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Wu W, Li Y, He J, Yang J, Liu Y. Resveratrol shields against cisplatin-induced ototoxicity through epigenetic lncRNA GAS5 modulation of miR-455-5p/PTEN pathway. Int Immunopharmacol 2024; 138:112464. [PMID: 38917526 DOI: 10.1016/j.intimp.2024.112464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/06/2024] [Accepted: 06/08/2024] [Indexed: 06/27/2024]
Abstract
BACKGROUND Our previous research demonstrated that resveratrol counters DDP-induced ototoxicity by upregulating miR-455-5p, which targets PTEN. This study aimed to elucidate the underlying mechanisms involving GAS5 and DNA methyltransferase 1 (DNMT1) in resveratrol's protective action. METHODS A luciferase reporter assay and RNA immunoprecipitation (RIP) assay were employed to study the binding between GAS5 and miR-455-5p, as well as between miR-455-5p and PTEN. HEI-OC1 cells treated with DDP were transfected with vectors for GAS5, si-GAS5, DNMT1, si-DNMT1, and miR-455-5p mimics, as well as PTEN. Subsequently, they were treated with resveratrol and exposed to DDP, both separately and in combination. The distribution of CpG islands in the GAS5 promoter was identified using MethyPrimer, and methylation-specific PCR (MSP) was conducted to determine the methylation levels of GAS5. Chromatin immunoprecipitation (ChIP) was utilized to examine the interaction between DNMT1 and GAS5. The viability of HEI-OC1 cells, catalase (CAT) activity, apoptosis, and ROS levels were assessed using the CCK-8 assay, CAT assay, TUNEL staining, and flow cytometry, respectively. An in vivo mouse model was developed to measure auditory brainstem response (ABR) thresholds, while RT-qPCR and Western blot analysis were employed to evaluate molecular levels. RESULTS Our study discovered that GAS5 acts as a sponge for miR-455-5p, thereby increasing PTEN expression in DDP-treated HEI-OC1 cells. This process was reversed upon treatment with resveratrol. Importantly, DNMT1 promoted the methylation of the GAS5 promoter, leading to the suppression of GAS5 expression. This suppression enhanced the effectiveness of resveratrol in combating DDP-induced apoptosis and ROS in HEI-OC1 cells and amplified its protective effect against DDP's ototoxicity in vivo. CONCLUSIONS Our research emphasizes the significance of the DNMT1/GAS5/miR-455-5p/PTEN axis as a promising new route to boost resveratrol's effectiveness against DDP-induced ototoxicity.
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Affiliation(s)
- Wenjin Wu
- Department of Otorhinolaryngology-Head& Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai Jiaotong University School of Medicine Ear Institute, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Yingru Li
- Department of Otorhinolaryngology-Head& Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai Jiaotong University School of Medicine Ear Institute, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Jingchun He
- Department of Otorhinolaryngology-Head& Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai Jiaotong University School of Medicine Ear Institute, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Jun Yang
- Department of Otorhinolaryngology-Head& Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai Jiaotong University School of Medicine Ear Institute, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Yupeng Liu
- Department of Otorhinolaryngology-Head& Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai Jiaotong University School of Medicine Ear Institute, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China.
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Kupke J, Klimmt J, Mudlaff F, Schwab M, Lutsik P, Plass C, Sticht C, Oliveira AMM. Dnmt3a1 regulates hippocampus-dependent memory via the downstream target Nrp1. Neuropsychopharmacology 2024; 49:1528-1539. [PMID: 38499720 PMCID: PMC11319347 DOI: 10.1038/s41386-024-01843-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/04/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024]
Abstract
Epigenetic factors are well-established players in memory formation. Specifically, DNA methylation is necessary for the formation of long-term memory in multiple brain regions including the hippocampus. Despite the demonstrated role of DNA methyltransferases (Dnmts) in memory formation, it is unclear whether individual Dnmts have unique or redundant functions in long-term memory formation. Furthermore, the downstream processes controlled by Dnmts during memory consolidation have not been investigated. In this study, we demonstrated that Dnmt3a1, the predominant Dnmt in the adult brain, is required for long-term spatial object recognition and contextual fear memory. Using RNA sequencing, we identified an activity-regulated Dnmt3a1-dependent genomic program in which several genes were associated with functional and structural plasticity. Furthermore, we found that some of the identified genes are selectively dependent on Dnmt3a1, but not its isoform Dnmt3a2. Specifically, we identified Neuropilin 1 (Nrp1) as a downstream target of Dnmt3a1 and further demonstrated the involvement of Nrp1 in hippocampus-dependent memory formation. Importantly, we found that Dnmt3a1 regulates hippocampus-dependent memory via Nrp1. In contrast, Nrp1 overexpression did not rescue memory impairments triggered by reduced Dnmt3a2 levels. Taken together, our study uncovered a Dnmt3a-isoform-specific mechanism in memory formation, identified a novel regulator of memory, and further highlighted the complex and highly regulated functions of distinct epigenetic regulators in brain function.
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Affiliation(s)
- Janina Kupke
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, the Netherlands
| | - Julien Klimmt
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany
- Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilians-University Munich, 81377, Munich, Germany
| | - Franziska Mudlaff
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany
- Integrated Program in Neuroscience, McGill University, Montreal, QC, H3A 2B4, Canada
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal, QC, H3G 1A4, Canada
| | - Maximilian Schwab
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Carsten Sticht
- Next Generation Sequencing Core Facility, Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
| | - Ana M M Oliveira
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany.
- Department of Molecular and Cellular Cognition Research, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany.
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3
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Chen T, Mahdadi S, Vidal M, Desbène-Finck S. Non-nucleoside inhibitors of DNMT1 and DNMT3 for targeted cancer therapy. Pharmacol Res 2024; 207:107328. [PMID: 39079576 DOI: 10.1016/j.phrs.2024.107328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024]
Abstract
DNA methylation can deactivate tumor suppressor genes thus causing cancers. Two DNA methylation inhibitors have been approved by the Food and Drug Administration (FDA) and have entered clinical use. However, these inhibitors are nucleoside analogues that can be incorporated into DNA or RNA and induce significant side effects. DNMT1 and DNMT3 are key enzymes involved in DNA methylation. In the acute myeloid leukemia model, a non-nucleoside DNMT1-specific inhibitor has shown lower toxicity and improved pharmacokinetics compared to traditional nucleoside drugs. DNMT3 is also implicated in certain specific cancers. Thus, developing non-nucleoside inhibitors for DNMT1 or DNMT3 can help in understanding their roles in carcinogenesis and provide targeted treatment options in certain cancers. Although no non-nucleoside inhibitors have yet entered clinical trials, in this review, we focus on DNMT1 or DNMT3 selective inhibitors. For DNMT1 selective inhibitors, we have compiled information on the repurposed drugs, derivative compounds and selective inhibitors identified through virtual screening. Additionally, we have outlined potential targets for DNMT1, including protein-protein complex, RNA mimics and aptamers. Compared to DNMT1, research on DNMT3-specific inhibitors has been less extensive. In this context, our exploration has identified a limited number of molecular inhibitors, and we have proposed specific long non-coding RNAs (lncRNAs) as potential contributors to the selective inhibition of DNMT3. This collective effort aims to offer valuable insights into the development of non-nucleoside inhibitors that selectively target DNMT1 or DNMT3.
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Affiliation(s)
- Ting Chen
- UMR 8038 CNRS, U1268 INSERM, UFR de pharmacie, Université Paris cité, 75270, France
| | - Syrine Mahdadi
- UMR 8038 CNRS, U1268 INSERM, UFR de pharmacie, Université Paris cité, 75270, France
| | - Michel Vidal
- UMR 8038 CNRS, U1268 INSERM, UFR de pharmacie, Université Paris cité, 75270, France; Toxicology, Cochin Hospital, HUPC, APHP, Paris 75014, France
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Li J, Yao P, Tang K, Zhao X, Liu X, Liu Q, Wei T, Xuan H, Bian S, Guo Y, Yang Z, Zhang ZQ, Zhang L. Functional Aptamers In Vitro Evolution for Intranuclear Blockage of RNA-Protein Interaction. J Am Chem Soc 2024. [PMID: 39167715 DOI: 10.1021/jacs.4c08824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Over the last 30 years, despite considerable research and endeavors aimed at harnessing aptamers as pharmaceutical molecules, the progress in developing aptamer-based drugs has been falling short of expectations. Sequential steps of affinity molecule acquisition and functional screening are typically required for discovering affinity-based macromolecule therapeutics, which can be time-consuming and limiting in candidate selection. Additionally, aptamers often necessitate tedious postselection modifications to overcome pharmacokinetic limitations, which usually impede the binding affinity. Herein, we propose a novel in vitro screening platform termed Functional Aptamers in vitro Evolution (FAIVE), which integrates affinity molecule acquisition with functional screening and introduces chemical diversity during the process. This platform aims to rapidly generate functional aptamers capable of binding to target proteins and regulating their functions. Illustrated by targeting intranuclear RNA-protein interactions involving HIV-1 Tat protein and TAR RNA, FAIVE demonstrates a selection of functional aptamers with significant intracellular blocking effects. The study also explores lipid nanoparticle delivery systems to enhance intracellular delivery efficiency, expanding aptamer targeting potential to broader intracellular and intranuclear domains. This study emphasizes the potential of FAIVE to expedite the development of aptamer-based drugs and facilitate the creation of more versatile and effective therapeutics.
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Affiliation(s)
- Jun Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xian, Shaanxi 710119, China
| | - Panzhu Yao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ke Tang
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xuyang Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiyang Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Qinguo Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Tongxuan Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Hong Xuan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Siqi Bian
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ying Guo
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhi-Qi Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xian, Shaanxi 710119, China
| | - Liqin Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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Rao X, Yang S, Lü S, Yang P. DNA Methylation Dynamics in Response to Drought Stress in Crops. PLANTS (BASEL, SWITZERLAND) 2024; 13:1977. [PMID: 39065503 PMCID: PMC11280950 DOI: 10.3390/plants13141977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024]
Abstract
Drought is one of the most hazardous environmental factors due to its severe damage on plant growth, development and productivity. Plants have evolved complex regulatory networks and resistance strategies for adaptation to drought stress. As a conserved epigenetic regulation, DNA methylation dynamically alters gene expression and chromosome interactions in plants' response to abiotic stresses. The development of omics technologies on genomics, epigenomics and transcriptomics has led to a rapid increase in research on epigenetic variation in non-model crop species. In this review, we summarize the most recent findings on the roles of DNA methylation under drought stress in crops, including methylating and demethylating enzymes, the global methylation dynamics, the dual regulation of DNA methylation on gene expression, the RNA-dependent DNA methylation (RdDM) pathway, alternative splicing (AS) events and long non-coding RNAs (lnc RNAs). We also discuss drought-induced stress memory. These epigenomic findings provide valuable potential for developing strategies to improve crop drought tolerance.
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Affiliation(s)
| | | | | | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (X.R.); (S.Y.); (S.L.)
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6
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Lai Z, Shu Q, Song Y, Tang A, Tian J. Effect of DNA methylation on the osteogenic differentiation of mesenchymal stem cells: concise review. Front Genet 2024; 15:1429844. [PMID: 39015772 PMCID: PMC11250479 DOI: 10.3389/fgene.2024.1429844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 06/10/2024] [Indexed: 07/18/2024] Open
Abstract
Mesenchymal stem cells (MSCs) have promising potential for bone tissue engineering in bone healing and regeneration. They are regarded as such due to their capacity for self-renewal, multiple differentiation, and their ability to modulate the immune response. However, changes in the molecular pathways and transcription factors of MSCs in osteogenesis can lead to bone defects and metabolic bone diseases. DNA methylation is an epigenetic process that plays an important role in the osteogenic differentiation of MSCs by regulating gene expression. An increasing number of studies have demonstrated the significance of DNA methyltransferases (DNMTs), Ten-eleven translocation family proteins (TETs), and MSCs signaling pathways about osteogenic differentiation in MSCs. This review focuses on the progress of research in these areas.
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Affiliation(s)
- Zhihao Lai
- Department of Rehabilitation Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qing Shu
- Department of Rehabilitation Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yue Song
- Department of Rehabilitation Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- College of Sports Medicine, Wuhan Sports University, Wuhan, China
| | - Ao Tang
- Department of Rehabilitation Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- College of Sports Medicine, Wuhan Sports University, Wuhan, China
| | - Jun Tian
- Department of Rehabilitation Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
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7
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Heydari R, Karimi P, Meyfour A. Long non-coding RNAs as pathophysiological regulators, therapeutic targets and novel extracellular vesicle biomarkers for the diagnosis of inflammatory bowel disease. Biomed Pharmacother 2024; 176:116868. [PMID: 38850647 DOI: 10.1016/j.biopha.2024.116868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing disease of the gastrointestinal (GI) system that includes two groups, Crohn's disease (CD) and ulcerative colitis (UC). To cope with these two classes of IBD, the investigation of pathogenic mechanisms and the discovery of new diagnostic and therapeutic approaches are crucial. Long non-coding RNAs (lncRNAs) which are non-coding RNAs with a length of longer than 200 nucleotides have indicated significant association with the pathology of IBD and strong potential to be used as accurate biomarkers in diagnosing and predicting responses to the IBD treatment. In the current review, we aim to investigate the role of lncRNAs in the pathology and development of IBD. We first describe recent advances in research on dysregulated lncRNAs in the pathogenesis of IBD from the perspective of epithelial barrier function, intestinal immunity, mitochondrial function, and intestinal autophagy. Then, we highlight the possible translational role of lncRNAs as therapeutic targets, diagnostic biomarkers, and predictors of therapeutic response in colon tissues and plasma samples. Finally, we discuss the potential of extracellular vesicles and their lncRNA cargo in the pathophysiology, diagnosis, and treatment of IBD.
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Affiliation(s)
- Raheleh Heydari
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Padideh Karimi
- CRTD/Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden 01307, Germany
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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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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Bittel AJ, Chen YW. DNA Methylation in the Adaptive Response to Exercise. Sports Med 2024; 54:1419-1458. [PMID: 38561436 DOI: 10.1007/s40279-024-02011-6] [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] [Accepted: 02/23/2024] [Indexed: 04/04/2024]
Abstract
Emerging evidence published over the past decade has highlighted the role of DNA methylation in skeletal muscle function and health, including as an epigenetic transducer of the adaptive response to exercise. In this review, we aim to synthesize the latest findings in this field to highlight: (1) the shifting understanding of the genomic localization of altered DNA methylation in response to acute and chronic aerobic and resistance exercise in skeletal muscle (e.g., promoter, gene bodies, enhancers, intergenic regions, un-annotated regions, and genome-wide methylation); (2) how these global/regional methylation changes relate to transcriptional activity following exercise; and (3) the factors (e.g., individual demographic or genetic features, dietary, training history, exercise parameters, local epigenetic characteristics, circulating hormones) demonstrated to alter both the pattern of DNA methylation after exercise, and the relationship between DNA methylation and gene expression. Finally, we discuss the changes in non-CpG methylation and 5-hydroxymethylation after exercise, as well as the importance of emerging single-cell analyses to future studies-areas of increasing focus in the field of epigenetics. We anticipate that this review will help generate a framework for clinicians and researchers to begin developing and testing exercise interventions designed to generate targeted changes in DNA methylation as part of a personalized exercise regimen.
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Affiliation(s)
- Adam J Bittel
- Research Center for Genetic Medicine, Children's National Hospital, 111 Michigan Ave NW, Washington, DC, 20010, USA.
| | - Yi-Wen Chen
- Research Center for Genetic Medicine, Children's National Hospital, 111 Michigan Ave NW, Washington, DC, 20010, USA
- Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Science, 111 Michigan Ave NW, Washington, DC, 20010, USA
- Department of Integrative Systems Biology, Institute for Biomedical Sciences, The George Washington University, 2121 I St NW, Washington, DC, 20052, USA
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Zhang Y, Guo W, Wen H, Shi Y, Gao W, Chen X, Wang T, Wang W, Wu W. Analysis of lncRNA-related studies of ivermectin-sensitive and -resistant strains of Haemonchus contortus. Parasitol Res 2024; 123:226. [PMID: 38814484 DOI: 10.1007/s00436-024-08238-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
In this study, 858 novel long non-coding RNAs (lncRNAs) were predicted as sensitive and resistant strains of Haemonchus contortus to ivermectin. These lncRNAs underwent bioinformatic analysis. In total, 205 lncRNAs significantly differed using log2 (difference multiplicity) > 1 or log2 (difference multiplicity) < - 1 and FDR < 0.05 as the threshold for significant difference analysis. We selected five lncRNAs based on significant differences in expression, cis-regulation, and their association with the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. These expressions of lncRNAs, namely MSTRG.12610.1, MSTRG.8169.1, MSTRG.6355.1, MSTRG.980.1, and MSTRG.9045.1, were significantly downregulated. These findings were consistent with the results of transcriptomic sequencing. We further investigated the relative expression of target gene mRNAs and the regulation of mRNA and miRNA, starting with lncRNA cis-regulation of mRNA, and constructed a lncRNA-mRNA-miRNA network regulation. After a series of statistical analyses, we finally screened out UGT8, Unc-116, Fer-related kinase-1, GGPP synthase 1, and sart3, which may be involved in developing drug resistance under the regulation of their corresponding lncRNAs. The findings of this study provide a novel direction for future studies on drug resistance targets.
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Affiliation(s)
- Yanmin Zhang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Inner Mongolia, China
| | - Wenrui Guo
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Inner Mongolia, China
| | - Haifeng Wen
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Inner Mongolia, China
| | - Yaqin Shi
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Inner Mongolia, China
| | - Wa Gao
- Inner Mongolia Key Laboratory of Tick-Borne Infectious Diseases, Inner Mongolia, China
| | - Xindi Chen
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Inner Mongolia, China
| | - Tengyu Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Inner Mongolia, China
| | - Wenlong Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Inner Mongolia, China.
| | - Weijie Wu
- Hinggan League Agricultural and Animal Husbandry Technology Extension Centre, Ulanhot, China.
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Di Martino P, Marcozzi V, Bibbò S, Ghinassi B, Di Baldassarre A, Gaggi G, Di Credico A. Unraveling the Epigenetic Landscape: Insights into Parkinson's Disease, Amyotrophic Lateral Sclerosis, and Multiple Sclerosis. Brain Sci 2024; 14:553. [PMID: 38928553 PMCID: PMC11202179 DOI: 10.3390/brainsci14060553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Parkinson's disease (PD), multiple sclerosis (MS), and amyotrophic lateral sclerosis (ALS) are examples of neurodegenerative movement disorders (NMDs), which are defined by a gradual loss of motor function that is frequently accompanied by cognitive decline. Although genetic abnormalities have long been acknowledged as significant factors, new research indicates that epigenetic alterations are crucial for the initiation and development of disease. This review delves into the complex interactions that exist between the pathophysiology of NMDs and epigenetic mechanisms such DNA methylation, histone modifications, and non-coding RNAs. Here, we examine how these epigenetic changes could affect protein aggregation, neuroinflammation, and gene expression patterns, thereby influencing the viability and functionality of neurons. Through the clarification of the epigenetic terrain underpinning neurodegenerative movement disorders, this review seeks to enhance comprehension of the underlying mechanisms of the illness and augment the creation of innovative therapeutic strategies.
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Affiliation(s)
- Pierpaolo Di Martino
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
| | - Valentina Marcozzi
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
| | - Sandra Bibbò
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
- Cell Reprogramming and Differentiation Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Barbara Ghinassi
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
- Cell Reprogramming and Differentiation Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
- UdA-Tech Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Angela Di Baldassarre
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
- Cell Reprogramming and Differentiation Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
- UdA-Tech Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Giulia Gaggi
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
- Cell Reprogramming and Differentiation Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
- UdA-Tech Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Andrea Di Credico
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
- Cell Reprogramming and Differentiation Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
- UdA-Tech Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
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12
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Liu Y, Sun Y, Yang J, Wu D, Yu S, Liu J, Hu T, Luo J, Zhou H. DNMT1-targeting remodeling global DNA hypomethylation for enhanced tumor suppression and circumvented toxicity in oral squamous cell carcinoma. Mol Cancer 2024; 23:104. [PMID: 38755637 PMCID: PMC11097543 DOI: 10.1186/s12943-024-01993-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/03/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND The faithful maintenance of DNA methylation homeostasis indispensably requires DNA methyltransferase 1 (DNMT1) in cancer progression. We previously identified DNMT1 as a potential candidate target for oral squamous cell carcinoma (OSCC). However, how the DNMT1- associated global DNA methylation is exploited to regulate OSCC remains unclear. METHODS The shRNA-specific DNMT1 knockdown was employed to target DNMT1 on oral cancer cells in vitro, as was the use of DNMT1 inhibitors. A xenografted OSCC mouse model was established to determine the effect on tumor suppression. High-throughput microarrays of DNA methylation, bulk and single-cell RNA sequencing analysis, multiplex immunohistochemistry, functional sphere formation and protein immunoblotting were utilized to explore the molecular mechanism involved. Analysis of human samples revealed associations between DNMT1 expression, global DNA methylation and collaborative molecular signaling with oral malignant transformation. RESULTS We investigated DNMT1 expression boosted steadily during oral malignant transformation in human samples, and its inhibition considerably minimized the tumorigenicity in vitro and in a xenografted OSCC model. DNMT1 overexpression was accompanied by the accumulation of cancer-specific DNA hypomethylation during oral carcinogenesis; conversely, DNMT1 knockdown caused atypically extensive genome-wide DNA hypomethylation in cancer cells and xenografted tumors. This novel DNMT1-remodeled DNA hypomethylation pattern hampered the dual activation of PI3K-AKT and CDK2-Rb and inactivated GSK3β collaboratively. When treating OSCC mice, targeting DNMT1 achieved greater anticancer efficacy than the PI3K inhibitor, and reduced the toxicity of blood glucose changes caused by the PI3K inhibitor or combination of PI3K and CDK inhibitors as well as adverse insulin feedback. CONCLUSIONS Targeting DNMT1 remodels a novel global DNA hypomethylation pattern to facilitate anticancer efficacy and minimize potential toxic effects via balanced signaling synergia. Our study suggests DNMT1 is a crucial gatekeeper regarding OSCC destiny and treatment outcome.
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Affiliation(s)
- Yangfan Liu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yu Sun
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
- School of Stomatology, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Jin Yang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Deyang Wu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Shuang Yu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Junjiang Liu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Tao Hu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jingjing Luo
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Hongmei Zhou
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
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13
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Wen J, Wu Y, Luo Q. DNA methyltransferases-associated long non-coding RNA PRKCQ-AS1 regulate DNA methylation in myelodysplastic syndrome. Int J Lab Hematol 2024. [PMID: 38679027 DOI: 10.1111/ijlh.14297] [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: 08/18/2023] [Accepted: 04/08/2024] [Indexed: 05/01/2024]
Abstract
INTRODUCTION Myelodysplastic syndrome (MDS) is a group of clonal hematopoietic stem cell disorders. DNA hypermethylation is considered to be the key mechanism of pathogenesis for MDS. Studies have demonstrated that DNA methylation can be regulated by the co-effect between long non-coding RNAs (lncRNAs) and DNA methyltransferases (DNMTs). The aim of this study was to identify DNMTs-associated differentially expressed (DE) lncRNAs, which may be a novel diagnostic and therapeutic target for MDS. METHODS Two gene expression profile datasets (GSE4619 and GSE19429) were downloaded from the Gene Expression Omnibus (GEO) database. Systematic bioinformatics analysis was conducted. Then we verified the expression of PRKCQ-AS1 in MDS patients and features in SKM-1 cells. RESULTS Bioinformatics analysis revealed that the DNMT-associated DE-lncRNA PRKCQ-AS1 was functionally related to DNA methylation. The target genes of PRKCQ-AS1 associated with DNA methylation are mainly methionine synthetase (MTR) and ten-eleven-translocation 1 (TET1). Moreover, the high expression of PRKCQ-AS1 was verified in real MDS cases. Further cellular analysis in SKM-1 cells revealed that overexpressed PRKCQ-AS1 promoted methylation levels of long interspersed nuclear element 1 (LINE-1) and cell proliferation, and apparently elevated both mRNA and protein levels of MTR and TET1, while knockdown of PRKCQ-AS1 showed opposite trend in SKM-1 cells. CONCLUSION DNMT-associated DE-lncRNA PRKCQ-AS1 may affects DNA methylation levels by regulating MTR and TET1.
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Affiliation(s)
- Jian Wen
- Department of Hematology, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, Guangxi Zhuang Autonomous Region, China
| | - Yongbin Wu
- Department of Laboratory Medicine, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, Guangxi Zhuang Autonomous Region, China
| | - Quanfang Luo
- Department of Hematology, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, Guangxi Zhuang Autonomous Region, China
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14
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Werner A, Kanhere A, Wahlestedt C, Mattick JS. Natural antisense transcripts as versatile regulators of gene expression. Nat Rev Genet 2024:10.1038/s41576-024-00723-z. [PMID: 38632496 DOI: 10.1038/s41576-024-00723-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
Long non-coding RNAs (lncRNAs) are emerging as a major class of gene products that have central roles in cell and developmental biology. Natural antisense transcripts (NATs) are an important subset of lncRNAs that are expressed from the opposite strand of protein-coding and non-coding genes and are a genome-wide phenomenon in both eukaryotes and prokaryotes. In eukaryotes, a myriad of NATs participate in regulatory pathways that affect expression of their cognate sense genes. Recent developments in the study of NATs and lncRNAs and large-scale sequencing and bioinformatics projects suggest that whether NATs regulate expression, splicing, stability or translation of the sense transcript is influenced by the pattern and degrees of overlap between the sense-antisense pair. Moreover, epigenetic gene regulatory mechanisms prevail in somatic cells whereas mechanisms dependent on the formation of double-stranded RNA intermediates are prevalent in germ cells. The modulating effects of NATs on sense transcript expression make NATs rational targets for therapeutic interventions.
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Affiliation(s)
| | | | | | - John S Mattick
- University of New South Wales, Sydney, New South Wales, Australia
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15
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Guo JK, Blanco MR, Walkup WG, Bonesteele G, Urbinati CR, Banerjee AK, Chow A, Ettlin O, Strehle M, Peyda P, Amaya E, Trinh V, Guttman M. Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo. Mol Cell 2024; 84:1271-1289.e12. [PMID: 38387462 PMCID: PMC10997485 DOI: 10.1016/j.molcel.2024.01.026] [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: 10/06/2023] [Revised: 12/01/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
Polycomb repressive complex 2 (PRC2) is reported to bind to many RNAs and has become a central player in reports of how long non-coding RNAs (lncRNAs) regulate gene expression. Yet, there is a growing discrepancy between the biochemical evidence supporting specific lncRNA-PRC2 interactions and functional evidence demonstrating that PRC2 is often dispensable for lncRNA function. Here, we revisit the evidence supporting RNA binding by PRC2 and show that many reported interactions may not occur in vivo. Using denaturing purification of in vivo crosslinked RNA-protein complexes in human and mouse cell lines, we observe a loss of detectable RNA binding to PRC2 and chromatin-associated proteins previously reported to bind RNA (CTCF, YY1, and others), despite accurately mapping bona fide RNA-binding sites across others (SPEN, TET2, and others). Taken together, these results argue for a critical re-evaluation of the broad role of RNA binding to orchestrate various chromatin regulatory mechanisms.
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Affiliation(s)
- Jimmy K Guo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Mario R Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Ward G Walkup
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Grant Bonesteele
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Carl R Urbinati
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Biology, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Abhik K Banerjee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Olivia Ettlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mackenzie Strehle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Parham Peyda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Enrique Amaya
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Vickie Trinh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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16
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Valyaeva AA, Sheval EV. Nonspecific Interactions in Transcription Regulation and Organization of Transcriptional Condensates. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:688-700. [PMID: 38831505 DOI: 10.1134/s0006297924040084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 06/05/2024]
Abstract
Eukaryotic cells are characterized by a high degree of compartmentalization of their internal contents, which ensures precise and controlled regulation of intracellular processes. During many processes, including different stages of transcription, dynamic membraneless compartments termed biomolecular condensates are formed. Transcription condensates contain various transcription factors and RNA polymerase and are formed by high- and low-specificity interactions between the proteins, DNA, and nearby RNA. This review discusses recent data demonstrating important role of nonspecific multivalent protein-protein and RNA-protein interactions in organization and regulation of transcription.
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Affiliation(s)
- Anna A Valyaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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Liu J, Zhong X. Epiallelic variation of non-coding RNA genes and their phenotypic consequences. Nat Commun 2024; 15:1375. [PMID: 38355746 PMCID: PMC10867003 DOI: 10.1038/s41467-024-45771-5] [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: 05/24/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
Epigenetic variations contribute greatly to the phenotypic plasticity and diversity. Current functional studies on epialleles have predominantly focused on protein-coding genes, leaving the epialleles of non-coding RNA (ncRNA) genes largely understudied. Here, we uncover abundant DNA methylation variations of ncRNA genes and their significant correlations with plant adaptation among 1001 natural Arabidopsis accessions. Through genome-wide association study (GWAS), we identify large numbers of methylation QTL (methylQTL) that are independent of known DNA methyltransferases and enriched in specific chromatin states. Proximal methylQTL closely located to ncRNA genes have a larger effect on DNA methylation than distal methylQTL. We ectopically tether a DNA methyltransferase MQ1v to miR157a by CRISPR-dCas9 and show de novo establishment of DNA methylation accompanied with decreased miR157a abundance and early flowering. These findings provide important insights into the genetic basis of epigenetic variations and highlight the contribution of epigenetic variations of ncRNA genes to plant phenotypes and diversity.
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Affiliation(s)
- Jie Liu
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Xuehua Zhong
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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18
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Miao LL, Wang JW, Liu HH, Gao S, Fan YC, Wang K. Hypomethylation of glycine dehydrogenase promoter in peripheral blood mononuclear cells is a new diagnostic marker of hepatitis B virus-associated hepatocellular carcinoma. Hepatobiliary Pancreat Dis Int 2024; 23:35-42. [PMID: 36878837 DOI: 10.1016/j.hbpd.2023.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/01/2023] [Indexed: 03/08/2023]
Abstract
BACKGROUND Glycine dehydrogenase (GLDC) plays an important role in the initiation and proliferation of several human cancers. In this study, we aimed to detect the methylation status of GLDC promoter and its diagnostic value for hepatitis B virus-associated hepatocellular carcinoma (HBV-HCC). METHODS We enrolled 197 patients, 111 with HBV-HCC, 51 with chronic hepatitis B (CHB), and 35 healthy controls (HCs). The methylation status of GLDC promoter in peripheral mononuclear cells (PBMCs) was identified by methylation specific polymerase chain reaction (MSP). The mRNA expression was examined using real-time quantitative polymerase chain reaction (qPCR). RESULTS The methylation frequency of the GLDC promoter was significantly lower in HBV-HCC patients (27.0%) compared to that in CHB patients (68.6%) and HCs (74.3%) (P < 0.001). The methylated group had lower alanine aminotransferase level (P = 0.035) and lower rates of tumor node metastasis (TNM) III/IV (P = 0.043) and T3/T4 (P = 0.026). TNM stage was identified to be an independent factor for GLDC promoter methylation. GLDC mRNA levels in CHB patients and HCs were significantly lower than those in HBV-HCC patients (P = 0.022 and P < 0.001, respectively). GLDC mRNA levels were significantly higher in HBV-HCC patients with unmethylated GLDC promoters than those with methylated GLDC promoters (P = 0.003). The diagnostic accuracy of alpha-fetoprotein (AFP) combined with GLDC promoter methylation for HBV-HCC was improved compared with that of AFP alone (AUC: 0.782 vs. 0.630, P < 0.001). In addition, GLDC promoter methylation was an independent predictor for overall survival of HBV-HCC patients (P = 0.038). CONCLUSIONS The methylation frequency of GLDC promoter was lower in PBMCs from HBV-HCC patients than that from patients with CHB and HCs. The combination of AFP and GLDC promoter hypomethylation significantly improved the diagnostic accuracy of HBV-HCC.
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Affiliation(s)
- Li-Li Miao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China; Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Jing-Wen Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Hui-Hui Liu
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Shuai Gao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Yu-Chen Fan
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China; Institute of Hepatology, Shandong University, Jinan 250012, China
| | - Kai Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China; Institute of Hepatology, Shandong University, Jinan 250012, China.
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19
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Wu Y, Song T, Xu Q. R-LOOPs on Short Tandem Repeat Expansion Disorders in Neurodegenerative Diseases. Mol Neurobiol 2023; 60:7185-7195. [PMID: 37540313 DOI: 10.1007/s12035-023-03531-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/24/2023] [Indexed: 08/05/2023]
Abstract
Expansions of short tandem repeats (STRs) have been found to be present in more than 50 diseases and have a close connection with neurodegenerative diseases. Transcriptional silencing and R-LOOP formation, RNA-mediated sequestration of RNA-binding proteins (RBPs), gain-of-function (GOF) proteins containing expanded repeats, and repeat-associated non-AUG (RAN) translation of toxic repeat peptides are some potential molecular mechanisms underlying STR expansion disorders. R-LOOP, a byproduct of transcription, is a three-stranded nucleic acid structure with abnormal accumulation that participates in the pathogenesis of STR expansion disorders by inducing DNA damage and genome instability. R-LOOPs can engender a series of DNA damage, such as DNA double-strand breaks (DSBs), single-strand breaks (SSBs), DNA recombination, or mutations in the DNA replication, transcription, or repair processes. In this review, we provide an in-depth discussion of recent advancements in R-LOOP and systematically elaborate on its genetic destabilizing effects in several neurodegenerative diseases. These molecular mechanisms will provide novel targets for drug design and therapeutic upgrading of these devastating diseases.
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Affiliation(s)
- Yiting Wu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Tingwei Song
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China.
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.
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20
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Song J, Gooding AR, Hemphill WO, Love BD, Robertson A, Yao L, Zon LI, North TE, Kasinath V, Cech TR. Structural basis for inactivation of PRC2 by G-quadruplex RNA. Science 2023; 381:1331-1337. [PMID: 37733873 PMCID: PMC11191771 DOI: 10.1126/science.adh0059] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023]
Abstract
Polycomb repressive complex 2 (PRC2) silences genes through trimethylation of histone H3K27. PRC2 associates with numerous precursor messenger RNAs (pre-mRNAs) and long noncoding RNAs (lncRNAs) with a binding preference for G-quadruplex RNA. In this work, we present a 3.3-Å-resolution cryo-electron microscopy structure of PRC2 bound to a G-quadruplex RNA. Notably, RNA mediates the dimerization of PRC2 by binding both protomers and inducing a protein interface composed of two copies of the catalytic subunit EZH2, thereby blocking nucleosome DNA interaction and histone H3 tail accessibility. Furthermore, an RNA-binding loop of EZH2 facilitates the handoff between RNA and DNA, another activity implicated in PRC2 regulation by RNA. We identified a gain-of-function mutation in this loop that activates PRC2 in zebrafish. Our results reveal mechanisms for RNA-mediated regulation of a chromatin-modifying enzyme.
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Affiliation(s)
- Jiarui Song
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Anne R. Gooding
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Wayne O. Hemphill
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Brittney D. Love
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
- Stem Cell Program, Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Anne Robertson
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
- Stem Cell Program, Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Liqi Yao
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Leonard I. Zon
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
- Stem Cell Program, Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Trista E. North
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
- Stem Cell Program, Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Vignesh Kasinath
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Thomas R. Cech
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
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21
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Mikaeili H, Habib AM, Yeung CWL, Santana-Varela S, Luiz AP, Panteleeva K, Zuberi S, Athanasiou-Fragkouli A, Houlden H, Wood JN, Okorokov AL, Cox JJ. Molecular basis of FAAH-OUT-associated human pain insensitivity. Brain 2023; 146:3851-3865. [PMID: 37222214 PMCID: PMC10473560 DOI: 10.1093/brain/awad098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/03/2023] [Accepted: 03/10/2023] [Indexed: 05/25/2023] Open
Abstract
Chronic pain affects millions of people worldwide and new treatments are needed urgently. One way to identify novel analgesic strategies is to understand the biological dysfunctions that lead to human inherited pain insensitivity disorders. Here we report how the recently discovered brain and dorsal root ganglia-expressed FAAH-OUT long non-coding RNA (lncRNA) gene, which was found from studying a pain-insensitive patient with reduced anxiety and fast wound healing, regulates the adjacent key endocannabinoid system gene FAAH, which encodes the anandamide-degrading fatty acid amide hydrolase enzyme. We demonstrate that the disruption in FAAH-OUT lncRNA transcription leads to DNMT1-dependent DNA methylation within the FAAH promoter. In addition, FAAH-OUT contains a conserved regulatory element, FAAH-AMP, that acts as an enhancer for FAAH expression. Furthermore, using transcriptomic analyses in patient-derived cells we have uncovered a network of genes that are dysregulated from disruption of the FAAH-FAAH-OUT axis, thus providing a coherent mechanistic basis to understand the human phenotype observed. Given that FAAH is a potential target for the treatment of pain, anxiety, depression and other neurological disorders, this new understanding of the regulatory role of the FAAH-OUT gene provides a platform for the development of future gene and small molecule therapies.
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Affiliation(s)
- Hajar Mikaeili
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Abdella M Habib
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Charlix Wai-Lok Yeung
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Sonia Santana-Varela
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Ana P Luiz
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Kseniia Panteleeva
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Sana Zuberi
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | | | - Henry Houlden
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London WC1N 3BG, UK
| | - John N Wood
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Andrei L Okorokov
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - James J Cox
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
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22
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Biswas S, Kang K, Ng KP, Radivoyevitch T, Schalper K, Zhang H, Lindner DJ, Thomas A, MacPherson D, Gastman B, Schrump DS, Wong KK, Velcheti V, Saunthararajah Y. Neuroendocrine lineage commitment of small cell lung cancers can be leveraged into p53-independent non-cytotoxic therapy. Cell Rep 2023; 42:113016. [PMID: 37597186 PMCID: PMC10528072 DOI: 10.1016/j.celrep.2023.113016] [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: 02/22/2023] [Revised: 07/10/2023] [Accepted: 08/04/2023] [Indexed: 08/21/2023] Open
Abstract
Small cell lung cancers (SCLCs) rapidly resist cytotoxic chemotherapy and immune checkpoint inhibitor (ICI) treatments. New, non-cross-resistant therapies are thus needed. SCLC cells are committed into neuroendocrine lineage then maturation arrested. Implicating DNA methyltransferase 1 (DNMT1) in the maturation arrests, we find (1) the repression mark methylated CpG, written by DNMT1, is retained at suppressed neuroendocrine-lineage genes, even as other repression marks are erased; (2) DNMT1 is recurrently amplified, whereas Ten-Eleven-Translocation 2 (TET2), which functionally opposes DNMT1, is deleted; (3) DNMT1 is recruited into neuroendocrine-lineage master transcription factor (ASCL1, NEUROD1) hubs in SCLC cells; and (4) DNMT1 knockdown activated ASCL1-target genes and released SCLC cell-cycling exits by terminal lineage maturation, which are cycling exits that do not require the p53/apoptosis pathway used by cytotoxic chemotherapy. Inhibiting DNMT1/corepressors with clinical compounds accordingly extended survival of mice with chemorefractory and ICI-refractory, p53-null, disseminated SCLC. Lineage commitment of SCLC cells can hence be leveraged into non-cytotoxic therapy able to treat chemo/ICI-refractory SCLC.
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Affiliation(s)
- Sudipta Biswas
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kai Kang
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kwok Peng Ng
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Tomas Radivoyevitch
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kurt Schalper
- Department of Pathology, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Hua Zhang
- Thoracic Oncology Program, Langone-Laura and Isaac Perlmutter Cancer Center, New York University, New York, NY 10016, USA
| | - Daniel J Lindner
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Anish Thomas
- Experimental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Brian Gastman
- Department of Plastic Surgery, Surgery Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - David S Schrump
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kwok-Kin Wong
- Thoracic Oncology Program, Langone-Laura and Isaac Perlmutter Cancer Center, New York University, New York, NY 10016, USA
| | - Vamsidhar Velcheti
- Thoracic Oncology Program, Langone-Laura and Isaac Perlmutter Cancer Center, New York University, New York, NY 10016, USA.
| | - Yogen Saunthararajah
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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23
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Khojastehpour S, Foroughi F, Gheibi N, Mohammadi Z, Ahmadi MH, Nasirian N, Maali A, Azad M. The Association of Methylation Status and Expression Level of MyoD1 with DNMT1 Expression Level in Breast Cancer Patients. Int J Hematol Oncol Stem Cell Res 2023; 17:133-144. [PMID: 37817971 PMCID: PMC10560649 DOI: 10.18502/ijhoscr.v17i3.13303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 05/22/2023] [Indexed: 10/12/2023] Open
Abstract
Background: Breast cancer (BC) is the most common malignancy in women worldwide. The methylation status of MyoD1, a tumor suppressor gene, is enrolled in various cancers, i.e., BC. Various studies showed the impact of MyoD1 epigenetic dysregulation in BC. This study aimed to investigate the methylation status and expression level of MyoD1 in BC patients and its association with the expression of DNMT1. Materials and Methods: This case-control study was conducted on 30 cases (pathology-confirmed ductal carcinoma) and 18 controls (fibroadenoma and fibrocystic masses), referred to Velayat Hospital, Qazvin, Iran. The expression of the MyoD1 and DNMT1 and the promoter methylation of the MyoD1 were evaluated in tissue blocks of BC patient masses using qRT-PCR and MS-PCR assays, respectively. SPSS 24.0 was used to analyze the data. Results: The MyoD1 promoter is hypermethylated in BC patients compared to controls (p =0.001). The expression level of MyoD1 in BC patients was significantly reduced compared to controls (fold change =0.13, p =0.042). In addition, in BC patients, the reduced expression level of MyoD1 was significantly associated with methylation of the MyoD1 promoter (p =0.001). There is no significant difference between the expression level of DNMT1 in BC patients and controls (p =0.197). A significant association is found between the expression of DNMT1 and the methylation status of the MyoD1 promoter (p =0.038). Discussion: The expression level of MyoD1 is affected by the methylation status of the promoter of this gene. Moreover, the expression level and methylation status of MyoD1 are correlated with clinical parameters.
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Affiliation(s)
- Sahar Khojastehpour
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Farshad Foroughi
- Department of Immunology, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
- Cellular and Molecular Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Nematollah Gheibi
- Cellular and Molecular Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Zahra Mohammadi
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mohammad Hossein Ahmadi
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Neda Nasirian
- Department of Pathology, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Amirhosein Maali
- Department of Immunology, Pasteur Institute of Iran, Tehran, Iran
- Department of Medical Biotechnology, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mehdi Azad
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
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24
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Huang LA, Lin C, Yang L. Plumbing mysterious RNAs in "dark genome" for the conquest of human diseases. Mol Ther 2023; 31:1577-1595. [PMID: 37165619 PMCID: PMC10278048 DOI: 10.1016/j.ymthe.2023.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/11/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
Next-generation sequencing has revealed that less than 2% of transcribed genes are translated into proteins, with a large portion transcribed into noncoding RNAs (ncRNAs). Among these, long noncoding RNAs (lncRNAs) represent the largest group and are pervasively transcribed throughout the genome. Dysfunctions in lncRNAs have been found in various diseases, highlighting their potential as therapeutic, diagnostic, and prognostic targets. However, challenges, such as unknown molecular mechanisms and nonspecific immune responses, and issues of drug specificity and delivery present obstacles in translating lncRNAs into clinical applications. In this review, we summarize recent publications that have explored lncRNA functions in human diseases. We also discuss challenges and future directions for developing lncRNA treatments, aiming to bridge the gap between functional studies and clinical potential and inspire further exploration in the field.
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Affiliation(s)
- Lisa A Huang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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25
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 426] [Impact Index Per Article: 426.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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26
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Yang L, Lin Y, Wang C, Fan P. circSnd1 promotes atherosclerosis progression through the miR-485-3p/Olr1 signaling pathway. Heliyon 2023; 9:e17366. [PMID: 37426804 PMCID: PMC10329125 DOI: 10.1016/j.heliyon.2023.e17366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 07/11/2023] Open
Abstract
Background Circular RNAs (circRNAs) participate in the development of atherosclerotic cardiovascular disease. Identifying and verifying the key competing endogenous RNA (ceRNA) network related to atherosclerosis (AS) is significant for understanding the development of AS. The aim of this study was to investigate the circRNA-miRNA‒mRNA network, identify a key circRNA and explore its role in the development of atherosclerosis. Methods Differentially expressed mRNAs (DEMs) and circRNAs (DECs) in the AS model were obtained from datasets in the Gene Expression Omnibus (GEO) database. R software and Cytoscape software were used to construct and visualize the ceRNA network. The dual-luciferase reporter experiment and the RNA pull-down experiment were used to verify the selected ceRNA axis. siRNA targeting circRNA, miRNA mimic, miRNA inhibitor, or gene overexpression plasmid was used for in vitro functional studies. ELISA and western blotting were used to detect inflammation and lipid transport-related proteins. Furthermore, an AS mouse model was established and treated with recombinant adeno-associated viral vectors to further verify the influence of the selected ceRNA axis on the occurrence and/or development of AS. Results A total of 497 DEMs were enriched in 25 pathways, based on which the circ_0082139 (circSnd1)/miR-485-3p/Olr1 axis was selected. In vitro, the interaction among the three molecules of this axis was validated and it was found to affect inflammation and lipid transport, which were characterized by the significant change of inflammatory factors (Il-6, Il-8, Tnf-α, Mcp-1, Vcam-1, and Icam-1), and lipid transport-related genes, including Abca1, Abcg1, Ldlr, Hdlbp, Lp-pla2, and Srebp-1c. Through animal experiments, we further verified that the circSnd1/miR-485-3p/Olr1 axis regulated these molecules and participated in the formation and/or development of AS in vivo. Conclusions The circSnd1/miR-485-3p/Olr1 axis participates in the formation and development of atherosclerosis by regulating inflammation and lipid transport.
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27
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Cabej NR. On the origin and nature of nongenetic information in eumetazoans. Ann N Y Acad Sci 2023. [PMID: 37154677 DOI: 10.1111/nyas.15001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nongenetic information implies all the forms of biological information not related to genes and DNA in general. Despite the deep scientific relevance of the concept, we currently lack reliable knowledge about its carriers and origins; hence, we still do not understand its true nature. Given that genes are the targets of nongenetic information, it appears that a parsimonious approach to find the ultimate source of that information is to trace back the sequential steps of the causal chain upstream of the target genes up to the ultimate link as the source of the nongenetic information. From this perspective, I examine seven nongenetically determined phenomena: placement of locus-specific epigenetic marks on DNA and histones, changes in snRNA expression patterns, neural induction of gene expression, site-specific alternative gene splicing, predator-induced morphological changes, and cultural inheritance. Based on the available evidence, I propose a general model of the common neural origin of all these forms of nongenetic information in eumetazoans.
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Affiliation(s)
- Nelson R Cabej
- Department of Biology, University of Tirana, Tirana, Albania
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28
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Verhoeff TJ, Holloway AF, Dickinson JL. Non-coding RNA regulation of integrins and their potential as therapeutic targets in cancer. Cell Oncol (Dordr) 2023; 46:239-250. [PMID: 36512308 PMCID: PMC10060301 DOI: 10.1007/s13402-022-00752-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Integrins are integral to cell signalling and management of the extracellular matrix, and exquisite regulation of their expression is essential for a variety of cell signalling pathways, whilst disordered regulation is a key driver of tumour progression and metastasis. Most recently non-coding RNAs in the form of micro-RNA (miRNA) and long non-coding RNA (lncRNA) have emerged as a key mechanism by which tissue dependent gene expression is controlled. Whilst historically these molecules have been poorly understood, advances in 'omic' technologies and a greater understanding of non-coding regions of the genome have revealed that non-coding RNAs make up a large proportion of the transcriptome. CONCLUSIONS AND PERSPECTIVES This review examines the regulation of integrin genes by ncRNAs, provides and overview of their mechanism of action and highlights how exploitation of these discoveries is informing the development of novel chemotherapeutic agents in the treatment of cancer. MiRNA molecules have been the most extensively characterised and negatively regulate most integrin genes, classically regulating genes through binding to recognition sequences in the mRNA 3'-untranslated regions of gene transcripts. LncRNA mechanisms of action are now being elucidated and appear to be more varied and complex, and may counter miRNA molecules, directly engage integrin mRNA transcripts, and guide or block both transcription factors and epigenetic machinery at integrin promoters or at other points in integrin regulation. Integrins as therapeutic targets are of enormous interest given their roles as oncogenes in a variety of tumours, and emerging therapeutics mimicking ncRNA mechanisms of action are already being trialled.
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Affiliation(s)
- Tristan Joseph Verhoeff
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart (Tasmania), Australia
| | - Adele F Holloway
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart (Tasmania), Australia
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart (Tasmania), Australia.
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29
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Jansson-Fritzberg LI, Sousa CI, Smallegan MJ, Song JJ, Gooding AR, Kasinath V, Rinn JL, Cech TR. DNMT1 inhibition by pUG-fold quadruplex RNA. RNA (NEW YORK, N.Y.) 2023; 29:346-360. [PMID: 36574982 PMCID: PMC9945446 DOI: 10.1261/rna.079479.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Aberrant DNA methylation is one of the earliest hallmarks of cancer. DNMT1 is responsible for methylating newly replicated DNA, but the precise regulation of DNMT1 to ensure faithful DNA methylation remains poorly understood. A link between RNA and chromatin-associated proteins has recently emerged, and several studies have shown that DNMT1 can be regulated by a variety of RNAs. In this study, we have confirmed that human DNMT1 indeed interacts with multiple RNAs, including its own nuclear mRNA. Unexpectedly, we found that DNMT1 exhibits a strong and specific affinity for GU-rich RNAs that form a pUG-fold, a noncanonical G-quadruplex. We find that pUG-fold-capable RNAs inhibit DNMT1 activity by inhibiting binding of hemimethylated DNA, and we additionally provide evidence for multiple RNA binding modes with DNMT1. Together, our data indicate that a human chromatin-associated protein binds to and is regulated by pUG-fold RNA.
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Affiliation(s)
- Linnea I Jansson-Fritzberg
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Camila I Sousa
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Michael J Smallegan
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Jessica J Song
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Anne R Gooding
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Vignesh Kasinath
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - John L Rinn
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Thomas R Cech
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
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30
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Song J, Gooding AR, Hemphill WO, Kasinath V, Cech TR. Structural basis for inactivation of PRC2 by G-quadruplex RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527314. [PMID: 36798278 PMCID: PMC9934548 DOI: 10.1101/2023.02.06.527314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The histone methyltransferase PRC2 (Polycomb Repressive Complex 2) silences genes via successively attaching three methyl groups to lysine 27 of histone H3. PRC2 associates with numerous pre-mRNA and lncRNA transcripts with a binding preference for G-quadruplex RNA. Here, we present a 3.3Ã…-resolution cryo-EM structure of PRC2 bound to a G-quadruplex RNA. Notably, RNA mediates the dimerization of PRC2 by binding both protomers and inducing a protein interface comprised of two copies of the catalytic subunit EZH2, which limits nucleosome DNA interaction and occludes H3 tail accessibility to the active site. Our results reveal an unexpected mechanism for RNA-mediated inactivation of a chromatin-modifying enzyme. Furthermore, the flexible loop of EZH2 that helps stabilize RNA binding also facilitates the handoff between RNA and DNA, an activity implicated in PRC2 regulation by RNA. One-Sentence Summary Cryo-EM structure of RNA-bound PRC2 dimer elucidates an unexpected mechanism of PRC2 inhibition by RNA.
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Targeted systematic evolution of an RNA platform neutralizing DNMT1 function and controlling DNA methylation. Nat Commun 2023; 14:99. [PMID: 36609400 PMCID: PMC9823104 DOI: 10.1038/s41467-022-35222-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/23/2022] [Indexed: 01/09/2023] Open
Abstract
DNA methylation is a fundamental epigenetic modification regulating gene expression. Aberrant DNA methylation is the most common molecular lesion in cancer cells. However, medical intervention has been limited to the use of broadly acting, small molecule-based demethylating drugs with significant side-effects and toxicities. To allow for targeted DNA demethylation, we integrated two nucleic acid-based approaches: DNMT1 interacting RNA (DiR) and RNA aptamer strategy. By combining the RNA inherent capabilities of inhibiting DNMT1 with an aptamer platform, we generated a first-in-class DNMT1-targeted approach - aptaDiR. Molecular modelling of RNA-DNMT1 complexes coupled with biochemical and cellular assays enabled the identification and characterization of aptaDiR. This RNA bio-drug is able to block DNA methylation, impair cancer cell viability and inhibit tumour growth in vivo. Collectively, we present an innovative RNA-based approach to modulate DNMT1 activity in cancer or diseases characterized by aberrant DNA methylation and suggest the first alternative strategy to overcome the limitations of currently approved non-specific hypomethylating protocols, which will greatly improve clinical intervention on DNA methylation.
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Wang J, Yang C, Cao H, Yang J, Meng W, Yu M, Yu L, Wang B. Hypermethylation-Mediated lncRNA MAGI2-AS3 Downregulation Facilitates Malignant Progression of Laryngeal Squamous Cell Carcinoma via Interacting With SPT6. Cell Transplant 2023; 32:9636897231154574. [PMID: 36852700 PMCID: PMC9986895 DOI: 10.1177/09636897231154574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have an effect on the occurrence and progression of a considerable number of diseases, especially cancer. Existing research has suggested that MAGI2 antisense RNA 3 (MAGI2-AS3) takes on a critical significance in the development of hepatocellular carcinoma and lung cancer. However, the functions of MAGI2-AS3 in laryngeal squamous cell carcinoma (LSCC) remain unclear. In this study, MAGI2-AS3 expression level in LSCC tissue and cell lines was detected, and the effect of MAGI2-AS3 overexpressed on LSCC phenotypes and the possible influence mechanisms were examined. MAGI2-AS3 was downregulated in the tissues of LSCC patients versus non-tumor tissues, and it was correlated with advanced TNM (tumor, node, metastasis) stage and lymph node metastases, as indicated by the results of this study. MAGI2-AS3 inhibited the proliferation, migration, and invasion of LSCC cells in vitro and in vivo. Furthermore, the hypermethylation level of the MAGI2-AS3 promoter region was indicated by bisulfite genomic sequencing and methylation-specific polymerase chain reaction, such that MAGI2-AS3 expression was downregulated. Besides, MAGI2-AS3 promoter hypermethylation was regulated by DNA methyltransferase 1 (DNMT1), and MAGI2-AS3 expression was reversed by 5-Aza-2'-deoxycytidine (5-Aza). Moreover, the result of the RNA pull-down experiment suggested that 38 proteins were enriched in the MAGI2-AS3 group versus the control group in TU177 cells. To be specific, SPT6 (ie, a conserved protein) was enriched by fold change >10. SPT6 knockdown reduced the antitumor effect of MAGI2-AS3 in TU177 and AMC-HN-8 cells. Meanwhile, SPT6 overexpression inhibited the proliferation, metastasis, and invasion of TU177 and AMC-HN-8 cells. As revealed by the above findings, DNMT1-regulated MAGI2-AS3 promoter hypermethylation led to downregulated MAGI2-AS3 expression, such that the presence and progression of LSCC were inhibited in an SPT6 binding-dependent manner.
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Affiliation(s)
- Jiantao Wang
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Chuan Yang
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Huan Cao
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jianwang Yang
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Wenxia Meng
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Miaomiao Yu
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lei Yu
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Baoshan Wang
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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Symeonidis A, Chatzilygeroudi T, Chondrou V, Sgourou A. Contingent Synergistic Interactions between Non-Coding RNAs and DNA-Modifying Enzymes in Myelodysplastic Syndromes. Int J Mol Sci 2022; 23:ijms232416069. [PMID: 36555712 PMCID: PMC9785516 DOI: 10.3390/ijms232416069] [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: 11/21/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematopoietic stem cell disorders with maturation and differentiation defects exhibiting morphological dysplasia in one or more hematopoietic cell lineages. They are associated with peripheral blood cytopenias and by increased risk for progression into acute myelogenous leukemia. Among their multifactorial pathogenesis, age-related epigenetic instability and the error-rate DNA methylation maintenance have been recognized as critical factors for both the initial steps of their pathogenesis and for disease progression. Although lower-risk MDS is associated with an inflammatory bone marrow microenvironment, higher-risk disease is delineated by immunosuppression and clonal expansion. "Epigenetics" is a multidimensional level of gene regulation that determines the specific gene networks expressed in tissues under physiological conditions and guides appropriate chromatin rearrangements upon influence of environmental stimulation. Regulation of this level consists of biochemical modifications in amino acid residues of the histone proteins' N-terminal tails and their concomitant effects on chromatin structure, DNA methylation patterns in CpG dinucleotides and the tissue-specific non-coding RNAs repertoire, which are directed against various gene targets. The role of epigenetic modifications is widely recognized as pivotal both in gene expression control and differential molecular response to drug therapies in humans. Insights to the potential of synergistic cooperations of epigenetic mechanisms provide new avenues for treatment development to comfort human diseases with a known epigenetic shift, such as MDS. Hypomethylating agents (HMAs), such as epigenetic modulating drugs, have been widely used in the past years as first line treatment for elderly higher-risk MDS patients; however, just half of them respond to therapy and are benefited. Rational outcome predictors following epigenetic therapy in MDS and biomarkers associated with disease relapse are of high importance to improve our efforts in developing patient-tailored clinical approaches.
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Affiliation(s)
- Argiris Symeonidis
- Hematology Division & Stem Cell Transplantation Unit, Department of Internal Medicine, University Hospital of Patras, 26504 Patras, Greece
- Medical School University of Patras, University Campus, 26500 Patras, Greece
| | - Theodora Chatzilygeroudi
- Hematology Division & Stem Cell Transplantation Unit, Department of Internal Medicine, University Hospital of Patras, 26504 Patras, Greece
| | - Vasiliki Chondrou
- Biology Laboratory, School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
| | - Argyro Sgourou
- Biology Laboratory, School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
- Correspondence:
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Wang Q, Zhang W, Yin D, Tang Z, Zhang E, Wu W. Gene amplification-driven lncRNA SNHG6 promotes tumorigenesis via epigenetically suppressing p27 expression and regulating cell cycle in non-small cell lung cancer. Cell Death Dis 2022; 8:485. [PMID: 36494339 PMCID: PMC9734177 DOI: 10.1038/s41420-022-01276-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been validated to play essential roles in non-small cell lung carcinoma (NSCLC) progression. In this study, through systematically screening GSE33532 and GSE29249 from Gene Expression Omnibus (GEO) database and bioinformatics analysis, we found the significant upregulation of SNHG6 in NSCLC. The activation of SNHG6 was driven by copy number amplification and high expression of SNHG6 indicated a poor prognosis. Functionally, the knockdown of SNHG6 inhibited NSCLC cell proliferation, migration, and suppressed the G1/S transition of the cell cycle. SNHG6 overexpression had the opposite effects. Mechanically, SNHG6 recruited EZH2 to the promoter region of p27 and increased H3K27me3 enrichment, thus epigenetically repressing the expression of p27, regulating the cell cycle, and promoting tumorigenesis of NSCLC. SNHG6 silencing restrained tumor growth in vivo and suppressed the expressions of cell cycle-related proteins in the G1/S transition. In conclusion, our study uncovered a novel mechanism of SNHG6 activation and its function. SNHG6 can be considered a potential target for the diagnosis and treatment of NSCLC in the future.
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Affiliation(s)
- Qi Wang
- grid.412676.00000 0004 1799 0784Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Zhang
- grid.412676.00000 0004 1799 0784Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Dandan Yin
- grid.410745.30000 0004 1765 1045Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Zhong Fu Road, Gulou District, Nanjing, Jiangsu 210003 PR China
| | - Zaibin Tang
- grid.412676.00000 0004 1799 0784Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Erbao Zhang
- grid.89957.3a0000 0000 9255 8984Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Weibing Wu
- grid.412676.00000 0004 1799 0784Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Yang Z, Xu F, Teschendorff AE, Zhao Y, Yao L, Li J, He Y. Insights into the role of long non-coding RNAs in DNA methylation mediated transcriptional regulation. Front Mol Biosci 2022; 9:1067406. [PMID: 36533073 PMCID: PMC9755597 DOI: 10.3389/fmolb.2022.1067406] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 09/12/2023] Open
Abstract
DNA methylation is one of the most important epigenetic mechanisms that governing regulation of gene expression, aberrant DNA methylation patterns are strongly associated with human malignancies. Long non-coding RNAs (lncRNAs) have being discovered as a significant regulator on gene expression at the epigenetic level. Emerging evidences have indicated the intricate regulatory effects between lncRNAs and DNA methylation. On one hand, transcription of lncRNAs are controlled by the promoter methylation, which is similar to protein coding genes, on the other hand, lncRNA could interact with enzymes involved in DNA methylation to affect the methylation pattern of downstream genes, thus regulating their expression. In addition, circular RNAs (circRNAs) being an important class of noncoding RNA are also found to participate in this complex regulatory network. In this review, we summarize recent research progress on this crosstalk between lncRNA, circRNA, and DNA methylation as well as their potential functions in complex diseases including cancer. This work reveals a hidden layer for gene transcriptional regulation and enhances our understanding for epigenetics regarding detailed mechanisms on lncRNA regulatory function in human cancers.
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Affiliation(s)
- Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Feng Xu
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Andrew E. Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yi Zhao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Lei Yao
- Experiment Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jian Li
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yungang He
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
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Corral A, Alcala M, Carmen Duran-Ruiz M, Arroba AI, Ponce-Gonzalez JG, Todorčević M, Serra D, Calderon-Dominguez M, Herrero L. Role of long non-coding RNAs in adipose tissue metabolism and associated pathologies. Biochem Pharmacol 2022; 206:115305. [DOI: 10.1016/j.bcp.2022.115305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022]
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Li W, Wang YY, Xiao L, Ding J, Wang L, Wang F, Sun T. Mysterious long noncoding RNAs and their relationships to human disease. Front Mol Biosci 2022; 9:950408. [PMID: 36406273 PMCID: PMC9666423 DOI: 10.3389/fmolb.2022.950408] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 10/18/2022] [Indexed: 11/29/2022] Open
Abstract
Increasingly studies have shown that the formation mechanism of many human diseases is very complex, which is determined by environmental factors and genetic factors rather than fully following Mendel's genetic law of inheritance. Long non-coding RNA (lncRNA) is a class of endogenous non-protein coding RNA with a length greater than 200 nt, which has attracted much attention in recent years. Studies have shown that lncRNAs have a wide range of biological functions, such as roles in gene imprinting, cell cycle progression, apoptosis, senescence, cell differentiation, and stress responses, and that they regulate the life processes of mammals at various levels, such as epigenetic transcription, processing, modification, transport, translation and degradation. Analyzing the characteristics of lncRNAs and revealing their internal roles can not only deepen our understanding of human physiological and pathological processes, but also provide new ideas and solutions for the diagnosis, prevention and treatment of some diseases. This article mainly reviews the biological characteristics of lncRNAs and their relationship with some diseases, so as to provide references for the related research of lncRNAs.
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Affiliation(s)
- Wenchao Li
- Ningxia Key Laboratory of Craniocerebral Disease, Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan, China,The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Yang Yang Wang
- Ningxia Key Laboratory of Craniocerebral Disease, Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan, China
| | - Lifei Xiao
- Ningxia Key Laboratory of Craniocerebral Disease, Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan, China
| | - Jiangwei Ding
- Ningxia Key Laboratory of Craniocerebral Disease, Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan, China
| | - Lei Wang
- Ningxia Key Laboratory of Craniocerebral Disease, Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan, China
| | - Feng Wang
- Zhejiang University School of Medicine, Hangzhou, China,*Correspondence: Tao Sun, ; Feng Wang,
| | - Tao Sun
- Ningxia Key Laboratory of Craniocerebral Disease, Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan, China,*Correspondence: Tao Sun, ; Feng Wang,
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Sherazi SAM, Abbasi A, Jamil A, Uzair M, Ikram A, Qamar S, Olamide AA, Arshad M, Fried PJ, Ljubisavljevic M, Wang R, Bashir S. Molecular hallmarks of long non-coding RNAs in aging and its significant effect on aging-associated diseases. Neural Regen Res 2022; 18:959-968. [PMID: 36254975 PMCID: PMC9827784 DOI: 10.4103/1673-5374.355751] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Aging is linked to the deterioration of many physical and cognitive abilities and is the leading risk factor for Alzheimer's disease. The growing aging population is a significant healthcare problem globally that researchers must investigate to better understand the underlying aging processes. Advances in microarrays and sequencing techniques have resulted in deeper analyses of diverse essential genomes (e.g., mouse, human, and rat) and their corresponding cell types, their organ-specific transcriptomes, and the tissue involved in aging. Traditional gene controllers such as DNA- and RNA-binding proteins significantly influence such programs, causing the need to sort out long non-coding RNAs, a new class of powerful gene regulatory elements. However, their functional significance in the aging process and senescence has yet to be investigated and identified. Several recent researchers have associated the initiation and development of senescence and aging in mammals with several well-reported and novel long non-coding RNAs. In this review article, we identified and analyzed the evolving functions of long non-coding RNAs in cellular processes, including cellular senescence, aging, and age-related pathogenesis, which are the major hallmarks of long non-coding RNAs in aging.
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Affiliation(s)
- Syed Aoun Mehmood Sherazi
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Islamabad, Pakistan
| | - Asim Abbasi
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Abdullah Jamil
- Department of Pharmacology, Government College University, Faisalabad, Pakistan
| | - Mohammad Uzair
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Islamabad, Pakistan
| | - Ayesha Ikram
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Shanzay Qamar
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | | | - Muhammad Arshad
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Islamabad, Pakistan
| | - Peter J. Fried
- Department of Neurology, Berenson-Allen Center for Noninvasive Brain Stimulation and Division of Cognitive Neurology, Beth Israel Deaconess Medical Center (KS 158), Harvard Medical School, Boston, MA, USA
| | - Milos Ljubisavljevic
- Department of Physiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ran Wang
- Department of Psychiatry, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China,Mental Health Institute of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Shahid Bashir
- Neuroscience Center, King Fahad Specialist Hospital, Dammam, Saudi Arabia,Correspondence to: Shahid Bashir, .
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Ma Z, Wang Y, Quan Y, Wang Z, Liu Y, Ding Z. Maternal obesity alters methylation level of cytosine in CpG island for epigenetic inheritance in fetal umbilical cord blood. Hum Genomics 2022; 16:34. [PMID: 36045397 PMCID: PMC9429776 DOI: 10.1186/s40246-022-00410-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Over the past few decades, global maternal obesity prevalence has rapidly increased. This condition may induce long-lasting pathophysiological effects on either fetal or infant health that could be attributable to unknown unique changes in the umbilical blood composition. METHODS A total of 34 overweight/obese and 32 normal-weight pregnant women were recruited. Fifteen umbilical blood samples including 8 overweight/obese subjects and 7 normal weight women were sequenced using Targeted Bisulfite Sequencing technology to detect the average methylation level of cytosine and identify the differentially methylated region (DMR). GO and KEGG analyses were then employed to perform pathway enrichment analysis of DMR-related genes and promoters. Moreover, the mRNA levels of methylation-related genes histone deacetylases (HDACs) and DNA methyltransferases (DNMTs) were characterized in the samples obtained from these two groups. RESULTS Average methylated cytosine levels in both the CpG islands (CGI) and promoter significantly decreased in overweight/obese groups. A total of 1669 DMRs exhibited differences in their DNA methylation status between the overweight/obese and control groups. GO and KEGG analyses revealed that DMR-related genes and promoters were enriched in the metabolism, cancer and cardiomyopathy signaling pathways. Furthermore, the HDACs and DNMTs mRNA levels trended to decline in overweight/obese groups. CONCLUSIONS Decreased methylated cytosine levels in overweight/obese women induce the gene expression activity at a higher level than in the control group. DMRs between these two groups in the fetal blood may contribute to the changes in gene transcription that underlie the increased risk of metabolic disorders, cancers and cardiomyopathy in their offspring.
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Affiliation(s)
- Zhuoyao Ma
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China
| | - Yingjin Wang
- Department of Obstetrics and Gynecology, Shanghai Eighth People's Hospital, Shanghai, 200235, China
| | - Yanmei Quan
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China
| | - Zhijie Wang
- Department of Obstetrics and Gynecology, Shanghai Eighth People's Hospital, Shanghai, 200235, China.
| | - Yue Liu
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China.
| | - Zhide Ding
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China.
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Yousuf A, Ahmed N, Qurashi A. Non-canonical DNA/RNA structures associated with the pathogenesis of Fragile X-associated tremor/ataxia syndrome and Fragile X syndrome. Front Genet 2022; 13:866021. [PMID: 36110216 PMCID: PMC9468596 DOI: 10.3389/fgene.2022.866021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS) and fragile X syndrome (FXS) are primary examples of fragile X-related disorders (FXDs) caused by abnormal expansion of CGG repeats above a certain threshold in the 5′-untranslated region of the fragile X mental retardation (FMR1) gene. Both diseases have distinct clinical manifestations and molecular pathogenesis. FXTAS is a late-adult-onset neurodegenerative disorder caused by a premutation (PM) allele (CGG expansion of 55–200 repeats), resulting in FMR1 gene hyperexpression. On the other hand, FXS is a neurodevelopmental disorder that results from a full mutation (FM) allele (CGG expansions of ≥200 repeats) leading to heterochromatization and transcriptional silencing of the FMR1 gene. The main challenge is to determine how CGG repeat expansion affects the fundamentally distinct nature of FMR1 expression in FM and PM ranges. Abnormal CGG repeat expansions form a variety of non-canonical DNA and RNA structures that can disrupt various cellular processes and cause distinct effects in PM and FM alleles. Here, we review these structures and how they are related to underlying mutations and disease pathology in FXS and FXTAS. Finally, as new CGG expansions within the genome have been identified, it will be interesting to determine their implications in disease pathology and treatment.
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Fonouni-Farde C, Christ A, Blein T, Legascue MF, Ferrero L, Moison M, Lucero L, Ramírez-Prado JS, Latrasse D, Gonzalez D, Benhamed M, Quadrana L, Crespi M, Ariel F. The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants. Genome Biol 2022; 23:181. [PMID: 36038910 PMCID: PMC9422110 DOI: 10.1186/s13059-022-02750-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/17/2022] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO), are emerging as important regulators of three-dimensional chromatin conformation and gene transcriptional activity. RESULTS Here, we show that in addition to the PRC1-component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), APOLO interacts with the methylcytosine-binding protein VARIANT IN METHYLATION 1 (VIM1), a conserved homolog of the mammalian DNA methylation regulator UBIQUITIN-LIKE CONTAINING PHD AND RING FINGER DOMAINS 1 (UHRF1). The APOLO-VIM1-LHP1 complex directly regulates the transcription of the auxin biosynthesis gene YUCCA2 by dynamically determining DNA methylation and H3K27me3 deposition over its promoter during the plant thermomorphogenic response. Strikingly, we demonstrate that the lncRNA UHRF1 Protein Associated Transcript (UPAT), a direct interactor of UHRF1 in humans, can be recognized by VIM1 and LHP1 in plant cells, despite the lack of sequence homology between UPAT and APOLO. In addition, we show that increased levels of APOLO or UPAT hamper VIM1 and LHP1 binding to YUCCA2 promoter and globally alter the Arabidopsis transcriptome in a similar manner. CONCLUSIONS Collectively, our results uncover a new mechanism in which a plant lncRNA coordinates Polycomb action and DNA methylation through the interaction with VIM1, and indicates that evolutionary unrelated lncRNAs with potentially conserved structures may exert similar functions by interacting with homolog partners.
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Affiliation(s)
- Camille Fonouni-Farde
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Aurélie Christ
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - Thomas Blein
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - María Florencia Legascue
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Lucía Ferrero
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Michaël Moison
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Leandro Lucero
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Juan Sebastián Ramírez-Prado
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - David Latrasse
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - Daniel Gonzalez
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Moussa Benhamed
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - Leandro Quadrana
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, 75005, Paris, France
| | - Martin Crespi
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina.
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Zhang Y, Qiao X, Liu L, Han W, Liu Q, Wang Y, Xie T, Tang Y, Wang T, Meng J, Ye A, He S, Chen R, Chen C. Long noncoding RNA MAGI2-AS3 regulates the H2O2 level and cell senescence via HSPA8. Redox Biol 2022; 54:102383. [PMID: 35797800 PMCID: PMC9287730 DOI: 10.1016/j.redox.2022.102383] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Yingmin Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinhua Qiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lihui Liu
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wensheng Han
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qinghua Liu
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuanyuan Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ting Xie
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiheng Tang
- University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tiepeng Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiao Meng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Aojun Ye
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shunmin He
- University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Runsheng Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chang Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Liu YC, Kwon J, Fabiani E, Xiao Z, Liu YV, Follo MY, Liu J, Huang H, Gao C, Liu J, Falconi G, Valentini L, Gurnari C, Finelli C, Cocco L, Liu JH, Jones AI, Yang J, Yang H, Thoms JAI, Unnikrishnan A, Pimanda JE, Pan R, Bassal MA, Voso MT, Tenen DG, Chai L. Demethylation and Up-Regulation of an Oncogene after Hypomethylating Therapy. N Engl J Med 2022; 386:1998-2010. [PMID: 35613022 PMCID: PMC9514878 DOI: 10.1056/nejmoa2119771] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Although hypomethylating agents are currently used to treat patients with cancer, whether they can also reactivate and up-regulate oncogenes is not well elucidated. METHODS We examined the effect of hypomethylating agents on SALL4, a known oncogene that plays an important role in myelodysplastic syndrome and other cancers. Paired bone marrow samples that were obtained from two cohorts of patients with myelodysplastic syndrome before and after treatment with a hypomethylating agent were used to explore the relationships among changes in SALL4 expression, treatment response, and clinical outcome. Leukemic cell lines with low or undetectable SALL4 expression were used to study the relationship between SALL4 methylation and expression. A locus-specific demethylation technology, CRISPR-DNMT1-interacting RNA (CRISPR-DiR), was used to identify the CpG island that is critical for SALL4 expression. RESULTS SALL4 up-regulation after treatment with hypomethylating agents was observed in 10 of 25 patients (40%) in cohort 1 and in 13 of 43 patients (30%) in cohort 2 and was associated with a worse outcome. Using CRISPR-DiR, we discovered that demethylation of a CpG island within the 5' untranslated region was critical for SALL4 expression. In cell lines and patients, we confirmed that treatment with a hypomethylating agent led to demethylation of the same CpG region and up-regulation of SALL4 expression. CONCLUSIONS By combining analysis of patient samples with CRISPR-DiR technology, we found that demethylation and up-regulation of an oncogene after treatment with a hypomethylating agent can indeed occur and should be further studied. (Funded by Associazione Italiana per la Ricerca sul Cancro and others.).
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Affiliation(s)
- Yao-Chung Liu
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Junsu Kwon
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Emiliano Fabiani
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Zhijian Xiao
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Yanjing V Liu
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Matilde Y Follo
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Jinqin Liu
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Huijun Huang
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Chong Gao
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Jun Liu
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Giulia Falconi
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Lia Valentini
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Carmelo Gurnari
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Carlo Finelli
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Lucio Cocco
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Jin-Hwang Liu
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Adrianna I Jones
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Junyu Yang
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Henry Yang
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Julie A I Thoms
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Ashwin Unnikrishnan
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - John E Pimanda
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Rongqing Pan
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Mahmoud A Bassal
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Maria T Voso
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Daniel G Tenen
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
| | - Li Chai
- From the Department of Pathology, Brigham and Women's Hospital (Y.-C.L., C. Gao, Jun Liu, J.Y., L. Chai), Harvard Stem Cell Institute, Harvard Medical School (A.I.J., M.A.B., D.G.T.), and the Department of Medical Oncology, Dana-Farber Cancer Institute (R.P.) - all in Boston; the Division of Hematology, Department of Medicine, Taipei Veterans General Hospital (Y.-C.L.), and the Faculty of Medicine and the Program in Molecular Medicine, Institute of Biopharmaceutical Sciences, School of Life Science, National Yang Ming Chiao Tung University (Y.-C.L., J.-H.L.) - both in Taipei, Taiwan; the Cancer Science Institute of Singapore, Singapore (J.K., Y.V.L., H.Y., M.A.B., D.G.T.); the Department of Biomedicine and Prevention, University of Rome Tor Vergata (E.F., G.F., L.V., C. Gurnari, M.T.V.), and UniCamillus-Saint Camillus International University of Health Sciences (E.F.), Rome, and Cellular Signaling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna (M.Y.F., L. Cocco), and IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli" (C.F.), Bologna - all in Italy; the National Clinical Research Center for Blood Diseases and State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China (Z.X., Jinqin Liu, H.H.); and the School of Medical Sciences and Lowy Cancer Research Centre (J.A.I.T., J.E.P.) and Prince of Wales Clinical School and Lowy Cancer Research Centre (A.U., J.E.P.), Faculty of Medicine, University of New South Wales, Sydney, and the Department of Hematology, Prince of Wales Hospital, Randwick, NSW (J.E.P.) - both in Australia
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Jia L, Wang J, Luoreng Z, Wang X, Wei D, Yang J, Hu Q, Ma Y. Progress in Expression Pattern and Molecular Regulation Mechanism of LncRNA in Bovine Mastitis. Animals (Basel) 2022; 12:ani12091059. [PMID: 35565486 PMCID: PMC9105470 DOI: 10.3390/ani12091059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Bovine mastitis is an inflammatory disease of the mammary glands that causes serious harm to cow health and huge economic losses. Susceptibility or resistance to mastitis in individual cows is mainly determined by genetic factors, including coding genes and non-coding genes. Long non-coding RNAs (lncRNAs) are non-coding RNA molecules with a length of more than 200 nucleotides (nt) that have recently been discovered. They can regulate a variety of diseases of humans and animals, especially the immune response and inflammatory disease process. This paper reviews the role of long non-coding RNA (lncRNA) in inflammatory diseases, emphasizes on the latest research progress of lncRNA expression and the molecular regulatory mechanism in bovine mastitis, and looks forward to the research and application prospect of lncRNA in bovine mastitis, intending to provide a reference for scientific researchers to systematically understand this research field. Abstract Bovine mastitis is an inflammatory disease caused by pathogenic microbial infection, trauma, or other factors. Its morbidity is high, and it is difficult to cure, causing great harm to the health of cows and the safety of dairy products. Susceptibility or resistance to mastitis in individual cows is mainly determined by genetic factors, including coding genes and non-coding genes. Long non-coding RNAs (lncRNAs) are a class of endogenous non-coding RNA molecules with a length of more than 200 nucleotides (nt) that have recently been discovered. They can regulate the immune response of humans and animals on three levels (transcription, epigenetic modification, and post-transcription), and are widely involved in the pathological process of inflammatory diseases. Over the past few years, extensive findings revealed basic roles of lncRNAs in inflammation, especially bovine mastitis. This paper reviews the expression pattern and mechanism of long non-coding RNA (lncRNA) in inflammatory diseases, emphasizes on the latest research progress of the lncRNA expression pattern and molecular regulatory mechanism in bovine mastitis, analyzes the molecular regulatory network of differentially expressed lncRNAs, and looks forward to the research and application prospect of lncRNA in bovine mastitis, laying a foundation for molecular breeding and the biological therapy of bovine mastitis.
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Affiliation(s)
- Li Jia
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Jinpeng Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Zhuoma Luoreng
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
- Correspondence: (Z.L.); (X.W.)
| | - Xingping Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
- Correspondence: (Z.L.); (X.W.)
| | - Dawei Wei
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Jian Yang
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Qichao Hu
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Yun Ma
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
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Teo WW, Cao X, Wu CS, Tan HK, Zhou Q, Gao C, Vanuytsel K, Kumar SS, Murphy GJ, Yang H, Chai L, Tenen DG. Non-coding RNA LEVER sequestration of PRC2 can mediate long range gene regulation. Commun Biol 2022; 5:343. [PMID: 35411071 PMCID: PMC9001699 DOI: 10.1038/s42003-022-03250-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 03/09/2022] [Indexed: 11/20/2022] Open
Abstract
Polycomb Repressive Complex 2 (PRC2) is an epigenetic regulator required for gene silencing during development. Although PRC2 is a well-established RNA-binding complex, the biological function of PRC2-RNA interaction has been controversial. Here, we study the gene-regulatory role of the inhibitory PRC2-RNA interactions. We report a nuclear long non-coding RNA, LEVER, which mapped 236 kb upstream of the β-globin cluster as confirmed by Nanopore sequencing. LEVER RNA interacts with PRC2 in its nascent form, and this prevents the accumulation of the H3K27 repressive histone marks within LEVER locus. Interestingly, the accessible LEVER chromatin, in turn, suppresses the chromatin interactions between the ε-globin locus and β-globin locus control region (LCR), resulting in a repressive effect on ε-globin gene expression. Our findings validate that the nascent RNA-PRC2 interaction inhibits local PRC2 function in situ. More importantly, we demonstrate that such a local process can in turn regulate the expression of neighboring genes. Identification of a long non-coding RNA LEVER, that inhibits the Polycomb Repressive Complex 2 (PRC2) and controls nearby embryonic form of beta-globin gene, provides additional evidence for PRC2-RNA functional interaction.
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Affiliation(s)
- Wei Wen Teo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Xinang Cao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chan-Shuo Wu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Hong Kee Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,National University of Singapore, Graduate School for Integrative Sciences and Engineering, Singapore, Singapore
| | - Qiling Zhou
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Chong Gao
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Kim Vanuytsel
- Section of Hematology and Medical Oncology, School of Medicine, Boston University, Boston, MA, USA.,Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
| | - Sara S Kumar
- Section of Hematology and Medical Oncology, School of Medicine, Boston University, Boston, MA, USA.,Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
| | - George J Murphy
- Section of Hematology and Medical Oncology, School of Medicine, Boston University, Boston, MA, USA.,Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Li Chai
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore. .,Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA. .,Harvard Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA.
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Mojally M, Sharmin E, Alhindi Y, Obaid NA, Almaimani R, Althubiti M, Idris S, Abdelghany AH, Refaat B, Al-Amodi HS, Abdalla AN, Kamel HFM. Hydrogel films of methanolic Mentha piperita extract and silver nanoparticles enhance wound healing in rats with diabetes Type I. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2022. [DOI: 10.1080/16583655.2022.2054607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mariam Mojally
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Eram Sharmin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Yosra Alhindi
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Najla A. Obaid
- Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Riyad Almaimani
- Department of Biochemistry, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mohamed Althubiti
- Department of Biochemistry, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Shakir Idris
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | | | - Bassem Refaat
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Hiba S. Al-Amodi
- Department of Biochemistry, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ashraf N. Abdalla
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Hala F. M. Kamel
- Department of Biochemistry, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
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LncRNA-mediated DNA methylation: an emerging mechanism in cancer and beyond. J Exp Clin Cancer Res 2022; 41:100. [PMID: 35292092 PMCID: PMC8922926 DOI: 10.1186/s13046-022-02319-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/08/2022] [Indexed: 02/07/2023] Open
Abstract
DNA methylation is one of the most important epigenetic mechanisms to regulate gene expression, which is highly dynamic during development and specifically maintained in somatic cells. Aberrant DNA methylation patterns are strongly associated with human diseases including cancer. How are the cell-specific DNA methylation patterns established or disturbed is a pivotal question in developmental biology and cancer epigenetics. Currently, compelling evidence has emerged that long non-coding RNA (lncRNA) mediates DNA methylation in both physiological and pathological conditions. In this review, we provide an overview of the current understanding of lncRNA-mediated DNA methylation, with emphasis on the roles of this mechanism in cancer, which to the best of our knowledge, has not been systematically summarized. In addition, we also discuss the potential clinical applications of this mechanism in RNA-targeting drug development.
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Shen Y, Qu B, Shen N. Expanding Roles of Noncoding RNAs in the Pathogenesis of Systemic Lupus Erythematosus. Curr Rheumatol Rep 2022; 24:64-75. [PMID: 35239107 DOI: 10.1007/s11926-022-01058-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE OF REVIEW The exact pathogenesis of systemic lupus erythematosus (SLE) remains unclear. Accumulating finds have indicated the roles of the non-coding RNAs (ncRNAs) acting as novel epigenetic regulatory elements in the dysfunction of the immune system in SLE. This review will introduce recent studies on how ncRNAs are involved in the development of SLE. RECENT FINDINGS Recent advances in ncRNAs biology have greatly expanded our understanding of epigenetic regulation of immune responses and inflammation, and increasing evidence suggests ncRNAs are important players in SLE development. Identifications of abnormal expression patterns of ncRNAs and relevant biological impacts in lupus patients have revealed their potential as novel biomarkers and therapeutic targets for SLE. The dysregulation of ncRNAs contributes to the immunopathogenesis of SLE. Clarifying the functions and mechanisms of SLE-associated ncRNAs provides new opportunities for disease biomarkers and targeted therapies.
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Affiliation(s)
- Yiwei Shen
- Department of Rheumatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Shandong Middle Road, Shanghai, 200001, China
| | - Bo Qu
- Department of Rheumatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Shandong Middle Road, Shanghai, 200001, China
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China
| | - Nan Shen
- Department of Rheumatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Shandong Middle Road, Shanghai, 200001, China.
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China.
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032, China.
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50
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Li Y, Darabi R. Role of epigenetics in cellular reprogramming; from iPSCs to disease modeling and cell therapy. J Cell Biochem 2022; 123:147-154. [PMID: 34668236 PMCID: PMC8860854 DOI: 10.1002/jcb.30164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/31/2021] [Accepted: 10/08/2021] [Indexed: 02/03/2023]
Abstract
Epigenetics play a fundamental role in induced pluripotent stem cell (iPSC) technology due to their effect on iPSC's reprogramming efficiency and their subsequent role in iPSC differentiation toward a specific lineage. Epigenetics can skew the differentiation course of iPSCs toward a specific lineage based on the epigenetic memory of the source cells, or even lead to acquisition of new cell phenotypes, due to its aberrations during reprogramming. This viewpoint discusses key features of the epigenetic process during iPSC reprogramming/differentiation and outlines important epigenetic factors that need to be considered for successful generation and differentiation of iPSCs for downstream applications.
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Affiliation(s)
- Yong Li
- Department of Orthopaedic Surgery, BioMedical Engineering, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, USA
| | - Radbod Darabi
- Center for Stem Cell and Regenerative Medicine (CSCRM), The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
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