-5p is age-associated and highly expressed in nurse workers, and localized in the cytoplasm of neurons, where it is partly co-localized with its target, Rab8A. We determined that miR-279c-5p agomir suppressed Rab8A expression in forager workers, consequently decreasing insulin content, resulting in the behavioral shift to 'nurse-like' behaviors, while the decrease in miR-279c-5p increased Rab8A expression and increased insulin content in nurse workers, leading to the behavioral shift to 'foraging-like' behaviors. Moreover, insulin could rescue the 'foraging behavior' induced by feeding miR-279c-5p to nurse workers. The overexpression and suppression of miR-279c-5p in vivo caused an obvious behavioral transition between foragers and nurses, and insulin synthesis was affected by miR-279c-5p by regulating the direct target Rab8A. CONCLUSION We first report that miR-279c-5p is a novel regulator that promotes labor division by negatively regulating the target gene Rab8A by controlling insulin production in ants. This miRNA-mediated mechanism is significant for understanding the behavioral plasticity of social insects between complex factors and potentially provides new targets for controlling red imported fire ants. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Jie Chen
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Yunjie Ma
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Ziying Guan
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Qin Liu
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Qingxing Shi
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Guojun Qi
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Ting Chen
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Lihua Lyu
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
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29
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Rezaee D, Saadatpour F, Akbari N, Zoghi A, Najafi S, Beyranvand P, Zamani-Rarani F, Rashidi MA, Bagheri-Mohammadi S, Bakhtiari M. The role of microRNAs in the pathophysiology of human central nervous system: A focus on neurodegenerative diseases. Ageing Res Rev 2023; 92:102090. [PMID: 37832609 DOI: 10.1016/j.arr.2023.102090] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023]
Abstract
microRNAs (miRNAs) are suggested to play substantial roles in regulating the development and various physiologic functions of the central nervous system (CNS). These include neurogenesis, cell fate and differentiation, morphogenesis, formation of dendrites, and targeting non-neural mRNAs. Notably, deregulation of an increasing number of miRNAs is associated with several neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis and CNS tumors. They are particularly known to affect the amyloid β (Aβ) cleavage and accumulation, tau protein homeostasis, and expression of alpha-synuclein (α-syn), Parkin, PINK1, and brain-derived neurotrophic factor (BDNF) that play pivotal roles in the pathogenesis of neurodegenerative diseases. These include miR-16, miR-17-5p, miR-20a, miR-106a, miR-106b, miR-15a, miR-15b, miR-103, miR-107, miR-298, miR-328, miR-195, miR-485, and miR-29. In CNS tumors, several miRNAs, including miR-31, miR-16, and miR-21 have been identified to modulate tumorigenesis through impacting tumor invasion and apoptosis. In this review article, we have a look at the recent advances on our knowledge about the role of miRNAs in human brain development and functions, neurodegenerative diseases, and their clinical potentials.
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Affiliation(s)
- Delsuz Rezaee
- School of Allied Medical Sciences, Ilam University of Medical Sciences, Ilam, Iran
| | - Fatemeh Saadatpour
- Molecular Virology Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Nayyereh Akbari
- Brain Mapping Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Anahita Zoghi
- Brain Mapping Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Parisa Beyranvand
- Department of Molecular Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Fahimeh Zamani-Rarani
- Department of Anatomical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Rashidi
- Student Research Committee, Department of Occupational Health and Safety, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeid Bagheri-Mohammadi
- Department of Physiology and Neurophysiology Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Bakhtiari
- Department of Anatomical Sciences, Behbahan Faculty of Medical Sciences, Behbahan, Iran
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30
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Kaeffer B. Human Breast Milk miRNAs: Their Diversity and Potential for Preventive Strategies in Nutritional Therapy. Int J Mol Sci 2023; 24:16106. [PMID: 38003296 PMCID: PMC10671413 DOI: 10.3390/ijms242216106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
The endogenous miRNAs of breast milk are the products of more than 1000 nonprotein-coding genes, giving rise to mature small regulatory molecules of 19-25 nucleotides. They are incorporated in macromolecular complexes, loaded on Argonaute proteins, sequestrated in exosomes and lipid complexes, or present in exfoliated cells of epithelial, endothelial, or immune origins. Their expression is dependent on the stage of lactation; however, their detection depends on progress in RNA sequencing and the reappraisal of the definition of small RNAs. Some miRNAs from plants are detected in breast milk, opening the possibility of the stimulation of immune cells from the allergy repertoire. Each miRNA harbors a seeding sequence, which targets mRNAs, gene promoters, or long noncoding RNAs. Their activities depend on their bioavailability. Efficient doses of miRNAs are estimated to be roughly 100 molecules in the cytoplasm of target cells from in vitro and in vivo experiments. Each miRNA is included in networks of stimulation/inhibition/sequestration, driving the expression of cellular phenotypes. Three types of stress applied during lactation to manipulate miRNA supply were explored using rodent offspring: a foster mother, a cafeteria diet, and early weaning. This review presents the main mature miRNAs described from current mothers' cohorts and their bioavailability in experimental models as well as studies assessing the potential of miR-26 or miR-320 miRNA families to alter offspring phenotypes.
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Affiliation(s)
- Bertrand Kaeffer
- Nantes Université, INRAE, UMR 1280, PhAN, F-44000 Nantes, France
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31
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Kumar D, Kirti PB. The genus Arachis: an excellent resource for studies on differential gene expression for stress tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1275854. [PMID: 38023864 PMCID: PMC10646159 DOI: 10.3389/fpls.2023.1275854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
Peanut Arachis hypogaea is a segmental allotetraploid in the section Arachis of the genus Arachis along with the Section Rhizomataceae. Section Arachis has several diploid species along with Arachis hypogaea and A. monticola. The section Rhizomataceae comprises polyploid species. Several species in the genus are highly tolerant to biotic and abiotic stresses and provide excellent sets of genotypes for studies on differential gene expression. Though there were several studies in this direction, more studies are needed to identify more and more gene combinations. Next generation RNA-seq based differential gene expression study is a powerful tool to identify the genes and regulatory pathways involved in stress tolerance. Transcriptomic and proteomic study of peanut plants under biotic stresses reveals a number of differentially expressed genes such as R genes (NBS-LRR, LRR-RLK, protein kinases, MAP kinases), pathogenesis related proteins (PR1, PR2, PR5, PR10) and defense related genes (defensin, F-box, glutathione S-transferase) that are the most consistently expressed genes throughout the studies reported so far. In most of the studies on biotic stress induction, the differentially expressed genes involved in the process with enriched pathways showed plant-pathogen interactions, phenylpropanoid biosynthesis, defense and signal transduction. Differential gene expression studies in response to abiotic stresses, reported the most commonly expressed genes are transcription factors (MYB, WRKY, NAC, bZIP, bHLH, AP2/ERF), LEA proteins, chitinase, aquaporins, F-box, cytochrome p450 and ROS scavenging enzymes. These differentially expressed genes are in enriched pathways of transcription regulation, starch and sucrose metabolism, signal transduction and biosynthesis of unsaturated fatty acids. These identified differentially expressed genes provide a better understanding of the resistance/tolerance mechanism, and the genes for manipulating biotic and abiotic stress tolerance in peanut and other crop plants. There are a number of differentially expressed genes during biotic and abiotic stresses were successfully characterized in peanut or model plants (tobacco or Arabidopsis) by genetic manipulation to develop stress tolerance plants, which have been detailed out in this review and more concerted studies are needed to identify more and more gene/gene combinations.
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Affiliation(s)
- Dilip Kumar
- Department of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Pulugurtha Bharadwaja Kirti
- Agri Biotech Foundation, Professor Jayashankar Telangana State (PJTS) Agricultural University, Hyderabad, Telangana, India
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32
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Chen WT, Luo Y, Chen XM, Xiao JH. Role of exosome-derived miRNAs in diabetic wound angiogenesis. Mol Cell Biochem 2023:10.1007/s11010-023-04874-1. [PMID: 37891446 DOI: 10.1007/s11010-023-04874-1] [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: 06/20/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023]
Abstract
Chronic wounds with high disability are among the most common and serious complications of diabetes. Angiogenesis dysfunction impair wound healing in patients with diabetes. Compared with traditional therapies that can only provide symptomatic treatment, stem cells-owing to their powerful paracrine properties, can alleviate the pathogenesis of chronic diabetic wounds and even cure them. Exosome-derived microRNAs (miRNAs), important components of stem cell paracrine signaling, have been reported for therapeutic use in various disease models, including diabetic wounds. Exosome-derived miRNAs have been widely reported to be involved in regulating vascular function and have promising applications in the repair and regeneration of skin wounds. Therefore, this article aims to review the current status of the pathophysiology of exosome-derived miRNAs in the diabetes-induced impairment of wound healing, along with current knowledge of the underlying mechanisms, emphasizing the regulatory mechanism of angiogenesis, we hope to document the emerging theoretical basis for improving wound repair by restoring angiogenesis in diabetes.
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Affiliation(s)
- Wen-Ting Chen
- Institute of Medicinal Biotechnology, Affiliated Hospital of Zunyi Medical University, 149 Dalian Road, Huichuan District, Zunyi, 563003, China
| | - Yi Luo
- Institute of Medicinal Biotechnology, Affiliated Hospital of Zunyi Medical University, 149 Dalian Road, Huichuan District, Zunyi, 563003, China
- Guizhou Provincial Universities Key Laboratory of Medicinal Biotechnology & Research Center for Translational Medicine, Affiliated Hospital of Zunyi Medical University, 149 Dalian Road, Huichuan District, Zunyi, 563003, China
| | - Xue-Mei Chen
- Institute of Medicinal Biotechnology, Affiliated Hospital of Zunyi Medical University, 149 Dalian Road, Huichuan District, Zunyi, 563003, China
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, 149 Dalian Road, Huichuan District, Zunyi, 563003, China
| | - Jian-Hui Xiao
- Institute of Medicinal Biotechnology, Affiliated Hospital of Zunyi Medical University, 149 Dalian Road, Huichuan District, Zunyi, 563003, China.
- Guizhou Provincial Universities Key Laboratory of Medicinal Biotechnology & Research Center for Translational Medicine, Affiliated Hospital of Zunyi Medical University, 149 Dalian Road, Huichuan District, Zunyi, 563003, China.
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, 149 Dalian Road, Huichuan District, Zunyi, 563003, China.
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Alrushaid N, Khan FA, Al-Suhaimi E, Elaissari A. Progress and Perspectives in Colon Cancer Pathology, Diagnosis, and Treatments. Diseases 2023; 11:148. [PMID: 37987259 PMCID: PMC10660546 DOI: 10.3390/diseases11040148] [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: 07/31/2023] [Revised: 09/03/2023] [Accepted: 10/17/2023] [Indexed: 11/22/2023] Open
Abstract
Worldwide, colon cancer is the third most frequent malignancy and the second most common cause of death. Although it can strike anybody at any age, colon cancer mostly affects the elderly. Small, non-cancerous cell clusters inside the colon, commonly known as polyps, are typically where colon cancer growth starts. But over time, if left untreated, these benign polyps may develop into malignant tissues and develop into colon cancer. For the diagnosis of colon cancer, with routine inspection of the colon region for polyps, several techniques, including colonoscopy and cancer scanning, are used. In the case identifying the polyps in the colon area, efforts are being taken to surgically remove the polyps as quickly as possible before they become malignant. If the polyps become malignant, then colon cancer treatment strategies, such as surgery, chemotherapy, targeted therapy, and immunotherapy, are applied to the patients. Despite the recent improvements in diagnosis and prognosis, the treatment of colorectal cancer (CRC) remains a challenging task. The objective of this review was to discuss how CRC is initiated, and its various developmental stages, pathophysiology, and risk factors, and also to explore the current state of colorectal cancer diagnosis and treatment, as well as recent advancements in the field, such as new screening methods and targeted therapies. We examined the limitations of current methods and discussed the ongoing need for research and development in this area. While this topic may be serious and complex, we hope to engage and inform our audience on this important issue.
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Affiliation(s)
- Noor Alrushaid
- Universite Claude Bernard Lyon-1, CNRS, ISA-UMR 5280, 69100 Villeurbanne, France;
- Department of Stem Cell Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Firdos Alam Khan
- Department of Stem Cell Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Ebtesam Al-Suhaimi
- Biology Department, College of Science, Institute of Research & Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Abdelhamid Elaissari
- Universite Claude Bernard Lyon-1, CNRS, ISA-UMR 5280, 69100 Villeurbanne, France;
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Chao Y, Gu T, Zhang Z, Wu T, Wang J, Bi Y. The role of miRNAs carried by extracellular vesicles in type 2 diabetes and its complications. J Diabetes 2023; 15:838-852. [PMID: 37583355 PMCID: PMC10590682 DOI: 10.1111/1753-0407.13456] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/30/2023] [Indexed: 08/17/2023] Open
Abstract
Diabetes poses severe global public health problems and places heavy burdens on the medical and economic systems of society. Type 2 diabetes (T2D) accounts for 90% of these cases. Diabetes also often accompanies serious complications that threaten multiple organs such as the brain, eyes, kidneys, and the cardiovascular system. MicroRNAs (miRNAs) carried by extracellular vesicles (EV-miRNAs) are considered to mediate cross-organ and cross-cellular communication and have a vital role in the pathophysiology of T2D. They also offer promising sources of diabetes-related biomarkers and serve as effective therapeutic targets. Here, we briefly reviewed studies of EV-miRNAs in T2D and related complications. Specially, we innovatively explore the targeting nature of miRNA action due to the target specificity of vesicle binding, aiding mechanism understanding as well as the detection and treatment of diseases.
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Affiliation(s)
- Yining Chao
- Department of Endocrinology, Endocrine and Metabolic Disease Medical Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingChina
- Branch of National Clinical Research Centre for Metabolic DiseasesNanjingChina
| | - Tianwei Gu
- Department of Endocrinology, Endocrine and Metabolic Disease Medical Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingChina
- Branch of National Clinical Research Centre for Metabolic DiseasesNanjingChina
| | - Zhou Zhang
- Department of Endocrinology, Endocrine and Metabolic Disease Medical Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingChina
- Branch of National Clinical Research Centre for Metabolic DiseasesNanjingChina
| | - Tianyu Wu
- Department of Endocrinology, Endocrine and Metabolic Disease Medical Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingChina
- Branch of National Clinical Research Centre for Metabolic DiseasesNanjingChina
| | - Jin Wang
- Department of Endocrinology, Endocrine and Metabolic Disease Medical Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingChina
- Branch of National Clinical Research Centre for Metabolic DiseasesNanjingChina
| | - Yan Bi
- Department of Endocrinology, Endocrine and Metabolic Disease Medical Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingChina
- Branch of National Clinical Research Centre for Metabolic DiseasesNanjingChina
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Wu Q, Li L, Jia Y, Xu T, Zhou X. Advances in studies of circulating microRNAs: origination, transportation, and distal target regulation. J Cell Commun Signal 2023; 17:445-455. [PMID: 36357651 PMCID: PMC9648873 DOI: 10.1007/s12079-022-00705-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/07/2022] [Indexed: 11/12/2022] Open
Abstract
In the past few years, numerous advances emerged in terms of circulating microRNA(miRNA) regulating gene expression by circulating blood to the distal tissues and cells. This article reviewed and summarized the process of circulating miRNAs entering the circulating system to exert gene regulation, especially exogenous miRNAs (such as plant miRNAs), from the perspective of the circulating miRNAs source (cell secretion or gastrointestinal absorption), the transport form and pharmacokinetics in circulating blood, and the evidence of distal regulation to gene expression, thereby providing a basis for their in-depth research and even application prospects.
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Affiliation(s)
- Qingni Wu
- Evidence Based Medicine Research Center, Jiangxi University of Chinese Medicine, 330004, Nanchang, China
| | - Longxue Li
- Laboratory Animal Science and Technology Center, Jiangxi University of Chinese Medicine, 330004, Nanchang, China
- Key Laboratory of Animal Model of TCM Syndromes of Depression, Jiangxi Administration of traditional Chinese Medicine, 330004, Nanchang, China
| | - Yao Jia
- Evidence Based Medicine Research Center, Jiangxi University of Chinese Medicine, 330004, Nanchang, China
| | - Tielong Xu
- Evidence Based Medicine Research Center, Jiangxi University of Chinese Medicine, 330004, Nanchang, China.
| | - Xu Zhou
- Evidence Based Medicine Research Center, Jiangxi University of Chinese Medicine, 330004, Nanchang, China.
- Key Laboratory of Drug-Targeting and Drug Delivery System of Sichuan Province, 610000, Chengdu, China.
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36
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Dhakal P, Tayara H, Chong KT. An ensemble of stacking classifiers for improved prediction of miRNA-mRNA interactions. Comput Biol Med 2023; 164:107242. [PMID: 37473564 DOI: 10.1016/j.compbiomed.2023.107242] [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: 05/01/2023] [Revised: 06/21/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that play a crucial role in regulating gene expression at the post-transcriptional level by binding to potential target sites of messenger RNAs (mRNAs), facilitated by the Argonaute family of proteins. Selecting the conservative candidate target sites (CTS) is a challenging step, considering that most of the existing computational algorithms primarily focus on canonical site types, which is a time-consuming and inefficient utilization of miRNA target site interactions. We developed a stacking classifier algorithm that addresses the CTS selection criteria using feature-encoding techniques that generates feature vectors, including k-mer nucleotide composition, dinucleotide composition, pseudo-nucleotide composition, and sequence order coupling. This innovative stacking classifier algorithm surpassed previous state-of-the-art algorithms in predicting functional miRNA targets. We evaluated the performance of the proposed model on 10 independent test datasets and obtained an average accuracy of 79.77%, which is a significant improvement of 7.26 % over previous models. This improvement shows that the proposed method has great potential for distinguishing highly functional miRNA targets and can serve as a valuable tool in biomedical and drug development research.
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Affiliation(s)
- Priyash Dhakal
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju-si, 54896, Jeollabuk-do, Republic of Korea
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju-si, 54896, Jeollabuk-do, Republic of Korea.
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju-si, 54896, Jeollabuk-do, Republic of Korea; Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju-si, 54896, Jeollabuk-do, Republic of Korea.
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37
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Wang X, Wang X, Jiang T, Zhang Z, Xie N, Yang G. MiR-22-3p suppresses NSCLC cell migration and EMT via targeting RAC1 expression. Funct Integr Genomics 2023; 23:281. [PMID: 37620594 PMCID: PMC10449966 DOI: 10.1007/s10142-023-01211-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: 07/05/2023] [Revised: 08/04/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
Previous studies have demonstrated the tumor-suppressive function of microRNA-22-3p (miR-22-3p) in several cancers, whereas the significance of miR-22-3p in non-small cell lung cancer (NSCLC) remains unclear. In this study, we explored the biological function and molecular mechanism of miR-22-3p in NSCLC cells. First, we assessed the expression of miR-22-3p in NSCLC tissues and cells based on RT-qPCR and TCGA database. Compared with normal lung tissues and cells, miR-22-3p expression was dramatically decreased in lung cancer tissues and cells. miR-22-3p expression was also correlated with lymph node metastasis and tumor size, but not TNM stages. We further explored the in vitro function of miR-22-3p on the migration and epithelial-mesenchymal transition (EMT) of NSCLC cells. The results showed that overexpression of miR-22-3p suppressed the migration and EMT of NSCLC cells, whereas silencing miR-22-3p showed the opposite effect. Luciferase assay demonstrated that RAS-related C3 botulinum toxin substrate 1 (RAC1) was the target gene for miR-22-3p. Mechanistically, we demonstrated that miR-22-3p suppressed the cell migration and EMT via downregulation of RAC1 because the inhibitory effect of miR-22-3p on cell migration and EMT of NSCLC cells was reversed by RAC1 overexpression. Based on these novel data, the miR-22-3p/RAC1 axis may be an alternative target in the therapeutic intervention of NSCLC.
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Affiliation(s)
- Xuejiao Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of the Air Force Medical University, Baqiao District, Xinsi Road 569, Xi'an, Shaanxi, China
| | - Xiaobin Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of the Air Force Medical University, Baqiao District, Xinsi Road 569, Xi'an, Shaanxi, China
| | - Tao Jiang
- Department of Thoracic Surgery, The Second Affiliated Hospital of the Air Force Medical University, Baqiao District, Xinsi Road 569, Xi'an, Shaanxi, China
| | - Zhipei Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of the Air Force Medical University, Baqiao District, Xinsi Road 569, Xi'an, Shaanxi, China
| | - Nianlin Xie
- Department of Thoracic Surgery, The Second Affiliated Hospital of the Air Force Medical University, Baqiao District, Xinsi Road 569, Xi'an, Shaanxi, China.
| | - Guang Yang
- Department of Thoracic Surgery, The Second Affiliated Hospital of the Air Force Medical University, Baqiao District, Xinsi Road 569, Xi'an, Shaanxi, China.
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Zhang MH, Yuan YF, Liu LJ, Wei YX, Yin WY, Zheng LZY, Tang YY, Lv Z, Zhu F. Dysregulated microRNAs as a biomarker for diagnosis and prognosis of hepatitis B virus-associated hepatocellular carcinoma. World J Gastroenterol 2023; 29:4706-4735. [PMID: 37664153 PMCID: PMC10473924 DOI: 10.3748/wjg.v29.i31.4706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/29/2023] [Accepted: 08/01/2023] [Indexed: 08/18/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignancy with a high incidence and fatality rate worldwide. Hepatitis B virus (HBV) infection is one of the most important risk factors for its occurrence and development. Early detection of HBV-associated HCC (HBV-HCC) can improve clinical decision-making and patient outcomes. Biomarkers are extremely helpful, not only for early diagnosis, but also for the development of therapeutics. MicroRNAs (miRNAs), a subset of non-coding RNAs approximately 22 nucleotides in length, have increasingly attracted scientists' attention due to their potential utility as biomarkers for cancer detection and therapy. HBV profoundly impacts the expression of miRNAs potentially involved in the development of hepatocarcinogenesis. In this review, we summarize the current progress on the role of miRNAs in the diagnosis and treatment of HBV-HCC. From a molecular standpoint, we discuss the mechanism by which HBV regulates miRNAs and investigate the exact effect of miRNAs on the promotion of HCC. In the near future, miRNA-based diagnostic, prognostic, and therapeutic applications will make their way into the clinical routine.
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Affiliation(s)
- Ming-He Zhang
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Yu-Feng Yuan
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Li-Juan Liu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Yu-Xin Wei
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei Province, China
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Wan-Yue Yin
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Lan-Zhuo-Yin Zheng
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei Province, China
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Ying-Ying Tang
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei Province, China
- Department of Neurology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Zhao Lv
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Fan Zhu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei Province, China
- Hubei Province Key Laboratory of Allergy & Immunology, Wuhan University, Wuhan 430071, Hubei Province, China
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Chen J, Liu Q, Yuan L, Shen W, Shi Q, Qi G, Chen T, Zhang Z. Osa-miR162a Enhances the Resistance to the Brown Planthopper via α-Linolenic Acid Metabolism in Rice ( Oryza sativa). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:11847-11859. [PMID: 37493591 DOI: 10.1021/acs.jafc.3c02637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The brown planthopper (BPH) is the most serious pest causing yield losses in rice. MicroRNAs (miRNAs) are emerging as key modulators of plant-pest interactions. In the study, we found that osa-miR162a is induced in response to BPH attack in the seedling stage and tunes rice resistance to the BPH via the α-linolenic acid metabolism pathway as indicated by gas chromatography/liquid chromatography-mass spectrometry analysis. Overexpression of osa-miR162a inhibited the development and growth of the BPH and simultaneously reduced the release of 3-hexenal and 3-hexen-1-ol to block host recognition in the BPH. Moreover, knockdown of OsDCL1, which is targeted by osa-miR162a, inhibited α-linolenic acid metabolism to enhance the resistance to the BPH, which was similar to that in miR162a-overexpressing plants. Our study revealed a novel defense mechanism mediated by plant miRNAs developed during the long-term evolution of plant-host interaction, provided new ideas for the identification of rice resistance resources, and promoted a better understanding of pest control.
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Affiliation(s)
- Jie Chen
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, Guangdong, China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Qin Liu
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, Guangdong, China
| | - Longyu Yuan
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, Guangdong, China
| | - Wenzhong Shen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MARA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research Institute, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
| | - Qingxing Shi
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, Guangdong, China
| | - Guojun Qi
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, Guangdong, China
| | - Ting Chen
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, Guangdong, China
| | - Zhenfei Zhang
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, Guangdong, China
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40
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Otsuka K, Nishiyama H, Kuriki D, Kawada N, Ochiya T. Connecting the dots in the associations between diet, obesity, cancer, and microRNAs. Semin Cancer Biol 2023; 93:52-69. [PMID: 37156343 DOI: 10.1016/j.semcancer.2023.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/27/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023]
Abstract
The prevalence of obesity has reached pandemic levels worldwide, leading to a lower quality of life and higher health costs. Obesity is a major risk factor for noncommunicable diseases, including cancer, although obesity is one of the major preventable causes of cancer. Lifestyle factors, such as dietary quality and patterns, are also closely related to the onset and development of obesity and cancer. However, the mechanisms underlying the complex association between diet, obesity, and cancer remain unclear. In the past few decades, microRNAs (miRNAs), a class of small non-coding RNAs, have been demonstrated to play critical roles in biological processes such as cell differentiation, proliferation, and metabolism, highlighting their importance in disease development and suppression and as therapeutic targets. miRNA expression levels can be modulated by diet and are involved in cancer and obesity-related diseases. Circulating miRNAs can also mediate cell-to-cell communications. These multiple aspects of miRNAs present challenges in understanding and integrating their mechanism of action. Here, we introduce a general consideration of the associations between diet, obesity, and cancer and review the current knowledge of the molecular functions of miRNA in each context. A comprehensive understanding of the interplay between diet, obesity, and cancer could be valuable for the development of effective preventive and therapeutic strategies in future.
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Affiliation(s)
- Kurataka Otsuka
- Tokyo NODAI Research Institure, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan; R&D Division, Kewpie Corporation, 2-5-7, Sengawa-cho, Chofu-shi, Tokyo 182-0002, Japan; Division of Molecular and Cellular Medicine, Institute of Medical Science, Tokyo Medical University, 6-7-1, Nishishinjyuku, Shinjuku-ku, Tokyo 160-0023, Japan; Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.
| | - Hiroshi Nishiyama
- R&D Division, Kewpie Corporation, 2-5-7, Sengawa-cho, Chofu-shi, Tokyo 182-0002, Japan
| | - Daisuke Kuriki
- R&D Division, Kewpie Corporation, 2-5-7, Sengawa-cho, Chofu-shi, Tokyo 182-0002, Japan
| | - Naoki Kawada
- R&D Division, Kewpie Corporation, 2-5-7, Sengawa-cho, Chofu-shi, Tokyo 182-0002, Japan
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, Institute of Medical Science, Tokyo Medical University, 6-7-1, Nishishinjyuku, Shinjuku-ku, Tokyo 160-0023, Japan
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41
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Shen Z, Yang Q, Luo L, Li T, Ke Z, Li T, Chen J, Meng X, Xiang H, Li C, Zhou Z, Chen P, Pan G. Non-coding RNAs identification and regulatory networks in pathogen-host interaction in the microsporidia congenital infection. BMC Genomics 2023; 24:420. [PMID: 37495972 PMCID: PMC10373312 DOI: 10.1186/s12864-023-09490-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/28/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND The interaction networks between coding and non-coding RNAs (ncRNAs) including long non-coding RNA (lncRNA), covalently closed circular RNA (circRNA) and miRNA are significant to elucidate molecular processes of biological activities and interactions between host and pathogen. Congenital infection caused by vertical transmission of microsporidia N. bombycis can result in severe economic losses in the silkworm-feeding industry. However, little is known about ncRNAs that take place in the microsporidia congenital infection. Here we conducted whole-transcriptome RNA-Seq analyses to identify ncRNAs and regulatory networks for both N. bombycis and host including silkworm embryos and larvae during the microsporidia congenital infection. RESULTS A total of 4,171 mRNAs, 403 lncRNA, 62 circRNAs, and 284 miRNAs encoded by N. bombycis were identified, among which some differentially expressed genes formed cross-talk and are involved in N. bombycis proliferation and infection. For instance, a lncRNA/circRNA competing endogenous RNA (ceRNA) network including 18 lncRNAs, one circRNA, and 20 miRNAs was constructed to describe 14 key parasites genes regulation, such as polar tube protein 3 (PTP3), ricin-B-lectin, spore wall protein 4 (SWP4), and heat shock protein 90 (HSP90). Regarding host silkworm upon N. bombycis congenital infection, a total of 14,889 mRNAs, 3,038 lncRNAs, 19,039 circRNAs, and 3,413 miRNAs were predicted based on silkworm genome with many differentially expressed coding and non-coding genes during distinct developmental stages. Different species of RNAs form interacting network to modulate silkworm biological processes, such as growth, metamorphosis and immune responses. Furthermore, a lncRNA/circRNA ceRNA network consisting of 140 lncRNAs, five circRNA, and seven miRNAs are constructed hypothetically to describe eight key host genes regulation, such as Toll-6, Serpin-6, inducible nitric oxide synthase (iNOS) and Caspase-8. Notably, cross-species analyses indicate that parasite and host miRNAs play a vital role in pathogen-host interaction in the microsporidia congenital infection. CONCLUSION This is the first comprehensive pan-transcriptome study inclusive of both N. bombycis and its host silkworm with a specific focus on the microsporidia congenital infection, and show that ncRNA-mediated regulation plays a vital role in the microsporidia congenital infection, which provides a new insight into understanding the basic biology of microsporidia and pathogen-host interaction.
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Affiliation(s)
- Zigang Shen
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Qiong Yang
- Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, People's Republic of China
| | - Lie Luo
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Tangxin Li
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Zhuojun Ke
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Tian Li
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Jie Chen
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Xianzhi Meng
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Heng Xiang
- College of Animal Science and Technology, Southwest University, Chongqing, People's Republic of China
| | - Chunfeng Li
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Zeyang Zhou
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
- College of Life Sciences, Chongqing Normal University, Chongqing, People's Republic of China
| | - Ping Chen
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China.
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, People's Republic of China.
| | - Guoqing Pan
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China.
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China.
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Song P, Chen X, Zhang P, Zhou Y, Zhou R. miR-200b/MYBL2/CDK1 suppresses proliferation and induces senescence through cell cycle arrest in ovine granulosa cells. Theriogenology 2023; 207:19-30. [PMID: 37257219 DOI: 10.1016/j.theriogenology.2023.05.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
Normal growth of granulosa cells (GCs) is essential for follicular development. miR-200b plays a vital role in litter size, estrous cycle, ovulation, and follicular development in sheep. However, it is unclear that the specific effect and regulatory mechanism of miR-200b on ovine GCs. miR-200b mimic inhibited GCs proliferation and induced cellular senescence through downregulating mitochondrial membrane potential (MMP), concentration of ATP and mitochondrial respiratory chain complex Ⅰ, and upregulating SA-β-gal positive rate and ROS production. A total of 597 differentially expressed genes were identified by RNA-Seq in GCs transfected with miR-200b mimic and mimic NC, and they were involved in cell cycle and cellular senescence. miR-200b directly targeted and downregulated MYBL2 and CDK1. Overexpression of MYBL2 promoted GCs proliferation and genes expression (CDK1, CDC20, MAD2L1 and FOXM1), which were suppressed by miR-200b mimic. Furthermore, MYBL2 negatively regulated miR-200b-induced GC senescence. In conclusion, miR-200b/MYBL2/CDK1 regulated proliferation and senescence through cell cycle pathway in ovine granulosa cells. Our study provides a novel insight that miR-200b regulates ovine follicular development.
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Affiliation(s)
- Pengyan Song
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, Hebei Province, 071001, China
| | - Xiaoyong Chen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, Hebei Province, 071001, China
| | - Peiying Zhang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, Hebei Province, 071001, China
| | - Ying Zhou
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, Hebei Province, 071001, China
| | - Rongyan Zhou
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, Hebei Province, 071001, China.
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43
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Teng L, Zhang X, Wang R, Lin K, Zeng M, Chen H, Cao F. miRNA transcriptome reveals key miRNAs and their targets contributing to the difference in Cd tolerance of two contrasting maize genotypes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 256:114881. [PMID: 37030049 DOI: 10.1016/j.ecoenv.2023.114881] [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: 11/29/2022] [Revised: 03/06/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Soil cadmium (Cd) contamination is a global environmental and food safety production issue. microRNAs (miRNAs) are proven to be involved in plant growth and development, and abiotic/biotic stress response, but their role in Cd tolerance is largely unknown in maize. To understand the genetic basis of Cd tolerance, two maize genotypes differing in Cd tolerance (L42, a sensitive genotype and L63, a tolerant genotype) were selected, and miRNA sequencing was carried out at nine-day-old seedlings exposed to 24 h Cd stress (5 μM CdCl2). A total of 151 differentially expressed miRNAs were identified, including 20 known miRNAs and 131 novel miRNAs. The results revealed that 90 and 22 miRNAs were up-regulated and down-regulated by Cd in Cd-tolerant genotype L63, and there were 23 and 43 miRNAs in Cd-sensitive genotype L42, respectively. Twenty-six miRNAs were up-regulated in L42 and unchanged or down-regulated in L63, or unchanged in L42 and down-regulated in L63. There were 108 miRNAs that were up-regulated in L63 and unchanged or down-regulated in L42, or unchanged in L63 and down-regulated in L42. Their target genes were enriched mainly in peroxisomes, glutathione (GSH) metabolism, ABC transporter, and ubiquitin-protease system. Among them, target genes involved in the peroxisome pathway and GSH metabolism might play key roles in Cd tolerance in L63. Besides, several ABC transporters which might involve in Cd uptake and transport were identified. The differentially expressed miRNAs or target genes could be used for breeding low grain Cd accumulation and high Cd tolerance cultivars in maize.
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Affiliation(s)
- Lidong Teng
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Xueqing Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Runfeng Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Kaina Lin
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Meng Zeng
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Hao Chen
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China; Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Fangbin Cao
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.
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44
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Ohashi-Ito K, Iwamoto K, Yamagami A, Nakano T, Fukuda H. HD-ZIP III-dependent local promotion of brassinosteroid synthesis suppresses vascular cell division in Arabidopsis root apical meristem. Proc Natl Acad Sci U S A 2023; 120:e2216632120. [PMID: 37011193 PMCID: PMC10104508 DOI: 10.1073/pnas.2216632120] [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: 09/29/2022] [Accepted: 02/22/2023] [Indexed: 04/05/2023] Open
Abstract
Spatiotemporal control of cell division in the meristem is vital for plant growth. In the stele of the root apical meristem (RAM), procambial cells divide periclinally to increase the number of vascular cell files. Class III homeodomain leucine zipper (HD-ZIP III) proteins are key transcriptional regulators of RAM development and suppress the periclinal division of vascular cells in the stele; however, the mechanism underlying the regulation of vascular cell division by HD-ZIP III transcription factors (TFs) remains largely unknown. Here, we performed transcriptome analysis to identify downstream genes of HD-ZIP III and found that HD-ZIP III TFs positively regulate brassinosteroid biosynthesis-related genes, such as CONSTITUTIVE PHOTOMORPHOGENIC DWARF (CPD), in vascular cells. Introduction of pREVOLUTA::CPD in a quadruple loss-of-function mutant of HD-ZIP III genes partly rescued the phenotype in terms of the vascular defect in the RAM. Treatment of a quadruple loss-of-function mutant, a gain-of-function mutant of HD-ZIP III, and the wild type with brassinosteroid and a brassinosteroid synthesis inhibitor also indicated that HD-ZIP III TFs act together to suppress vascular cell division by increasing brassinosteroid levels. Furthermore, brassinosteroid application suppressed the cytokinin response in vascular cells. Together, our findings suggest that the suppression of vascular cell division by HD-ZIP III TFs is caused, at least in part, by the increase in brassinosteroid levels through the transcriptional activation of brassinosteroid biosynthesis genes in the vascular cells of the RAM. This elevated brassinosteroid level suppresses cytokinin response in vascular cells, inhibiting vascular cell division in the RAM.
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Affiliation(s)
- Kyoko Ohashi-Ito
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0033, Japan
| | - Kuninori Iwamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0033, Japan
| | - Ayumi Yamagami
- Department of Plant Gene and Totipotency, Graduate School of Biostudies, Kyoto University, Kyoto606-8502, Japan
| | - Takeshi Nakano
- Department of Plant Gene and Totipotency, Graduate School of Biostudies, Kyoto University, Kyoto606-8502, Japan
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0033, Japan
- Department of Bioscience and Biotechnology, Faculty of Environmental Sciences, Kyoto University of Advanced Science, Kyoto621-8555, Japan
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45
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Qu Q, Chen X, Ning B, Zhang X, Nie H, Zeng L, Chen H, Fu X. Prediction of miRNA-disease associations by neural network-based deep matrix factorization. Methods 2023; 212:1-9. [PMID: 36813017 DOI: 10.1016/j.ymeth.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/17/2023] [Accepted: 02/10/2023] [Indexed: 02/23/2023] Open
Abstract
MicroRNA(miRNA) is a class of short non-coding RNAs with a length of about 22 nucleotides, which participates in various biological processes of cells. A number of studies have shown that miRNAs are closely related to the occurrence of cancer and various human diseases. Therefore, studying miRNA-disease associations is helpful to understand the pathogenesis of diseases as well as the prevention, diagnosis, treatment and prognosis of diseases. Traditional biological experimental methods for studying miRNA-disease associations have disadvantages such as expensive equipment, time-consuming and labor-intensive. With the rapid development of bioinformatics, more and more researchers are committed to developing effective computational methods to predict miRNA-disease associations in roder to reduce the time and money cost of experiments. In this study, we proposed a neural network-based deep matrix factorization method named NNDMF to predict miRNA-disease associations. To address the problem that traditional matrix factorization methods can only extract linear features, NNDMF used neural network to perform deep matrix factorization to extract nonlinear features, which makes up for the shortcomings of traditional matrix factorization methods. We compared NNDMF with four previous classical prediction models (IMCMDA, GRMDA, SACMDA and ICFMDA) in global LOOCV and local LOOCV, respectively. The AUCs achieved by NNDMF in two cross-validation methods were 0.9340 and 0.8763, respectively. Furthermore, we conducted case studies on three important human diseases (lymphoma, colorectal cancer and lung cancer) to validate the effectiveness of NNDMF. In conclusion, NNDMF could effectively predict the potential miRNA-disease associations.
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Affiliation(s)
- Qiang Qu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Xia Chen
- School of Basic Education, Changsha Aeronautical Vocational and Technical College, Changsha, China
| | - Bin Ning
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Xiang Zhang
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Hao Nie
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Li Zeng
- College of Life and Environmental Science, Hunan University of Art and Science, Changde, China
| | - Haowen Chen
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.
| | - Xiangzheng Fu
- Research Institute of Hunan University in Chongqing, Chongqing, China.
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Kim IK, Song BW, Lim S, Kim SW, Lee S. The Role of Epicardial Adipose Tissue-Derived MicroRNAs in the Regulation of Cardiovascular Disease: A Narrative Review. BIOLOGY 2023; 12:biology12040498. [PMID: 37106699 PMCID: PMC10135702 DOI: 10.3390/biology12040498] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
Cardiovascular diseases have been leading cause of death worldwide for many decades, and obesity has been acknowledged as a risk factor for cardiovascular diseases. In the present review, human epicardial adipose tissue-derived miRNAs reported to be differentially expressed under pathologic conditions are discussed and summarized. The results of the literature review indicate that some of the epicardial adipose tissue-derived miRNAs are believed to be cardioprotective, while some others show quite the opposite effects depending on the underlying pathologic conditions. Furthermore, they suggest that that the epicardial adipose tissue-derived miRNAs have great potential as both a diagnostic and therapeutic modality. Nevertheless, mainly due to highly limited availability of human samples, it is very difficult to make any generalized claims on a given miRNA in terms of its overall impact on the cardiovascular system. Therefore, further functional investigation of a given miRNA including, but not limited to, the study of its dose effect, off-target effects, and potential toxicity is required. We hope that this review can provide novel insights to transform our current knowledge on epicardial adipose tissue-derived miRNAs into clinically viable therapeutic strategies for preventing and treating cardiovascular diseases.
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Affiliation(s)
- Il-Kwon Kim
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si 25601, Republic of Korea
- International St. Mary’s Hospital, Catholic Kwandong University, Incheon 22711, Republic of Korea
| | - Byeong-Wook Song
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si 25601, Republic of Korea
- International St. Mary’s Hospital, Catholic Kwandong University, Incheon 22711, Republic of Korea
| | - Soyeon Lim
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si 25601, Republic of Korea
- International St. Mary’s Hospital, Catholic Kwandong University, Incheon 22711, Republic of Korea
| | - Sang-Woo Kim
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si 25601, Republic of Korea
- International St. Mary’s Hospital, Catholic Kwandong University, Incheon 22711, Republic of Korea
| | - Seahyoung Lee
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si 25601, Republic of Korea
- International St. Mary’s Hospital, Catholic Kwandong University, Incheon 22711, Republic of Korea
- Correspondence:
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Gu C, Mo W, Wang K, Gao M, Chen J, Zhang F, Shen J. Exosomal miR-370-3p increases the permeability of blood-brain barrier in ischemia/reperfusion stroke of brain by targeting MPK1. Aging (Albany NY) 2023; 15:1931-1943. [PMID: 37000151 PMCID: PMC10085611 DOI: 10.18632/aging.204573] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/23/2023] [Indexed: 04/01/2023]
Abstract
Ischemia/reperfusion (I/R) damage induced by stroke poses a serious hazard to human life, while mechanism of blood-brain barrier (BBB) dysfunction is still unknown. To imitate stroke induced ischemia conditions in vivo, the rat model of cerebral I/R damage was created by middle cerebral artery occlusion (MCAO). In vitro, the rat microvascular endothelial cell line bEND.3 was subjected to oxygen-glucose deprivation/reperfusion (OGD/R). Evans blue was used to evaluate the permeability of the blood-brain barrier (BBB). To evaluate gene expression at the mRNA and protein levels, researchers used real-time PCR and western blotting. Infarct volume and BBB permeability were considerably higher in cerebral (I/R) animals than in the Sham group. Exosomal miR-370-3p expression was shown to be higher in the brains of I/R injured rats and OGD/R treatment bEND.3. The BBB permeability was considerably increased when miR-370-3p was downregulated in OGD/R pretreated bEND.3. miR-370-3p regulates MAPK1 expression by targeting it. In bEND.3, OGD/R therapy increased BBB permeability substantially. OGD/R was inhibited by miR-370-3p mimic transfection, while miR-370-3p mimic was abolished by co-transfection with MAPK1 overexpression lentivirus. In cerebral I/R damage, exosomal miR-370-3p targets MAPK1 and aggregates BBB permeability.
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Affiliation(s)
- Caifeng Gu
- Center of Emergency and Intensive Care Unit, Jinshan Hospital, Fudan University, Shanghai, China
| | - Weichun Mo
- Center of Emergency and Intensive Care Unit, Jinshan Hospital, Fudan University, Shanghai, China
| | - Kunlun Wang
- Center of Emergency and Intensive Care Unit, Jinshan Hospital, Fudan University, Shanghai, China
| | - Mingqiang Gao
- Center of Emergency and Intensive Care Unit, Jinshan Hospital, Fudan University, Shanghai, China
| | - Junfeng Chen
- Center of Emergency and Intensive Care Unit, Jinshan Hospital, Fudan University, Shanghai, China
| | - Feng Zhang
- Center of Emergency and Intensive Care Unit, Jinshan Hospital, Fudan University, Shanghai, China
| | - Jie Shen
- Center of Emergency and Intensive Care Unit, Jinshan Hospital, Fudan University, Shanghai, China
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Kirstein N, Dokaneheifard S, Cingaram PR, Valencia MG, Beckedorff F, Gomes Dos Santos H, Blumenthal E, Tayari MM, Gaidosh GS, Shiekhattar R. The Integrator complex regulates microRNA abundance through RISC loading. SCIENCE ADVANCES 2023; 9:eadf0597. [PMID: 36763664 PMCID: PMC9916992 DOI: 10.1126/sciadv.adf0597] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
MicroRNA (miRNA) homeostasis is crucial for the posttranscriptional regulation of their target genes during development and in disease states. miRNAs are derived from primary transcripts and are processed from a hairpin precursor intermediary to a mature 22-nucleotide duplex RNA. Loading of the duplex into the Argonaute (AGO) protein family is pivotal to miRNA abundance and its posttranscriptional function. The Integrator complex plays a key role in protein coding and noncoding RNA maturation, RNA polymerase II pause-release, and premature transcriptional termination. Here, we report that loss of Integrator results in global destabilization of mature miRNAs. Enhanced ultraviolet cross-linking and immunoprecipitation of Integrator uncovered an association with duplex miRNAs before their loading onto AGOs. Tracing miRNA fate from biogenesis to stabilization by incorporating 4-thiouridine in nascent transcripts pinpointed a critical role for Integrator in miRNA assembly into AGOs.
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Affiliation(s)
- Nina Kirstein
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Sadat Dokaneheifard
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Pradeep Reddy Cingaram
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Monica Guiselle Valencia
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Felipe Beckedorff
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Helena Gomes Dos Santos
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Ezra Blumenthal
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
- Medical Scientist Training Program and Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mina Masoumeh Tayari
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Gabriel Stephen Gaidosh
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Ramin Shiekhattar
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
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49
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Jabeer A, Temiz M, Bakir-Gungor B, Yousef M. miRdisNET: Discovering microRNA biomarkers that are associated with diseases utilizing biological knowledge-based machine learning. Front Genet 2023; 13:1076554. [PMID: 36712859 PMCID: PMC9877296 DOI: 10.3389/fgene.2022.1076554] [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: 10/21/2022] [Accepted: 12/30/2022] [Indexed: 01/14/2023] Open
Abstract
During recent years, biological experiments and increasing evidence have shown that microRNAs play an important role in the diagnosis and treatment of human complex diseases. Therefore, to diagnose and treat human complex diseases, it is necessary to reveal the associations between a specific disease and related miRNAs. Although current computational models based on machine learning attempt to determine miRNA-disease associations, the accuracy of these models need to be improved, and candidate miRNA-disease relations need to be evaluated from a biological perspective. In this paper, we propose a computational model named miRdisNET to predict potential miRNA-disease associations. Specifically, miRdisNET requires two types of data, i.e., miRNA expression profiles and known disease-miRNA associations as input files. First, we generate subsets of specific diseases by applying the grouping component. These subsets contain miRNA expressions with class labels associated with each specific disease. Then, we assign an importance score to each group by using a machine learning method for classification. Finally, we apply a modeling component and obtain outputs. One of the most important outputs of miRdisNET is the performance of miRNA-disease prediction. Compared with the existing methods, miRdisNET obtained the highest AUC value of .9998. Another output of miRdisNET is a list of significant miRNAs for disease under study. The miRNAs identified by miRdisNET are validated via referring to the gold-standard databases which hold information on experimentally verified microRNA-disease associations. miRdisNET has been developed to predict candidate miRNAs for new diseases, where miRNA-disease relation is not yet known. In addition, miRdisNET presents candidate disease-disease associations based on shared miRNA knowledge. The miRdisNET tool and other supplementary files are publicly available at: https://github.com/malikyousef/miRdisNET.
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Affiliation(s)
- Amhar Jabeer
- Department of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri, Turkey
| | - Mustafa Temiz
- Department of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri, Turkey,*Correspondence: Malik Yousef, ; Mustafa Temiz,
| | - Burcu Bakir-Gungor
- Department of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri, Turkey
| | - Malik Yousef
- Department of Information Systems, Zefat Academic College, Zefat, Israel,Galilee Digital Health Research Center (GDH), Zefat Academic College, Zefat, Israel,*Correspondence: Malik Yousef, ; Mustafa Temiz,
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50
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Torrez RM, Ohi MD, Garner AL. Structural Insights into the Advances and Mechanistic Understanding of Human Dicer. Biochemistry 2023; 62:1-16. [PMID: 36534787 DOI: 10.1021/acs.biochem.2c00570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The RNase III endoribonuclease Dicer was discovered to be associated with cleavage of double-stranded RNA in 2001. Since then, many advances in our understanding of Dicer function have revealed that the enzyme plays a major role not only in microRNA biology but also in multiple RNA interference-related pathways. Yet, there is still much to be learned regarding Dicer structure-function in relation to how Dicer and Dicer-like enzymes initiate their cleavage reaction and release the desired RNA product. This Perspective describes the latest advances in Dicer structural studies, expands on what we have learned from this data, and outlines key gaps in knowledge that remain to be addressed. More specifically, we focus on human Dicer and highlight the intermediate processing steps where there is a lack of structural data to understand how the enzyme traverses from pre-cleavage to cleavage-competent states. Understanding these details is necessary to model Dicer's function as well as develop more specific microRNA-targeted therapeutics for the treatment of human diseases.
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Affiliation(s)
- Rachel M Torrez
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States.,Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Melanie D Ohi
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States.,Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109, United States
| | - Amanda L Garner
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
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