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Li Z, Huang J, Zhang S, Zhang W, Si X. Non coding RNA biomarkers in pemphigus disease. Clin Chim Acta 2025:120381. [PMID: 40412588 DOI: 10.1016/j.cca.2025.120381] [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: 04/28/2025] [Revised: 05/21/2025] [Accepted: 05/21/2025] [Indexed: 05/27/2025]
Abstract
Pemphigus represents a group of potentially life-threatening autoimmune blistering diseases characterized by the production of pathogenic autoantibodies against desmosomal cadherins, leading to loss of cell adhesion. Early and accurate diagnosis remains critical for optimal management, yet current diagnostic approaches largely rely on invasive biopsies and serological assays that do not always predict disease progression or therapeutic response. In this context, the identification of reliable biomarkers is essential to enhance diagnostic precision, monitor disease activity, and guide treatment strategies. Non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), have emerged as promising biomarker candidates due to their stability in body fluids, tissue- and disease-specific expression patterns, and regulatory functions in immune processes. Increasing evidence suggests that dysregulated ncRNAs play significant roles in the immunopathogenesis of pemphigus, influencing cytokine signaling, immune cell differentiation, and keratinocyte adhesion. Therefore, herein, we summarize current findings on the involvement of specific miRNAs and lncRNAs in pemphigus pathogenesis, their diagnostic and prognostic potential, and the emerging therapeutic opportunities based on modulating ncRNA expression. Additionally, we address the limitations and challenges associated with clinical translation of ncRNA research and highlight future directions that may facilitate the incorporation of ncRNAs into personalized medicine approaches for pemphigus patients.
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Affiliation(s)
- ZhuQing Li
- School of Clinical Medicine, Shandong Second Medical University, WeiFang, ShanDong 261000, China
| | - JinJin Huang
- School of Clinical Medicine, Shandong Second Medical University, WeiFang, ShanDong 261000, China
| | - ShuCheng Zhang
- Shandong First Medical University, JiNan, ShanDong 250014, China
| | - WenJuan Zhang
- JiNing Medical University, JiNing, ShanDong 272067, China
| | - Xiaoqing Si
- Department of Dermatology, The first Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250014, China.
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2
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Mishra S, Garg P, Trivedi M, Srivastava P. Multiple system biology approaches reveals the role of the hsa-miR-21 in increasing risk of neurological disorders in patients suffering from hypertension. J Hum Hypertens 2025:10.1038/s41371-025-01027-3. [PMID: 40389629 DOI: 10.1038/s41371-025-01027-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2024] [Revised: 04/11/2025] [Accepted: 05/02/2025] [Indexed: 05/21/2025]
Abstract
Hypertension is a prevalent disease that substantially elevates the risk of neurological disorders such as dementia, stroke and Parkinson's disease. MicroRNAs (miRNAs) play a critical role in the regulation of gene expression related to brain function and disorders. Understanding the involvement of miRNAs in these conditions could provide new insights into potential therapeutic targets. The main objective of this study is to target and investigate microRNAs (miRNAs) associated with neurological disorders in patients suffering from hypertension. The genes involved in hypertension were identified from various databases including GeneCard, MalaCard, DisGeNet, OMIM & GEO2R. The key gene for hypertension was identified using a systems biology approach. Also, potent phytochemical for hypertension was determined by computer-aided drug-designing approach. Functional miRNAs were determined for the key target gene using miRNet analytics platform by hypergeometric tests. Further, the gene-miRNA interaction was determined and enrichment analysis was done. RPS27A was identified as a key target gene for hypertension. Naringenin showed effective molecular interaction with RPS27A with a binding energy score (-6.28). Further, a list of miRNAs which were targeting brain disorders was determined from miRNet. A gene-miRNA network was constructed using the PSRR tool for Parkinson's Disease, Autism Spectrum Disorder, Acute Cerebral Infarction, ACTH-Secreting Pituitary Adenoma, & Ependymoma. Further, miRNA 21 & miRNA 16 were found to be associated with four of the neurological disorders. The study identifies specific miRNAs that may serve as potential biomarkers for brain disorders in hypertensive patients. Targeting these miRNAs could open new avenues for therapeutic strategies aimed at mitigating neurological damage in this patient population.
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Affiliation(s)
- Sanjana Mishra
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, India
| | - Prekshi Garg
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, India
| | - Mala Trivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, India.
| | - Prachi Srivastava
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, India.
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3
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Pedreañez A, Vargas R, Carrero Y, Hernández-Fonseca JP, Hernández-Fonseca H, Mosquera J. Role of Angiotensin II in Venezuelan Equine Encephalitis: Narrative Review. Rev Med Virol 2025; 35:e70040. [PMID: 40317791 DOI: 10.1002/rmv.70040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2025] [Revised: 04/15/2025] [Accepted: 04/29/2025] [Indexed: 05/07/2025]
Abstract
Venezuelan equine encephalitis virus (VEEV) is an alphavirus in the family Togaviridae, transmitted by a mosquito bite and is highly infectious in aerosol form. Inflammation plays a role of antiviral response as well as development of lethal encephalitis. Infection through a mosquito bite is biphasic, beginning with an inflammatory process and viral replication in different organs with subsequent infiltration to the central nervous system (CNS), inducing encephalitis. The direct route is through inhalation of aerosols containing the virus with direct brain infection through the olfactory nerve. Significant damage is due to exacerbated inflammation in the host. Angiotensin II (Ang II) is a molecule with high pro-inflammatory capacity, which has been found to be upregulated in the brain of VEEV-infected rats, suggesting its role in the pathogenesis of this disease. Limited information regarding the association of Ang II expression with VEEV brain infection has been reported. The aim of this review is to highlight published reports indicating a possible association between Ang II expression and VEEV-induced encephalitis. Several studies reflect a possible expression and function of Ang II during VEEV infection. Factors such as the relationship of Ang II with proteins involved in viral replication and entry into the cell (furin, Rab5, Rab7), activation of protein kinase C (necessary for the phosphorylation of VEEV), presence of microRNAs related to viral biology, increased permeability of the blood-brain barrier, and use of transcription pathways common to Ang II and VEEV, may conceivable an association of Ang II with the pathogenesis of VEEV encephalitis.
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Affiliation(s)
- Adriana Pedreañez
- Cátedra de Inmunología, Facultad de Medicina, Escuela de Bioanálisis, Universidad del Zulia, Maracaibo, Venezuela
| | - Renata Vargas
- Facultad de Medicina, Instituto de Investigaciones Clínicas 'Dr. Américo Negrette', Universidad del Zulia, Maracaibo, Venezuela
| | - Yenddy Carrero
- Facultad de Medicina, Instituto de Investigaciones Clínicas 'Dr. Américo Negrette', Universidad del Zulia, Maracaibo, Venezuela
| | - Juan P Hernández-Fonseca
- Facultad de Medicina, Instituto de Investigaciones Clínicas 'Dr. Américo Negrette', Universidad del Zulia, Maracaibo, Venezuela
- Servicio de Microscopia Electrónica del Centro Nacional de Biotecnología (CNB-CSIC), Madrid, España
| | - Hugo Hernández-Fonseca
- Department of Anatomy, Physiology and Pharmacology, School of Veterinary Medicine, Saint George's University, True Blue, Grenada
| | - Jesús Mosquera
- Facultad de Medicina, Instituto de Investigaciones Clínicas 'Dr. Américo Negrette', Universidad del Zulia, Maracaibo, Venezuela
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4
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Zhao L, Huang J, Fu X, Li Y, Wu S. IHNV induced miR-19-3p modulates immune response of rainbow trout (Oncorhynchus mykiss) by targeting DHX58-dependent RLR signaling pathway. FISH & SHELLFISH IMMUNOLOGY 2025; 160:110200. [PMID: 39954832 DOI: 10.1016/j.fsi.2025.110200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 01/16/2025] [Accepted: 02/12/2025] [Indexed: 02/17/2025]
Abstract
miR-19-3p has been implicated in various pathological and physiological processes, including immune response, inflammation, oncogenesis and cell damage. However, its function in rainbow trout (Oncorhynchus mykiss) has not been well elucidated. In this study, the expression patterns of miR-19-3p and target gene DExH-Box helicase 58 (DHX58) in rainbow trout infected with infectious hematopoietic necrosis virus (IHNV) were detected, and regulatory mechanism and function of miR-19-3p were investigated by overexpression and inhibition experiment in vitro and in vivo. Expression patterns showed that miR-19-3p and DHX58 displayed significant time-dependent changes in IHNV-infected rainbow trout intestines, skins, gills, and liver cells, and their expression were negatively correlated at multiple time points. In vitro, the targeting relationship between miR-19-3p and DHX58 was confirmed by dual-luciferase reporter assay and RNA immunoprecipitation assay, and overexpression of miR-19-3p significantly suppressed the expression of DHX58 and downstream genes interferon regulatory factor 3 (IRF3), interferon regulatory factor 7 (IRF7), interferon (IFN), myxovirus 1 (MX1), interferon-stimulated gene 15 (ISG15), nuclear factor kappa-B (NF-κB), and interleukin-1 beta (IL-1β), whereas the expression levels of DHX58 and downstream genes were significantly increased after transfecting miR-19-3p inhibitor. In vivo, agomiR-19-3p significantly inhibited the expression of DHX58, and then reduced the expression levels of IRF3, IRF7, IFN, MX1, NF-κB, IL-1β, tumor necrosis factor-α (TNFα), and ISG15. Additionally, overexpression of miR-19-3p significantly increased IHNV copies and cell proliferation number, and suppressed apoptosis, while the opposite results were obtained after miR-19-3p repressing. This study confirmed that miR-19-3p regulates rainbow trout antiviral immune by DHX58-mediated interferon pathway in vitro and in vivo, which provides potential for using miRNAs as anti-viral target drugs.
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Affiliation(s)
- Lu Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xujuan Fu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yongjuan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China; College of Science, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Shenji Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
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Akhgari H, Ahmadi A, Rezaei A, Mohammadi A, Safaralizadeh R. Enhanced expression of miR-128 in peripheral blood mononuclear cells: a potent candidate diagnostic biomarker for multiple sclerosis. Neurol Res 2025; 47:393-401. [PMID: 40122134 DOI: 10.1080/01616412.2025.2481443] [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: 07/02/2024] [Accepted: 03/12/2025] [Indexed: 03/25/2025]
Abstract
OBJECTIVES Millions of people worldwide, especially young adults, are affected by multiple sclerosis (MS), a demyelinating and autoimmune condition of the central nervous system (CNS). Many studies have focused on the diagnostic value of miRNAs circulating in body fluids of MS patients. Thus, this study aimed to assess the expression of miR-128 and its potential as a biomarker for MS in the Iranian population. METHODS This study recruited 85 MS patients and 30 healthy matched controls. Following the collection of blood samples, serum was isolated. RNA was then extracted, cDNA was synthesized, and miR-128 expression was measured by real-time PCR. RESULTS There was significant overexpression of miR-128 in MS patients in comparison with healthy controls (p-value <0.0001). In addition, there was a rather notable association between the subtypes of MS samples and the expression levels of miR-128. ROC analysis showed an AUC of 0.9111 (95%CI 0.85-0.97, p-value <0.0001) with sensitivity and specificity of 80.00% and 93.33%, respectively. CONCLUSION The expression of miR-128 was significantly higher in PBMCs of MS patients in comparison with healthy controls. Additionally, miR-128 could be an excellent biomarker for MS patient diagnosis.
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Affiliation(s)
- Hossein Akhgari
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Alireza Ahmadi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Abedeh Rezaei
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Ali Mohammadi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
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6
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Jiang M, Yang K, Zhang C, Xu D. Novel Sensing Strategy for MicroRNA via DSN-RCA Dual Amplification and Optical Tweezer-Assisted Suspension Bead Arrays. Anal Chem 2025; 97:9014-9022. [PMID: 40247710 DOI: 10.1021/acs.analchem.5c00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2025]
Abstract
Traditional microRNA detection methods have some limitations that cannot be ignored. Enzyme-catalyzed nucleic acid amplification has gradually become an important method in bioanalysis and is expected to be a substitute for traditional methods. Combining enzymes with different functions provides a wide range of analytical design possibilities to create high-performance sensing strategies. Meanwhile, the optical tweezers that produce the tightly focused laser beam are integrated with a suspension bead array that fully concentrates the signal labels, contributing to stable signal output and improved detection efficiency. Herein, we have developed a novel "DSN-RCA dual amplification and optical tweezer-assisted suspension bead array imaging" sensing strategy for highly efficient detection of microRNA-21 (miRNA-21). The conversion of low abundance targets into bulk fluorescence signal probes was achieved by duplex-specific nuclease (DSN), and signal enrichment on bead supports rather than dispersion in solution was realized by rolling circle amplification (RCA) in one step. The synergistic integration of dual amplification and the application of bead supports effectively improved the sensitivity and specificity. Finally, the suspension bead array was created by the modified optical tweezer system, which realized the high-quality imaging analysis and improved the detection efficiency. The proposed sensing strategy achieved a limit of detection (LOD) as low as 5.90 pM with excellent specificity, stability, and reproducibility and was successfully applied to human serum samples, which has great potential for application in clinical serological research.
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Affiliation(s)
- Min Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, PR China
| | - Kaihan Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, PR China
| | - Chenchen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, PR China
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, PR China
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7
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Saadh MJ, Saeed TN, Alfarttoosi KH, Sanghvi G, Roopashree R, Thakur V, Lakshmi L, Kubaev A, Taher WM, Alwan M, Jawad MJ, Al-Nuaimi AMA. Exosomes and MicroRNAs: key modulators of macrophage polarization in sepsis pathophysiology. Eur J Med Res 2025; 30:298. [PMID: 40247413 PMCID: PMC12007276 DOI: 10.1186/s40001-025-02561-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2025] [Accepted: 04/06/2025] [Indexed: 04/19/2025] Open
Abstract
Sepsis is a highly dangerous and complex condition that can result in death. It is characterized by a strong reaction to an infection, causing dysfunction in multiple bodily systems and a high risk of mortality. The transformation of macrophages is a vital stage in the procedure as they possess the capability to interchange between two separate types: M1, which promotes inflammation, and M2, which inhibits inflammation. The choice greatly affects the immune response of the host. This analysis underscores the rapidly expanding roles of exosomes and microRNAs (miRNAs) in regulating the trajectory of macrophage polarization during episodes of sepsis. Exosomes, extremely small extracellular vesicles, facilitate cellular communication by transferring biologically active compounds, including miRNAs, proteins, and lipids. We investigate the impact of changes in exosome production and composition caused by sepsis on macrophage polarization and function. Unique microRNAs present in exosomes play a significant role in controlling crucial signaling pathways that govern the phenotype of macrophages. Through thorough examination of recent progress in this area, we clarify the ways in which miRNAs derived from exosomes can either aggravate or alleviate the inflammatory reactions that occur during sepsis. This revelation not only deepens our comprehension of the underlying mechanisms of sepsis, but it also reveals potential new biomarkers and targets for treatment. This assessment aims to amalgamate diverse research investigations and propose potential avenues for future investigations on the influence that exosomes and miRNAs have on macrophage polarization and the body's response to sepsis. These entities are essential for controlling the host's reaction to sepsis and hold important functions in this mechanism.
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Affiliation(s)
- Mohamed J Saadh
- Faculty of Pharmacy, Middle East University, Amman, 11831, Jordan
| | - Tamara Nazar Saeed
- Department of Medical Laboratory Technics, College of Health and Medical Technology, Alnoor University, Mosul, Iraq.
| | | | - Gaurav Sanghvi
- Department of Microbiology, Faculty of Science, Marwadi University Research Center, Marwadi University, Rajkot, Gujarat, 360003, India
| | - R Roopashree
- Department of Chemistry and Biochemistry, School of Sciences, JAIN (Deemed to Be University), Bangalore, Karnataka, India
| | - Vishal Thakur
- Centre for Research Impact & Outcome, Chitkara University Institute of Engineering and Technology, Chitkara University, Rajpura, 140401, Punjab, India
| | - L Lakshmi
- Department of Nursing, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Aziz Kubaev
- Department of Maxillofacial Surgery, Samarkand State Medical University, 18 Amir Temur Street, 140100, Samarkand, Uzbekistan
| | - Waam Mohammed Taher
- College of Nursing, National University of Science and Technology, Dhi Qar, Iraq
| | - Mariem Alwan
- Pharmacy College, Al-Farahidi University, Baghdad, Iraq
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Webb J, Zhao M, Campbell AH, Paul NA, Cummins SF, Eamens AL. The microRNA Pathway of Macroalgae: Its Similarities and Differences to the Plant and Animal microRNA Pathways. Genes (Basel) 2025; 16:442. [PMID: 40282402 PMCID: PMC12026948 DOI: 10.3390/genes16040442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2025] [Revised: 03/31/2025] [Accepted: 04/05/2025] [Indexed: 04/29/2025] Open
Abstract
In plants and animals, the microRNA (miRNA) class of small regulatory RNA plays an essential role in controlling gene expression in all aspects of development, to respond to environmental stress, or to defend against pathogen attack. This well-established master regulatory role for miRNAs has led to each protein-mediated step of both the plant and animal miRNA pathways being thoroughly characterized. Furthermore, this degree of characterization has led to the development of a suite of miRNA-based technologies for gene expression manipulation for fundamental research or for use in industrial or medical applications. In direct contrast, molecular research on the miRNA pathway of macroalgae, specifically seaweeds (marine macroalgae), remains in its infancy. However, the molecular research conducted to date on the seaweed miRNA pathway has shown that it shares functional features specific to either the plant or animal miRNA pathway. In addition, of the small number of seaweed species where miRNA data is available, little sequence conservation of individual miRNAs exists. These preliminary findings show the pressing need for substantive research into the seaweed miRNA pathway to advance our current understanding of this essential gene expression regulatory process. Such research will also generate the knowledge required to develop novel miRNA-based technologies for use in seaweeds. In this review, we compare and contrast the seaweed miRNA pathway to those well-characterized pathways of plants and animals and outline the low degree of miRNA sequence conservation across the polyphyletic group known as the seaweeds.
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Affiliation(s)
- Jessica Webb
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia (M.Z.); (A.H.C.); (N.A.P.); (S.F.C.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Min Zhao
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia (M.Z.); (A.H.C.); (N.A.P.); (S.F.C.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Alexandra H. Campbell
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia (M.Z.); (A.H.C.); (N.A.P.); (S.F.C.)
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Nicholas A. Paul
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia (M.Z.); (A.H.C.); (N.A.P.); (S.F.C.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Scott F. Cummins
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia (M.Z.); (A.H.C.); (N.A.P.); (S.F.C.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Andrew L. Eamens
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia (M.Z.); (A.H.C.); (N.A.P.); (S.F.C.)
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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Xu C, Yang L, Cheng T, Wang Z, Liu C, Shao J. Sodium Houttuyfonate Ameliorates DSS-induced Colitis Aggravated by Candida albicans through Dectin-1/NF-κB/miR-32-5p/NFKBIZ Axis Based on Intestinal microRNA Profiling. Inflammation 2025; 48:820-838. [PMID: 38963571 DOI: 10.1007/s10753-024-02091-6] [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: 05/14/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
Our previous research indicated that Sodium houttuyfonate (SH) can effectively ameliorate dextran sulfate sodium (DSS)-induced colitis exacerbated by Candida albicans. However, the underlying protective mechanism of SH remains unclear. Therefore, in this study, a mice colitis model was infected with C. albicans, and the total colonic miRNAs were assessed. Furthermore, the differentially expressed miRNAs were enriched, clustered, and analyzed. Moreover, based on the dual luciferase analysis of NFKBIZ modulation by miR-32-5p, the in vitro and in vivo therapeutic effects of SH on inflammatory response, fungal burden, oxidative stress, and apoptosis were assessed at transcriptional and translational levels in the presence of agonist and antagonist. A total of 1157 miRNAs were identified, 84 of which were differentially expressed. Furthermore, qRT-PCR validated that SH treatment improved 17 differentially expressed miRNAs with > fourfold upregulation or > sixfold downregulation. Similar to most differentially altered miRNA, C. albicans significantly increased Dectin-1, NF-κB, TNF-α, IL-1β, IL-17A, and decreased miR-32-5p which negatively targeted NFKBIZ. In addition, SH treatment reduced inflammatory response and fungal burden in a colitis model with C. albicans infection. Further analyses indicated that in C. albicans infected Caco2 cells, SH inhibited fungal growth, oxidative stress, and apoptosis by increasing Dectin-1, NF-κB, NFKBIZ, TNF-α, IL-1β, IL-17A, and decreasing miR-32-5p. Therefore, SH can ameliorate the severity of colitis aggravated by C. albicans via the Dectin-1/NF-κB/miR-32-5p/NFKBIZ axis.
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Affiliation(s)
- Chen Xu
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China
| | - Liu Yang
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China
| | - Ting Cheng
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China
| | - Zixu Wang
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China
| | - Chengcheng Liu
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China
| | - Jing Shao
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China.
- Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China.
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10
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Rahman MS, Ghorai S, Panda K, Santiago MJ, Aggarwal S, Wang T, Rahman I, Chinnapaiyan S, Unwalla HJ. Dr. Jekyll or Mr. Hyde: The multifaceted roles of miR-145-5p in human health and disease. Noncoding RNA Res 2025; 11:22-37. [PMID: 39736851 PMCID: PMC11683234 DOI: 10.1016/j.ncrna.2024.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 10/14/2024] [Accepted: 11/09/2024] [Indexed: 01/01/2025] Open
Abstract
MicroRNAs (miRNAs) are classified as small, non-coding RNAs that play crucial roles in diverse biological processes, including cellular development, differentiation, growth, and metabolism. MiRNAs regulate gene expression by recognizing complementary sequences within messenger RNA (mRNA) molecules. Recent studies have revealed that miR-145-5p functions as a tumor suppressor in several cancers, including lung, liver, and breast cancers. Notably, miR-145-5p plays a vital role in the pathophysiology underlying HIV and chronic obstructive pulmonary diseases associated with cigarette smoke. This miRNA is abundant in biofluids and shows potential as a biomarker for the diagnosis and prognosis of several infectious diseases, such as hepatitis B, tuberculosis, and influenza. Additionally, numerous studies have indicated that other non-coding RNAs, including long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), can regulate miR-145-5p. Given the significance of miR-145-5p, a comprehensive overview focusing on its roles in health and disease is essential. This review discusses the dual role of miR-145-5p as a protagonist and antagonist in important human diseases, with particular emphasis on disorders of the respiratory, digestive, nervous, reproductive, endocrine, and urinary systems.
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Affiliation(s)
- Md. Sohanur Rahman
- Department of Cellular and Molecular Medicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Suvankar Ghorai
- Department of Cellular and Molecular Medicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Kingshuk Panda
- Department of Cellular and Molecular Medicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Maria J. Santiago
- Department of Cellular and Molecular Medicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Saurabh Aggarwal
- Department of Cellular and Molecular Medicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Ting Wang
- Department of Cellular and Molecular Medicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
- Center for Translational Science, Florida International University, Port Saint Lucie, FL 34987, USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Srinivasan Chinnapaiyan
- Department of Cellular and Molecular Medicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Hoshang J. Unwalla
- Department of Cellular and Molecular Medicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
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11
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Solaimani M, Hosseinzadeh S, Abasi M. Non-coding RNAs, a double-edged sword in breast cancer prognosis. Cancer Cell Int 2025; 25:123. [PMID: 40170036 PMCID: PMC11959806 DOI: 10.1186/s12935-025-03679-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 02/06/2025] [Indexed: 04/03/2025] Open
Abstract
Cancer is a rising issue worldwide, and numerous studies have focused on understanding the underlying reasons for its occurrence and finding proper ways to defeat it. By applying technological advances, researchers are continuously uncovering and updating treatments in cancer therapy. Their vast functions in the regulation of cell growth and proliferation and their significant role in the progression of diseases, including cancer. This review provides a comprehensive analysis of ncRNAs in breast cancer, focusing on long non-coding RNAs such as HOTAIR, MALAT1, and NEAT1, as well as microRNAs such as miR-21, miR-221/222, and miR-155. These ncRNAs are pivotal in regulating cell proliferation, metastasis, drug resistance, and apoptosis. Additionally, we discuss experimental approaches that are useful for studying them and highlight the advantages and challenges of each method. We then explain the results of these clinical trials and offer insights for future studies by discussing major existing gaps. On the basis of an extensive number of studies, this review provides valuable insights into the potential of ncRNAs in cancer therapy. Key findings show that even though the functions of ncRNAs are vast and undeniable in cancer, there are still complications associated with their therapeutic use. Moreover, there is an absence of sufficient experiments regarding their application in mouse models, which is an area to work on. By emphasizing the crucial role of ncRNAs, this review underscores the need for innovative approaches and further studies to explore their potential in cancer therapy.
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Affiliation(s)
- Maryam Solaimani
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
| | - Sahar Hosseinzadeh
- Faculty of Pharmacy and Medical Biotechnology, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mozhgan Abasi
- Immunogenetics Research Center, Department of Tissue Engineering and Applied Cell Sciences, Faculty of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, PO Box: 48175/861, Sari, Iran.
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12
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Boucher J, Pépin G, Goyer B, Hubert A, Bazié WW, Vitry J, Barabé F, Gilbert C. Exploring the relationship between extracellular vesicles, the dendritic cell immunoreceptor, and microRNA-155 in an in vivo model of HIV-1 infection to understand the disease and develop new treatments. FASEB J 2025; 39:e70475. [PMID: 40111214 DOI: 10.1096/fj.202402692rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 03/05/2025] [Accepted: 03/11/2025] [Indexed: 03/22/2025]
Abstract
HIV-1 infection induces persistent immune system activation despite antiretroviral therapy. New immunomodulatory targets might be required to restore immune competence. The dendritic cells immunoreceptor (DCIR) can bind HIV-1 and regulate immune functions and extracellular vesicles (EVs) production. EVs have emerged as biomarkers and a non-invasive tool to monitor HIV-1 progression. In people living with HIV-1, an increase in the size and abundance of EVs is associated with a decline in the CD4/CD8 T cells ratio, a key marker of immune dysfunction. Analysis of host nucleic acids within EVs has revealed an enrichment of microRNA-155 (miR-155) during HIV-1 infection. Experiments have demonstrated that miR-155-rich EVs enhance HIV-1 infection in vitro. A humanized NSG-mouse model was established to assess the in vivo impact of miR-155-rich EVs. Co-production of the virus with miR-155-rich EVs heightened the viral load and lowered the CD4/CD8 ratio in the mice. Upon euthanasia, EVs were isolated from plasma for size and quantity assessment. Consistent with findings in individuals with HIV-1, increased EV size and abundance were inversely correlated with the CD4/CD8 ratio. Next, by using the virus co-product with EV-miR-155, we tested a DCIR inhibitor to limit infection and immune damage in a humanized mouse model. DCIR inhibition reduced infection and partially restored immune functions. Finally, viral particles and various EV subtypes can convey HIV-1 RNA. HIV-1 RNA was predominantly associated with large EVs (200-1000 nm) rather than small EVs (50-200 nm). Viral loads in large EVs strongly correlated with blood and tissue markers of immune activation. The humanized mice model has proven its applicability to studying the roles of EVs on HIV-1 infection and investigating the impact of DCIR inhibition.
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Affiliation(s)
- Julien Boucher
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, Quebec, Canada
| | - Gabriel Pépin
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, Quebec, Canada
| | - Benjamin Goyer
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, Quebec, Canada
| | - Audrey Hubert
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, Quebec, Canada
| | - Wilfried Wenceslas Bazié
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, Quebec, Canada
- Programme de Recherche Sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso, Burkina Faso
| | - Julien Vitry
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, Quebec, Canada
| | - Frédéric Barabé
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, Quebec, Canada
- Département de médecine, Faculté de médecine, Université Laval, Québec, Quebec, Canada
| | - Caroline Gilbert
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, Quebec, Canada
- Département de Microbiologie-Infectiologie et d'Immunologie, Faculté de Médecine, Université Laval, Québec, Quebec, Canada
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13
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Lim SY, Boyd SC, Diefenbach RJ, Rizos H. Circulating MicroRNAs: functional biomarkers for melanoma prognosis and treatment. Mol Cancer 2025; 24:99. [PMID: 40156012 PMCID: PMC11951542 DOI: 10.1186/s12943-025-02298-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Accepted: 03/10/2025] [Indexed: 04/01/2025] Open
Abstract
MicroRNAs (miRNAs) hold significant promise as circulating cancer biomarkers and unlike many other molecular markers, they can provide valuable insights that extend beyond tumour biology. The expression of circulating miRNAs may parallel the cellular composition and dynamic activity within the tumour microenvironment and reveal systemic immune responses. The functional complexity of miRNAs-where a single miRNA can regulate multiple messenger RNAs (mRNAs) to fine tune fundamental processes, and a single mRNA can be targeted by multiple miRNAs-underscores their broad significance and impact. However, this complexity poses significant challenges for translating miRNA research into clinical practice. In melanoma, specific miRNA signatures have shown notable diagnostic, prognostic and predictive value, with lineage-specific and immune-related miRNAs frequently identified as valuable markers. In this review, we explore the role of circulating miRNAs as potential biomarkers in melanoma, and highlight the current status and advances required to translate miRNA research into therapeutic opportunities.
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Affiliation(s)
- Su Yin Lim
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- Melanoma Institute of Australia, The University of Sydney, Sydney, NSW, Australia
| | - Suzanah C Boyd
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- Melanoma Institute of Australia, The University of Sydney, Sydney, NSW, Australia
| | - Russell J Diefenbach
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- Melanoma Institute of Australia, The University of Sydney, Sydney, NSW, Australia
| | - Helen Rizos
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.
- Melanoma Institute of Australia, The University of Sydney, Sydney, NSW, Australia.
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14
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Seida M, Ogami K, Yoshino S, Suzuki HI. Fine Regulation of MicroRNAs in Gene Regulatory Networks and Pathophysiology. Int J Mol Sci 2025; 26:2861. [PMID: 40243428 PMCID: PMC11988966 DOI: 10.3390/ijms26072861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2025] [Revised: 03/19/2025] [Accepted: 03/20/2025] [Indexed: 04/18/2025] Open
Abstract
MicroRNAs (miRNAs) are ~22-nucleotide small non-coding RNAs that play critical roles in gene regulation. The discovery of miRNAs in Caenorhabditis elegans in 1993 by the research groups of Victor Ambros and Gary Ruvkun opened a new era in RNA research. Typically, miRNAs act as negative regulators of gene expression by binding to complementary sequences within the 3' untranslated regions of their target mRNAs. This interaction results in translational repression and/or target destabilization. The expression levels and activities of miRNAs are fine-tuned by multiple factors, including the miRNA biogenesis pathway, variability in target recognition, super-enhancers, post-transcriptional modifications, and target-directed miRNA degradation. Together, these factors form complex mechanisms that govern gene regulation and underlie several pathological conditions, including Argonaute syndrome, genetic diseases driven by super-enhancer-associated miRNAs, and miRNA-deadenylation-associated bone marrow failure syndromes. In addition, as miRNA genes have evolved rapidly in vertebrates, miRNA regulation in the brain is characterized by several unique features. In this review, we summarize recent insights into the role of miRNAs in human diseases, focusing on miRNA biogenesis; regulatory mechanisms, such as super-enhancers; and the impact of post-transcriptional modifications. By exploring these mechanisms, we highlight the intricate and multifaceted roles of miRNAs in health and disease.
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Affiliation(s)
- Mayu Seida
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Koichi Ogami
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Seiko Yoshino
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya 464-8601, Japan
- Center for One Medicine Innovative Translational Research (COMIT), Nagoya University, Nagoya 464-8601, Japan
- Inamori Research Institute for Science (InaRIS), Kyoto 600-8411, Japan
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15
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Costa S, La Rocca G, Cavalieri V. Epigenetic Regulation of Chromatin Functions by MicroRNAs and Long Noncoding RNAs and Implications in Human Diseases. Biomedicines 2025; 13:725. [PMID: 40149701 PMCID: PMC11939841 DOI: 10.3390/biomedicines13030725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 03/12/2025] [Accepted: 03/14/2025] [Indexed: 03/29/2025] Open
Abstract
The bulk of RNA produced from the genome of complex organisms consists of a very large number of transcripts lacking protein translational potential and collectively known as noncoding RNAs (ncRNAs). Initially thought to be mere products of spurious transcriptional noise, ncRNAs are now universally recognized as pivotal players in cell regulatory networks across a broad spectrum of biological processes. Owing to their critical regulatory roles, ncRNA dysfunction is closely associated with the etiopathogenesis of various human malignancies, including cancer. As such, ncRNAs represent valuable diagnostic biomarkers as well as potential targets for innovative therapeutic intervention. In this review, we focus on microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), the two most extensively studied classes in the field of ncRNA biology. After outlining key concepts of miRNA and lncRNA biogenesis pathways, we examine their multiple roles in mediating epigenetic regulation of gene expression and chromatin organization. Finally, by providing numerous examples of specific miRNAs and lncRNAs, we discuss how dysregulation of these mechanisms contributes to the onset and/or progression of various human diseases.
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Affiliation(s)
| | | | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STeBiCeF), University of Palermo, Viale delle Scienze Bld. 16, 90128 Palermo, Italy
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16
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Khan A, Smagghe G, Li S, Shakeel M, Yang G, Ahmed N. Insect metamorphosis and chitin metabolism under miRNA regulation: a review with current advances. PEST MANAGEMENT SCIENCE 2025. [PMID: 40079237 DOI: 10.1002/ps.8758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2024] [Revised: 02/15/2025] [Accepted: 02/21/2025] [Indexed: 03/14/2025]
Abstract
Insect metamorphosis is a complex developmental process regulated by microRNAs (miRNAs) and hormonal signaling pathways. Key genes driving insect ontogenic changes are precisely modulated by miRNAs, which interact with 20-hydroxyecdysone (20E) and juvenile hormone (JH) to coordinate developmental transitions. Over the past decade, significant progress has been made in understanding miRNA biogenesis, their regulatory roles in gene expression, and their involvement in critical biological processes, including metamorphosis and chitin metabolism. miRNAs are now recognized as essential regulators of chitin metabolism and hormonal signaling, ensuring precise control of insect development. Disrupting the expression of participating genes in hormone signaling pathways through miRNAs leads to aberrant metamorphosis and consequent lethal outcomes, highlighting their potential as targets for pest control. This review summarizes current advances in miRNA-mediated regulation of insect metamorphosis and chitin metabolism, with a focus on their interactions with 20E and JH signaling pathways. By integrating recent findings, we provide insights into the molecular mechanisms underlying miRNA function in developmental transitions and their potential applications in insect pest management strategies. © 2025 Society of Chemical Industry.
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Affiliation(s)
- Ashraf Khan
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, China
- Institute of Plant and Environmental Protection, National Agricultural Research Center, Pakistan Agricultural Research Council, Islamabad, Pakistan
| | - Guy Smagghe
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, China
- Molecular and Cellular Life Sciences, Department of Biology, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Shangwei Li
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, China
| | - Muhammad Shakeel
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, China
| | - Guangming Yang
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, China
- Guizhou Institute of Biology, Guiyang, China
| | - Nazeer Ahmed
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
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17
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Su F, Zhao W, Zhao F, Cao M, Zhu T, Lv W, Li B. Pyrococcus furiosus Argonaute-Based Fluorometric Biosensor for One-Tube Detection of Cancer-Associated Single Nucleotide Polymorphisms in MicroRNAs. Anal Chem 2025; 97:4678-4686. [PMID: 39982863 DOI: 10.1021/acs.analchem.4c07109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2025]
Abstract
MicroRNA-related single nucleotide polymorphisms (miR-SNPs) are promising biomarkers for cancer diagnostics, yet accurate detection methods remain limited. Here, we introduce a ligation-triggered Pyrococcus furiosus Argonaute (PfAgo) cleavage (LTAC) strategy for the sensitive detection of miR-SNPs, demonstrated using the rs11614913 SNP in miR-196a2, which is associated with nonsmall cell lung cancer (NSCLC). The mutant miR-196a2T serves as a scaffold for the formation of guide DNA (gDNA) catalyzed by the SplintR ligase, leading to PfAgo activation and enhanced fluorescence. In contrast, wild-type miR-196a2C cannot facilitate gDNA formation and thus fails to activate PfAgo. This method exhibits a linear relationship with the logarithm of the miR-196a2T concentration over a range of 0.2 pM to 100 nM, achieving a low detection limit of 0.15 pM. Analysis of NSCLC patient samples using LTAC reveals elevated levels of the rs11614913 SNP in miR-196a2 compared to healthy controls, underscoring the diagnostic potential of LTAC.
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Affiliation(s)
- Fengli Su
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 211166, China
| | - Wentao Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 211166, China
| | - Furong Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 211166, China
| | - Min Cao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 211166, China
| | - Tianjiao Zhu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 211166, China
| | - Wei Lv
- Department of Pharmacy, The Jiangyin Clinical College of Xuzhou Medical University, Jiangyin 214400, China
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 211166, China
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18
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Golovina E, Eaton C, Cox V, Andel J, Savvulidi Vargova K. Mechanism of Action of circRNA/miRNA Network in DLBCL. Noncoding RNA 2025; 11:22. [PMID: 40126346 PMCID: PMC11932212 DOI: 10.3390/ncrna11020022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2024] [Revised: 02/06/2025] [Accepted: 02/27/2025] [Indexed: 03/25/2025] Open
Abstract
Circular RNAs (circRNAs) make up approximately 10% of the human transcriptome. CircRNAs belong to the broad group of non-coding RNAs and characteristically are formed by backsplicing into a stable circular loop. Their main role is to regulate transcription through the inhibition of miRNAs' expression, termed miRNA sponging. CircRNAs promote tumorigenesis/lymphomagenesis by competitively binding to miRNAs at miRNA binding sites. In diffuse large B-cell lymphoma (DLBCL), several circRNAs have been identified and their expression is related to both progression and response to therapy. DLBCL is the most prevalent and aggressive subtype of B-cell lymphomas and accounts for about 25% to 30% of all non-Hodgkin lymphomas. DLBCL displays great heterogeneity concerning histopathology, biology, and genetics. Patients who have relapsed or have refractory disease after first-line therapy have a very poor prognosis, demonstrating an important unmet need for new treatment options. As more circRNAs are identified in the future, we will better understand their biological roles and potential use in treating cancer, including DLBCL. For example, circAmotl1 promotes nuclear translocation of MYC and upregulation of translational targets of MYC, thus enhancing lymphomagenesis. Another example is circAPC, which is significantly downregulated in DLBCL and correlates with disease aggressiveness and poor prognosis. CircAPC increases expression of the host gene adenomatous polyposis coli (APC), and in doing so inactivates the canonical Wnt/β-catenin signaling and restrains DLBCL growth. MiRNAs belong to the non-coding regulatory molecules that significantly contribute to lymphomagenesis through their target mRNAs. In DLBCL, among the highly expressed miRNAs, are miR-155-5p and miR-21-5p, which regulate NF-ĸB and PI3K/AKT signaling pathways. The aim of this review is to describe the function and mechanism of regulation of circRNAs on miRNAs' expression in DLBCL. This will help us to better understand the regulatory network of circRNA/miRNA/mRNA, and to propose novel therapeutic targets to treat DLBCL.
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Affiliation(s)
- Elena Golovina
- First Faculty of Medicine, Institute of Pathological Physiology, Charles University, 12108 Prague, Czech Republic; (E.G.); (C.E.)
| | - Cory Eaton
- First Faculty of Medicine, Institute of Pathological Physiology, Charles University, 12108 Prague, Czech Republic; (E.G.); (C.E.)
| | - Virginia Cox
- First Faculty of Medicine, Institute of Pathological Physiology, Charles University, 12108 Prague, Czech Republic; (E.G.); (C.E.)
| | - Jozef Andel
- First Faculty of Medicine, Institute of Pathological Physiology, Charles University, 12108 Prague, Czech Republic; (E.G.); (C.E.)
- Faculty of Science, Molecular Biology and Genetics of Eukaryotes, Charles University, 12800 Prague, Czech Republic
| | - Karina Savvulidi Vargova
- First Faculty of Medicine, Institute of Pathological Physiology, Charles University, 12108 Prague, Czech Republic; (E.G.); (C.E.)
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Wu B, Zhang X, Zhao J, Zeng B, Cao Z. Identification and analysis of miRNA - mRNA regulatory modules associated with resistance to bacterial leaf streak in rice. BMC Genomics 2025; 26:207. [PMID: 40025448 PMCID: PMC11874638 DOI: 10.1186/s12864-025-11404-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2024] [Accepted: 02/25/2025] [Indexed: 03/04/2025] Open
Abstract
BACKGROUND B: acterial leaf streak (BLS) is a bacterial disease that severely affects rice leaves, leading to significant yield reductions. microRNAs (miRNAs) are short non-coding RNAs extensively involved in the growth, development, and stress responses of plants and animals. However, miRNAs that regulate the response of rice to bacterial leaf streak are still relatively scarce. RESULTS: The indica rice variety Dular exhibits resistance to BLS, whereas the variety 9311 is highly susceptible to the disease. By conducting miRNA sequencing and transcriptome sequencing on both Dular and 9311 before and after BLS inoculation, we identified 19 miRNAs that were significantly downregulated at both 12 and 24 h post-inoculation in Dular, and 9 miRNAs that were significantly upregulated at the same time points in 9311. Additionally, through degradome sequencing, we identified 23 miRNA- mRNA regulatory modules that likely play crucial roles in rice resistance to BLS, and 4 miRNA- mRNA regulatory modules that may be important in rice susceptibility to the disease. DISCUSSION: Current studies on rice disease resistance miRNAs primarily focus on those involved in resistance to rice blast and bacterial blight, with the miRNA-target mRNA regulatory mechanisms for BLS remaining unclear. This study has identified miRNA-mRNA modules that may play significant roles in rice responses to BLS, contributing to the understanding of the miRNA regulatory network involved in rice defense against BLS infection.
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Affiliation(s)
- Baowei Wu
- Jiangxi Super-Rice Research and Development Center, Jiangxi Provincial Key Laboratory of Rice Germplasm Innovation and Breeding, Jiangxi Academy of Agricultural Sciences, National Engineering Research Center for Rice, Nanchang, 330200, China
| | - Xiaoyu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jialiang Zhao
- Jiangxi Super-Rice Research and Development Center, Jiangxi Provincial Key Laboratory of Rice Germplasm Innovation and Breeding, Jiangxi Academy of Agricultural Sciences, National Engineering Research Center for Rice, Nanchang, 330200, China
| | - Bohong Zeng
- Jiangxi Super-Rice Research and Development Center, Jiangxi Provincial Key Laboratory of Rice Germplasm Innovation and Breeding, Jiangxi Academy of Agricultural Sciences, National Engineering Research Center for Rice, Nanchang, 330200, China
| | - Zhibin Cao
- Jiangxi Super-Rice Research and Development Center, Jiangxi Provincial Key Laboratory of Rice Germplasm Innovation and Breeding, Jiangxi Academy of Agricultural Sciences, National Engineering Research Center for Rice, Nanchang, 330200, China.
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20
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Tesarova T, Fiala O, Hora M, Vaclavikova R. Non-coding transcriptome profiles in clear-cell renal cell carcinoma. Nat Rev Urol 2025; 22:151-174. [PMID: 39242964 DOI: 10.1038/s41585-024-00926-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2024] [Indexed: 09/09/2024]
Abstract
Clear-cell renal cell carcinoma (ccRCC) is a common urological malignancy with an increasing incidence. The development of molecular biomarkers that can predict the response to treatment and guide personalized therapy selection would substantially improve patient outcomes. Dysregulation of non-coding RNA (ncRNA) has been shown to have a role in the pathogenesis of ccRCC. Thus, an increasing number of studies are being carried out with a focus on the identification of ncRNA biomarkers in ccRCC tissue samples and the connection of these markers with patients' prognosis, pathological stage and grade (including metastatic potential), and therapy outcome. RNA sequencing analysis led to the identification of several ncRNA biomarkers that are dysregulated in ccRCC and might have a role in ccRCC development. These ncRNAs have the potential to be prognostic and predictive biomarkers for ccRCC, with prospective applications in personalized treatment selection. Research on ncRNA biomarkers in ccRCC is advancing, but clinical implementation remains preliminary owing to challenges in validation, standardization and reproducibility. Comprehensive studies and integration of ncRNAs into clinical trials are essential to accelerate the clinical use of these biomarkers.
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Affiliation(s)
- Tereza Tesarova
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic.
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.
| | - Ondrej Fiala
- Department of Oncology and Radiotherapeutics, Faculty of Medicine in Pilsen and University Hospital, Charles University, Pilsen, Czech Republic
- Laboratory of Cancer Treatment and Tissue Regeneration, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Milan Hora
- Department of Urology, Faculty of Medicine in Pilsen and University Hospital, Charles University, Pilsen, Czech Republic
| | - Radka Vaclavikova
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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21
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Kawasumi R, Kawamura T, Yamashita K, Tominaga Y, Harada A, Ito E, Takeda M, Kita S, Shimomura I, Miyagawa S. Systemic administration of induced pluripotent stem cell-derived mesenchymal stem cells improves cardiac function through extracellular vesicle-mediated tissue repair in a rat model of ischemic cardiomyopathy. Regen Ther 2025; 28:253-261. [PMID: 39834593 PMCID: PMC11745812 DOI: 10.1016/j.reth.2024.12.008] [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: 10/27/2024] [Revised: 12/03/2024] [Accepted: 12/11/2024] [Indexed: 01/22/2025] Open
Abstract
Introduction Systemic administration of induced pluripotent stem cell-derived mesenchymal stem cells (iPS-MSCs) has a therapeutic effect on myocardial ischemia. However, the therapeutic mechanism underlying systemic iPS-MSC-based therapy for ischemic cardiomyopathy (ICM) remains unclear. We investigated the therapeutic effects of iPS-MSCs through extracellular vesicle (EV)-mediated tissue repair in a rat model of ICM. Methods A rat ICM model was created by left anterior descending coronary artery ligation. iPS-MSCs were administered intravenously every week for four weeks in the iPS-MSC group, whereas saline was administered to the control group. Alix, a protein involved in the biogenesis of EVs, was knocked down, and Alix-knockdown iPS-MSCs were administered to the siAlix group. We analyzed sequential cardiac function using echocardiography, histological analysis, cell tracking analysis with fluorescent dyes, and comprehensive RNA sequencing of the border zone of the myocardium after treatment. Results Left ventricular ejection fraction (LVEF) was significantly improved in the iPS-MSC group compared with that in the control group. In the siAlix group, LVEF was significantly lower than that in the iPS-MSC group. Histological analysis showed a significant decrease in fibrosis area and significant increase in microvascular density in the iPS-MSC group. A cell-tracking assay revealed iPS-MSC accumulation in the border zone of the myocardium during the acute phase. Comprehensive microRNA sequencing analysis revealed that EVs from iPS-MSCs contained miRNAs associated with anti-fibrosis and angiogenesis. Gene ontology analysis of differentially expressed genes in myocardial tissue also showed upregulation of pathways related to antifibrosis and neovascularization and downregulation of pathways linked to inflammation and T-cell differentiation. Conclusions Systemic administration of iPS-MSCs improved cardiac function through EV-mediated angiogenetic and antifibrotic effects in an ICM, suggesting the clinical possibility of treating chronic heart failure.
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Affiliation(s)
- Ryo Kawasumi
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Takuji Kawamura
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Kizuku Yamashita
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yuji Tominaga
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Akima Harada
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Emiko Ito
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Maki Takeda
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Shunbun Kita
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Adipose Management, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Iichiro Shimomura
- Department of Adipose Management, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shigeru Miyagawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
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22
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Akbarzadeh A, Gerami MH, Farrokhi MR, Shapoori S, Jafarinia M. Therapeutic prospects of microRNAs derived from mesenchymal stem cell extracellular vesicles in rheumatoid arthritis: a comprehensive overview. Mol Cell Biochem 2025; 480:1275-1286. [PMID: 39105963 DOI: 10.1007/s11010-024-05082-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 07/29/2024] [Indexed: 08/07/2024]
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by inflammatory joint damage. Recent studies have focused on the significance of microRNAs (miRNAs) in the pathogenesis of RA. Mesenchymal stem cells (MSCs) have emerged as a potential therapeutic option for RA based on their regenerative and immunomodulatory properties. MSCs release extracellular vesicles (EVs) containing miRNAs that can modulate immune and inflammatory responses. This article provides a comprehensive overview of the current evidence on the existence of various MSCs-derived miRNAs involved in the pathophysiology, characterization, and treatment of RA. An overview of the miRNA profiles in MSC-EVs is provided, along with an examination of their impact on various cell types implicated in RA pathogenesis, including synovial fibroblasts, macrophages, and T cells. Furthermore, the therapeutic capability of MSC-EVs for miRNA-based therapies in RA is discussed. In total, this review can present an extensive view of the complex interaction between EVs and MSC-derived miRNAs in RA and thus suggest valuable strategies for developing new therapeutic approaches to target this debilitating disease.
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Affiliation(s)
- Armin Akbarzadeh
- Department of Orthopedic Surgery, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hadi Gerami
- Department of Orthopedic Surgery, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Majid Reza Farrokhi
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Neurosurgery, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shima Shapoori
- Center for Research in Medical Devices (CÚRAM), University of Galway, Galway, Ireland
| | - Morteza Jafarinia
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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23
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Qi Y, Yu J, Lou M, Yu Y, Li R, Zhang Z, Dai Y, Lao K, Cao M, Gou X. Lab on a single microbead: An enzyme-free strategy for the sensitive detection of microRNA via efficient localized catalytic hairpin assembly. Anal Chim Acta 2025; 1340:343659. [PMID: 39863312 DOI: 10.1016/j.aca.2025.343659] [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: 12/03/2024] [Accepted: 01/11/2025] [Indexed: 01/27/2025]
Abstract
BACKGROUND Accurate quantification of microRNA (miRNA) is of great significance because it provides opportunities for the accurate early diagnosis of a series of human diseases including cancers. Currently, complicated nucleic acid amplification technologies are always required for the highly sensitive miRNA detection. The introduction of nucleic acid signal amplification coupled with various enzymes will inevitably lead to tedious work and increase the complexity of the analysis process. It is still urgently desired to develop enzyme-free yet sensitive assays that enable the sensitive analysis of miRNA in complicated biological samples. RESULTS A single microbead (MB)-based localized catalytic hairpin assembly (CHA) strategy is proposed for the sensitive analysis of microRNA (miRNA). This rationally designed CHA strategy allows target miRNA to walk only on a single MB which can create a micro-amplification zone, initiating a highly efficient localized CHA reaction, generating a large number of fluorescent DNA duplexes on the surface of single MB. The efficient localized CHA on single MB can not only greatly suppress the nonspecific reaction between two hairpin probes, thus decreasing the background signal, but also greatly enhance the brightness of MB owing to the highly-concentrated fluorescence enrichment on only one MB. Therefore, highly sensitive quantification of miRNA has been achieved by measuring the fluorescence signal on MB using a confocal fluorescence microscope. This new strategy exhibits a detection limit of 1.09 pM for let-7a detection, and enables high specificity of distinguishing homologous miRNA family members. SIGNIFICANCE This is the first report by only using one single MB as a carrier to conduct localized CHA, rendering highly-concentrated fluorescence enrichment on only one MB and a dramatic increase in sensitivity. This single MB-based localized CHA strategy has been successfully applied to the accurate analysis of miRNA target in complex biological sample.
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Affiliation(s)
- Yan Qi
- Institute of Basic and Translational Medicine & Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China; Engineering Research Center of Brain Diseases Drug Development, Universities of Shaanxi Province, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China
| | - Jiangtao Yu
- Institute of Basic and Translational Medicine & Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China; Engineering Research Center of Brain Diseases Drug Development, Universities of Shaanxi Province, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China
| | - Ming Lou
- Stomatology College of Xi'an Medical University, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China
| | - Yameng Yu
- Institute of Basic and Translational Medicine & Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China; Engineering Research Center of Brain Diseases Drug Development, Universities of Shaanxi Province, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China
| | - Ruohan Li
- Yantai Yongqi Technical Consulting Service Co., Ltd., Yantai, 264003, Shandong Province, PR China
| | - Zhenhao Zhang
- Institute of Basic and Translational Medicine & Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China; Engineering Research Center of Brain Diseases Drug Development, Universities of Shaanxi Province, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China
| | - Yuxuan Dai
- Institute of Basic and Translational Medicine & Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China; Engineering Research Center of Brain Diseases Drug Development, Universities of Shaanxi Province, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China
| | - Kejing Lao
- Institute of Basic and Translational Medicine & Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China; Engineering Research Center of Brain Diseases Drug Development, Universities of Shaanxi Province, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China
| | - Meng Cao
- Institute of Basic and Translational Medicine & Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China; Engineering Research Center of Brain Diseases Drug Development, Universities of Shaanxi Province, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China
| | - Xingchun Gou
- Institute of Basic and Translational Medicine & Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China; Engineering Research Center of Brain Diseases Drug Development, Universities of Shaanxi Province, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, PR China.
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24
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Yin C, Liufu C, Ye S, Zhu T, Jiang J, Wang M, Zhou L, Yao L, Wang Y, Shi B. Tumor-derived exosomal KPNA2 activates fibroblasts and interacts with KIFC1 to promote bladder cancer progression, a process inhibited by miR-26b-5p. Cell Mol Biol Lett 2025; 30:20. [PMID: 39956902 PMCID: PMC11830183 DOI: 10.1186/s11658-025-00687-w] [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: 07/09/2024] [Accepted: 01/07/2025] [Indexed: 02/18/2025] Open
Abstract
BACKGROUND Recent studies have illuminated the complexities of treating advanced bladder cancer (BCa), underscoring the importance of comprehending its molecular mechanisms for creating novel therapies. While the role of Karyopherin a2 (KPNA2) in promoting BCa growth is established, the precise mechanism remains elusive. METHODS To investigate the regulatory role of KPNA2 in BCa, we employed a comprehensive approach integrating clinical case data and bioinformatics analysis to evaluate the expression of KPNA2 in BCa tissues. Mechanisms promoting cancer by KPNA2 were examined using both in vivo and in vitro models. RESULTS Our research reveals that miR-26b-5p acts as an anticancer factor by targeting and inhibiting KPNA2 expression. Furthermore, we have observed that the interaction between KPNA2 and Kinesin Family Member C1 (KIFC1) facilitates the transition of BCa cells into the G2/M phase, thereby promoting tumor advancement via activation of the Phosphoinositide 3-kinase (PI3K)- Protein Kinase B (AKT) pathway. Importantly, this investigation is the first to identify KPNA2 expression in exosomes originating from BCa tissues. Plasma exosomes from patients with BCa exhibited notably increased levels of KPNA2 compared with healthy controls, suggesting KPNA2 as a potential new tumor indicator. Additionally, KPNA2 from BCa cells triggered the conversion of fibroblasts into cancer-associated fibroblasts (CAFs), which secreted elevated levels of interleukin-6 (IL-6), contributing to a tumor-supporting environment. CONCLUSIONS These findings suggest that KPNA2 is a key gene that promotes BCa progression, can potentially be a novel tumor marker, and may serve as a new therapeutic target for BCa.
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Affiliation(s)
- Cong Yin
- Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, No. 3002, Sungangxi Road, Shenzhen, 518035, People's Republic of China
- Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Cen Liufu
- Shantou University Medical College, Shantou, 515041, China
- Department of Urology, Peking University Shenzhen Hospital, Institute of Urology, Shenzhen PKU-HKUST Medical Center, Shenzhen, 518036, China
| | - Shuai Ye
- Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, No. 3002, Sungangxi Road, Shenzhen, 518035, People's Republic of China
- Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Tao Zhu
- Shantou University Medical College, Shantou, 515041, China
- Department of Urology, Peking University Shenzhen Hospital, Institute of Urology, Shenzhen PKU-HKUST Medical Center, Shenzhen, 518036, China
| | - Jiahao Jiang
- Department of Urology, Shenzhen Second People's Hospital, Clinical College of Anhui Medical University, Shenzhen, 518035, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Mingxia Wang
- Department of Urology, Peking University Shenzhen Hospital, Institute of Urology, Shenzhen PKU-HKUST Medical Center, Shenzhen, 518036, China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, No. 8 Xishiku St., Xicheng District, Beijing, 100034, People's Republic of China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, No. 8 Xishiku St., Xicheng District, Beijing, 100034, China
| | - Lin Yao
- Department of Urology, Peking University First Hospital, No. 8 Xishiku St., Xicheng District, Beijing, 100034, People's Republic of China.
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, No. 8 Xishiku St., Xicheng District, Beijing, 100034, China.
| | - Yan Wang
- Department of Urology, Peking University Shenzhen Hospital, Institute of Urology, Shenzhen PKU-HKUST Medical Center, Shenzhen, 518036, China.
| | - Bentao Shi
- Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, No. 3002, Sungangxi Road, Shenzhen, 518035, People's Republic of China.
- Shenzhen University Health Science Center, Shenzhen, 518055, China.
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25
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Huang L, Liao C, Xiong Z, Chen Z, Zhang S. Hsa-miR-526b-5p Regulates the Sensitivity of Colorectal Cancer to 5-Fluorouracil by Targeting TP53 in Organoid Models. Biochem Genet 2025:10.1007/s10528-025-11045-y. [PMID: 39953363 DOI: 10.1007/s10528-025-11045-y] [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: 06/06/2024] [Accepted: 01/27/2025] [Indexed: 02/17/2025]
Abstract
This study aimed to explore the mechanisms through which microRNAs (miRNAs) regulate 5-fluorouracil (5-FU) sensitivity in colorectal cancer (CRC) using organoid models. Fresh tissue samples from CRC tumors were collected, and CRC organoids were isolated and cultured. The consistency between CRC organoids and their derived tissues was validated. CRC organoids were treated with 5-FU, and ATP activity was measured. High-throughput sequencing of CRC organoids, combined with Gene Expression Omnibus (GEO) data analysis, was performed to examine miRNA expression following 5-FU treatment. Next, we investigated the cellular function of miR-526b-5p in CRC organoids and cells. Dual-luciferase reporter assays validated the binding of miR-526b-5p to the 3' UTR of TP53 mRNA. We successfully established CRC organoids that exhibited characteristics consistent with their source tissues. 5-FU treatment suppressed the proliferation and ATP activity of CRC organoids. High-throughput sequencing of CRC organoids, combined with GEO data analysis and quantitative reverse transcription polymerase chain reaction (qRT-PCR) validation, revealed that hsa-miR-526b-5p levels were elevated following 5-FU treatment in CRC organoids and cells. Furthermore, hsa-miR-526b-5p was upregulated in CRC tissues compared to adjacent normal tissues, correlating with poor survival in CRC patients. Overexpression of hsa-miR-526b-5p mitigated the inhibitory effects of 5-FU on CRC organoid proliferation, migration, invasion, and ferroptosis. In contrast, silencing of hsa-miR-526b-5p impaired cell function and ferroptosis. Additionally, overexpression of hsa-miR-526b-5p decreased TP53 mRNA and protein levels while increasing the expression of SLC7A11 mRNA and protein. Silencing of hsa-miR-526b-5p resulted in the opposite effect. hsa-miR-526b-5p directly targeted and inhibited TP53 expression. Overexpression of TP53 diminished the promotive effect of hsa-miR-526b-5p on ferroptosis-related proteins GPX4 and SLC7A11, whereas inhibition of TP53 reversed the impact of hsa-miR-526b-5p silencing. Our study demonstrates that hsa-miR-526b-5p targets TP53 to regulate 5-FU sensitivity in CRC through the ferroptosis pathway based on CRC organoid models.
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Affiliation(s)
- Lizhe Huang
- Colorectal Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, 530021, China
| | - Cun Liao
- Colorectal Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, 530021, China
| | - Zuming Xiong
- Colorectal Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, 530021, China
| | - Zhongyang Chen
- Colorectal Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, 530021, China
| | - Sen Zhang
- Colorectal Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, 530021, China.
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26
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Balali MR, Taghizadeh M, Alizadeh M, Karami Y, Karimi F, Khatami SH, Taheri-Anganeh M, Ehtiati S, Movahedpour A, Mahmoudi R, Ghasemi H. MicroRNA biosensors for detection of chronic kidney disease. Clin Chim Acta 2025; 567:120081. [PMID: 39653321 DOI: 10.1016/j.cca.2024.120081] [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: 10/06/2024] [Revised: 12/04/2024] [Accepted: 12/04/2024] [Indexed: 12/13/2024]
Abstract
Chronic kidney disease (CKD) is a prevalent health condition characterized by gradual kidney function loss. Early detection is crucial for the effective management and treatment of CKD. A promising biomarker for various diseases, including chronic kidney disease, is microRNAs (miRNAs), which are becoming increasingly important due to their stability and differential expression in various disease-related states, including CKD. Recent developments in microRNA biosensors have made it possible to detect miRNAs associated with CKD in a sensitive and specific manner. This review article discusses the current state of microRNA biosensors for detecting CKD and highlights their potential applications in clinical settings. Various microRNA biosensors, including electrochemical, optical, and nanomaterial-based sensors, are explored for their ability to detect specific miRNAs linked to CKD progression. The advantages and limitations of these biosensors are evaluated, focusing on factors such as sensitivity, specificity, and ease of use. Overall, microRNA biosensors are promising diagnostic tools for early detection of CKD. However, challenges such as standardizing protocols, validating in large cohorts, and translating to clinical practice remain to be addressed. Future research efforts should aim to overcome these limitations to fully realize the potential of microRNA biosensors in improving the diagnosis and management of CKD.
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Affiliation(s)
| | - Mohammad Taghizadeh
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Alizadeh
- Student Research Committee, Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yousof Karami
- Department of Clinical Science, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - Seyyed Hossein Khatami
- Student Research Committee, Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Sajad Ehtiati
- Student Research Committee, Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ahmad Movahedpour
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran.
| | - Reza Mahmoudi
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran.
| | - Hassan Ghasemi
- Research Center for Environmental Contaminants (RCEC), Abadan University of Medical Sciences, Abadan, Iran.
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27
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Li Y, Chen S, Rao H, Cui S, Chen G. MicroRNA Gets a Mighty Award. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2414625. [PMID: 39836690 PMCID: PMC11831481 DOI: 10.1002/advs.202414625] [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: 11/09/2024] [Revised: 12/29/2024] [Indexed: 01/23/2025]
Abstract
Recent advancements in microRNAs (miRNAs) research have revealed their key roles in both normal physiological processes and pathological conditions, leading to potential applications in diagnostics and therapeutics. However, the path forward is fraught with several scientific and technical challenges. This review article briefly explores the milestones of the discovery, biogenesis, functions, and application for clinical diagnostic and therapeutic strategies of miRNAs. The potential challenges and future directions are also discussed to fully harness their capabilities.
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Affiliation(s)
- Yu Li
- Department of Human Cell Biology and GeneticsJoint Laboratory of Guangdong‐Hong Kong Universities for Vascular Homeostasis and DiseasesSchool of MedicineSouthern University of Science and TechnologyShenzhenGuangdong518055China
| | - Sijie Chen
- Department of Human Cell Biology and GeneticsJoint Laboratory of Guangdong‐Hong Kong Universities for Vascular Homeostasis and DiseasesSchool of MedicineSouthern University of Science and TechnologyShenzhenGuangdong518055China
| | - Hai Rao
- Department of BiochemistryKey University Laboratory of Metabolism and Health of GuangdongSchool of MedicineSouthern University of Science and TechnologyShenzhenGuangdong518055China
| | - Shengjin Cui
- Clinical LaboratoryThe University of Hong Kong‐Shenzhen HospitalShenzhenGuangdong518053China
| | - Guoan Chen
- Department of Human Cell Biology and GeneticsJoint Laboratory of Guangdong‐Hong Kong Universities for Vascular Homeostasis and DiseasesSchool of MedicineSouthern University of Science and TechnologyShenzhenGuangdong518055China
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28
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De Sousa P, Seitz H. [Nobel Prize in physiology or medicine 2024: Victor Ambros and Gary Ruvkun - The discovery of microRNAs, revealing a New World in genetics]. Med Sci (Paris) 2025; 41:180-185. [PMID: 40028957 DOI: 10.1051/medsci/2025012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2025] Open
Abstract
Le prix Nobel 2024 de physiologie ou médecine a récompensé Victor Ambros et Gary Ruvkun pour leur découverte du premier microARN en 1993. Attirés par le phénotype intriguant d’un mutant du ver nématode Cænorhabditis elegans, dont le gène muté semblait échapper aux méthodes habituelles d’identification, les deux chercheurs et leurs équipes ont mis au jour une nouvelle classe de régulateurs de l’expression des gènes. Leurs découvertes, admirables de rigueur et de clairvoyance (leurs articles de 1993 révélaient déjà plusieurs des propriétés essentielles des microARN), sont trop longtemps restées négligées par la communauté scientifique, avant de susciter un véritable engouement quelques années plus tard.
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Affiliation(s)
- Pauline De Sousa
- Institut de génétique humaine, UMR 9002 CNRS et Université de Montpellier, Montpellier, France
| | - Hervé Seitz
- Institut de génétique humaine, UMR 9002 CNRS et Université de Montpellier, Montpellier, France
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29
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Yamamoto K, Chiba M. MicroRNA‑21‑5p expression in extracellular vesicles is increased in the blood of aging mice and in vascular endothelial cells induced by ionizing radiation. Exp Ther Med 2025; 29:22. [PMID: 39650777 PMCID: PMC11621913 DOI: 10.3892/etm.2024.12772] [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: 08/16/2024] [Accepted: 10/25/2024] [Indexed: 12/11/2024] Open
Abstract
In recent years, the Japanese population has been aging and the risk of contracting various age-related diseases has increased. Thus, there is a need to analyze components that are characteristic of aging and examine their association with diseases to detect age-related diseases at an early stage. In the present study, microRNAs (miRNAs/miRs) in serum extracellular vesicles (EVs) of 82-102-week-old mice were analyzed to identify miRNAs characteristic of aging. Increased expression of mmu-miR-21a-5p was observed. These miRNAs may be derived from senescent vascular endothelial cells, and RNA-sequencing data (GSE130727) of HUVECs induced to senesce by 4 Gy of radiation revealed that the miRNAs were involved in the cell cycle and DNA repair. Annotations to senescence-related pathways were also identified. Reduced expression of the miR-21-5p target gene, which has an identical sequence in humans and mice, was confirmed. In HUVECs induced to age under similar conditions, increased senescence-associated β-galactosidase activity and increased intracellular miR-21-5p expression were observed. A portion of the miR-21-5p was secreted extracellularly by internalizing tetraspanin-positive EVs, and miR-21-5p was secreted into the extracellular space. The present study also demonstrated that miR-21-5p expression was upregulated and extracellular secretion of miR-21-5p was enhanced during vascular endothelial cell senescence. These findings suggested that increased serum miR-21-5p represents a biomarker for vascular endothelial cell senescence.
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Affiliation(s)
- Keisuke Yamamoto
- Department of Bioscience and Laboratory Medicine, Graduate School of Health Sciences, Hirosaki University, Hirosaki, Aomori 036-8564, Japan
| | - Mitsuru Chiba
- Department of Bioscience and Laboratory Medicine, Graduate School of Health Sciences, Hirosaki University, Hirosaki, Aomori 036-8564, Japan
- Research Center for Biomedical Sciences, Hirosaki University, Hirosaki, Aomori 036-8564, Japan
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Su J, Liu T, Wang M, Xu W, Liu J, Lan J, Chen Y, Xu H, Guo D, Lai Z. Enhanced stability of hairpin-functionalized DNA tetrahedral nanostructures for miRNA detection in plasma from ischemic stroke patients. Anal Chim Acta 2025; 1334:343419. [PMID: 39638466 DOI: 10.1016/j.aca.2024.343419] [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: 10/17/2024] [Revised: 11/06/2024] [Accepted: 11/11/2024] [Indexed: 12/07/2024]
Abstract
The enzyme-free amplification technique using the Hybridization Chain Reaction (HCR) is gaining traction for its efficiency in miRNA analysis. Conventional HCR (C-HCR) with hairpin probes faces challenges due to enzymatic degradation in body fluids, leading to potential false-positive results. This study addresses the critical need for a more reliable method that resists enzymatic breakdown and improves diagnostic accuracy for detecting miRNA related to ischemic stroke. We have developed a novel DNA tetrahedral nanostructures-mediated HCR (DTN-HCR) platform for the precise detection of microRNA-25 (miR-25), a biomarker for ischemic stroke. Incorporating two unique DNA tetrahedral nanostructures with embedded hairpin structures (DTN-HP1 and DTN-HP2), this platform activates upon miR-25 binding, initiating a robust DTN-HCR reaction. This reaction forms extensive DNA tetrahedron clusters that significantly boost the fluorescence signal, enabling detection thresholds as low as 5.4 pM. The method showcases exceptional specificity by distinguishing target miRNA from close analogues and maintains structural integrity against DNase I and fetal bovine serum (FBS), verified through polyacrylamide gel electrophoresis (PAGE). It successfully differentiates ischemic stroke patients from healthy controls by analyzing peripheral blood-derived miRNAs. This study concludes that the DTN-HCR platform substantially enhances the specificity and stability of miRNA detection, marking a significant advancement in non-enzymatic miRNA analysis techniques. With its capability to accurately identify ischemic stroke biomarkers at very low concentrations and its resistance to enzymatic degradation, the DTN-HCR method presents a valuable diagnostic tool for ischemic stroke, potentially improving early detection and monitoring in a clinical environment.
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Affiliation(s)
- Jiansheng Su
- Department of Anesthesiology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
| | - Tingshan Liu
- Department of Anesthesiology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
| | - Min Wang
- Department of Anesthesiology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
| | - Wansong Xu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian, 350108, China
| | - Junle Liu
- Department of Anesthesiology, Xiamen Third Hospital Affiliated to Fujian University of Traditional Chinese Medicine, Xiamen, Fujian, 361199, China
| | - Jianning Lan
- Department of Anesthesiology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
| | - Yujuan Chen
- Department of Anesthesiology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
| | - Huo Xu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian, 350108, China.
| | - Danhua Guo
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, Fujian, 350001, China.
| | - Zhongmeng Lai
- Department of Anesthesiology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China.
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Chen Z, Chen W, Xu C, Song H, Ji X, Jiang H, Duan H, Li Z, Gao W, Yao T, Zhang Z, He L, Yin Y, Yang N, Tian W, Wu J, Li X. Near-infrared fluorogenic RNA for in vivo imaging and sensing. Nat Commun 2025; 16:518. [PMID: 39788937 PMCID: PMC11718054 DOI: 10.1038/s41467-024-55093-1] [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: 01/07/2024] [Accepted: 11/29/2024] [Indexed: 01/12/2025] Open
Abstract
Fluorogenic RNA aptamers have various applications, including use as fluorescent tags for imaging RNA trafficking and as indicators of RNA-based sensors that exhibit fluorescence upon binding small-molecule fluorophores in living cells. Current fluorogenic RNA:fluorophore complexes typically emit visible fluorescence. However, it is challenging to develop fluorogenic RNA with near-infrared (NIR) fluorescence for in vivo imaging and sensing studies. To address this issue, we identify and modulate red fluorescent protein-like fluorophores to bind Squash, a highly folded fluorogenic RNA. One of these fluorophores, DFQL-1T, exhibits photostable NIR fluorescence when bound to Squash, enabling RNA visualization in living mammalian cells and mice. With Squash:DFQL-1T complexes, we generate RNA-based sensors for detecting non-coding RNAs and small molecule targets in living mammalian cells and in mice. These studies reveal a fluorogenic RNA:fluorophore complex that can be readily developed into NIR fluorescent RNA tags for in vivo imaging and sensing.
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Affiliation(s)
- Zhenyin Chen
- Interdisciplinary Science Center, State Key Laboratory of Integrated Management of Pest Insects and Rodents,Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- Department of Pulmonary and Critical Care Medicine, the Affiliated Hospital of Southwest Medical University, 646000, Luzhou, Sichuan, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Wei Chen
- Centre for Medical Genetics, School of Life Sciences, Central South University, 410078, Changsha, China
- Hengyang Key Laboratory of Cellular Stress Biology, Hengyang Medical School, University of South China, 421001, Hengyang, Hunan, China
| | - Cun Xu
- Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012, Changchun, China
| | - Haozhi Song
- Interdisciplinary Science Center, State Key Laboratory of Integrated Management of Pest Insects and Rodents,Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xin Ji
- Interdisciplinary Science Center, State Key Laboratory of Integrated Management of Pest Insects and Rodents,Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Haodong Jiang
- Interdisciplinary Science Center, State Key Laboratory of Integrated Management of Pest Insects and Rodents,Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Hongtao Duan
- College of Life Sciences, Hebei University, 071002, Baoding, Hebei, China
| | - Zehao Li
- College of Life Sciences, Hebei University, 071002, Baoding, Hebei, China
| | - Wankai Gao
- Interdisciplinary Science Center, State Key Laboratory of Integrated Management of Pest Insects and Rodents,Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Tuoxin Yao
- College of Life Sciences, Hunan Normal University, 410081, Changsha, China
| | - Zhongxuan Zhang
- Interdisciplinary Science Center, State Key Laboratory of Integrated Management of Pest Insects and Rodents,Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Liuqin He
- College of Life Sciences, Hunan Normal University, 410081, Changsha, China
| | - Yulong Yin
- Yuelushan Laboratory, 410128, Changsha, China
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Nanyang Yang
- Centre for Medical Genetics, School of Life Sciences, Central South University, 410078, Changsha, China
| | - Wenjing Tian
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012, Changchun, China
| | - Jiahui Wu
- Department of Chemistry, University of Massachusetts, 01003, Amherst, MA, USA
| | - Xing Li
- Interdisciplinary Science Center, State Key Laboratory of Integrated Management of Pest Insects and Rodents,Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
- Department of Pulmonary and Critical Care Medicine, the Affiliated Hospital of Southwest Medical University, 646000, Luzhou, Sichuan, China.
- College of Life Sciences, Hebei University, 071002, Baoding, Hebei, China.
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Wu H, Lyu X, Xu M, Chen Y, Liao S, Zhang G, Lin Y, Cai X. A Multifunctional miRNA Delivery System Based on Tetrahedral Framework Nucleic Acids for Regulating Inflammatory Periodontal Ligament Stem Cells and Attenuating Periodontitis Bone Loss. ACS APPLIED MATERIALS & INTERFACES 2025; 17:560-571. [PMID: 39679863 DOI: 10.1021/acsami.4c17195] [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: 12/17/2024]
Abstract
Periodontitis is a chronic inflammatory disease that leads to periodontal tissue damage and tooth loss. Therefore, controlling inflammatory bone loss and promoting osteogenesis is a crucial challenge clinically. MicroRNA (miRNA) based gene therapy has shown substantial prospects in recent years, but its application has been limited due to structural instability and easy degradation by enzymes. Research has shown that miRNA-200c is regarded as a key miRNA by regulating multiple signaling pathways during the process of bone resorption. Tetrahedral framework nucleic acid (tFNA) can be considered an ideal carrier of miRNA due to its good tissue permeability, cell uptake efficiency, and biocompatibility. This study developed a tFNA system carrying miR-200c, named T-200c, to exert various biological effects in human periodontal ligament stem cells (PDLSCs). The activation of the NF-κB pathway is diminished, whereas the Akt/β-catenin pathway is enhanced, resulting in a notable decrease in the release of diverse inflammatory mediators and cellular reactive oxygen species. This modulation fosters cell proliferation and osteogenic differentiation, thereby rejuvenating the functionality of PDLSCs. These changes offer a viable alternative for the treatment of periodontitis and the regeneration of periodontal tissues.
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Affiliation(s)
- Haoyan Wu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiaoying Lyu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Mengzhuo Xu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ye Chen
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shengnan Liao
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Geru Zhang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, Sichuan 610041, China
- National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, Sichuan 610041, China
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Marceca GP, Romano G, Acunzo M, Nigita G. ncRNA Editing: Functional Characterization and Computational Resources. Methods Mol Biol 2025; 2883:455-495. [PMID: 39702721 DOI: 10.1007/978-1-0716-4290-0_20] [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: 12/21/2024]
Abstract
Non-coding RNAs (ncRNAs) play crucial roles in gene expression regulation, translation, and disease development, including cancer. They are classified by size in short and long non-coding RNAs. This chapter focuses on the functional implications of adenosine-to-inosine (A-to-I) RNA editing in both short (e.g., miRNAs) and long ncRNAs. RNA editing dynamically alters the sequence and structure of primary transcripts, impacting ncRNA biogenesis and function. Notable findings include the role of miRNA editing in promoting glioblastoma invasiveness, characterizing RNA editing hotspots across cancers, and its implications in thyroid cancer and ischemia. This chapter also highlights bioinformatics resources and next-generation sequencing (NGS) technologies that enable comprehensive ncRNAome studies and genome-wide RNA editing detection. Dysregulation of RNA editing machinery has been linked to various human diseases, emphasizing the potential of RNA editing as a biomarker and therapeutic target. This overview integrates current knowledge and computational tools for studying ncRNA editing, providing insights into its biological significance and clinical applications.
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Affiliation(s)
| | - Giulia Romano
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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Uno H, Takeuchi H, Abe I, Yoshino T, Taguchi T, Hirakawa Y, Matsunaga T, Tanaka T. PCR- and wash-free detection of serum miRNA via signaling probe hybridization. Biotechnol Bioeng 2025; 122:159-166. [PMID: 39397338 DOI: 10.1002/bit.28859] [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: 07/23/2024] [Revised: 09/26/2024] [Accepted: 09/30/2024] [Indexed: 10/15/2024]
Abstract
Detection of microRNAs (miRNAs) in the serum is an effective liquid biopsy technique for cancer diagnosis. However, conventional diagnostic methods are time-consuming and complex. Therefore, in this study, we established a signaling probe-based DNA microarray system for miRNA detection. PCR, fluorescence labeling, and washing are not necessary for signaling probes. Four probes were designed using different miRNAs as diagnostic cancer markers. The developed system is useful for various miRNAs, regardless of their target lengths (18-26-mer) and GC content (36%-89%). Here, all the assays were performed within 40 min. Overall, our signaling probe-based DNA hybridization system facilitates the simple and rapid detection of serum miRNAs without the need for gene amplification, fluorescence labeling and washing.
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Affiliation(s)
- Haruka Uno
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hiyori Takeuchi
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Ishin Abe
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | | | - Yuko Hirakawa
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Yokogawa Electric Corporation, Tokyo, Japan
| | - Tadashi Matsunaga
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
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35
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Tian J, He Y, Zhang Z, Zhu Y, Ren H, Zhang L, Li L, Li W, Zhang W, Xiao T, Zhou H, Li X. miR-224-5p Suppresses Non-Small Cell Lung Cancer via IL6ST-Mediated Regulation of the JAK2/STAT3 Pathway. Thorac Cancer 2025; 16:e15516. [PMID: 39840666 PMCID: PMC11751714 DOI: 10.1111/1759-7714.15516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Revised: 11/14/2024] [Accepted: 12/04/2024] [Indexed: 01/23/2025] Open
Abstract
BACKGROUND Our study aimed to explore the specific functions and potential mechanisms of miR-224-5p in non-small cell lung cancer (NSCLC). METHODS We first analyzed the expression of miR-224-5p in NSCLC patients and cell lines through the GEO database and qRT-PCR analysis. Then, we used MTT assays, wound healing assays, Transwell assays, and western blotting to evaluate the effects of miR-224-5p on NSCLC cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT). Furthermore, we used a xenograft tumor model to evaluate the effect of miR-224-5p on NSCLC tumor growth. Potential binding targets of miR-224-5p were further identified through the target prediction databases, and the relationships between miR-224-5p, its targets, and downstream signaling pathways were further verified using luciferase reporter gene assays and western blotting. RESULTS The GEO database and qRT-PCR analysis indicated that miR-224-5p was significantly downregulated in NSCLC patients and cell lines. Functional assays indicated that inhibiting miR-224-5p could enhance the proliferation, migration, invasion, and EMT of NSCLC cells, as well as accelerate tumor growth. In contrast, overexpression of miR-224-5p inhibited these processes. We identified IL6ST (interleukin 6 signal transducer) as a binding target of miR-224-5p. We observed that miR-224-5p could bind to and inhibit IL6ST expression and JAK2/STAT3 signaling pathway, and the inhibition of NSCLC tumor growth and JAK2/STAT3 pathway by miR-224-5p could be reversed by IL6ST overexpression. CONCLUSION Our study demonstrated that miR-224-5p inhibited NSCLC by targeting IL6ST, thereby downregulating the JAK2/STAT3 signaling pathway.
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Affiliation(s)
- Jiao Tian
- Department of Thoracic Surgery, Tianjin First Central Hospital, School of MedicineNankai UniversityTianjinChina
- State Key Laboratory of Medicinal Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Yiming He
- Department of Thoracic Surgery, Tianjin First Central Hospital, School of MedicineNankai UniversityTianjinChina
- State Key Laboratory of Medicinal Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Zihui Zhang
- Department of Thoracic Surgery, Tianjin First Central Hospital, School of MedicineNankai UniversityTianjinChina
- State Key Laboratory of Medicinal Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Yuxin Zhu
- Department of Thoracic Surgery, Tianjin First Central Hospital, School of MedicineNankai UniversityTianjinChina
- State Key Laboratory of Medicinal Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Haixia Ren
- Department of Thoracic Surgery, Tianjin First Central Hospital, School of MedicineNankai UniversityTianjinChina
- State Key Laboratory of Medicinal Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Liang Zhang
- Department of Thoracic Surgery, Tianjin First Central Hospital, School of MedicineNankai UniversityTianjinChina
- State Key Laboratory of Medicinal Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Lei Li
- Department of Thoracic Surgery, Tianjin First Central Hospital, School of MedicineNankai UniversityTianjinChina
- State Key Laboratory of Medicinal Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Wei Li
- Department of Thoracic Surgery, Tianjin First Central Hospital, School of MedicineNankai UniversityTianjinChina
- State Key Laboratory of Medicinal Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Weidong Zhang
- Department of Thoracic Surgery, Tianjin First Central Hospital, School of MedicineNankai UniversityTianjinChina
- State Key Laboratory of Medicinal Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Ting Xiao
- Department of Thoracic Surgery, Tianjin First Central Hospital, School of MedicineNankai UniversityTianjinChina
- State Key Laboratory of Medicinal Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
- State Key Laboratory of Separation Membranes and Membrane Processes, Tianjin Key Laboratory of Green Chemical Technology and Process Engineering, School of Pharmaceutical SciencesTiangong UniversityTianjinChina
| | - Honggang Zhou
- Department of Thoracic Surgery, Tianjin First Central Hospital, School of MedicineNankai UniversityTianjinChina
- State Key Laboratory of Medicinal Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Xiaoping Li
- Department of Thoracic Surgery, Tianjin First Central Hospital, School of MedicineNankai UniversityTianjinChina
- State Key Laboratory of Medicinal Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
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Quah S, Subramanian G, Tan JSL, Utami KH, Sampath P. MicroRNAs: a symphony orchestrating evolution and disease dynamics. Trends Mol Med 2025; 31:21-35. [PMID: 39112313 DOI: 10.1016/j.molmed.2024.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/13/2024] [Accepted: 07/08/2024] [Indexed: 01/11/2025]
Abstract
The genesis of human disease lies in our evolutionary past. Evolution has featured a general trend towards increased morphological complexity, partly conferred by expansion in gene regulatory capacity via microRNA (miRNA) innovation. Many human diseases are directly related to the evolved roles of these miRNAs, and miRNA-based therapies are emerging as an appealing strategy for precision medicine. We focus on three categories of human disease - cancer, inflammation-linked pathologies, and neurological disorders - which are highly prevalent and are associated with substantial disease burden worldwide. In each category we discuss the pathogenic roles of miRNAs in the context of their evolved functions, as well as current and potential advances in targeting these miRNAs for disease therapy.
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Affiliation(s)
- Shan Quah
- A*STAR Skin Research Labs (A*SRL), Agency for Science, Technology, and Research (A*STAR), 8A Biomedical Grove #06-06 Immunos, Singapore 138648, Republic of Singapore
| | - Gowtham Subramanian
- A*STAR Skin Research Labs (A*SRL), Agency for Science, Technology, and Research (A*STAR), 8A Biomedical Grove #06-06 Immunos, Singapore 138648, Republic of Singapore
| | - Jonathan S L Tan
- A*STAR Skin Research Labs (A*SRL), Agency for Science, Technology, and Research (A*STAR), 8A Biomedical Grove #06-06 Immunos, Singapore 138648, Republic of Singapore
| | | | - Prabha Sampath
- A*STAR Skin Research Labs (A*SRL), Agency for Science, Technology, and Research (A*STAR), 8A Biomedical Grove #06-06 Immunos, Singapore 138648, Republic of Singapore; Genome Institute of Singapore, Agency for Science, Technology, and Research, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Republic of Singapore; Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Republic of Singapore; Skin Research Institute of Singapore (SRIS), 11 Mandalay Road #17-01 Clinical Sciences Building, Singapore 308232, Republic of Singapore.
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Rakhmetullina A, Lukasik A, Zielenkiewicz P. An Overview of miRNA and miRNA Target Analysis Tools. Methods Mol Biol 2025; 2900:43-71. [PMID: 40380052 DOI: 10.1007/978-1-0716-4398-3_2] [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: 05/19/2025]
Abstract
MicroRNA molecules have been shown to play various significant roles in many physiological and pathophysiological processes in living organisms. The tremendous interest in these molecules has led to the significant development and constant release of a number of computational tools useful for basic as well as advanced miRNA-related analyses. These approaches have various constantly evolving utilities, such as detection, target prediction, functional annotation, and many others. In this chapter, we provide an overview of several computational tools useful for broadly defined plant miRNA analysis. We have added to the Tools4miRs new databases that provide extensive information on small noncoding RNA sequences. Additionally, several tools within the platform have been updated, now featuring comprehensive references and accessible links, ensuring users have access to the most recent and relevant research findings.
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Affiliation(s)
- Aizhan Rakhmetullina
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Lukasik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
- Department of Plant Molecular Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Warsaw, Poland.
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Sahu VK, Parida AS, Ranjan A, Madhyastha H, Basu S. miRVim: Three-dimensional miRNA Structure Database. Microrna 2025; 14:59-72. [PMID: 39171462 DOI: 10.2174/0122115366307988240809045125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/10/2024] [Accepted: 06/19/2024] [Indexed: 08/23/2024]
Abstract
INTRODUCTION MicroRNAs (miRNAs), a distinct category of non-coding RNAs, exert multifaceted regulatory functions in a variety of organisms, including humans, animals, and plants. The inventory of identified miRNAs stands at approximately 60,000 among all species and 1,926 in Homo sapiens manifests miRNA expression. Their theranostic role has been explored by researchers over the last few decades, positioning them as prominent therapeutic targets as our understanding of RNA targeting advances. However, limited availability of experimentally determined miRNA structures has constrained drug discovery efforts relying on virtual screening or computational methods, including machine learning and artificial intelligence. METHODS To address this lacuna, miRVim has been developed, providing a repository of human miRNA structures derived from both two-dimensional (MXFold2, CentroidFold, and RNAFold) and three-dimensional (RNAComposer and 3dRNA) structure prediction algorithms, in addition to experimentally available structures from the RCSB PDB repository. RESULTS miRVim contains 13,971 predicted secondary structures and 17,045 predicted three-dimensional structures filling the gap of unavailability of miRNA structure data bank. This database aims to facilitate computational data analysis for drug discovery, opening new avenues for advancing technologies such as machine learning-based predictions in the field of RNA biology. CONCLUSION The publicly accessible structures provided by miRVim, available at https://mirna.in/miRVim, offer a valuable resource for the research community, advancing the field of miRNA-related computational analysis and drug discovery.
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Affiliation(s)
- Vishal Kumar Sahu
- Cancer and Translational Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, (DYPBBI), Dr. D.Y. Patil Vidyapeeth (Deemed to be University), Tathawade, Pune, 411033, India
| | - Ankita Subhadarsani Parida
- Cancer and Translational Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, (DYPBBI), Dr. D.Y. Patil Vidyapeeth (Deemed to be University), Tathawade, Pune, 411033, India
- Department of Bioinformatics, Central University of South Bihar, Gaya, India
| | - Amit Ranjan
- Cancer and Translational Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, (DYPBBI), Dr. D.Y. Patil Vidyapeeth (Deemed to be University), Tathawade, Pune, 411033, India
| | - Harishkumar Madhyastha
- Department of Cardiovascular Physiology, Faculty of Medicine, University of Miyazaki, Miyazaki, 8891692, Japan
| | - Soumya Basu
- Cancer and Translational Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, (DYPBBI), Dr. D.Y. Patil Vidyapeeth (Deemed to be University), Tathawade, Pune, 411033, India
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Janga H, Schmerer N, Aznaourova M, Schulte LN. Non-coding RNA Networks in Infection. Methods Mol Biol 2025; 2883:53-77. [PMID: 39702704 DOI: 10.1007/978-1-0716-4290-0_3] [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: 12/21/2024]
Abstract
In the face of global health challenges posed by infectious diseases and the emergence of drug-resistant pathogens, the exploration of cellular non-coding RNA (ncRNA) networks has unveiled new dimensions in infection research. Particularly microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have emerged as instrumental players in ensuring a balance between protection against hyper-inflammatory conditions and the effective elimination of pathogens. Specifically, ncRNAs, such as the miRNA miR-155 or the lncRNAs MaIL1 (macrophage interferon-regulatory lncRNA 1), and LUCAT1 (lung cancer-associated transcript 1) have been recurrently linked to infectious and inflammatory diseases. Together with other ncRNAs, discussed in this chapter, they form a complex regulatory network shaping the host response to pathogens. Additionally, some pathogens exploit these ncRNAs to establish and sustain infections, underscoring their dual roles in host protection and colonization. Despite the substantial progress made, the vast majority of ncRNA loci remains unexplored, with ongoing research likely to reveal novel ncRNA categories and expand our understanding of their roles in infections. This chapter consolidates current insights into ncRNA-mediated regulatory networks, highlighting their contributions to severe diseases and their potential as targets and biomarkers for innovative therapeutic strategies.
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Affiliation(s)
| | - Nils Schmerer
- Institute for Lung Research, Philipps University, Marburg, Germany
| | | | - Leon N Schulte
- Institute for Lung Research, Philipps University, Marburg, Germany.
- German Center for Lung Research, Giessen, Germany.
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Hill M, Stapleton S, Nguyen PT, Sais D, Deutsch F, Gay VC, Marsh DJ, Tran N. The potential regulation of the miR-17-92a cluster by miR-21. Int J Biochem Cell Biol 2025; 178:106705. [PMID: 39615668 DOI: 10.1016/j.biocel.2024.106705] [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: 05/30/2024] [Revised: 10/31/2024] [Accepted: 11/26/2024] [Indexed: 12/16/2024]
Abstract
MicroRNAs (miRNA,miRs) are small noncoding RNAs that are ubiquitously expressed in all mammalian cells. Their primary function is the regulation of nascent RNA transcripts by direct binding to regions on the target. There is now exciting data to suggest that these miRNAs can bind to other miRNAs, and this may have a broader impact on gene regulation in disease states. The oncomiR miR-21 is one of the highest-expressing miRNAs in cancer cells, and in this study, we characterise which miRNAs could be potential targets of miR-21. In cancer cells delivered with a miR-21 mimic, there was an observable shift of the miRNA milieu. We demonstrate that the miR-17-92a cluster, which harbours six miRNA members, may be a target for miR-21 regulation. Additionally, the primary transcript of miR-17-92a was reduced in the presence of miR-21. In the broader context of miR:miR regulation, overexpression of miR-21 shifted the expression of more than 150 miRNAs, including those known to regulate genes in cancer pathways such as the MAPK signalling and FoxO pathways. This study expands upon our limited understanding of miR:miR regulatory network and reinforces the concept that miRNAs can regulate each other, thereby influencing broader gene networks.
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Affiliation(s)
- Meredith Hill
- School of Biomedical Engineering, Faculty of Engineering, and Information Technology, University of Technology Sydney, Australia
| | - Sarah Stapleton
- School of Biomedical Engineering, Faculty of Engineering, and Information Technology, University of Technology Sydney, Australia
| | | | - Dayna Sais
- School of Biomedical Engineering, Faculty of Engineering, and Information Technology, University of Technology Sydney, Australia
| | - Fiona Deutsch
- School of Biomedical Engineering, Faculty of Engineering, and Information Technology, University of Technology Sydney, Australia
| | - Valerie C Gay
- School of Electrical and Data Engineering, Faculty of Engineering, and Information Technology, University of Technology Sydney, Australia
| | - Deborah J Marsh
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Australia
| | - Nham Tran
- School of Biomedical Engineering, Faculty of Engineering, and Information Technology, University of Technology Sydney, Australia.
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Sood S, Tiwari A, Sangwan J, Vohra M, Sinha NR, Tripathi R, Sangwan VS, Mohan RR. Role of epigenetics in corneal health and disease. Prog Retin Eye Res 2025; 104:101318. [PMID: 39547455 PMCID: PMC11710990 DOI: 10.1016/j.preteyeres.2024.101318] [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: 09/03/2024] [Revised: 11/12/2024] [Accepted: 11/13/2024] [Indexed: 11/17/2024]
Abstract
Epigenetics plays a vital role in corneal health and diseases. Epigenetic changes regulate the expression of genes by altering the accessibility of chromatin via histone modifications, DNA methylation and miRNAs without altering DNA sequence. Ocular trauma and infections are common causes of corneal damage, vision impairment, and mono/bilateral blindness worldwide. Mounting literature shows that epigenetic modifications can modulate corneal clarity, function, and pathogenesis including inflammation, wound healing, fibrosis, and neovascularization. Additionally, epigenetic modifications can be targeted to reverse corneal pathologies and develop interventional therapies. However, current understanding on how epigenetic modifications lead to corneal abnormalities and diseases is limited. This review provides in-depth knowledge and mechanistic understanding of epigenetics alterations in corneal pathogenesis, and information on potential epigenetic targets for treatment of corneal diseases.
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Affiliation(s)
- Swati Sood
- Departments of Veterinary Medicine & Surgery, College of Veterinary Medicine University of Missouri, Columbia, MO, USA
| | - Anil Tiwari
- Departments of Veterinary Medicine & Surgery, College of Veterinary Medicine University of Missouri, Columbia, MO, USA; Eicher-Shroff Centre for Stem Cells Research (ESC-SCR), Dr. Shroff Charity Eye Hospital, Delhi, India
| | - Jyoti Sangwan
- Eicher-Shroff Centre for Stem Cells Research (ESC-SCR), Dr. Shroff Charity Eye Hospital, Delhi, India
| | - Mehak Vohra
- Eicher-Shroff Centre for Stem Cells Research (ESC-SCR), Dr. Shroff Charity Eye Hospital, Delhi, India
| | - Nishant R Sinha
- Departments of Veterinary Medicine & Surgery, College of Veterinary Medicine University of Missouri, Columbia, MO, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA; Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Ratnakar Tripathi
- Departments of Veterinary Medicine & Surgery, College of Veterinary Medicine University of Missouri, Columbia, MO, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Virender S Sangwan
- Eicher-Shroff Centre for Stem Cells Research (ESC-SCR), Dr. Shroff Charity Eye Hospital, Delhi, India
| | - Rajiv R Mohan
- Departments of Veterinary Medicine & Surgery, College of Veterinary Medicine University of Missouri, Columbia, MO, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA; Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, MO, USA.
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Barrero-Torres DM, Herrera-Torres G, Pérez J, Martínez-Moreno Á, Martínez-Moreno FJ, Flores-Velázquez LM, Buffoni L, Rufino-Moya PJ, Ruiz-Campillo MT, Molina-Hernández V. Unraveling the microRNAs Involved in Fasciolosis: Master Regulators of the Host-Parasite Crosstalk. Int J Mol Sci 2024; 26:204. [PMID: 39796061 PMCID: PMC11719827 DOI: 10.3390/ijms26010204] [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: 11/22/2024] [Revised: 12/24/2024] [Accepted: 12/24/2024] [Indexed: 01/13/2025] Open
Abstract
Fasciolosis is a neglected tropical disease caused by helminth parasites of the genus Fasciola spp., including Fasciola hepatica (F. hepatica) and Fasciola gigantica (F. gigantica), being a major zoonotic problem of human and animal health. Its control with antihelminthics is becoming ineffective due to the increase in parasite resistance. Developing new therapeutic protocols is crucial to a deeper knowledge of the molecular bases in the host-parasite interactions. The high-throughput omics technologies have dramatically provided unprecedented insights into the complexity of the molecular host-parasite crosstalk. MicroRNAs (miRNAs) are key players as critical regulators in numerous biological processes, modifying the gene expression of cells by degradation of messenger RNA (mRNA), regulating transcription and translation functions, protein positioning, cell cycle integrity, differentiation and apoptosis. The large-scale exploration of miRNAs, including the miRNome, has offered great scientific knowledge of steps in fasciolosis, further scrutinizing the pathogenesis, the growth and development of their strains and their interaction with the host for the survival of the different parasite stages. This review compiles the updated knowledge related to miRNAs involved in fasciolosis and the generated miRNome, highlighting the importance of these key molecules in the host-parasite interactions and the pathogenesis of Fasciola spp. directing towards the development of new biotherapeutic protocols for the control of fasciolosis.
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Affiliation(s)
- Diana María Barrero-Torres
- Departamento de Anatomía y Anatomía Patológica Comparadas y Toxicología, UIC Zoonosis y Enfermedades Emergentes (ENZOEM), Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad Animal, 14071 Córdoba, Spain; (D.M.B.-T.); (G.H.-T.); (J.P.); (L.M.F.-V.)
| | - Guillem Herrera-Torres
- Departamento de Anatomía y Anatomía Patológica Comparadas y Toxicología, UIC Zoonosis y Enfermedades Emergentes (ENZOEM), Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad Animal, 14071 Córdoba, Spain; (D.M.B.-T.); (G.H.-T.); (J.P.); (L.M.F.-V.)
| | - José Pérez
- Departamento de Anatomía y Anatomía Patológica Comparadas y Toxicología, UIC Zoonosis y Enfermedades Emergentes (ENZOEM), Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad Animal, 14071 Córdoba, Spain; (D.M.B.-T.); (G.H.-T.); (J.P.); (L.M.F.-V.)
| | - Álvaro Martínez-Moreno
- Departamento de Sanidad Animal (Área de Parasitología), UIC Zoonosis y Enfermedades Emergentes (ENZOEM), Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad Animal, 14071 Córdoba, Spain; (Á.M.-M.); (F.J.M.-M.); (L.B.); (P.J.R.-M.)
| | - Francisco Javier Martínez-Moreno
- Departamento de Sanidad Animal (Área de Parasitología), UIC Zoonosis y Enfermedades Emergentes (ENZOEM), Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad Animal, 14071 Córdoba, Spain; (Á.M.-M.); (F.J.M.-M.); (L.B.); (P.J.R.-M.)
| | - Luis Miguel Flores-Velázquez
- Departamento de Anatomía y Anatomía Patológica Comparadas y Toxicología, UIC Zoonosis y Enfermedades Emergentes (ENZOEM), Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad Animal, 14071 Córdoba, Spain; (D.M.B.-T.); (G.H.-T.); (J.P.); (L.M.F.-V.)
- Unidad de Anatomía, Histología y Patología Veterinaria, Escuela de Medicina Veterinaria, Facultad de Ciencias Naturales, Universidad San Sebastián, Campus Puerto Montt, Puerto Montt 5480000, Chile
| | - Leandro Buffoni
- Departamento de Sanidad Animal (Área de Parasitología), UIC Zoonosis y Enfermedades Emergentes (ENZOEM), Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad Animal, 14071 Córdoba, Spain; (Á.M.-M.); (F.J.M.-M.); (L.B.); (P.J.R.-M.)
| | - Pablo José Rufino-Moya
- Departamento de Sanidad Animal (Área de Parasitología), UIC Zoonosis y Enfermedades Emergentes (ENZOEM), Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad Animal, 14071 Córdoba, Spain; (Á.M.-M.); (F.J.M.-M.); (L.B.); (P.J.R.-M.)
| | - María Teresa Ruiz-Campillo
- Departamento de Anatomía y Anatomía Patológica Comparadas y Toxicología, UIC Zoonosis y Enfermedades Emergentes (ENZOEM), Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad Animal, 14071 Córdoba, Spain; (D.M.B.-T.); (G.H.-T.); (J.P.); (L.M.F.-V.)
| | - Verónica Molina-Hernández
- Departamento de Anatomía y Anatomía Patológica Comparadas y Toxicología, UIC Zoonosis y Enfermedades Emergentes (ENZOEM), Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad Animal, 14071 Córdoba, Spain; (D.M.B.-T.); (G.H.-T.); (J.P.); (L.M.F.-V.)
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Zhang Y, Li Y, Han H, Wang X, Gao S, Zhao Q, Bieerdebieke H, Xu L, Zang Q, Wang H, Bai P, Lin K. Identification of miRNAs Involved in Olfactory Regulation in Antennae of Beet Webworm, Loxostege sticticalis (Lepidoptera: Pyralidae). Life (Basel) 2024; 14:1705. [PMID: 39768411 PMCID: PMC11677245 DOI: 10.3390/life14121705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Revised: 12/13/2024] [Accepted: 12/14/2024] [Indexed: 01/11/2025] Open
Abstract
The beet webworm, Loxostege sticticalis, is a typical migratory pest. Although miRNAs participate in many physiological functions, little is known about the functions of miRNAs in olfactory regulation. In this study, 1120 (869 known and 251 novel) miRNAs were identified in the antennae of L. sticticalis by using high-throughput sequencing technology. Among the known miRNAs, 189 from 49 families were insect-specific, indicating that these miRNAs might play unique roles in insects. Furthermore, based on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, we found that 3647 and 1393 miRNAs were associated with localization and the regulation of localization, respectively, and 80 miRNAs were enriched in the neuroactive ligand-receptor interaction pathway. These miRNAs might be involved in the olfactory system of L. sticticalis. Notably, qRT-PCR showed that most of the tested miRNAs presented similar expression patterns compared with the RNA-seq data and that miR-87-3, novel-miR-78, and novel-miR-142 were significantly differentially expressed in the antennae of males and females. In addition, 21 miRNAs were predicted to target 23 olfactory genes, including 10 odorant-binding proteins (OBPs), 3 chemosensory proteins (CSPs), 4 odorant receptors (ORs), 1 ionotropic receptor (IR), and 5 gustatory receptors (GRs). The olfactory-related miRNAs exhibited low-abundance transcripts, except undef-miR-55 and undef-miR-523, and gender-biased expression was not observed for olfactory-related miRNAs. Our findings provide an overview of the potential miRNAs involved in olfactory regulation, which may provide important information on the function of miRNAs in the insect olfactory system.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Biohazard Monitoring, Green Prevention and Control for Artificial Grassland, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (Y.Z.); (S.G.); (Q.Z.); (L.X.); (H.W.)
| | - Yanyan Li
- Research Center for Grassland Entomology, Inner Mongolia Agricultural University, Hohhot 010020, China; (Y.L.); (H.H.)
| | - Haibin Han
- Research Center for Grassland Entomology, Inner Mongolia Agricultural University, Hohhot 010020, China; (Y.L.); (H.H.)
| | - Xiaoling Wang
- Xilin Gol League Agricultural and Animal Husbandry Technology Promotion Center, Xilinhot 026000, China;
| | - Shujing Gao
- Key Laboratory of Biohazard Monitoring, Green Prevention and Control for Artificial Grassland, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (Y.Z.); (S.G.); (Q.Z.); (L.X.); (H.W.)
| | - Qing Zhao
- Key Laboratory of Biohazard Monitoring, Green Prevention and Control for Artificial Grassland, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (Y.Z.); (S.G.); (Q.Z.); (L.X.); (H.W.)
| | - Halima Bieerdebieke
- The Center for Grassland Biological Disaster Prevention of Xinjiang Uygur Autonomous Region, Urumqi 830049, China;
| | - Linbo Xu
- Key Laboratory of Biohazard Monitoring, Green Prevention and Control for Artificial Grassland, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (Y.Z.); (S.G.); (Q.Z.); (L.X.); (H.W.)
| | - Qicong Zang
- Heilongjiang Province Grassland Station, Harbin 150069, China;
| | - Hui Wang
- Key Laboratory of Biohazard Monitoring, Green Prevention and Control for Artificial Grassland, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (Y.Z.); (S.G.); (Q.Z.); (L.X.); (H.W.)
| | - Penghua Bai
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Kejian Lin
- Key Laboratory of Biohazard Monitoring, Green Prevention and Control for Artificial Grassland, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (Y.Z.); (S.G.); (Q.Z.); (L.X.); (H.W.)
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Wang Z, Wang PS, Yang C. Dysregulation of Long Non-coding RNAs-the Novel lnc in Metal Toxicity and Carcinogenesis. Curr Environ Health Rep 2024; 12:3. [PMID: 39715843 PMCID: PMC11755759 DOI: 10.1007/s40572-024-00468-1] [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] [Accepted: 12/11/2024] [Indexed: 12/25/2024]
Abstract
PURPOSE OF REVIEW Metals are common environmental pollutants. Acute and chronic exposures to non-essential toxic metals or excessive essential metals cause various diseases including cancer in humans. However, the underlying mechanisms have not been well understood. Long non-coding RNAs (lncRNAs) refer to RNA transcripts that have more than 200 nucleotides but do not have significant protein coding capacities. While lncRNAs were once considered transcription noise, they have become increasingly recognized as crucial players in various physiological and pathogenesis processes. The goal of this article is to review and discuss recent studies that show important roles of lncRNA dysregulations in metal toxicity and carcinogenesis. RECENT FINDINGS Recent studies showed that metal exposures dysregulate expression of lncRNAs in cultured cells, animals and humas. However, only a few studies determined the mechanisms of how metal exposure dysregulated expression of lncRNAs. The majority of the studies reported the association of abnormally expressed lncRNAs with various toxic effects of metal exposures, only limited studies established causal relationships demonstrating causal roles of dysregulated lncRNAs in metal toxicity and carcinogenesis. Mechanistically, most studies reported that dysregulated lncRNAs functioned as microRNA sponges to regulate gene expression, much less studies explored other mechanisms of lncRNA actions. It is evident that metal exposures dysregulate expression of lncRNAs, which may serve as novel mediators in metal toxicity and carcinogenesis. Further studies are needed to establish dysregulated lncRNAs as potential diagnostic biomarkers and therapeutic targets for metal exposure-associated diseases.
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Affiliation(s)
- Zhishan Wang
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, 11794, USA
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, 101 Nicolls Road, Stony Brook, NY, 11794, USA
| | - Po-Shun Wang
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Chengfeng Yang
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, 11794, USA.
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, 101 Nicolls Road, Stony Brook, NY, 11794, USA.
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Hall I, O'Steen M, Gold S, C Keane S, Weidmann CA. Template switching enables chemical probing of native RNA structures. RNA (NEW YORK, N.Y.) 2024; 31:113-125. [PMID: 39438135 DOI: 10.1261/rna.079926.123] [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: 12/13/2023] [Accepted: 09/26/2024] [Indexed: 10/25/2024]
Abstract
RNAs are often studied in nonnative sequence contexts to facilitate structural studies. However, seemingly innocuous changes to an RNA sequence may perturb the native structure and generate inaccurate or ambiguous structural models. To facilitate the investigation of native RNA secondary structure by selective 2' hydroxyl acylation analyzed by primer extension (SHAPE), we engineered an approach that couples minimal enzymatic steps to RNA chemical probing and mutational profiling (MaP) reverse transcription (RT) methods-a process we call template switching and mutational profiling (Switch-MaP). In Switch-MaP, RT templates and additional library sequences are added postprobing through ligation and template switching, capturing reactivities for every nucleotide. For a candidate SAM-I riboswitch, we compared RNA structure models generated by the Switch-MaP approach to those of traditional primer-based MaP, including RNAs with or without appended structure cassettes. Primer-based MaP masked reactivity data in the 5' and 3' ends of the RNA, producing ambiguous ensembles inconsistent with the conserved SAM-I riboswitch secondary structure. Structure cassettes enabled unambiguous modeling of an aptamer-only construct but introduced nonnative interactions in the full-length riboswitch. In contrast, Switch-MaP provided reactivity data for all nucleotides in each RNA and enabled unambiguous modeling of secondary structure, consistent with the conserved SAM-I fold. Switch-MaP is a straightforward alternative approach to primer-based and cassette-based chemical probing methods that precludes primer masking and the formation of alternative secondary structures due to nonnative sequence elements.
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Affiliation(s)
- Ian Hall
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Martin O'Steen
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sophie Gold
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sarah C Keane
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Chase A Weidmann
- Department of Biological Chemistry, Center for RNA Biomedicine, Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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Li X, Qin W, Wang W, Liu W, Dong T, Liu A, Cai H, Xu Z, Zeng J. Screening and Studying of Blood miRNAs as Potential Diagnostic Markers for Papillary Thyroid Carcinoma. Onco Targets Ther 2024; 17:1173-1185. [PMID: 39678015 PMCID: PMC11645959 DOI: 10.2147/ott.s489559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Accepted: 12/03/2024] [Indexed: 12/17/2024] Open
Abstract
Objective MiRNAs play a pivotal role in tumorigenesis and development by exerting negative regulation on the expression of target genes. In this study, bioinformatics techniques and online database were employed to investigate the specific miRNA-target gene regulatory network in PTC, which was subsequently validated using human blood samples and compared to existing tumor markers. Methods The miRNA (GSE50901) and Gene Expression (GSE113629) chip screening data of human PTC tissues were retrieved from GEO database. A comparative analysis was conducted using the GEO2R to identify differentially expressed miRNAs and target genes of the patients with PTC. Prediction of the miRNA-target gene regulatory network, related signal transduction pathways, biological effects and their relationship to prognosis was performed based on GO, KEGG, qRT-PCR detection of human blood samples, analysis of correlation on the existing pathological tumor markers, and ROC. Results Compared to the corresponding normal thyroid tissues, a total of 2116 miRNAs were found to be differentially expressed in PTC patients, including 1968 up-regulated and 148 down-regulated genes. The abnormally expressed genes primarily participated in signal pathways associated with tumorigenesis and abnormal gene transcription. By utilizing data from the GEO database, five miRNAs closely linked to PTC prognosis were identified, which were miR-221-3p, miR-222-3p, miR-182-5p, miR-135a-5p, and miR-34a-5p, with elucidating the target genes. Experimental validation, correlation analysis with tumor markers along with bioinformatics analysis revealed a significant increase in expression levels of miR-182-5p in PTC patients which positively correlated with poor prognosis. These molecules could play crucial roles in both initiation and progression of PTC. Conclusion This study identified potential novel blood-based miRNA biomarkers for PTC through bioinformatics analysis combined with the detection of human blood samples, thereby offering new possibilities for significant biomarkers associated with diagnosis and prognosis of PTC.
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Affiliation(s)
- Xize Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Jinan, 250012, People’s Republic of China
| | - Wen Qin
- The Hospital Wing, Shandong University, Jinan, 250012, People’s Republic of China
| | - Wenting Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Jinan, 250012, People’s Republic of China
| | - Weilin Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Jinan, 250012, People’s Republic of China
| | - Tianyi Dong
- Department of Breast and Thyroid Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, People’s Republic of China
| | - Aixiang Liu
- Department of Clinical Laboratory, Zaozhuang Municipal Hospital, Zaozhuang, 277102, People’s Republic of China
| | - Haojie Cai
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Jinan, 250012, People’s Republic of China
| | - Zhouhan Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Jinan, 250012, People’s Republic of China
| | - Jiping Zeng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Jinan, 250012, People’s Republic of China
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, 266113, People’s Republic of China
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Drula R, Calin GA. MicroRNAs: where brilliance, perseverance, and ambition converged. J Clin Invest 2024; 135:e189625. [PMID: 39656547 PMCID: PMC11735086 DOI: 10.1172/jci189625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2025] Open
Affiliation(s)
- Rares Drula
- Translational Molecular Pathology Department
| | - George A. Calin
- Translational Molecular Pathology Department
- Leukemia Department, and
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Huang K, Qi Y. miRNA in mechanobiology: The exploration needs to continue. MECHANOBIOLOGY IN MEDICINE 2024; 2:100101. [PMID: 40395226 PMCID: PMC12082168 DOI: 10.1016/j.mbm.2024.100101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Accepted: 11/06/2024] [Indexed: 05/22/2025]
Abstract
The 2024 Nobel Prize in Physiology or Medicine has once again sparked considerable interest in microRNA (miRNA). Recent advances have unveiled that miRNAs play critical roles in mediating the effects of mechanical stimuli on gene expression, cellular functions, tissue development, and disease progression. This perspective summarized the history of miRNA research and highlighted the promising research directions of miRNAs in the field of mechanobiology.
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Affiliation(s)
- Kai Huang
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang, 200240, Shanghai, China
| | - Yingxin Qi
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang, 200240, Shanghai, China
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Li W, Yu L. Role and therapeutic perspectives of extracellular vesicles derived from liver and adipose tissue in metabolic dysfunction-associated steatotic liver disease. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2024; 52:355-369. [PMID: 38833340 DOI: 10.1080/21691401.2024.2360008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 05/22/2024] [Indexed: 06/06/2024]
Abstract
The global epidemic of metabolic diseases has led to the emergence of metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction-associated steatohepatitis (MASH), which pose a significant threat to human health. Despite recent advances in research on the pathogenesis and treatment of MASLD/MASH, there is still a lack of more effective and targeted therapies. Extracellular vesicles (EVs) discovered in a wide range of tissues and body fluids encapsulate different activated biomolecules and mediate intercellular communication. Recent studies have shown that EVs derived from the liver and adipose tissue (AT) play vital roles in MASLD/MASH pathogenesis and therapeutics, depending on their sources and intervention types. Besides, adipose-derived stem cell (ADSC)-derived EVs appear to be more effective in mitigating MASLD/MASH. This review presents an overview of the definition, extraction strategies, and characterisation of EVs, with a particular focus on the biogenesis and release of exosomes. It also reviews the effects and potential molecular mechanisms of liver- and AT-derived EVs on MASLD/MASH, and emphasises the contribution and clinical therapeutic potential of ADSC-derived EVs. Furthermore, the future perspective of EV therapy in a clinical setting is discussed.
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Affiliation(s)
- Wandi Li
- Senior Department of Burns and Plastic Surgery, the Fourth Medical Center of PLA General Hospital, Haidian District, Beijing, P.R. China
| | - Lili Yu
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, P.R. China
- Endocrine Department, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang Medical University, Henan, P.R. China
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Xiang W, Yang F, Pu X, Zhao S, Wang P. A New Perspective on Pig Genetics and Breeding: microRNA. Reprod Domest Anim 2024; 59:e14751. [PMID: 39639849 DOI: 10.1111/rda.14751] [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: 07/21/2024] [Revised: 11/05/2024] [Accepted: 11/17/2024] [Indexed: 12/07/2024]
Abstract
microRNA (miRNA) is a class of small non-coding RNA molecules that are widely expressed in organisms and play an important role in the regulation of gene expression at the post-transcriptional level. In recent years, researchers have begun to explore its effects on the development of domestic animals and have begun to think about its potential role in modern molecular breeding. Increasing evidence shows that miRNA play a central role in the regulation of pig fertility, pork product quality and disease resistance. Understanding the physiological mechanism of miRNA will be able to better guide future breeding work. In this paper, we will review the research progress of the function and mechanism of miRNA in combination with the above economic characteristics of pigs. The reported miRNA and their target genes were sorted out to evaluate their potential role in improving economic traits such as pig fertility, meat quality and disease resistance, to provide a reference for modern pig molecular breeding.
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Affiliation(s)
- Wei Xiang
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, China
| | - Fan Yang
- College of Bioengineering, Chongqing University, Chongqing, China
| | - Xiufen Pu
- College of Bioengineering, Chongqing University, Chongqing, China
| | - Shuang Zhao
- College of Bioengineering, Chongqing University, Chongqing, China
| | - Pingqing Wang
- College of Bioengineering, Chongqing University, Chongqing, China
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