1
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Li Q, Wang Q, Wang R, Zhang L, Liu Z. The frameshifting element in coronaviruses: structure, function, and potential as a therapeutic target. Trends Pharmacol Sci 2025:S0165-6147(25)00069-0. [PMID: 40382241 DOI: 10.1016/j.tips.2025.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 04/15/2025] [Accepted: 04/15/2025] [Indexed: 05/20/2025]
Abstract
The frameshifting element (FSE) comprises a slippery heptanucleotide sequence followed by a downstream RNA structure, such as a pseudoknot or stem-loop. Found in various RNA viruses, FSE regulates viral replication via programmed -1 ribosomal frameshifting (-1 PRF), making it a potential broad-spectrum antiviral target. Advances in RNA structural analysis have elucidated the dynamic conformations and cross-viral diversity of FSE, with the SARS-CoV-2 outbreak further highlighting its role in viral replication. Efforts to develop antiviral drugs targeting FSE have progressed through virtual and phenotypic screening. In this review, we explore the evolution, structure, and function of FSE in coronaviruses, evaluate recent advances in FSE-targeted drug development, and discuss their design advantages, efficacy, and challenges, providing insights for future antiviral strategies.
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Affiliation(s)
- Qi Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China; Ningbo Institute of Marine Medicine, Peking University, Zhejiang, 315832, China
| | - Rui Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China; Ningbo Institute of Marine Medicine, Peking University, Zhejiang, 315832, China.
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2
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Liu T, Xu L, Chung K, Sisto LJ, Hwang J, Zhang C, Van Zandt MC, Pyle AM. Molecular insights into de novo small-molecule recognition by an intron RNA structure. Proc Natl Acad Sci U S A 2025; 122:e2502425122. [PMID: 40339124 PMCID: PMC12088405 DOI: 10.1073/pnas.2502425122] [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: 01/31/2025] [Accepted: 04/01/2025] [Indexed: 05/10/2025] Open
Abstract
Despite the promise of vastly expanding the druggable genome, rational design of RNA-targeting ligands remains challenging as it requires the rapid identification of hits and visualization of the resulting cocomplexes for guiding optimization. Here, we leveraged high-throughput screening, medicinal chemistry, and structural biology to identify a de novo splicing inhibitor against a large and highly folded fungal group I intron. High-resolution cryoEM structures of the intron in different liganded states not only reveal molecular interactions that rationalize experimental structure-activity relationship but also shed light on a unique strategy whereby RNA-associated metal ions and RNA conformation exhibit exceptional plasticity in response to small-molecule binding. This study reveals general principles that govern RNA-ligand recognition, the interplay between chemical bonding specificity, and dynamic responses within an RNA target.
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Affiliation(s)
- Tianshuo Liu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
| | - Ling Xu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
- HHMI, Chevy Chase, MD 20815
| | - Kevin Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
| | - Luke J Sisto
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
- New England Discovery Partners, Branford, CT 06405
| | - Jimin Hwang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
| | - Chengxin Zhang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
| | | | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
- HHMI, Chevy Chase, MD 20815
- Department of Chemistry, Yale University, New Haven, CT 06511
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3
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Liu Y, Whitfield TW, Bell GW, Guo R, Flamier A, Young RA, Jaenisch R. Exploring the complexity of MECP2 function in Rett syndrome. Nat Rev Neurosci 2025:10.1038/s41583-025-00926-1. [PMID: 40360671 DOI: 10.1038/s41583-025-00926-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2025] [Indexed: 05/15/2025]
Abstract
Rett syndrome (RTT) is a neurodevelopmental disorder that is mainly caused by mutations in the methyl-DNA-binding protein MECP2. MECP2 is an important epigenetic regulator that plays a pivotal role in neuronal gene regulation, where it has been reported to function as both a repressor and an activator. Despite extensive efforts in mechanistic studies over the past two decades, a clear consensus on how MECP2 dysfunction impacts molecular mechanisms and contributes to disease progression has not been reached. Here, we review recent insights from epigenomic, transcriptomic and proteomic studies that advance our understanding of MECP2 as an interacting hub for DNA, RNA and transcription factors, orchestrating diverse processes that are crucial for neuronal function. By discussing findings from different model systems, we identify crucial epigenetic details and cofactor interactions, enriching our understanding of the multifaceted roles of MECP2 in transcriptional regulation and chromatin structure. These mechanistic insights offer potential avenues for rational therapeutic design for RTT.
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Affiliation(s)
- Yi Liu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | | | - George W Bell
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Ruisi Guo
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Anthony Flamier
- Department of Neuroscience, Université de Montréal, Montreal, Quebec, Canada
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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4
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Fujiwara N, Ueno T, Yamazaki T, Hirose T. Unraveling architectural RNAs: Structural and functional blueprints of membraneless organelles and strategies for genome-scale identification. Biochim Biophys Acta Gen Subj 2025; 1869:130815. [PMID: 40348038 DOI: 10.1016/j.bbagen.2025.130815] [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: 01/05/2025] [Revised: 04/25/2025] [Accepted: 05/06/2025] [Indexed: 05/14/2025]
Abstract
Architectural RNAs (arcRNAs) are long noncoding RNAs that serve as structural scaffolds for membraneless organelles (MLOs), facilitating cellular organization and dynamic responses to stimuli. Acting as blueprints for MLO assembly, arcRNAs recruit specific proteins and nucleic acids to establish and maintain the internal structure of MLOs while coordinating their spatial relationships with other organelles. This organized framework enables precise spatiotemporal regulation, allowing for targeted control of transcription, RNA processing, and cellular responses to stress. Notably, arcRNAs exhibit the "semi-extractable" feature, a property derived from their stable binding to cellular structures, making them partially resistant to conventional RNA extraction methods. This unique feature serves as a useful criterion for identifying novel arcRNAs, providing an opportunity to accelerate research in long noncoding RNAs and deepen our understanding of their functional roles in cellular processes.
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Affiliation(s)
- Naoko Fujiwara
- Graduate School of Frontier Biosciences, The University of Osaka, Suita 565-0871, Japan
| | - Tsuyoshi Ueno
- Graduate School of Frontier Biosciences, The University of Osaka, Suita 565-0871, Japan
| | - Tomohiro Yamazaki
- Graduate School of Frontier Biosciences, The University of Osaka, Suita 565-0871, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, The University of Osaka, Suita 565-0871, Japan.
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5
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Chen X, Wang L, Xie J, Nowak JS, Luo B, Zhang C, Jia G, Zou J, Huang D, Glatt S, Yang Y, Su Z. RNA sample optimization for cryo-EM analysis. Nat Protoc 2025; 20:1114-1157. [PMID: 39548288 DOI: 10.1038/s41596-024-01072-1] [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: 08/04/2023] [Accepted: 09/12/2024] [Indexed: 11/17/2024]
Abstract
RNAs play critical roles in most biological processes. Although the three-dimensional (3D) structures of RNAs primarily determine their functions, it remains challenging to experimentally determine these 3D structures due to their conformational heterogeneity and intrinsic dynamics. Cryogenic electron microscopy (cryo-EM) has recently played an emerging role in resolving dynamic conformational changes and understanding structure-function relationships of RNAs including ribozymes, riboswitches and bacterial and viral noncoding RNAs. A variety of methods and pipelines have been developed to facilitate cryo-EM structure determination of challenging RNA targets with small molecular weights at subnanometer to near-atomic resolutions. While a wide range of conditions have been used to prepare RNAs for cryo-EM analysis, correlations between the variables in these conditions and cryo-EM visualizations and reconstructions remain underexplored, which continue to hinder optimizations of RNA samples for high-resolution cryo-EM structure determination. Here we present a protocol that describes rigorous screenings and iterative optimizations of RNA preparation conditions that facilitate cryo-EM structure determination, supplemented by cryo-EM data processing pipelines that resolve RNA dynamics and conformational changes and RNA modeling algorithms that generate atomic coordinates based on moderate- to high-resolution cryo-EM density maps. The current protocol is designed for users with basic skills and experience in RNA biochemistry, cryo-EM and RNA modeling. The expected time to carry out this protocol may range from 3 days to more than 3 weeks, depending on the many variables described in the protocol. For particularly challenging RNA targets, this protocol could also serve as a starting point for further optimizations.
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Affiliation(s)
- Xingyu Chen
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Liu Wang
- The State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, National Center for Stomatology, Department of Cardiology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiahao Xie
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Jakub S Nowak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Bingnan Luo
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Chong Zhang
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Guowen Jia
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Jian Zou
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Dingming Huang
- The State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, National Center for Stomatology, Department of Cardiology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Department for Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Yang Yang
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.
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6
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Aguilar R, Rosenberg M, Levy V, Lee JT. An evolving landscape of PRC2-RNA interactions in chromatin regulation. Nat Rev Mol Cell Biol 2025:10.1038/s41580-025-00850-3. [PMID: 40307460 DOI: 10.1038/s41580-025-00850-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2025] [Indexed: 05/02/2025]
Abstract
A major unsolved problem in epigenetics is how RNA regulates Polycomb repressive complex 2 (PRC2), a complex that trimethylates histone H3 Lys27 (H3K27me3) to form repressive chromatin. Key questions include how PRC2 binds RNA in vivo and what the functional consequences of binding are. In this Perspective, we expound on the viewpoint that RNA is integral to the stepwise regulation of PRC2 activity. Using the long non-coding RNA XIST and X chromosome inactivation as a model, we discuss evidence indicating that RNA is involved in PRC2 recruitment onto chromatin, in induction of its catalytic activity and in its eviction from chromatin. Studies have also implicated RNA in controlling promoter-proximal pausing of RNA polymerase II. The cumulative data argue that the functional consequences of PRC2-RNA interactions crucially depend on RNA conformation. We recognize that alternative hypotheses exist and therefore we attempt to integrate contrary data. Thus, although an RNA-rich landscape is emerging for Polycomb complexes, additional work is required to resolve a broad range of data interpretations.
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Affiliation(s)
- Rodrigo Aguilar
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Michael Rosenberg
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Vered Levy
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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7
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Wang J. Genome-Wide Analysis of Stable RNA Secondary Structures across Multiple Organisms Using Chemical Probing Data: Insights into Short Structural Motifs and RNA-Targeting Therapeutics. Biochemistry 2025; 64:1817-1827. [PMID: 40131856 PMCID: PMC12005188 DOI: 10.1021/acs.biochem.4c00764] [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: 11/12/2024] [Revised: 03/10/2025] [Accepted: 03/14/2025] [Indexed: 03/27/2025]
Abstract
Small molecules targeting specific RNA-binding sites, including stable and transient RNA structures, are emerging as effective pharmacological approaches for modulating gene expression. However, little is understood about how stable RNA secondary structures are shared across organisms, which is an important factor in controlling drug selectivity. In this study, I provide an analytical pipeline named RNA secondary structure finder (R2S-Finder) to discover short, stable RNA structural motifs in humans, Escherichia coli (E. coli), SARS-CoV-2, and Zika virus by leveraging existing in vivo and in vitro genome-wide chemical RNA-probing datasets. I found several common features across the organisms. For example, apart from the well-documented tetraloops, AU-rich tetraloops are widely present in different organisms. I also validated that the 5' untranslated region (UTR) contains a higher proportion of stable structures than the coding sequences in humans and Zika virus. In general, stable structures predicted from in vitro (protein-free) and in vivo datasets are consistent across different organisms, indicating that stable structure formation is mostly driven by RNA folding, while a larger variation was found between in vitro and in vivo data for certain RNA types, such as human long intergenic noncoding RNAs (lincRNAs). Finally, I predicted stable three- and four-way RNA junctions that exist under both in vivo and in vitro conditions and can potentially serve as drug targets. All results of stable structures, stem-loops, internal loops, bulges, and n-way junctions have been collated in the R2S-Finder database (https://github.com/JingxinWangLab/R2S-Finder), which is coded in hyperlinked HTML pages and tabulated in CSV files.
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Affiliation(s)
- Jingxin Wang
- Section of Genetic Medicine,
Department of Medicine, Biological Sciences Division, University of Chicago, Chicago, Illinois 60637, United States
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8
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Wan L, Guo H, Hu F, Pan Y, Yang S, Jiang CY, Liu W, Wu X, Wu X. EZH2-mediated suppression of TIMP1 in spinal GABAergic interneurons drives microglial activation via MMP-9-TLR2/4-NLRP3 signaling in neuropathic pain. Brain Behav Immun 2025; 128:234-255. [PMID: 40209863 DOI: 10.1016/j.bbi.2025.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 03/31/2025] [Accepted: 04/03/2025] [Indexed: 04/12/2025] Open
Abstract
Effective management of neuropathic pain remains a significant challenge due to the limited understanding of its underlying mechanisms. We found that the FDA-approved enhancer of zeste homolog 2 (EZH2) inhibitor, EPZ6438, can prevent the development of neuropathic pain caused by chronic constriction injury (CCI). Therefore, we utilized EPZ6438 as a probe to investigate the molecular events involved in the early stage of neuropathic pain. RNA-seq analysis reveals that EPZ6438 significantly upregulates Timp1 transcription in the spinal cord of mice. As a specific endogenous inhibitor of MMP-9, tissue inhibitor of metalloproteinase 1 (TIMP1) levels significantly decrease in the cerebrospinal fluid of both neuropathic pain patients and the CCI rat models. Importantly, intrathecal administration of mouse recombinant TIMP1 protein (rmTIMP1) reverses CCI-induced mechanical and thermal hyperalgesia. Mechanistically, substance P released from primary sensory neurons suppresses TIMP1 in spinal GABAergic interneurons by elevating EZH2 expression, which enhances H3K27me3 enrichment at the Timp1 promoter. Blocking spinal NK1R effectively prevents the downregulation of TIMP1 and alleviates CCI-induced hyperalgesia. The imbalance between TIMP1 and MMP-9 leads to NLRP3 activation in spinal microglia and increases IL-1β maturation via TLR2/4 pathway. TIMP1 injection eliminates MMP-9-induced NLRP3 activation and blocks hyperalgesia, suggesting that TIMP1 is a critical gatekeeper in preventing neuroinflammation during neuropathic pain development.
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Affiliation(s)
- Li Wan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Haiyue Guo
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Fan Hu
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yinbing Pan
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Shuo Yang
- Department of Immunology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chun-Yi Jiang
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Wentao Liu
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Xuefeng Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China.
| | - Xudong Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China.
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9
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Zhang Y, Wang T, Wang Z, Shi X, Jin J. Functions and Therapeutic Potentials of Long Noncoding RNA in Skeletal Muscle Atrophy and Dystrophy. J Cachexia Sarcopenia Muscle 2025; 16:e13747. [PMID: 40034097 PMCID: PMC11876862 DOI: 10.1002/jcsm.13747] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 12/23/2024] [Accepted: 02/04/2025] [Indexed: 03/05/2025] Open
Abstract
Skeletal muscle is the most abundant tissue in the human body and is responsible for movement, metabolism, energy production and longevity. Muscle atrophy is a frequent complication of several diseases and occurs when protein degradation exceeds protein synthesis. Genetics, ageing, nerve injury, weightlessness, cancer, chronic diseases, the accumulation of metabolic byproducts and other stimuli can lead to muscle atrophy. Muscular dystrophy is a neuromuscular disorder, part of which is caused by the deficiency of dystrophin protein and is mostly related to genetics. Muscle atrophy and muscular dystrophy are accompanied by dynamic changes in transcriptomic, translational and epigenetic regulation. Multiple signalling pathways, such as the transforming growth factor-β (TGF-β) signalling pathway, the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/mechanistic target of rapamycin (mTOR) pathway, inflammatory signalling pathways, neuromechanical signalling pathways, endoplasmic reticulum stress and glucocorticoids signalling pathways, regulate muscle atrophy. A large number of long noncoding RNAs (lncRNAs) have been found to be abnormally expressed in atrophic muscles and dystrophic muscles and regulate the balance of muscle protein synthesis and degradation or dystrophin protein expression. These lncRNAs may serve as potential targets for treating muscle atrophy and muscular dystrophy. In this review, we summarized the known lncRNAs related to muscular dystrophy and muscle atrophy induced by denervation, ageing, weightlessness, cachexia and abnormal myogenesis, along with their molecular mechanisms. Finally, we explored the potential of using these lncRNAs as therapeutic targets for muscle atrophy and muscular dystrophy, including the methods of discovery and clinical application prospects for functional lncRNAs.
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Affiliation(s)
- Yidi Zhang
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Teng Wang
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Ziang Wang
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Xin'e Shi
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Jianjun Jin
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
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10
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Wu Y, Cheng S, Zhang T, Wang L, Li T, Zheng Y, Yang G, Wu X, Luo C, Chen T, Ou L. A novel lncRNA FLJ promotes castration resistance in prostate cancer through AR mediated autophagy. J Transl Med 2025; 23:255. [PMID: 40033417 PMCID: PMC11874752 DOI: 10.1186/s12967-025-06294-9] [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: 11/05/2024] [Accepted: 02/23/2025] [Indexed: 03/05/2025] Open
Abstract
BACKGROUND Progression to castration resistance is the leading cause of death in prostate cancer patients. Long non-coding RNAs (lncRNAs) have recently become a focal point in the regulation of cancer development. However, few lncRNAs associated with castration-resistant prostate cancer (CRPC) have been reported. METHODS Firstly, we explore the CRPC associated lncRNAs by RNA sequencing and validated using quantitative polymerase chain reaction (qRT-PCR) and RNA fluorescence in situ hybridization (RNA-FISH). The clinical significance of FLJ was evaluated in a collected cancer cohort. Functional loss assays were performed to assess the effects of FLJ on CRPC cells both in vitro and in vivo. The regulatory mechanism of FLJ was investigated using immunohistochemistry (IHC), qRT-PCR, dual-luciferase reporter assays, and chromatin immunoprecipitation (ChIP) assays. RESULTS FLJ is highly expressed in CRPC and is associated with higher stages and Gleason scores in prostate cancer. FLJ is strongly positively correlated with androgen receptor (AR), which acts as a transcription factor and directly binds to the FLJ promoter region to enhance its transcription. Knockdown of FLJ inhibits CRPC cell proliferation and increases sensitivity to castration and enzalutamide (ENZA) in vitro. Mechanistically, FLJ promotes castration resistance in prostate cancer cells by inhibiting AR nuclear import and cytoplasmic protein degradation, thereby activating the androgen-independent AR signaling pathway. Importantly, in vivo experiments showed that FLJ knockdown inhibited tumor growth and enhanced the therapeutic effect of ENZA. CONCLUSIONS This study identifies a novel regulatory mechanism by which lncRNA FLJ promotes CRPC progression. Sustained AR activation in CRPC acts as a transcription factor to upregulate FLJ expression. FLJ circumvents the traditional androgen-dependent survival mechanism by inhibiting AR nuclear entry and cytoplasmic protein degradation, thereby activating the AR signaling pathway. Targeting the FLJ-AR signaling axis may represent a novel therapeutic strategy for patients with castration-resistant prostate cancer.
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Affiliation(s)
- Yingying Wu
- Department of Clinical Laboratory, Chongqing University Fuling Hospital, Chongqing, China
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, No.1, Yi-Xue-Yuan Road, Yu-Zhong District, Chongqing, 400016, China
| | - Shaojie Cheng
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Ting Zhang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, No.1, Yi-Xue-Yuan Road, Yu-Zhong District, Chongqing, 400016, China
| | - Leilei Wang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, No.1, Yi-Xue-Yuan Road, Yu-Zhong District, Chongqing, 400016, China
| | - Ting Li
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, No.1, Yi-Xue-Yuan Road, Yu-Zhong District, Chongqing, 400016, China
| | - Yongbo Zheng
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guo Yang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaohou Wu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chunli Luo
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, No.1, Yi-Xue-Yuan Road, Yu-Zhong District, Chongqing, 400016, China
| | - Tingmei Chen
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, No.1, Yi-Xue-Yuan Road, Yu-Zhong District, Chongqing, 400016, China
| | - Liping Ou
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, No.1, Yi-Xue-Yuan Road, Yu-Zhong District, Chongqing, 400016, China.
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11
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An J, Wang H, Wei M, Yu X, Liao Y, Tan X, Hu C, Li S, Luo Y, Gui Y, Lin K, Wang Y, Huang L, Wang D. Identification of chemical inhibitors targeting long noncoding RNA through gene signature-based high throughput screening. Int J Biol Macromol 2025; 292:139119. [PMID: 39722392 DOI: 10.1016/j.ijbiomac.2024.139119] [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: 10/30/2024] [Revised: 12/18/2024] [Accepted: 12/21/2024] [Indexed: 12/28/2024]
Abstract
Scalable methods for functionally high-throughput screening of RNA-targeting small molecules are currently limited. Here, an RNA knockdown gene signature and high-throughput sequencing-based high-throughput screening (HTS2) were integrated to identify RNA-targeting compounds. We first generated a gene signature characterizing the knockdown of the long non-coding RNA LINC00973. Then, screening of 8199 compounds by HTS2 assay identified that treatments of Hesperadin and GSK1070916 significantly mimic the expression pattern of the LINC00973 knockdown gene signature. Functionally, cell phenotype changes after treatments of these two compounds also mimic the losing function of LINC00973 in multiple types of cancer cells. Mechanistically, the inhibitory action of these two compounds on LINC00973 primarily operates via the AURKB-mediated MAPK signaling pathway, resulting in reduced expression of the transcription factor c-Jun. Consequently, this leads to the suppression of LINC00973 transcription. Moreover, these two compounds significantly inhibit xenograft tumor growth in vivo. Clinically, we further found that breast tumors with high expression of LINC00973 also show relatively high expression of AURKB or JUN, and vice versa. In summary, we established a novel high-throughput screening strategy to identify small molecules capable of targeting RNA, provided two promising compounds targeting LINC00973 and further shed light on the underlying transcriptional upregulation mechanism of LINC00973 within cancer cells.
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Affiliation(s)
- Jun An
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Huili Wang
- School of Medicine, Tsinghua University, Beijing, China
| | - Mingming Wei
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiankuo Yu
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yile Liao
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xue Tan
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chao Hu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shengrong Li
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yan Luo
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yu Gui
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Kequan Lin
- Department of Cardiology of The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yumei Wang
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lijun Huang
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Dong Wang
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
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12
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Ding M, Wang D, Chen H, Kesner B, Grimm NB, Weissbein U, Lappala A, Jiang J, Rivera C, Lou J, Li P, Lee JT. A biophysical basis for the spreading behavior and limited diffusion of Xist. Cell 2025; 188:978-997.e25. [PMID: 39824183 PMCID: PMC11863002 DOI: 10.1016/j.cell.2024.12.004] [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: 07/22/2024] [Revised: 11/04/2024] [Accepted: 12/06/2024] [Indexed: 01/20/2025]
Abstract
Xist RNA initiates X inactivation as it spreads in cis across the chromosome. Here, we reveal a biophysical basis for its cis-limited diffusion. Xist RNA and HNRNPK together drive a liquid-liquid phase separation (LLPS) that encapsulates the chromosome. HNRNPK droplets pull on Xist and internalize the RNA. Once internalized, Xist induces a further phase transition and "softens" the HNRNPK droplet. Xist alters the condensate's deformability, adhesiveness, and wetting properties in vitro. Other Xist-interacting proteins are internalized and entrapped within the droplet, resulting in a concentration of Xist and protein partners within the condensate. We attribute LLPS to HNRNPK's RGG and Xist's repeat B (RepB) motifs. Mutating these motifs causes Xist diffusion, disrupts polycomb recruitment, and precludes the required mixing of chromosomal compartments for Xist's migration. Thus, we hypothesize that phase transitions in HNRNPK condensates allow Xist to locally concentrate silencing factors and to spread through internal channels of the HNRNPK-encapsulated chromosome.
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Affiliation(s)
- Mingrui Ding
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Danni Wang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Hui Chen
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Barry Kesner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Niklas-Benedikt Grimm
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Uri Weissbein
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Anna Lappala
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jiying Jiang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Carlos Rivera
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jizhong Lou
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Pilong Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
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13
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Chen Y, Ye X, Hu M, Hu Y, Ding J. Long non-coding RNAs in pancreatic cancer. Clin Chim Acta 2025; 566:120040. [PMID: 39536894 DOI: 10.1016/j.cca.2024.120040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 11/06/2024] [Accepted: 11/10/2024] [Indexed: 11/16/2024]
Abstract
This article reviews the recent advances in pathogenesis, diagnosis and treatment of pancreatic cancer, as well as the relationship between long non-coding RNA (lncRNA) in disease progression. Unfortunately, pancreatic cancer has no early symptoms and quickly invades surrounding tissue and organs, making it one of the deadliest. Accordingly, we urgently need to identify high-risk individuals with precancerous lesions through screening methods to identify early disease, provide better prevention strategies and improve overall survival. LncRNAs have a variety of biological functions in both physiologic and pathophysiologic states including tumor growth, differentiation and proliferation. Herein we review the biological functions, expression patterns, clinical significance and targeted therapy potential of lncRNAs to provide new approaches for diagnosis and treatment in pancreatic cancer.
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Affiliation(s)
- Yuan Chen
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, Zhejiang, China
| | - Xiaohua Ye
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, Zhejiang, China
| | - Minli Hu
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, Zhejiang, China
| | - Yibing Hu
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, Zhejiang, China
| | - Jin Ding
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, Zhejiang, China.
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14
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Sidharthan V, Sibley C, Dunne-Dombrink K, Yang M, Zahurancik W, Balaratnam S, Wilburn D, Schneekloth J, Gopalan V. Use of a small molecule microarray screen to identify inhibitors of the catalytic RNA subunit of Methanobrevibacter smithii RNase P. Nucleic Acids Res 2025; 53:gkae1190. [PMID: 39676671 PMCID: PMC11724310 DOI: 10.1093/nar/gkae1190] [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: 08/28/2024] [Revised: 11/13/2024] [Accepted: 11/18/2024] [Indexed: 12/17/2024] Open
Abstract
Despite interest in developing therapeutics that leverage binding pockets in structured RNAs-whose dysregulation leads to diseases-such drug discovery efforts are limited. Here, we have used a small molecule microarray (SMM) screen to find inhibitors of a large ribozyme: the Methanobrevibacter smithii RNase P RNA (Msm RPR, ∼300 nt). The ribonucleoprotein form of RNase P, which catalyzes the 5'-maturation of precursor tRNAs, is a suitable drug target as it is essential, structurally diverse across life domains, and present in low copy. From an SMM screen of 7,300 compounds followed by selectivity profiling, we identified 48 hits that bound specifically to the Msm RPR-the catalytic subunit in Msm (archaeal) RNase P. When we tested these hits in precursor-tRNA cleavage assays, we discovered that the drug-like M1, a diaryl-piperidine, inhibits Msm RPR (KI, 17 ± 1 μM) but not a structurally related archaeal RPR, and binds to Msm RPR with a KD(app) of 8 ± 3 μM. Structure-activity relationship analyses performed with synthesized analogs pinpointed groups in M1 that are important for its ability to inhibit Msm RPR. Overall, the SMM method offers prospects for advancing RNA druggability by identifying new privileged scaffolds/chemotypes that bind large, structured RNAs.
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Affiliation(s)
- Vaishnavi Sidharthan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Christopher D Sibley
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Kara Dunne-Dombrink
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Mo Yang
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Walter J Zahurancik
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Sumirtha Balaratnam
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Damien B Wilburn
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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15
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Shi H, Wang Z, Zhou L, Xu Z, Xie L, Kong R, Chang S. Status and Prospects of Research on Deep Learning-based De Novo Generation of Drug Molecules. Curr Comput Aided Drug Des 2025; 21:257-269. [PMID: 38321907 DOI: 10.2174/0115734099287389240126072433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
Abstract
Traditional molecular de novo generation methods, such as evolutionary algorithms, generate new molecules mainly by linking existing atomic building blocks. The challenging issues in these methods include difficulty in synthesis, failure to achieve desired properties, and structural optimization requirements. Advances in deep learning offer new ideas for rational and robust de novo drug design. Deep learning, a branch of machine learning, is more efficient than traditional methods for processing problems, such as speech, image, and translation. This study provides a comprehensive overview of the current state of research in de novo drug design based on deep learning and identifies key areas for further development. Deep learning-based de novo drug design is pivotal in four key dimensions. Molecular databases form the basis for model training, while effective molecular representations impact model performance. Common DL models (GANs, RNNs, VAEs, CNNs, DMs) generate drug molecules with desired properties. The evaluation metrics guide research directions by determining the quality and applicability of generated molecules. This abstract highlights the foundational aspects of DL-based de novo drug design, offering a concise overview of its multifaceted contributions. Consequently, deep learning in de novo molecule generation has attracted more attention from academics and industry. As a result, many deep learning-based de novo molecule generation types have been actively proposed.
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Affiliation(s)
- Huanghao Shi
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Zhichao Wang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Litao Zhou
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Zhiwang Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Liangxu Xie
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Ren Kong
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
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16
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Aguilar R, Mardones C, Moreno AA, Cepeda-Plaza M. A guide to RNA structure analysis and RNA-targeting methods. FEBS J 2024. [PMID: 39718192 DOI: 10.1111/febs.17368] [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: 08/10/2024] [Revised: 10/22/2024] [Accepted: 12/10/2024] [Indexed: 12/25/2024]
Abstract
RNAs are increasingly recognized as promising therapeutic targets, susceptible to modulation by strategies that include targeting with small molecules, antisense oligonucleotides, deoxyribozymes (DNAzymes), or CRISPR/Cas13. However, while drug development for proteins follows well-established paths for rational design based on the accurate knowledge of their three-dimensional structure, RNA-targeting strategies are challenging since comprehensive RNA structures are yet scarce and challenging to acquire. Numerous methods have been developed to elucidate the secondary and three-dimensional structure of RNAs, including X-ray crystallography, cryo-electron microscopy, nuclear magnetic resonance, SHAPE, DMS, and bioinformatic methods, yet they have often revealed flexible transcripts and co-existing populations rather than single-defined structures. Thus, researchers aiming to target RNAs face a critical decision: whether to acquire the detailed structure of transcripts in advance or to adopt phenotypic screens or sequence-based approaches that are independent of the structure. Still, even in strategies that seem to rely only on the nucleotide sequence (like the design of antisense oligonucleotides), researchers may need information about the accessibility of the compounds to the folded RNA molecule. In this concise guide, we provide an overview for researchers interested in targeting RNAs: We start by revisiting current methodologies for defining secondary or three-dimensional RNA structure and then we explore RNA-targeting strategies that may or may not require an in-depth knowledge of RNA structure. We envision that complementary approaches may expedite the development of RNA-targeting molecules to combat disease.
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Affiliation(s)
- Rodrigo Aguilar
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Constanza Mardones
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Adrian A Moreno
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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17
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Kiger NM, Schroeder SJ. SVALKA: A Long Noncoding Cis-Natural Antisense RNA That Plays a Role in the Regulation of the Cold Response of Arabidopsis thaliana. Noncoding RNA 2024; 10:59. [PMID: 39728604 DOI: 10.3390/ncrna10060059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Revised: 11/26/2024] [Accepted: 11/26/2024] [Indexed: 12/28/2024] Open
Abstract
RNA plays important roles in the regulation of gene expression in response to environmental stimuli. SVALKA, a long noncoding cis-natural antisense RNA, is a key component of regulating the response to cold temperature in Arabidopsis thaliana. There are three mechanisms through which SVALKA fine tunes the transcriptional response to cold temperatures. SVALKA regulates the expression of the CBF1 (C-Repeat Dehydration Binding Factor 1) transcription factor through a collisional transcription mechanism and a dsRNA and DICER mediated mechanism. SVALKA also interacts with Polycomb Repressor Complex 2 to regulate the histone methylation of CBF3. Both CBF1 and CBF3 are key components of the COLD REGULATED (COR) regulon that direct the plant's response to cold temperature over time, as well as plant drought adaptation, pathogen responses, and growth regulation. The different isoforms of SVALKA and its potential to form dynamic RNA conformations are important features in regulating a complex gene network in concert with several other noncoding RNA. This review will summarize the three mechanisms through which SVALKA participates in gene regulation, describe the ways that dynamic RNA structures support the function of regulatory noncoding RNA, and explore the potential for improving agricultural genetic engineering with a better understanding of the roles of noncoding RNA.
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Affiliation(s)
- Nicholas M Kiger
- School of Biological Sciences, University of Oklahoma, Norman, OK 73019, USA
| | - Susan J Schroeder
- School of Biological Sciences, University of Oklahoma, Norman, OK 73019, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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18
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Chen LL, Kim VN. Small and long non-coding RNAs: Past, present, and future. Cell 2024; 187:6451-6485. [PMID: 39547208 DOI: 10.1016/j.cell.2024.10.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Revised: 10/13/2024] [Accepted: 10/15/2024] [Indexed: 11/17/2024]
Abstract
Since the introduction of the central dogma of molecular biology in 1958, various RNA species have been discovered. Messenger RNAs transmit genetic instructions from DNA to make proteins, a process facilitated by housekeeping non-coding RNAs (ncRNAs) such as small nuclear RNAs (snRNAs), ribosomal RNAs (rRNAs), and transfer RNAs (tRNAs). Over the past four decades, a wide array of regulatory ncRNAs have emerged as crucial players in gene regulation. In celebration of Cell's 50th anniversary, this Review explores our current understanding of the most extensively studied regulatory ncRNAs-small RNAs and long non-coding RNAs (lncRNAs)-which have profoundly shaped the field of RNA biology and beyond. While small RNA pathways have been well documented with clearly defined mechanisms, lncRNAs exhibit a greater diversity of mechanisms, many of which remain unknown. This Review covers pivotal events in their discovery, biogenesis pathways, evolutionary traits, action mechanisms, functions, and crosstalks among ncRNAs. We also highlight their roles in pathophysiological contexts and propose future research directions to decipher the unknowns of lncRNAs by leveraging lessons from small RNAs.
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Affiliation(s)
- Ling-Ling Chen
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China; School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; New Cornerstone Science Laboratory, Shenzhen, China.
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
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19
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Tong Y, Childs-Disney JL, Disney MD. Targeting RNA with small molecules, from RNA structures to precision medicines: IUPHAR review: 40. Br J Pharmacol 2024; 181:4152-4173. [PMID: 39224931 DOI: 10.1111/bph.17308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/10/2024] [Accepted: 07/09/2024] [Indexed: 09/04/2024] Open
Abstract
RNA plays important roles in regulating both health and disease biology in all kingdoms of life. Notably, RNA can form intricate three-dimensional structures, and their biological functions are dependent on these structures. Targeting the structured regions of RNA with small molecules has gained increasing attention over the past decade, because it provides both chemical probes to study fundamental biology processes and lead medicines for diseases with unmet medical needs. Recent advances in RNA structure prediction and determination and RNA biology have accelerated the rational design and development of RNA-targeted small molecules to modulate disease pathology. However, challenges remain in advancing RNA-targeted small molecules towards clinical applications. This review summarizes strategies to study RNA structures, to identify small molecules recognizing these structures, and to augment the functionality of RNA-binding small molecules. We focus on recent advances in developing RNA-targeted small molecules as potential therapeutics in a variety of diseases, encompassing different modes of actions and targeting strategies. Furthermore, we present the current gaps between early-stage discovery of RNA-binding small molecules and their clinical applications, as well as a roadmap to overcome these challenges in the near future.
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Affiliation(s)
- Yuquan Tong
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - Jessica L Childs-Disney
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
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20
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Yang Y, Cheng H. Emerging Roles of ncRNAs in Type 2 Diabetes Mellitus: From Mechanisms to Drug Discovery. Biomolecules 2024; 14:1364. [PMID: 39595541 PMCID: PMC11592034 DOI: 10.3390/biom14111364] [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: 09/30/2024] [Revised: 10/23/2024] [Accepted: 10/26/2024] [Indexed: 11/28/2024] Open
Abstract
Type 2 diabetes mellitus (T2DM), a high-incidence chronic metabolic disorder, has emerged as a global health issue, where most patients need lifelong medication. Gaining insights into molecular mechanisms involved in T2DM development is expected to provide novel strategies for clinical prevention and treatment. Growing evidence validates that non-coding RNAs (ncRNAs) including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) function as crucial regulators in multiple biological processes of T2DM, inspiring various potential targets and drug candidates. In this review, we summarize the current understanding of ncRNA roles in T2DM and discuss the potential use of ncRNAs as targets and active molecules for drug discovery.
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Affiliation(s)
- Yue Yang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Hao Cheng
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
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21
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Wang J. Genome-Wide Identification of Stable RNA Secondary Structures Across Multiple Organisms Using Chemical Probing Data: Insights into Short Structural Motifs and RNA-Targeting Therapeutics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.08.617329. [PMID: 39416040 PMCID: PMC11482745 DOI: 10.1101/2024.10.08.617329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Small molecules targeting specific RNA binding sites, including stable and transient RNA structures, are emerging as effective pharmacological approaches for modulating gene expression. However, little is understood about how stable RNA secondary structures are shared across organisms, an important factor in controlling drug selectivity. In this study, I provide an analytical pipeline named RNA Secondary Structure Finder (R2S-Finder) to discover short, stable RNA structural motifs for humans, Escherichia coli ( E. coli ), SARS-CoV-2, and Zika virus by leveraging existing in vivo and in vitro genome-wide chemical RNA-probing datasets. I found several common features across organisms. For example, apart from the well-documented tetraloops, AU-rich tetraloops are widely present in different organisms. I also found that the 5' untranslated region (UTR) contains a higher proportion of stable structures than the coding sequences in humans, SARS-CoV-2, and Zika virus. In general, stable structures predicted from in vitro (protein-free) and in vivo datasets are consistent in humans, E. coli , and SARS-CoV-2, indicating that most stable structure formation were driven by RNA folding alone, while a larger variation was found between in vitro and in vivo data with certain RNA types, such as human long intergenic non-coding RNAs (lincRNAs). Finally, I predicted stable three- and four-way RNA junctions that exist both in vivo and in vitro conditions, which can potentially serve as drug targets. All results of stable sequences, stem-loops, internal loops, bulges, and three- and four-way junctions have been collated in the R2S-Finder database ( https://github.com/JingxinWangLab/R2S-Finder ), which is coded in hyperlinked HTML pages and tabulated in CSV files.
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22
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Lee Y, Lee JT. PRC2-RNA interactions: Viewpoint from YongWoo Lee and Jeannie T. Lee. Mol Cell 2024; 84:3586-3592. [PMID: 39366347 DOI: 10.1016/j.molcel.2024.09.006] [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: 09/06/2024] [Revised: 09/06/2024] [Accepted: 09/06/2024] [Indexed: 10/06/2024]
Abstract
Here, we expound on the view that Xist RNA directly controls Polycomb repressive complex 2 (PRC2) recruitment, off-loading to chromatin, catalytic activity, and eviction from chromatin. RNA-PRC2 interactions also control RNA polymerase II transcription pausing. Dynamic RNA folding determines PRC2 activity. Disparate studies and interpretations abound but can be reconciled.
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Affiliation(s)
- YongWoo Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
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23
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Cao X, Zhang Y, Ding Y, Wan Y. Identification of RNA structures and their roles in RNA functions. Nat Rev Mol Cell Biol 2024; 25:784-801. [PMID: 38926530 DOI: 10.1038/s41580-024-00748-6] [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: 05/28/2024] [Indexed: 06/28/2024]
Abstract
The development of high-throughput RNA structure profiling methods in the past decade has greatly facilitated our ability to map and characterize different aspects of RNA structures transcriptome-wide in cell populations, single cells and single molecules. The resulting high-resolution data have provided insights into the static and dynamic nature of RNA structures, revealing their complexity as they perform their respective functions in the cell. In this Review, we discuss recent technical advances in the determination of RNA structures, and the roles of RNA structures in RNA biogenesis and functions, including in transcription, processing, translation, degradation, localization and RNA structure-dependent condensates. We also discuss the current understanding of how RNA structures could guide drug design for treating genetic diseases and battling pathogenic viruses, and highlight existing challenges and future directions in RNA structure research.
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Affiliation(s)
- Xinang Cao
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Yueying Zhang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK.
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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24
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Xiao H, Zhang Y, Yang X, Yu S, Chen Z, Lu A, Zhang Z, Zhang G, Zhang BT. SMTRI: A deep learning-based web service for predicting small molecules that target miRNA-mRNA interactions. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102303. [PMID: 39281703 PMCID: PMC11401195 DOI: 10.1016/j.omtn.2024.102303] [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: 09/12/2023] [Accepted: 08/12/2024] [Indexed: 09/18/2024]
Abstract
Mature microRNAs (miRNAs) are short, single-stranded RNAs that bind to target mRNAs and induce translational repression and gene silencing. Many miRNAs discovered in animals have been implicated in diseases and have recently been pursued as therapeutic targets. However, conventional pharmacological screening for candidate small-molecule drugs can be time-consuming and labor-intensive. Therefore, developing a computational program to assist mature miRNA-targeted drug discovery in silico is desirable. Our previous work (https://doi.org/10.1002/advs.201903451) revealed that the unique functional loops formed during Argonaute-mediated miRNA-mRNA interactions have stable structural characteristics and may serve as potential targets for small-molecule drug discovery. Developing drugs specifically targeting disease-related mature miRNAs and their target mRNAs would avoid affecting unrelated ones. Here, we present SMTRI, a convolutional neural network-based approach for efficiently predicting small molecules that target RNA secondary structural motifs formed by interactions between miRNAs and their target mRNAs. Measured on three additional testing sets, SMTRI outperformed state-of-the-art algorithms by 12.9%-30.3% in AUC and 2.0%-18.4% in accuracy. Moreover, four case studies on the published experimentally validated RNA-targeted small molecules also revealed the reliability of SMTRI.
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Affiliation(s)
- Huan Xiao
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yihao Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Xin Yang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Sifan Yu
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ziqi Chen
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Zongkang Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Bao-Ting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
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25
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Devi C, Ranjan P, Raj S, Das P. Computational exploration of protein structure dynamics and RNA structural consequences of PKD1 missense variants: implications in ADPKD pathogenesis. 3 Biotech 2024; 14:211. [PMID: 39188533 PMCID: PMC11344749 DOI: 10.1007/s13205-024-04057-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024] Open
Abstract
We analyzed the impact of nine previously identified missense PKD1 variants from our studies, including c.6928G > A p.G2310R, c.8809G > A p.E2937K, c.2899 T > C p.W967R, c.6284A > G p.D2095G, c.6644G > A p.R2215Q, c.7810G > A p.D2604N, c.11249G > C p.R3750P, c.1001C > T p.T334M, and c.3101A > G p.N1034S on RNA structures and PC1 protein structure dynamics utilizing computational tools. RNA structure analysis was done using short RNA snippets of 41 nucleotides with the variant position at the 21st nucleotide, ensuring 20 bases on both sides. The secondary structures of these RNA snippets were predicted using RNAstructure. Structural changes of the mutants compared to the wild type were analyzed using the MutaRNA webserver. Molecular dynamics (MD) simulation of PC1 wild-type and mutant protein regions were performed using GROMACS 2018 (GROMOS96 54a7 force field). Findings revealed that five variants including c.8809G > A (p.E2937K), c.11249G > C (p.R3750P), c.3101A > G (p.N1034S), c.6928G > A (p.G2310R), c.6644G > A (p.R2215Q) exhibited major alterations in RNA structures and thereby their interactions with other proteins or RNAs affecting protein structure dynamics. While certain variants have minimal impact on RNA conformations, their observed alterations in MD simulations indicate impact on protein structure dynamics highlighting the importance of evaluating the functional consequences of genetic variants by considering both RNA and protein levels. The study also emphasizes that each missense variant exerts a unique impact on RNA stability, and protein structure dynamics, potentially contributing to the heterogeneous clinical manifestations and progression observed in Autosomal Dominant Polycystic Kidney Disease (ADPKD) patients offering a novel perspective in this direction. Thus, the utility of studying the structure dynamics through computational tools can help in prioritizing the variants for their functional implications, understanding the molecular mechanisms underlying variability in ADPKD presentation and developing targeted therapeutic interventions. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04057-9.
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Affiliation(s)
- Chandra Devi
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005 India
| | - Prashant Ranjan
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005 India
| | - Sonam Raj
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Parimal Das
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005 India
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26
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Coan M, Haefliger S, Ounzain S, Johnson R. Targeting and engineering long non-coding RNAs for cancer therapy. Nat Rev Genet 2024; 25:578-595. [PMID: 38424237 DOI: 10.1038/s41576-024-00693-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 03/02/2024]
Abstract
RNA therapeutics (RNATx) aim to treat diseases, including cancer, by targeting or employing RNA molecules for therapeutic purposes. Amongst the most promising targets are long non-coding RNAs (lncRNAs), which regulate oncogenic molecular networks in a cell type-restricted manner. lncRNAs are distinct from protein-coding genes in important ways that increase their therapeutic potential yet also present hurdles to conventional clinical development. Advances in genome editing, oligonucleotide chemistry, multi-omics and RNA engineering are paving the way for efficient and cost-effective lncRNA-focused drug discovery pipelines. In this Review, we present the emerging field of lncRNA therapeutics for oncology, with emphasis on the unique strengths and challenges of lncRNAs within the broader RNATx framework. We outline the necessary steps for lncRNA therapeutics to deliver effective, durable, tolerable and personalized treatments for cancer.
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Affiliation(s)
- Michela Coan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Simon Haefliger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland.
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Dublin, Ireland.
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27
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Yu J, Zhang Y, Xue Y, Pei H, Li B. Emerging roles of long noncoding RNAs in enzymes related intracellular metabolic pathways in cancer biology. Biomed Pharmacother 2024; 176:116831. [PMID: 38824835 DOI: 10.1016/j.biopha.2024.116831] [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: 02/03/2024] [Revised: 05/13/2024] [Accepted: 05/26/2024] [Indexed: 06/04/2024] Open
Abstract
Metabolic reprogramming plays critical roles in the development and progression of tumor by providing cancer cells with a sufficient supply of nutrients and other factors needed for fast-proliferating. Emerging evidence indicates that long noncoding RNAs (lncRNAs) are involved in the initiation of metastasis via regulating the metabolic reprogramming in various cancers. In this paper, we aim to summarize that lncRNAs could participate in intracellular nutrient metabolism including glucose, amino acid, lipid, and nucleotide, regardless of whether lncRNAs have tumor-promoting or tumor-suppressor function. Meanwhile, modulation of lncRNAs in glucose metabolic enzymes in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle (TCA) in cancer is reviewed. We also discuss therapeutic strategies targeted at interfering with enzyme activity to decrease the utilization of glucoses, amino acid, nucleotide acid and lipid in tumor cells. This review focuses on our current understanding of lncRNAs participating in cancer cell metabolic reprogramming, paving the way for further investigation into the combination of such approaches with existing anti-cancer therapies.
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Affiliation(s)
- Jing Yu
- Department of Nutrition and Food Hygiene, School of Public Health, Medical College of Soochow University, Suzhou 215123, China; Department of clinical laboratory Center, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Yue Zhang
- School of Clinical Medicine, Medical College of Soochow University, Suzhou 215123, China
| | - Yaqi Xue
- Department of Clinical Nutrition, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Hailong Pei
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Centre of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.
| | - Bingyan Li
- Department of Nutrition and Food Hygiene, School of Public Health, Medical College of Soochow University, Suzhou 215123, China.
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28
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Song Y, Cui J, Zhu J, Kim B, Kuo ML, Potts PR. RNATACs: Multispecific small molecules targeting RNA by induced proximity. Cell Chem Biol 2024; 31:1101-1117. [PMID: 38876100 DOI: 10.1016/j.chembiol.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/09/2024] [Accepted: 05/22/2024] [Indexed: 06/16/2024]
Abstract
RNA-targeting small molecules (rSMs) have become an attractive modality to tackle traditionally undruggable proteins and expand the druggable space. Among many innovative concepts, RNA-targeting chimeras (RNATACs) represent a new class of multispecific, induced proximity small molecules that act by chemically bringing RNA targets into proximity with an endogenous RNA effector, such as a ribonuclease (RNase). Depending on the RNA effector, RNATACs can alter the stability, localization, translation, or splicing of the target RNA. Although still in its infancy, this new modality has the potential for broad applications in the future to treat diseases with high unmet need. In this review, we discuss potential advantages of RNATACs, recent progress in the field, and challenges to this cutting-edge technology.
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Affiliation(s)
- Yan Song
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA.
| | - Jia Cui
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Jiaqiang Zhu
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Boseon Kim
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Mei-Ling Kuo
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Patrick Ryan Potts
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA.
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29
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Zhang Y, Wang L, Wang F, Chu X, Jiang JH. G-Quadruplex mRNAs Silencing with Inducible Ribonuclease Targeting Chimera for Precision Tumor Therapy. J Am Chem Soc 2024; 146:15815-15824. [PMID: 38832857 DOI: 10.1021/jacs.4c02091] [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: 06/06/2024]
Abstract
Ribonuclease targeting chimera (RIBOTAC) represents an emerging strategy for targeted therapy. However, RIBOTAC that is selectively activated by bio-orthogonal or cell-specific triggers has not been explored. We developed a strategy of inducible RIBOTAC (iRIBOTAC) that enables on-demand degradation of G-quadruplex (G4) RNAs for precision cancer therapy. iRIBOTAC is designed by coupling an RNA G4 binder with a caged ribonuclease recruiter, which can be decaged by a bio-orthogonal reaction, tumor-specific enzyme, or metabolite. A bivalent G4 binder is engineered by conjugating a near-infrared (NIR) fluorescence G4 ligand to a noncompetitive G4 ligand, conferring fluorescence activation on binding G4s with synergistically enhanced affinity. iRIBOTAC is demonstrated to greatly knockdown G4 RNAs upon activation under bio-orthogonal or cell-specific stimulus, with dysregulation of gene expressions involving cell killing, channel regulator activity, and metabolism as revealed by RNA sequencing. This strategy also shows a crucial effect on cell fate with remarkable biochemical hallmarks of apoptosis. Mice model studies demonstrate that iRIBOTAC allows selective imaging and growth suppression of tumors with bio-orthogonal and tumor-specific controls, highlighting G4 RNA targeting and inducible silencing as a valuable RIBOTAC paradigm for cancer therapy.
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Affiliation(s)
- Yuan Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Lingyan Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Fenglin Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
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30
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Gu S, Huang X, Luo S, Liu Y, Khoong Y, Liang H, Tu L, Xu R, Yang E, Zhao Y, Yao M, Zan T. Targeting the nuclear long noncoding transcript LSP1P5 abrogates extracellular matrix deposition by trans-upregulating CEBPA in keloids. Mol Ther 2024; 32:1984-1999. [PMID: 38553852 PMCID: PMC11184311 DOI: 10.1016/j.ymthe.2024.03.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 01/07/2024] [Accepted: 03/26/2024] [Indexed: 06/09/2024] Open
Abstract
Keloids are characterized by fibroblast hyperproliferation and excessive accumulation of extracellular matrix (ECM) and are a major global health care burden among cutaneous diseases. However, the function of long noncoding RNA (lncRNA)-mediated ECM remodeling during the pathogenesis of keloids is still unclear. Herein, we identified a long noncoding transcript, namely, lymphocyte-specific protein 1 pseudogene 5 (LSP1P5), that modulates ECM component deposition in keloids. First, high-throughput transcriptome analysis showed that LSP1P5 was selectively upregulated in keloids and correlated with more severe disease in a clinical keloid cohort. Therapeutically, the attenuation of LSP1P5 significantly decreased the expression of ECM markers (COL1, COL3, and FN1) both in vitro and in vivo. Intriguingly, an antifibrotic gene, CCAAT enhancer binding protein alpha (CEBPA), is a functional downstream candidate of LSP1P5. Mechanistically, LSP1P5 represses CEBPA expression by hijacking Suppressor of Zeste 12 to the promoter of CEBPA, thereby enhancing the polycomb repressive complex 2-mediated H3K27me3 and changing the chromosomal opening status of CEBPA. Taken together, these findings indicate that targeting LSP1P5 abrogates fibrosis in keloids through epigenetic regulation of CEBPA, revealing a novel antifibrotic therapeutic strategy that bridges our current understanding of lncRNA regulation, histone modification and ECM remodeling in keloids.
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Affiliation(s)
- Shuchen Gu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, P.R. China
| | - Xin Huang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, P.R. China
| | - Shenying Luo
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, P.R. China
| | - Yunhan Liu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, P.R. China
| | - Yimin Khoong
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, P.R. China
| | - Hsin Liang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, P.R. China
| | - Liying Tu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, P.R. China
| | - Ruoqing Xu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, P.R. China
| | - En Yang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, P.R. China
| | - Yixuan Zhao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, P.R. China.
| | - Min Yao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, P.R. China.
| | - Tao Zan
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, P.R. China.
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31
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Wu L, Zhao Z, Shin YJ, Yin Y, Raju A, Vaiyapuri TS, Idzham K, Son M, Lee Y, Sa JK, Chua JYH, Unal B, Zhai Y, Fan W, Huang L, Hu H, Gunaratne J, Nam DH, Jiang T, Tergaonkar V. Tumour microenvironment programming by an RNA-RNA-binding protein complex creates a druggable vulnerability in IDH-wild-type glioblastoma. Nat Cell Biol 2024; 26:1003-1018. [PMID: 38858501 PMCID: PMC11178504 DOI: 10.1038/s41556-024-01428-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024]
Abstract
Patients with IDH-wild-type glioblastomas have a poor five-year survival rate along with limited treatment efficacy due to immune cell (glioma-associated microglia and macrophages) infiltration promoting tumour growth and resistance. To enhance therapeutic options, our study investigated the unique RNA-RNA-binding protein complex LOC-DHX15. This complex plays a crucial role in driving immune cell infiltration and tumour growth by establishing a feedback loop between cancer and immune cells, intensifying cancer aggressiveness. Targeting this complex with blood-brain barrier-permeable small molecules improved treatment efficacy, disrupting cell communication and impeding cancer cell survival and stem-like properties. Focusing on RNA-RNA-binding protein interactions emerges as a promising approach not only for glioblastomas without the IDH mutation but also for potential applications beyond cancer, offering new avenues for developing therapies that address intricate cellular relationships in the body.
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Affiliation(s)
- Lele Wu
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Zheng Zhao
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yong Jae Shin
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Yiyun Yin
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Anandhkumar Raju
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Thamil Selvan Vaiyapuri
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Khaireen Idzham
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Miseol Son
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Yeri Lee
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Jason K Sa
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Joelle Yi Heng Chua
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Bilal Unal
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - You Zhai
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Wenhua Fan
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lijie Huang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Huimin Hu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Jayantha Gunaratne
- Laboratory of Translational Biomedical Proteomics, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Do-Hyun Nam
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
- Department of Neurosurgery, Samsung Medical Center, Seoul, Republic of Korea
| | - Tao Jiang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Vinay Tergaonkar
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore.
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Republic of Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Republic of Singapore.
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32
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Farzaneh M, Anbiyaee O, Azizidoost S, Nasrolahi A, Ghaedrahmati F, Kempisty B, Mozdziak P, Khoshnam SE, Najafi S. The Mechanisms of Long Non-coding RNA-XIST in Ischemic Stroke: Insights into Functional Roles and Therapeutic Potential. Mol Neurobiol 2024; 61:2745-2753. [PMID: 37932544 DOI: 10.1007/s12035-023-03740-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023]
Abstract
Ischemic stroke, which occurs due to the occlusion of cerebral arteries, is a common type of stroke. Recent research has highlighted the important role of long non-coding RNAs (lncRNAs) in the development of cerebrovascular diseases, specifically ischemic stroke. Understanding the functional roles of lncRNAs in ischemic stroke is crucial, given their potential contribution to the disease pathology. One noteworthy lncRNA is X-inactive specific transcript (XIST), which exhibits downregulation during the early stages of ischemic stroke and subsequent upregulation in later stages. XIST exert its influence on the development of ischemic stroke through interactions with multiple miRNAs and transcription factors. These interactions play a significant role in the pathogenesis of the condition. In this review, we have provided a comprehensive summary of the functional roles of XIST in ischemic stroke. By investigating the involvement of XIST in the disease process, we aim to enhance our understanding of the mechanisms underlying ischemic stroke and potentially identify novel therapeutic targets.
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Affiliation(s)
- Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Omid Anbiyaee
- Cardiovascular Research Center, Namazi Hospital, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shirin Azizidoost
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ava Nasrolahi
- Infectious Ophthalmologic Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Farhoodeh Ghaedrahmati
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bartosz Kempisty
- Department of Human Morphology and Embryology, Division of Anatomy, Wroclaw Medical University, Wrocław, Poland
- Institute of Veterinary Medicine, Department of Veterinary Surgery, Nicolaus Copernicus University, Torun, Poland
- North Carolina State University College of Agriculture and Life Sciences, Raleigh, NC, 27695, USA
| | - Paul Mozdziak
- North Carolina State University College of Agriculture and Life Sciences, Raleigh, NC, 27695, USA
| | - Seyed Esmaeil Khoshnam
- Persian Gulf Physiology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Ferrer J, Dimitrova N. Transcription regulation by long non-coding RNAs: mechanisms and disease relevance. Nat Rev Mol Cell Biol 2024; 25:396-415. [PMID: 38242953 PMCID: PMC11045326 DOI: 10.1038/s41580-023-00694-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2023] [Indexed: 01/21/2024]
Abstract
Long non-coding RNAs (lncRNAs) outnumber protein-coding transcripts, but their functions remain largely unknown. In this Review, we discuss the emerging roles of lncRNAs in the control of gene transcription. Some of the best characterized lncRNAs have essential transcription cis-regulatory functions that cannot be easily accomplished by DNA-interacting transcription factors, such as XIST, which controls X-chromosome inactivation, or imprinted lncRNAs that direct allele-specific repression. A growing number of lncRNA transcription units, including CHASERR, PVT1 and HASTER (also known as HNF1A-AS1) act as transcription-stabilizing elements that fine-tune the activity of dosage-sensitive genes that encode transcription factors. Genetic experiments have shown that defects in such transcription stabilizers often cause severe phenotypes. Other lncRNAs, such as lincRNA-p21 (also known as Trp53cor1) and Maenli (Gm29348) contribute to local activation of gene transcription, whereas distinct lncRNAs influence gene transcription in trans. We discuss findings of lncRNAs that elicit a function through either activation of their transcription, transcript elongation and processing or the lncRNA molecule itself. We also discuss emerging evidence of lncRNA involvement in human diseases, and their potential as therapeutic targets.
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Affiliation(s)
- Jorge Ferrer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Nadya Dimitrova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
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Liu Y, Wang Y, Liu B, Liu W, Ma Y, Cao Y, Yan S, Zhang P, Zhou L, Zhan Q, Wu N. Targeting lncRNA16 by GalNAc-siRNA conjugates facilitates chemotherapeutic sensibilization via the HBB/NDUFAF5/ROS pathway. SCIENCE CHINA. LIFE SCIENCES 2024; 67:663-679. [PMID: 38155279 DOI: 10.1007/s11427-023-2434-8] [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: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 12/30/2023]
Abstract
Chemoresistance is a significant barrier to effective cancer treatment. Potential mechanisms for chemoresistance include reactive oxygen species (ROS) accumulation and expression of chemoresistance-promoting genes. Here, we report a novel function of lncRNA16 in the inhibition of ROS generation and the progression of chemoresistance. By analyzing the serum levels of lncRNA16 in a cohort of 35 patients with non-small cell lung cancer (NSCLC) and paired serum samples pre- and post-treatment from 10 NSCLC patients receiving neoadjuvant platinum-based chemotherapy, performing immunohistochemistry (IHC) assays on 188 NSCLC tumor samples, using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) assays, as well as RNA immunoprecipitation (RIP) and RNA pull-down analyses, we discovered that patients with increased serum levels of lncRNA16 exhibited a poor response to platinum-based chemotherapy. The expression of hemoglobin subunit beta (HBB) and NDUFAF5 significantly increases with the development of chemoresistance. LncRNA16 binds to HBB and promotes HBB accumulation by inhibiting autophagy. LncRNA16 can also inhibit ROS generation via the HBB/NDUFAF5 axis and function as a scaffold to facilitate the colocalization of HBB and NDUFAF5 in the mitochondria. Importantly, preclinical studies in mouse models of chemo-resistant NSCLC have suggested that lncRNA16 targeting by trivalent N-acetylgalactosamine (GalNAc)-conjugated siRNA restores chemosensitivity and results in tumor growth inhibition with no detectable toxicity in vivo. Overall, lncRNA16 is a promising therapeutic target for overcoming chemoresistance, and the combination of first-line platinum-based chemotherapy with lncRNA16 intervention can substantially enhance anti-tumor efficacy.
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Affiliation(s)
- Yanfang Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Bing Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Wenzhong Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yuanyuan Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yiren Cao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Shi Yan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Panpan Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Oncology II, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Lixin Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Qimin Zhan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
- Peking University International Cancer Institute, Beijing, 100191, China.
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
| | - Nan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
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Tian R, Ghosh S. Mechanisms and functions of lncRNAs linked to autoimmune disease risk alleles. Adv Immunol 2024; 161:1-15. [PMID: 38763698 DOI: 10.1016/bs.ai.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Recent advances in human genomics technologies have helped uncover genetic risk alleles for many complex autoimmune diseases. Intriguingly, over 90% of genome-wide association study (GWAS) risk alleles reside within the non-coding regions of the genome. An emerging new frontier of functional and mechanistic studies have shed light on the functional relevance of risk alleles that lie within long noncoding RNAs (lncRNAs). Here, we review the mechanisms and functional implications of five evolutionarily conserved lncRNAs that display risk allele association with highly prevalent autoimmune diseases.
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Affiliation(s)
- Ruxiao Tian
- Department of Microbiology & Immunology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, United States
| | - Sankar Ghosh
- Department of Microbiology & Immunology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, United States.
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Wang M, Yan M, Tan L, Zhao X, Liu G, Zhang Z, Zhang J, Gao H, Qin W. Non-coding RNAs: targets for Chinese herbal medicine in treating myocardial fibrosis. Front Pharmacol 2024; 15:1337623. [PMID: 38476331 PMCID: PMC10928947 DOI: 10.3389/fphar.2024.1337623] [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: 11/13/2023] [Accepted: 02/07/2024] [Indexed: 03/14/2024] Open
Abstract
Cardiovascular diseases have become the leading cause of death in urban and rural areas. Myocardial fibrosis is a common pathological manifestation at the adaptive and repair stage of cardiovascular diseases, easily predisposing to cardiac death. Non-coding RNAs (ncRNAs), RNA molecules with no coding potential, can regulate gene expression in the occurrence and development of myocardial fibrosis. Recent studies have suggested that Chinese herbal medicine can relieve myocardial fibrosis through targeting various ncRNAs, mainly including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Thus, ncRNAs are novel drug targets for Chinese herbal medicine. Herein, we summarized the current understanding of ncRNAs in the pathogenesis of myocardial fibrosis, and highlighted the contribution of ncRNAs to the therapeutic effect of Chinese herbal medicine on myocardial fibrosis. Further, we discussed the future directions regarding the potential applications of ncRNA-based drug screening platform to screen drugs for myocardial fibrosis.
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Affiliation(s)
- Minghui Wang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
| | - Maocai Yan
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
| | - Liqiang Tan
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Xiaona Zhao
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
- School of Pharmacy, Weifang Medical University, Weifang, Shandong, China
| | - Guoqing Liu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
| | - Zejin Zhang
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Jing Zhang
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
| | - Honggang Gao
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
| | - Wei Qin
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
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Zhang L, Zhang H, Xie Q, Feng H, Li H, Li Z, Yang K, Ding J, Gao G. LncRNA-mediated cartilage homeostasis in osteoarthritis: a narrative review. Front Med (Lausanne) 2024; 11:1326843. [PMID: 38449881 PMCID: PMC10915071 DOI: 10.3389/fmed.2024.1326843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/08/2024] [Indexed: 03/08/2024] Open
Abstract
Osteoarthritis (OA) is a degenerative disease of cartilage that affects the quality of life and has increased in morbidity and mortality in recent years. Cartilage homeostasis and dysregulation are thought to be important mechanisms involved in the development of OA. Many studies suggest that lncRNAs are involved in cartilage homeostasis in OA and that lncRNAs can be used to diagnose or treat OA. Among the existing therapeutic regimens, lncRNAs are involved in drug-and nondrug-mediated therapeutic mechanisms and are expected to improve the mechanism of adverse effects or drug resistance. Moreover, targeted lncRNA therapy may also prevent or treat OA. The purpose of this review is to summarize the links between lncRNAs and cartilage homeostasis in OA. In addition, we review the potential applications of lncRNAs at multiple levels of adjuvant and targeted therapies. This review highlights that targeting lncRNAs may be a novel therapeutic strategy for improving and modulating cartilage homeostasis in OA patients.
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Affiliation(s)
- Li Zhang
- Department of Orthopedics, the Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- The First Clinical Medicine School, Nanchang University, Nanchang, China
| | - Hejin Zhang
- The Second Clinical Medicine School, Nanchang University, Nanchang, China
| | - Qian Xie
- The Third Clinical Medicine School, Nanchang University, Nanchang, China
| | - Haiqi Feng
- Queen Mary School, Nanchang University, Nanchang, China
| | - Haoying Li
- Queen Mary School, Nanchang University, Nanchang, China
| | - Zelin Li
- The First Clinical Medicine School, Nanchang University, Nanchang, China
| | - Kangping Yang
- Department of Orthopedics, the Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- The Second Clinical Medicine School, Nanchang University, Nanchang, China
| | - Jiatong Ding
- Department of Orthopedics, the Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- The Second Clinical Medicine School, Nanchang University, Nanchang, China
| | - Guicheng Gao
- Department of Orthopedics, the Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
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Button AC, Hall SD, Ashley EL, McHugh CA. Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA. RNA (NEW YORK, N.Y.) 2024; 30:240-255. [PMID: 38164599 PMCID: PMC10870365 DOI: 10.1261/rna.079713.123] [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: 08/24/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024]
Abstract
XIST noncoding RNA promotes the initiation of X chromosome silencing by recruiting the protein SPEN to one X chromosome in female mammals. The SPEN protein is also called SHARP (SMRT and HDAC-associated repressor protein) and MINT (Msx-2 interacting nuclear target) in humans. SPEN recruits N-CoR2 and HDAC3 to initiate histone deacetylation on the X chromosome, leading to the formation of repressive chromatin marks and silencing gene expression. We dissected the contributions of different RNA and protein regions to the formation of a human XIST-SPEN complex in vitro and identified novel sequence and structure determinants that may contribute to X chromosome silencing initiation. Binding of SPEN to XIST RNA requires RRM 4 of the protein, in contrast to the requirement of RRM 3 and RRM 4 for specific binding to SRA RNA. Measurements of SPEN binding to full-length, dimeric, trimeric, or other truncated versions of the A-repeat region revealed that high-affinity binding of XIST to SPEN in vitro requires a minimum of four A-repeat segments. SPEN binding to XIST A-repeat RNA changes the accessibility of the RNA at specific nucleotide sequences, as indicated by changes in RNA reactivity through chemical structure probing. Based on computational modeling, we found that inter-repeat duplexes formed by multiple A-repeats can present an unpaired adenosine in the context of a double-stranded region of RNA. The presence of this specific combination of sequence and structural motifs correlates with high-affinity SPEN binding in vitro. These data provide new information on the molecular basis of the XIST and SPEN interaction.
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Affiliation(s)
- Aileen C Button
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Simone D Hall
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Ethan L Ashley
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Colleen A McHugh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
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Kovachka S, Panosetti M, Grimaldi B, Azoulay S, Di Giorgio A, Duca M. Small molecule approaches to targeting RNA. Nat Rev Chem 2024; 8:120-135. [PMID: 38278932 DOI: 10.1038/s41570-023-00569-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 01/28/2024]
Abstract
The development of innovative methodologies to identify RNA binders has attracted enormous attention in chemical biology and drug discovery. Although antibiotics targeting bacterial ribosomal RNA have been on the market for decades, the renewed interest in RNA targeting reflects the need to better understand complex intracellular processes involving RNA. In this context, small molecules are privileged tools used to explore the biological functions of RNA and to validate RNAs as therapeutic targets, and they eventually are to become new drugs. Despite recent progress, the rational design of specific RNA binders requires a better understanding of the interactions which occur with the RNA target to reach the desired biological response. In this Review, we discuss the challenges to approaching this underexplored chemical space, together with recent strategies to bind, interact and affect biologically relevant RNAs.
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Affiliation(s)
- Sandra Kovachka
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
| | - Marc Panosetti
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
- Molecular Medicine Research Line, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Benedetto Grimaldi
- Molecular Medicine Research Line, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Stéphane Azoulay
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
| | - Audrey Di Giorgio
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
| | - Maria Duca
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France.
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40
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Bose R, Saleem I, Mustoe AM. Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states. Cell Chem Biol 2024; 31:17-35. [PMID: 38199037 PMCID: PMC10842484 DOI: 10.1016/j.chembiol.2023.12.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/21/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
RNA secondary structure plays essential roles in encoding RNA regulatory fate and function. Most RNAs populate ensembles of alternatively paired states and are continually unfolded and refolded by cellular processes. Measuring these structural ensembles and their contributions to cellular function has traditionally posed major challenges, but new methods and conceptual frameworks are beginning to fill this void. In this review, we provide a mechanism- and function-centric compendium of the roles of RNA secondary structural ensembles and minority states in regulating the RNA life cycle, from transcription to degradation. We further explore how dysregulation of RNA structural ensembles contributes to human disease and discuss the potential of drugging alternative RNA states to therapeutically modulate RNA activity. The emerging paradigm of RNA structural ensembles as central to RNA function provides a foundation for a deeper understanding of RNA biology and new therapeutic possibilities.
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Affiliation(s)
- Ritwika Bose
- Therapeutic Innovation Center (THINC), Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Irfana Saleem
- Therapeutic Innovation Center (THINC), Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony M Mustoe
- Therapeutic Innovation Center (THINC), Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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Alkan AH, Ensoy M, Cansaran-Duman D. Strategic and Innovative Roles of lncRNAs Regulated by Naturally-derived Small Molecules in Cancer Therapy. Curr Med Chem 2024; 31:6672-6691. [PMID: 37921177 DOI: 10.2174/0109298673264372230919102758] [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: 05/27/2023] [Revised: 07/22/2023] [Accepted: 08/17/2023] [Indexed: 11/04/2023]
Abstract
In the field of precision and personalized medicine, the next generation sequencing method has begun to take an active place as genome-wide screening applications in the diagnosis and treatment of diseases. Studies based on the determination of the therapeutic efficacy of personalized drug use in cancer treatment in the size of the transcriptome and its extension, lncRNA, have been increasing rapidly in recent years. Targeting and/or regulating noncoding RNAs (ncRNAs) consisting of long noncoding RNAs (lncRNAs) are promising strategies for cancer treatment. Within the scope of rapidly increasing studies in recent years, it has been shown that many natural agents obtained from biological organisms can potentially alter the expression of many lncRNAs associated with oncogenic functions. Natural agents include effective small molecules that provide anti-cancer effects and have been used as chemotherapy drugs or in combination with standard anti-cancer drugs used in routine treatment. In this review, it was aimed to provide detailed information about the potential of natural agents to regulate and/or target non-coding RNAs and their mechanisms of action to provide an approach for cancer therapy. The discovery of novel anti-cancer targets and subsequent development of effective drugs or combination strategies that are still needed for most cancers will be promising for cancer treatment.
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Affiliation(s)
- Ayşe Hale Alkan
- Biotechnology Institute, Ankara University, Keçiören, Ankara, Turkey
- Department of Molecular Biology and Genetics, Faculty of Science, Bartın University, Bartın, Turkey
| | - Mine Ensoy
- Biotechnology Institute, Ankara University, Keçiören, Ankara, Turkey
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Ao YQ, Gao J, Jiang JH, Wang HK, Wang S, Ding JY. Comprehensive landscape and future perspective of long noncoding RNAs in non-small cell lung cancer: it takes a village. Mol Ther 2023; 31:3389-3413. [PMID: 37740493 PMCID: PMC10727995 DOI: 10.1016/j.ymthe.2023.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/01/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a distinct subtype of RNA that lack protein-coding capacity but exert significant influence on various cellular processes. In non-small cell lung cancer (NSCLC), dysregulated lncRNAs act as either oncogenes or tumor suppressors, contributing to tumorigenesis and tumor progression. LncRNAs directly modulate gene expression, act as competitive endogenous RNAs by interacting with microRNAs or proteins, and associate with RNA binding proteins. Moreover, lncRNAs can reshape the tumor immune microenvironment and influence cellular metabolism, cancer cell stemness, and angiogenesis by engaging various signaling pathways. Notably, lncRNAs have shown great potential as diagnostic or prognostic biomarkers in liquid biopsies and therapeutic strategies for NSCLC. This comprehensive review elucidates the significant roles and diverse mechanisms of lncRNAs in NSCLC. Furthermore, we provide insights into the clinical relevance, current research progress, limitations, innovative research approaches, and future perspectives for targeting lncRNAs in NSCLC. By summarizing the existing knowledge and advancements, we aim to enhance the understanding of the pivotal roles played by lncRNAs in NSCLC and stimulate further research in this field. Ultimately, unraveling the complex network of lncRNA-mediated regulatory mechanisms in NSCLC could potentially lead to the development of novel diagnostic tools and therapeutic strategies.
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Affiliation(s)
- Yong-Qiang Ao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Gao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jia-Hao Jiang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hai-Kun Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Shuai Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Jian-Yong Ding
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
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Wang H, Li Y, Jiang S, Liu N, Zhou Q, Li Q, Chen Z, Lin Y, Chen C, Deng Y. LncRNA xist regulates sepsis associated neuroinflammation in the periventricular white matter of CLP rats by miR-122-5p/PKCη Axis. Front Immunol 2023; 14:1225482. [PMID: 38115999 PMCID: PMC10728298 DOI: 10.3389/fimmu.2023.1225482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/30/2023] [Indexed: 12/21/2023] Open
Abstract
Background Neuroinflammation is a common feature of many neurological diseases, and remains crucial for disease progression and prognosis. Activation of microglia and astrocytes can lead to neuroinflammation. However, little is known about the role of lncRNA xist and miR-122-5p in the pathogenesis of sepsis-associated neuroinflammation (SAN). This study aims to investigate the role of lncRNA xist and miR-122-5p in the pathogenesis of SAN. Methods Levels of miR-122-5p and proinflammatory mediators were detected in the cerebrospinal fluid (CSF) of patients with intracranial infection (ICI) by ELISA and qRT-PCR. miRNA expression in the periventricular white matter (PWM) in rats was analyzed by high-throughput sequencing. Levels of lncRNA xist, miR-122-5p and proinflammatory mediators in the PWM were measured using qRT-PCR and western blot. Bioinformatics analysis was used to predict the upstream and downstream of miR-122-5p. The interaction between miR-122-5p and its target protein was validated using luciferase reporter assay. BV2 and astrocytes were used to detect the expression of lncRNA xist, miR-122-5p. Results The level of miR-122-5p was significantly decreased in the CSF of ICI patients, while the expression of IL-1β and TNF-α were significantly upregulated. Furthermore, it was found that the expression of IL-1β and TNF-α were negatively correlated with the level of miR-122-5p. A high-throughput sequencing analysis showed that miR-122-5p expression was downregulated with 1.5-fold changes in the PWM of CLP rats compared with sham group. Bioinformatics analysis found that lncRNA xist and PKCη were the upstream and downstream target genes of miR-122-5p, respectively. The identified lncRNA xist and PKCη were significantly increased in the PWM of CLP rats. Overexpression of miR-122-5p or knockdown of lncRNA xist could significantly downregulate the level of PKCη and proinflammatory mediators from activated microglia and astrocytes. Meanwhile, in vitro investigation showed that silencing lncRNA xist or PKCη or enhancing the expression of miR-122-5p could obviously inhibit the release of proinflammatory mediators in activated BV2 cells and astrocytes. Conclusion LncRNA xist could regulate microglia and astrocytes activation in the PWM of CLP rats via miR-122-5p/PKCη axis, further mediating sepsis associated neuroinflammation.
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Affiliation(s)
- Huifang Wang
- Department of Intensive Care Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Yichen Li
- Department of Intensive Care Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Shuqi Jiang
- Department of Intensive Care Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Nan Liu
- Department of Intensive Care Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Department of Critical Care Medicine, Guangdong Provincial People’s Hospital, School of Medicine South China University of Technology, Guangzhou, China
| | - Qiuping Zhou
- Department of Intensive Care Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Qian Li
- Department of Intensive Care Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Zhuo Chen
- Department of Intensive Care Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Department of Critical Care Medicine, Guangdong Provincial People’s Hospital, School of Medicine South China University of Technology, Guangzhou, China
| | - Yiyan Lin
- Department of Intensive Care Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Chunbo Chen
- Department of Intensive Care Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Yiyu Deng
- Department of Intensive Care Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
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Dai Z, Wang S, Guo X, Wang Y, Yin H, Tan J, Mu C, Sun S, Liu H, Yang F. Gender dimorphism in hepatocarcinogenesis-DNA methylation modification regulated X-chromosome inactivation escape molecule XIST. Clin Transl Med 2023; 13:e1518. [PMID: 38148658 PMCID: PMC10751514 DOI: 10.1002/ctm2.1518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 12/02/2023] [Accepted: 12/06/2023] [Indexed: 12/28/2023] Open
Abstract
BACKGROUND Sex disparities constitute a significant issue in hepatocellular carcinoma (HCC). However, the mechanism of gender dimorphism in HCC is still not completely understood. METHODS 5-Hydroxymethylcytosine (5hmC)-Seal technology was utilised to detect the global 5hmC levels from four female and four male HCC samples. Methylation of XIST was detected by Sequenom MassARRAY methylation profiling between HCC tissues (T) and adjacent normal liver tissues (L). The role of Tet methylcytosine dioxygenase 2 (TET2) was investigated using diethylnitrosamine (DEN)-administered Tet2-/- female mice, which regulated XIST in hepatocarcinogenesis. All statistical analyses were carried out by GraphPad Prism 9.0 and SPSS version 19.0 software. RESULTS The results demonstrated that the numbers of 5hmC reads in the first exon of XIST from female HCC tissues (T) were remarkably lower than that in female adjacent normal liver tissues (L). Correspondingly, DNA methylation level of XIST first exon region was significantly increased in female T than in L. By contrast, no significant change was observed in male HCC patients. Compared to L, the expression of XIST in T was also significantly downregulated. Female patients with higher XIST in HCC had a higher overall survival (OS) and more extended recurrence-free survival (RFS). Moreover, TET2 can interact with YY1 binding to the promoter region of XIST and maintain the hypomethylation state of XIST. In addition, DEN-administered Tet2-/- mice developed more tumours than controls in female mice. CONCLUSIONS Our study provided that YY1 and TET2 could interact to form protein complexes binding to the promoter region of XIST, regulating the methylation level of XIST and then affecting the expression of XIST. This research will provide a new clue for studying sex disparities in hepatocarcinogenesis. HIGHLIGHTS XIST was significantly downregulated in HCC tissues and had gender disparity. Methylation levels in the XIST first exon were higher in female HCC tissues, but no significant change in male HCC patients. The TET2-YY1 complex regulate XIST expression in female hepatocytes. Other ways regulate XIST expression in male hepatocytes.
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Affiliation(s)
- Zhihui Dai
- Department of Medical GeneticsNaval Medical UniversityShanghaiChina
| | - Sijie Wang
- Department of Medical GeneticsNaval Medical UniversityShanghaiChina
- School of Health Science and EngineeringUniversity of Shanghai for Science and TechnologyShanghaiChina
| | - Xinggang Guo
- Third Department of Hepatic SurgeryEastern Hepatobiliary Surgery Hospital, Naval Medical UniversityShanghaiChina
| | - Yuefan Wang
- Department of Medical GeneticsNaval Medical UniversityShanghaiChina
- Third Department of Hepatic SurgeryEastern Hepatobiliary Surgery Hospital, Naval Medical UniversityShanghaiChina
| | - Haozan Yin
- Department of Medical GeneticsNaval Medical UniversityShanghaiChina
| | - Jian Tan
- Department of Medical GeneticsNaval Medical UniversityShanghaiChina
| | - Chenyang Mu
- Department of Medical GeneticsNaval Medical UniversityShanghaiChina
- School of Health Science and EngineeringUniversity of Shanghai for Science and TechnologyShanghaiChina
| | - Shu‐Han Sun
- Department of Medical GeneticsNaval Medical UniversityShanghaiChina
| | - Hui Liu
- Third Department of Hepatic SurgeryEastern Hepatobiliary Surgery Hospital, Naval Medical UniversityShanghaiChina
| | - Fu Yang
- Department of Medical GeneticsNaval Medical UniversityShanghaiChina
- Shanghai Key Laboratory of Medical BioprotectionShanghaiChina
- Key Laboratory of Biological Defense, Ministry of EducationShanghaiChina
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Liang X, Wang X. LncRNAs: Current understanding, future directions, and challenges. Animal Model Exp Med 2023; 6:505-507. [PMID: 38146076 PMCID: PMC10757209 DOI: 10.1002/ame2.12371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/03/2023] [Indexed: 12/27/2023] Open
Affiliation(s)
- Xiaolin Liang
- Department of Geriatrics, Gerontology Institute of Anhui Province, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
- Anhui Province Key Laboratory of Geriatric Immunology and Nutrition TherapyHefeiAnhuiChina
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Anhui Provincial Engineering Research Center for Elderly Care ProductsUniversity of Science and Technology of ChinaHefeiAnhuiChina
| | - Xiangting Wang
- Department of Geriatrics, Gerontology Institute of Anhui Province, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
- Anhui Province Key Laboratory of Geriatric Immunology and Nutrition TherapyHefeiAnhuiChina
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Anhui Provincial Engineering Research Center for Elderly Care ProductsUniversity of Science and Technology of ChinaHefeiAnhuiChina
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Obuse C, Hirose T. Functional domains of nuclear long noncoding RNAs: Insights into gene regulation and intracellular architecture. Curr Opin Cell Biol 2023; 85:102250. [PMID: 37806294 DOI: 10.1016/j.ceb.2023.102250] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/12/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023]
Abstract
Recent functional research on long noncoding RNAs (lncRNAs) has revealed their significant regulatory roles in gene expression and intracellular architecture. Well-characterized examples of such lncRNAs include Xist and NEAT1_2, which play critical roles in heterochromatin formation of inactive X-chromosomes and paraspeckle assembly, in mammalian cells. Both lncRNAs possess modular domain structures with multiple functionally distinct domains that serve as platforms for specific RNA-binding proteins (RBPs), which dictate the function of each lncRNA. Some of these RBPs bind characteristic RNA structures, which can be targeted by small chemical compounds that modulate lncRNA function by perturbing the interaction of RBPs with the RNA structures. Therefore, RNA structures hidden in lncRNAs represent a novel and potent type of therapeutic target.
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Affiliation(s)
- Chikashi Obuse
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan; Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita 565-0871, Japan
| | - Tetsuro Hirose
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita 565-0871, Japan.
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47
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Tang J, Sun Q, Xie Y, Zheng Q, Ding Y. Virus-like Iron-Gold Heterogeneous Nanoparticles for Drug Target Screening. Anal Chem 2023; 95:17187-17192. [PMID: 37962582 DOI: 10.1021/acs.analchem.3c01762] [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: 11/15/2023]
Abstract
Drug-target recognition has great impacts on revealing mechanisms of pharmacological activities, especially drug resistance and off-target effects. In recent years, chemoproteomics has been widely used for drug target screening and discovery due to its high-throughput, high accuracy, and sensitivity. However, there still remain challenges on how to efficiently and unambiguously track target proteins from complex biological matrices. Herein, we report a drug target screening method based on virus-like iron-gold heterogeneous nanoparticles (Au@Fe3O4 NPs). The unique structure of Au@Fe3O4 NPs not only maintains the magnetism of Fe3O4 NPs to facilitate protein enrichment and purification, but also increases drug modification by introducing more active sites on the surface of Au NPs. After coincubating the drug modified NPs with the cell lysate, the high loading of drug on the surface of Au@Fe3O4 NPs was beneficial for capturing target proteins with low abundance. This well-designed heterogeneous nanomaterial provides a novel strategy for improving the efficiency and accuracy of affinity-based proteomics.
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Affiliation(s)
- Jiayue Tang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Qi Sun
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxin Xie
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Qiuling Zheng
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Ya Ding
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
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48
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Keniry A, Blewitt ME. Chromatin-mediated silencing on the inactive X chromosome. Development 2023; 150:dev201742. [PMID: 37991053 DOI: 10.1242/dev.201742] [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: 11/23/2023]
Abstract
In mammals, the second X chromosome in females is silenced to enable dosage compensation between XX females and XY males. This essential process involves the formation of a dense chromatin state on the inactive X (Xi) chromosome. There is a wealth of information about the hallmarks of Xi chromatin and the contribution each makes to silencing, leaving the tantalising possibility of learning from this knowledge to potentially remove silencing to treat X-linked diseases in females. Here, we discuss the role of each chromatin feature in the establishment and maintenance of the silent state, which is of crucial relevance for such a goal.
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Affiliation(s)
- Andrew Keniry
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Marnie E Blewitt
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
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Prudent R, Lemoine H, Walsh J, Roche D. Affinity selection mass spectrometry speeding drug discovery. Drug Discov Today 2023; 28:103760. [PMID: 37660985 DOI: 10.1016/j.drudis.2023.103760] [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: 03/23/2023] [Revised: 07/21/2023] [Accepted: 08/29/2023] [Indexed: 09/05/2023]
Abstract
Affinity selection mass spectrometry (AS-MS) has gained momentum in drug discovery. This review summarizes how this technology has slowly risen as a new paradigm in hit identification and its potential synergy with DNA encoded library technology. It presents an overview of the recent results on challenging targets and perspectives on new areas of research, such as RNA targeting with small molecules. The versatility of the approach is illustrated and strategic drivers discussed in terms of the experience of a small-medium CRO and a big pharma organization.
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Affiliation(s)
| | | | - Jarrod Walsh
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Alderley Park, UK
| | - Didier Roche
- Edelris, Bioparc, Bioserra 1 Building, Lyon, France.
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50
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Wan J, Zhang Z, Wu C, Tian S, Zang Y, Jin G, Sun Q, Wang P, Luan X, Yang Y, Zhan X, Ye LL, Duan DD, Liu X, Zhang W. Astragaloside IV derivative HHQ16 ameliorates infarction-induced hypertrophy and heart failure through degradation of lncRNA4012/9456. Signal Transduct Target Ther 2023; 8:414. [PMID: 37857609 PMCID: PMC10587311 DOI: 10.1038/s41392-023-01660-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/10/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
Reversing ventricular remodeling represents a promising treatment for the post-myocardial infarction (MI) heart failure (HF). Here, we report a novel small molecule HHQ16, an optimized derivative of astragaloside IV, which effectively reversed infarction-induced myocardial remodeling and improved cardiac function by directly acting on the cardiomyocyte to reverse hypertrophy. The effect of HHQ16 was associated with a strong inhibition of a newly discovered Egr2-affiliated transcript lnc9456 in the heart. While minimally expressed in normal mouse heart, lnc9456 was dramatically upregulated in the heart subjected to left anterior descending coronary artery ligation (LADL) and in cardiomyocytes subjected to hypertrophic stimulation. The critical role of lnc9456 in cardiomyocyte hypertrophy was confirmed by specific overexpression and knockout in vitro. A physical interaction between lnc9456 and G3BP2 increased NF-κB nuclear translocation, triggering hypertrophy-related cascades. HHQ16 physically bound to lnc9456 with a high-affinity and induced its degradation. Cardiomyocyte-specific lnc9456 overexpression induced, but knockout prevented LADL-induced, cardiac hypertrophy and dysfunction. HHQ16 reversed the effect of lnc9456 overexpression while lost its protective role when lnc9456 was deleted, further confirming lnc9456 as the bona fide target of HHQ16. We further identified the human ortholog of lnc9456, also an Egr2-affiliated transcript, lnc4012. Similarly, lnc4012 was significantly upregulated in hypertrophied failing hearts of patients with dilated cardiomyopathy. HHQ16 also specifically bound to lnc4012 and caused its degradation and antagonized its hypertrophic effects. Targeted degradation of pathological increased lnc4012/lnc9456 by small molecules might serve as a novel promising strategy to regress infarction-induced cardiac hypertrophy and HF.
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Affiliation(s)
- Jingjing Wan
- School of Pharmacy, Second Military Medical University, Shanghai, PR China
| | - Zhen Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, PR China
| | - Chennan Wu
- School of Pharmacy, Second Military Medical University, Shanghai, PR China
| | - Saisai Tian
- School of Pharmacy, Second Military Medical University, Shanghai, PR China
| | - Yibei Zang
- School of Pharmacy, Second Military Medical University, Shanghai, PR China
| | - Ge Jin
- School of Pharmacy, Second Military Medical University, Shanghai, PR China
| | - Qingyan Sun
- China Institute of Pharmaceutical Industry, Shanghai, PR China
| | - Pin Wang
- Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, PR China
| | - Xin Luan
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, PR China
| | - Yili Yang
- China Regional Research Centre, International Centre of Genetic Engineering & Biotechnology, Taizhou, PR China
| | - Xuelin Zhan
- China Regional Research Centre, International Centre of Genetic Engineering & Biotechnology, Taizhou, PR China
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, PR China
| | - Lingyu Linda Ye
- Center for Phenomics of Traditional Chinese Medicine, Hospital of Traditional Chinese Medicine Affiliated to Southwest Medical University, Southwest Medical University, Luzhou, PR China
| | - Dayue Darrel Duan
- Center for Phenomics of Traditional Chinese Medicine, Hospital of Traditional Chinese Medicine Affiliated to Southwest Medical University, Southwest Medical University, Luzhou, PR China.
- Key Laboratory of Autoimmune Diseases and Precision Medicine, People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, PR China.
| | - Xia Liu
- School of Pharmacy, Second Military Medical University, Shanghai, PR China.
| | - Weidong Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, PR China.
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China.
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