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Liu X, Chen Q, Yin X, Wang X, Ran J, Yu W, Wang B. Study on chromatin regulation patterns of expression vectors in the PhiC31 integration site. Epigenetics 2024; 19:2337085. [PMID: 38595049 PMCID: PMC11008548 DOI: 10.1080/15592294.2024.2337085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 03/26/2024] [Indexed: 04/11/2024] Open
Abstract
The PhiC31 integration system allows for targeted and efficient transgene integration and expression by recognizing pseudo attP sites in mammalian cells and integrating the exogenous genes into the open chromatin regions of active chromatin. In order to investigate the regulatory patterns of efficient gene expression in the open chromatin region of PhiC31 integration, this study utilized Ubiquitous Chromatin Opening Element (UCOE) and activating RNA (saRNA) to modulate the chromatin structure in the promoter region of the PhiC31 integration vector. The study analysed the effects of DNA methylation and nucleosome occupancy changes in the integrated promoter on gene expression levels. The results showed that for the OCT4 promoter with moderate CG density, DNA methylation had a smaller impact on expression compared to changes in nucleosome positioning near the transcription start site, which was crucial for enhancing downstream gene expression. On the other hand, for the SOX2 promoter with high CG density, increased methylation in the CpG island upstream of the transcription start site played a key role in affecting high expression, but the positioning and clustering of nucleosomes also had an important influence. In conclusion, analysing the DNA methylation patterns, nucleosome positioning, and quantity distribution of different promoters can determine whether the PhiC31 integration site possesses the potential to further enhance expression or overcome transgene silencing effects by utilizing chromatin regulatory elements.
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Affiliation(s)
- Xueli Liu
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
- Pharmaceutical Department, Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Qina Chen
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
| | - Xudong Yin
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
| | - Xiao Wang
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
| | - Jinshan Ran
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
| | - Wei Yu
- Department of Pharmacy, 920th Hospital of Joint Logistics Support Force, PLA, Kunming, China
| | - Bin Wang
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
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2
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Wang L, Lin Y, Yao Z, Babu N, Lin W, Chen C, Du L, Cai S, Pan Y, Xiong X, Ye Q, Ren H, Zhang D, Chen Y, Yeung SCJ, Bremer E, Zhang H. Targeting undruggable phosphatase overcomes trastuzumab resistance by inhibiting multi-oncogenic kinases. Drug Resist Updat 2024; 76:101118. [PMID: 39094301 DOI: 10.1016/j.drup.2024.101118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 06/12/2024] [Accepted: 07/05/2024] [Indexed: 08/04/2024]
Abstract
AIMS Resistance to targeted therapy is one of the critical obstacles in cancer management. Resistance to trastuzumab frequently develops in the treatment for HER2+ cancers. The role of protein tyrosine phosphatases (PTPs) in trastuzumab resistance is not well understood. In this study, we aim to identify pivotal PTPs affecting trastuzumab resistance and devise a novel counteracting strategy. METHODS Four public datasets were used to screen PTP candidates in relation to trastuzumab responsiveness in HER2+ breast cancer. Tyrosine kinase (TK) arrays were used to identify kinases that linked to protein tyrosine phosphate receptor type O (PTPRO)-enhanced trastuzumab sensitivity. The efficacy of small activating RNA (saRNA) in trastuzumab-conjugated silica nanoparticles was tested for PTPRO upregulation and resistance mitigation in cell models, a transgenic mouse model, and human cancer cell line-derived xenograft models. RESULTS PTPRO was identified as the key PTP which influences trastuzumab responsiveness and patient survival. PTPRO de-phosphorated several TKs, including the previously overlooked substrate ERBB3, thereby inhibiting multiple oncogenic pathways associated with drug resistance. Notably, PTPRO, previously deemed "undruggable," was effectively upregulated by saRNA-loaded nanoparticles. The upregulated PTPRO simultaneously inhibited ERBB3, ERBB2, and downstream SRC signaling pathways, thereby counteracting trastuzumab resistance. CONCLUSIONS Antibody-conjugated saRNA represents an innovative approach for targeting "undruggable" PTPs.
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Affiliation(s)
- Lu Wang
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China; State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, China; Zhuhai Institute of Jinan University, Zhuhai, China
| | - Yusheng Lin
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, China; Zhuhai Institute of Jinan University, Zhuhai, China; Department of Thoracic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China; Department of Hematology, University of Groningen, University Medical Center Groningen, the Netherlands; Shantou University Medical College, Shantou, China
| | - Zhimeng Yao
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, China; Zhuhai Institute of Jinan University, Zhuhai, China; Department of Urology Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Nipun Babu
- Shantou University Medical College, Shantou, China
| | - Wan Lin
- Shantou University Medical College, Shantou, China
| | | | - Liang Du
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, China; Zhuhai Institute of Jinan University, Zhuhai, China
| | - Songwang Cai
- Department of Thoracic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yunlong Pan
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Xiao Xiong
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, China; Zhuhai Institute of Jinan University, Zhuhai, China
| | - Qiantao Ye
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, China; Zhuhai Institute of Jinan University, Zhuhai, China
| | - Hongzheng Ren
- Department of Pathology, Gongli Hospital of Shanghai Pudong New Area, Shanghai, China; Department of Pathology, Heping Hospital, Changzhi Medical College, Changzhi, China
| | - Dianzheng Zhang
- Department of Biomedical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA, USA
| | - Yexi Chen
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Sai-Ching Jim Yeung
- Department of Emergency Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Endocrine Neoplasia and Hormonal Disorders, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edwin Bremer
- Department of Hematology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Hao Zhang
- Department of Pathology, Gongli Hospital of Shanghai Pudong New Area, Shanghai, China; State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, China; Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China; Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China.
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3
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Bakrania A, Mo Y, Zheng G, Bhat M. RNA nanomedicine in liver diseases. Hepatology 2024:01515467-990000000-00569. [PMID: 37725757 DOI: 10.1097/hep.0000000000000606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
The remarkable impact of RNA nanomedicine during the COVID-19 pandemic has demonstrated the expansive therapeutic potential of this field in diverse disease contexts. In recent years, RNA nanomedicine targeting the liver has been paradigm-shifting in the management of metabolic diseases such as hyperoxaluria and amyloidosis. RNA nanomedicine has significant potential in the management of liver diseases, where optimal management would benefit from targeted delivery, doses titrated to liver metabolism, and personalized therapy based on the specific site of interest. In this review, we discuss in-depth the different types of RNA and nanocarriers used for liver targeting along with their specific applications in metabolic dysfunction-associated steatotic liver disease, liver fibrosis, and liver cancers. We further highlight the strategies for cell-specific delivery and future perspectives in this field of research with the emergence of small activating RNA, circular RNA, and RNA base editing approaches.
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Affiliation(s)
- Anita Bakrania
- Department of Medicine, Toronto General Hospital Research Institute, Toronto, Ontario, Canada
- Department of Medicine, Ajmera Transplant Program, University Health Network, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yulin Mo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Gang Zheng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mamatha Bhat
- Department of Medicine, Toronto General Hospital Research Institute, Toronto, Ontario, Canada
- Department of Medicine, Ajmera Transplant Program, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, Division of Gastroenterology, University Health Network and University of Toronto, Toronto, Ontario, Canada
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4
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Zhai P, Tong T, Wang X, Li C, Liu C, Qin X, Li S, Xie F, Mao J, Zhang J, Guo H. Nuclear miR-451a activates KDM7A and leads to cetuximab resistance in head and neck squamous cell carcinoma. Cell Mol Life Sci 2024; 81:282. [PMID: 38943031 PMCID: PMC11335205 DOI: 10.1007/s00018-024-05324-x] [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: 10/30/2023] [Revised: 05/29/2024] [Accepted: 06/16/2024] [Indexed: 06/30/2024]
Abstract
Cetuximab resistance has been a major challenge for head and neck squamous cell carcinoma (HNSCC) patients receiving targeted therapy. However, the mechanism that causes cetuximab resistance, especially microRNA (miRNA) regulation, remains unclear. Growing evidence suggests that miRNAs may act as "nuclear activating miRNAs" for targeting promoter regions or enhancers related to target genes. This study elucidates a novel mechanism underlying cetuximab resistance in HNSCC involving the nuclear activation of KDM7A transcription via miR-451a. Herein, small RNA sequencing, quantitative real-time polymerase chain reaction (qRT‒PCR) and fluorescence in situ hybridization (FISH) results provided compelling evidence of miR-451a nuclear enrichment in response to cetuximab treatment. Chromatin isolation via RNA purification, microarray analysis, and bioinformatic analysis revealed that miR-451a interacts with an enhancer region in KDM7A, activating its expression and further facilitating cetuximab resistance. It has also been demonstrated that the activation of KDM7A by nuclear miR-451a is induced by cetuximab treatment and is AGO2 dependent. Logistic regression analyses of 87 HNSCC samples indicated the significance of miR-451a and KDM7A in the development of cetuximab resistance. These discoveries support the potential of miR-451a and KDM7A as valuable biomarkers for cetuximab resistance and emphasize the function of nuclear-activating miRNAs.
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Affiliation(s)
- Peisong Zhai
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, People's Republic of China
| | - Tong Tong
- Department of Oral and Maxillofacial Surgery, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200001, People's Republic of China
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, 200002, People's Republic of China
| | - Xiaoning Wang
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, People's Republic of China
| | - Chuwen Li
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, People's Republic of China
| | - Chun Liu
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, People's Republic of China
| | - Xing Qin
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, People's Republic of China
| | - Shu Li
- Department of Clinical Laboratory, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People's Republic of China
| | - Fei Xie
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, People's Republic of China
| | - Jiayi Mao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People's Republic of China
| | - Jianjun Zhang
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, People's Republic of China.
| | - Haiyan Guo
- Department of Clinical Laboratory, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People's Republic of China.
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Xie R, Yuan S, Hu G, Zhan J, Jin K, Tang Y, Fan J, Zhao Y, Wang F, Chen C, Wang DW, Li H. Nuclear AGO2 promotes myocardial remodeling by activating ANKRD1 transcription in failing hearts. Mol Ther 2024; 32:1578-1594. [PMID: 38475992 PMCID: PMC11081878 DOI: 10.1016/j.ymthe.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/01/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024] Open
Abstract
Heart failure (HF) is manifested by transcriptional and posttranscriptional reprogramming of critical genes. Multiple studies have revealed that microRNAs could translocate into subcellular organelles such as the nucleus to modify gene expression. However, the functional property of subcellular Argonaute2 (AGO2), the core member of the microRNA machinery, has remained elusive in HF. AGO2 was found to be localized in both the cytoplasm and nucleus of cardiomyocytes, and robustly increased in the failing hearts of patients and animal models. We demonstrated that nuclear AGO2 rather than cytosolic AGO2 overexpression by recombinant adeno-associated virus (serotype 9) with cardiomyocyte-specific troponin T promoter exacerbated the cardiac dysfunction in transverse aortic constriction (TAC)-operated mice. Mechanistically, nuclear AGO2 activates the transcription of ANKRD1, encoding ankyrin repeat domain-containing protein 1 (ANKRD1), which also has a dual function in the cytoplasm as part of the I-band of the sarcomere and in the nucleus as a transcriptional cofactor. Overexpression of nuclear ANKRD1 recaptured some key features of cardiac remodeling by inducing pathological MYH7 activation, whereas cytosolic ANKRD1 seemed cardioprotective. For clinical practice, we found ivermectin, an antiparasite drug, and ANPep, an ANKRD1 nuclear location signal mimetic peptide, were able to prevent ANKRD1 nuclear import, resulting in the improvement of cardiac performance in TAC-induced HF.
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Affiliation(s)
- Rong Xie
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Shuai Yuan
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Guo Hu
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Jiabing Zhan
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Kunying Jin
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Yuyan Tang
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Jiahui Fan
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Yanru Zhao
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Feng Wang
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Chen Chen
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China.
| | - Dao Wen Wang
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China.
| | - Huaping Li
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China.
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6
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Nie X, Fan J, Dai B, Wen Z, Li H, Chen C, Wang DW. LncRNA CHKB-DT Downregulation Enhances Dilated Cardiomyopathy Through ALDH2. Circ Res 2024; 134:425-441. [PMID: 38299365 DOI: 10.1161/circresaha.123.323428] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
BACKGROUND Human cardiac long noncoding RNA (lncRNA) profiles in patients with dilated cardiomyopathy (DCM) were previously analyzed, and the long noncoding RNA CHKB (choline kinase beta) divergent transcript (CHKB-DT) levels were found to be mostly downregulated in the heart. In this study, the function of CHKB-DT in DCM was determined. METHODS Long noncoding RNA expression levels in the human heart tissues were measured via quantitative reverse transcription-polymerase chain reaction and in situ hybridization assays. A CHKB-DT heterozygous or homozygous knockout mouse model was generated using the clustered regularly interspaced palindromic repeat (CRISPR)/CRISPR-associated protein 9 system, and the adeno-associated virus with a cardiac-specific promoter was used to deliver the RNA in vivo. Sarcomere shortening was performed to assess the primary cardiomyocyte contractility. The Seahorse XF cell mitochondrial stress test was performed to determine the energy metabolism and ATP production. Furthermore, the underlying mechanisms were explored using quantitative proteomics, ribosome profiling, RNA antisense purification assays, mass spectrometry, RNA pull-down, luciferase assay, RNA-fluorescence in situ hybridization, and Western blotting. RESULTS CHKB-DT levels were remarkably decreased in patients with DCM and mice with transverse aortic constriction-induced heart failure. Heterozygous knockout of CHKB-DT in cardiomyocytes caused cardiac dilation and dysfunction and reduced the contractility of primary cardiomyocytes. Moreover, CHKB-DT heterozygous knockout impaired mitochondrial function and decreased ATP production as well as cardiac energy metabolism. Mechanistically, ALDH2 (aldehyde dehydrogenase 2) was a direct target of CHKB-DT. CHKB-DT physically interacted with the mRNA of ALDH2 and fused in sarcoma (FUS) through the GGUG motif. CHKB-DT knockdown aggravated ALDH2 mRNA degradation and 4-HNE (4-hydroxy-2-nonenal) production, whereas overexpression of CHKB-DT reversed these molecular changes. Furthermore, restoring ALDH2 expression in CHKB-DT+/- mice alleviated cardiac dilation and dysfunction. CONCLUSIONS CHKB-DT is significantly downregulated in DCM. CHKB-DT acts as an energy metabolism-associated long noncoding RNA and represents a promising therapeutic target against DCM.
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MESH Headings
- Animals
- Humans
- Mice
- Adenosine Triphosphate/metabolism
- Aldehyde Dehydrogenase, Mitochondrial/genetics
- Aldehyde Dehydrogenase, Mitochondrial/metabolism
- Cardiomyopathy, Dilated/genetics
- Cardiomyopathy, Dilated/metabolism
- Down-Regulation
- In Situ Hybridization, Fluorescence
- Mice, Knockout
- Mitochondria, Heart/metabolism
- Myocytes, Cardiac/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
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Affiliation(s)
- Xiang Nie
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College (X.N., J.F., B.D., Z.W., H.L., C.C., D.W.W.), Huazhong University of Science and Technology, Wuhan, China
| | - Jiahui Fan
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College (X.N., J.F., B.D., Z.W., H.L., C.C., D.W.W.), Huazhong University of Science and Technology, Wuhan, China
| | - Beibei Dai
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College (X.N., J.F., B.D., Z.W., H.L., C.C., D.W.W.), Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders (B.D., Z.W., H.L.), Huazhong University of Science and Technology, Wuhan, China
| | - Zheng Wen
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College (X.N., J.F., B.D., Z.W., H.L., C.C., D.W.W.), Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders (B.D., Z.W., H.L.), Huazhong University of Science and Technology, Wuhan, China
| | - Huaping Li
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College (X.N., J.F., B.D., Z.W., H.L., C.C., D.W.W.), Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders (B.D., Z.W., H.L.), Huazhong University of Science and Technology, Wuhan, China
| | - Chen Chen
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College (X.N., J.F., B.D., Z.W., H.L., C.C., D.W.W.), Huazhong University of Science and Technology, Wuhan, China
| | - Dao Wen Wang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College (X.N., J.F., B.D., Z.W., H.L., C.C., D.W.W.), Huazhong University of Science and Technology, Wuhan, China
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7
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Shi Y, Zhen X, Zhang Y, Li Y, Koo S, Saiding Q, Kong N, Liu G, Chen W, Tao W. Chemically Modified Platforms for Better RNA Therapeutics. Chem Rev 2024; 124:929-1033. [PMID: 38284616 DOI: 10.1021/acs.chemrev.3c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
RNA-based therapies have catalyzed a revolutionary transformation in the biomedical landscape, offering unprecedented potential in disease prevention and treatment. However, despite their remarkable achievements, these therapies encounter substantial challenges including low stability, susceptibility to degradation by nucleases, and a prominent negative charge, thereby hindering further development. Chemically modified platforms have emerged as a strategic innovation, focusing on precise alterations either on the RNA moieties or their associated delivery vectors. This comprehensive review delves into these platforms, underscoring their significance in augmenting the performance and translational prospects of RNA-based therapeutics. It encompasses an in-depth analysis of various chemically modified delivery platforms that have been instrumental in propelling RNA therapeutics toward clinical utility. Moreover, the review scrutinizes the rationale behind diverse chemical modification techniques aiming at optimizing the therapeutic efficacy of RNA molecules, thereby facilitating robust disease management. Recent empirical studies corroborating the efficacy enhancement of RNA therapeutics through chemical modifications are highlighted. Conclusively, we offer profound insights into the transformative impact of chemical modifications on RNA drugs and delineates prospective trajectories for their future development and clinical integration.
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Affiliation(s)
- Yesi Shi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Xueyan Zhen
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yiming Zhang
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yongjiang Li
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Seyoung Koo
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Qimanguli Saiding
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Na Kong
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Gang Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Wei Chen
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
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Yan J, Zhang H, Li G, Su J, Wei Y, Xu C. Lipid nanovehicles overcome barriers to systemic RNA delivery: Lipid components, fabrication methods, and rational design. Acta Pharm Sin B 2024; 14:579-601. [PMID: 38322344 PMCID: PMC10840434 DOI: 10.1016/j.apsb.2023.10.012] [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: 07/17/2023] [Revised: 09/24/2023] [Accepted: 10/08/2023] [Indexed: 02/08/2024] Open
Abstract
Lipid nanovehicles are currently the most advanced vehicles used for RNA delivery, as demonstrated by the approval of patisiran for amyloidosis therapy in 2018. To illuminate the unique superiority of lipid nanovehicles in RNA delivery, in this review, we first introduce various RNA therapeutics, describe systemic delivery barriers, and explain the lipid components and methods used for lipid nanovehicle preparation. Then, we emphasize crucial advances in lipid nanovehicle design for overcoming barriers to systemic RNA delivery. Finally, the current status and challenges of lipid nanovehicle-based RNA therapeutics in clinical applications are also discussed. Our objective is to provide a comprehensive overview showing how to utilize lipid nanovehicles to overcome multiple barriers to systemic RNA delivery, inspiring the development of more high-performance RNA lipid nanovesicles in the future.
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Affiliation(s)
- Jing Yan
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
- Institute of Medicine, Shanghai University, Shanghai 200444, China
| | - Hao Zhang
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
- Department of Orthopedics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Guangfeng Li
- Department of Orthopedics, Shanghai Zhongye Hospital, Shanghai 200941, China
| | - Jiacan Su
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
- Department of Orthopedics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
- Organoid Research Center, Shanghai University, Shanghai 200444, China
| | - Yan Wei
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
- Organoid Research Center, Shanghai University, Shanghai 200444, China
| | - Can Xu
- Department of Gastroenterology, Changhai Hospital, Shanghai 200433, China
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9
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Rehman SU, Ullah N, Zhang Z, Zhen Y, Din AU, Cui H, Wang M. Recent insights into the functions and mechanisms of antisense RNA: emerging applications in cancer therapy and precision medicine. Front Chem 2024; 11:1335330. [PMID: 38274897 PMCID: PMC10809404 DOI: 10.3389/fchem.2023.1335330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
The antisense RNA molecule is a unique DNA transcript consisting of 19-23 nucleotides, characterized by its complementary nature to mRNA. These antisense RNAs play a crucial role in regulating gene expression at various stages, including replication, transcription, and translation. Additionally, artificial antisense RNAs have demonstrated their ability to effectively modulate gene expression in host cells. Consequently, there has been a substantial increase in research dedicated to investigating the roles of antisense RNAs. These molecules have been found to be influential in various cellular processes, such as X-chromosome inactivation and imprinted silencing in healthy cells. However, it is important to recognize that in cancer cells; aberrantly expressed antisense RNAs can trigger the epigenetic silencing of tumor suppressor genes. Moreover, the presence of deletion-induced aberrant antisense RNAs can lead to the development of diseases through epigenetic silencing. One area of drug development worth mentioning is antisense oligonucleotides (ASOs), and a prime example of an oncogenic trans-acting long noncoding RNA (lncRNA) is HOTAIR (HOX transcript antisense RNA). NATs (noncoding antisense transcripts) are dysregulated in many cancers, and researchers are just beginning to unravel their roles as crucial regulators of cancer's hallmarks, as well as their potential for cancer therapy. In this review, we summarize the emerging roles and mechanisms of antisense RNA and explore their application in cancer therapy.
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Affiliation(s)
- Shahab Ur Rehman
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
| | - Numan Ullah
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
| | - Zhenbin Zhang
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
| | - Yongkang Zhen
- College of Animals Nutrition Yangzhou University, Yangzhou, China
| | - Aziz-Ud Din
- Department of Human Genetics, Hazara University Mansehra, Mansehra, Pakistan
| | - Hengmi Cui
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
- Institute of Epigenetics and Epigenomics Yangzhou University, College of Animal Nutrition Yangzhou University, Yangzhou, China
| | - Mengzhi Wang
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
- College of Animals Nutrition Yangzhou University, Yangzhou, China
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10
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Luo J, Ji Y, Chen N, Song G, Zhou S, Niu X, Yu D. Nuclear miR-150 enhances hepatic lipid accumulation by targeting RNA transcripts overlapping the PLIN2 promoter. iScience 2023; 26:107837. [PMID: 37736048 PMCID: PMC10509351 DOI: 10.1016/j.isci.2023.107837] [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: 06/08/2023] [Revised: 07/09/2023] [Accepted: 09/02/2023] [Indexed: 09/23/2023] Open
Abstract
Alcohol-associated liver disease is a prevalent chronic liver disease caused by excessive ethanol consumption. This study aims to investigate the role of miR-150 in regulating hepatic lipid homeostasis in alcoholic fatty liver (AFL). miR-150 was mainly distributed in the nucleus of hepatocytes and correlated with the degree of liver injury. The decreased expression of miR-150 observed in AFL was a compensatory response to ethanol-induced hepatic steatosis. Overexpression of miR-150 facilitated hepatic lipid accumulation in cellulo and exacerbated ethanol-induced liver steatosis in vivo. In silico analysis identified perilipin-2 (PLIN2) as a potential target gene of miR-150. miR-150 activated PLIN2 transcription by directly binding the RNA transcripts overlapping PLIN2 promoter and facilitating the recruitment of DNA helicase DHX9 and RNA polymeraseⅡ. Overall, our study provides fresh insights into the homeostasis regulation of hepatic steatosis induced by ethanol and identifies miR-150 as a pro-steatosis effector driving transcriptional PLIN2 gene activation.
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Affiliation(s)
- Jiao Luo
- School of Public Health, Qingdao University, Qingdao, China
| | - Yanan Ji
- School of Public Health, Qingdao University, Qingdao, China
| | - Ningning Chen
- School of Public Health, Qingdao University, Qingdao, China
| | - Ge Song
- School of Public Health, Qingdao University, Qingdao, China
| | - Shuyue Zhou
- School of Public Health, Qingdao University, Qingdao, China
| | - Xuan Niu
- School of Public Health, Qingdao University, Qingdao, China
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao, China
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11
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Wang M, Wang Y, Yang L, Du X, Li Q. Nuclear lncRNA NORSF reduces E2 release in granulosa cells by sponging the endogenous small activating RNA miR-339. BMC Biol 2023; 21:221. [PMID: 37858148 PMCID: PMC10588145 DOI: 10.1186/s12915-023-01731-x] [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: 05/28/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Functioning as a competing endogenous RNA (ceRNA) is the main action mechanism of most cytoplasmic lncRNAs. However, it is not known whether this mechanism of action also exists in the nucleus. RESULTS We identified four nuclear lncRNAs that are presented in granulosa cells (GCs) and were differentially expressed during sow follicular atresia. Notably, similar to cytoplasmic lncRNAs, these nuclear lncRNAs also sponge miRNAs in the nucleus of GCs through direct interactions. Furthermore, NORSF (non-coding RNA involved in sow fertility), one of the nuclear lncRNA acts as a ceRNA of miR-339. Thereby, it relieves the regulatory effect of miR-339 on CYP19A1 encoding P450arom, a rate-limiting enzyme for E2 synthesis in GCs. Interestingly, miR-339 acts as a saRNA that activates CYP19A1 transcription and enhances E2 release by GCs through altering histone modifications in the promoter by directly binding to the CYP19A1 promoter. Functionally, NORSF inhibited E2 release by GCs via the miR-339 and CYP19A1 axis. CONCLUSIONS Our findings highlight an unappreciated mechanism of nuclear lncRNAs and show it acts as a ceRNA, which may be a common lncRNA function in the cytoplasm and nucleus. We also identified a potential endogenous saRNA for improving female fertility and treating female infertility.
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Affiliation(s)
- Miaomiao Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Liu Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xing Du
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qifa Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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12
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Kwofie KD, Hernandez EP, Anisuzzaman, Kawada H, Koike Y, Sasaki S, Inoue T, Jimbo K, Mikami F, Ladzekpo D, Umemiya-Shirafuji R, Yamaji K, Tanaka T, Matsubayashi M, Alim MA, Dadzie SK, Iwanaga S, Tsuji N, Hatta T. RNA activation in ticks. Sci Rep 2023; 13:9341. [PMID: 37291173 PMCID: PMC10250327 DOI: 10.1038/s41598-023-36523-4] [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: 02/22/2023] [Accepted: 06/05/2023] [Indexed: 06/10/2023] Open
Abstract
RNA activation (RNAa) is a burgeoning area of research in which double-stranded RNAs (dsRNAs) or small activating RNAs mediate the upregulation of specific genes by targeting the promoter sequence and/or AU-rich elements in the 3'- untranslated region (3'-UTR) of mRNA molecules. So far, studies on the phenomenon have been limited to mammals, plants, bacteria, Caenorhabditis elegans, and recently, Aedes aegypti. However, it is yet to be applied in other arthropods, including ticks, despite the ubiquitous presence of argonaute 2 protein, which is an indispensable requirement for the formation of RNA-induced transcriptional activation complex to enable a dsRNA-mediated gene activation. In this study, we demonstrated for the first time the possible presence of RNAa phenomenon in the tick vector, Haemaphysalis longicornis (Asian longhorned tick). We targeted the 3'-UTR of a novel endochitinase-like gene (HlemCHT) identified previously in H. longicornis eggs for dsRNA-mediated gene activation. Our results showed an increased gene expression in eggs of H. longicornis endochitinase-dsRNA-injected (dsHlemCHT) ticks on day-13 post-oviposition. Furthermore, we observed that eggs of dsHlemCHT ticks exhibited relatively early egg development and hatching, suggesting a dsRNA-mediated activation of the HlemCHT gene in the eggs. This is the first attempt to provide evidence of RNAa in ticks. Although further studies are required to elucidate the detailed mechanism by which RNAa occurs in ticks, the outcome of this study provides new opportunities for the use of RNAa as a gene overexpression tool in future studies on tick biology, to reduce the global burden of ticks and tick-borne diseases.
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Affiliation(s)
- Kofi Dadzie Kwofie
- Department of Parasitology and Tropical Medicine, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana
| | - Emmanuel Pacia Hernandez
- Department of Parasitology and Tropical Medicine, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan
- Department of Veterinary Paraclinical Sciences, College of Veterinary Medicine, University of the Philippines at Los Baños, College, 4031, Laguna, Philippines
| | - Anisuzzaman
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Hayato Kawada
- Department of Parasitology and Tropical Medicine, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan
- Department of Molecular and Cellular Parasitology, Graduate School of Medical Sciences, Kitasato University, Sagamihara, Kanagawa, 252-0374, Japan
| | - Yuki Koike
- Department of Molecular and Cellular Parasitology, Graduate School of Medical Sciences, Kitasato University, Sagamihara, Kanagawa, 252-0374, Japan
| | - Sana Sasaki
- Department of Molecular and Cellular Parasitology, Graduate School of Medical Sciences, Kitasato University, Sagamihara, Kanagawa, 252-0374, Japan
| | - Takahiro Inoue
- Department of Molecular and Cellular Parasitology, Graduate School of Medical Sciences, Kitasato University, Sagamihara, Kanagawa, 252-0374, Japan
| | - Kei Jimbo
- Department of Molecular and Cellular Parasitology, Graduate School of Medical Sciences, Kitasato University, Sagamihara, Kanagawa, 252-0374, Japan
| | - Fusako Mikami
- Department of Parasitology and Tropical Medicine, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan
| | - Danielle Ladzekpo
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana
- Department of Environmental Parasitology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Rika Umemiya-Shirafuji
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
| | - Kayoko Yamaji
- Department of Tropical Medicine and Center for Medical Entomology, The Jikei University School of Medicine, Minato-ku, Tokyo, 105-8461, Japan
| | - Tetsuya Tanaka
- Laboratory of Infectious Diseases, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Makoto Matsubayashi
- Department of Veterinary Immunology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, Izumisano, Osaka, 598-8531, Japan
| | - Md Abdul Alim
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Samuel Kweku Dadzie
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana
| | - Shiroh Iwanaga
- Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
- Center for Infectious Disease Education and Research (CIDER), Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Naotoshi Tsuji
- Department of Parasitology and Tropical Medicine, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan
- Department of Molecular and Cellular Parasitology, Graduate School of Medical Sciences, Kitasato University, Sagamihara, Kanagawa, 252-0374, Japan
| | - Takeshi Hatta
- Department of Parasitology and Tropical Medicine, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan.
- Department of Molecular and Cellular Parasitology, Graduate School of Medical Sciences, Kitasato University, Sagamihara, Kanagawa, 252-0374, Japan.
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13
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MiRNAs in Hematopoiesis and Acute Lymphoblastic Leukemia. Int J Mol Sci 2023; 24:ijms24065436. [PMID: 36982511 PMCID: PMC10049736 DOI: 10.3390/ijms24065436] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 03/14/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common kind of pediatric cancer. Although the cure rates in ALL have significantly increased in developed countries, still 15–20% of patients relapse, with even higher rates in developing countries. The role of non-coding RNA genes as microRNAs (miRNAs) has gained interest from researchers in regard to improving our knowledge of the molecular mechanisms underlying ALL development, as well as identifying biomarkers with clinical relevance. Despite the wide heterogeneity reveled in miRNA studies in ALL, consistent findings give us confidence that miRNAs could be useful to discriminate between leukemia linages, immunophenotypes, molecular groups, high-risk-for-relapse groups, and poor/good responders to chemotherapy. For instance, miR-125b has been associated with prognosis and chemoresistance in ALL, miR-21 has an oncogenic role in lymphoid malignancies, and the miR-181 family can act either as a oncomiR or tumor suppressor in several hematological malignancies. However, few of these studies have explored the molecular interplay between miRNAs and their targeted genes. This review aims to state the different ways in which miRNAs could be involved in ALL and their clinical implications.
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14
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Herbert A, Pavlov F, Konovalov D, Poptsova M. Conserved microRNAs and Flipons Shape Gene Expression during Development by Altering Promoter Conformations. Int J Mol Sci 2023; 24:ijms24054884. [PMID: 36902315 PMCID: PMC10003719 DOI: 10.3390/ijms24054884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
The classical view of gene regulation draws from prokaryotic models, where responses to environmental changes involve operons regulated by sequence-specific protein interactions with DNA, although it is now known that operons are also modulated by small RNAs. In eukaryotes, pathways based on microRNAs (miR) regulate the readout of genomic information from transcripts, while alternative nucleic acid structures encoded by flipons influence the readout of genetic programs from DNA. Here, we provide evidence that miR- and flipon-based mechanisms are deeply connected. We analyze the connection between flipon conformation and the 211 highly conserved human miR that are shared with other placental and other bilateral species. The direct interaction between conserved miR (c-miR) and flipons is supported by sequence alignments and the engagement of argonaute proteins by experimentally validated flipons as well as their enrichment in promoters of coding transcripts important in multicellular development, cell surface glycosylation and glutamatergic synapse specification with significant enrichments at false discovery rates as low as 10-116. We also identify a second subset of c-miR that targets flipons essential for retrotransposon replication, exploiting that vulnerability to limit their spread. We propose that miR can act in a combinatorial manner to regulate the readout of genetic information by specifying when and where flipons form non-B DNA (NoB) conformations, providing the interactions of the conserved hsa-miR-324-3p with RELA and the conserved hsa-miR-744 with ARHGAP5 genes as examples.
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Affiliation(s)
- Alan Herbert
- InsideOutBio, 42 8th Street, Charlestown, MA 02129, USA
- Correspondence:
| | - Fedor Pavlov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia
| | - Dmitrii Konovalov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia
| | - Maria Poptsova
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia
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15
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Zhang Q, Guo Y, Kang M, Lin WH, Wu JC, Yu Y, Li LC, Sang A. p21CIP/WAF1 saRNA inhibits proliferative vitreoretinopathy in a rabbit model. PLoS One 2023; 18:e0282063. [PMID: 36821623 PMCID: PMC9949646 DOI: 10.1371/journal.pone.0282063] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
PURPOSE Proliferative vitreoretinopathy (PVR) is a disease process resulting from proliferation of retinal pigment epithelial (RPE) cells in the vitreous and periretinal area, leading to periretinal membrane formation and traction and eventually to postoperative failure after vitreo-retinal surgery for primary rhegmatogenous retinal detachment (RRD). The present study was designed to test the therapeutic potential of a p21CIP/WAF1 (p21) inducing saRNA for PVR. METHODS A chemically modified p21 saRNA (RAG1-40-53) was tested in cultured human RPE cells for p21 induction and for the inhibition of cell proliferation, migration and cell cycle progression. RAG1-40-53 was further conjugated to a cholesterol moiety and tested for pharmacokinetics and pharmacodynamics in rabbit eyes and for therapeutic effects after intravitreal administration in a rabbit PVR model established by injecting human RPE cells. RESULTS RAG1-40-53 (0.3 mg, 1 mg) significantly induced p21 expression in RPE cells and inhibited cell proliferation, the progression of cell cycle at the G0/G1 phase and TGF-β1 induced migration. After a single intravitreal injection into rabbit eyes, cholesterol-conjugated RAG1-40-53 exhibited sustained concentration in the vitreal humor beyond at least 8 days and prevented the progression of established PVR. CONCLUSION p21 saRNA could represent a novel therapeutics for PVR by exerting a antiproliferation and antimigration effect on RPE cells.
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Affiliation(s)
- Qi Zhang
- Department of Ophthalmology, Affiliated Hospital and Medical School of Nantong University, Nantong City, Jiangsu Province, China
- Dalian Medical University, Lvshunkou District, Dalian City, Liaoning Province, China
| | - Yangchen Guo
- Department of Ophthalmology, Affiliated Hospital and Medical School of Nantong University, Nantong City, Jiangsu Province, China
- Nantong University, Nantong City, Jiangsu Province, China
| | - Moorim Kang
- Ractigen Therapeutics, Nantong City, Jiangsu Province, China
| | - Wei-Hsiang Lin
- Ractigen Therapeutics, Nantong City, Jiangsu Province, China
| | - Jian-Cheng Wu
- Ractigen Therapeutics, Nantong City, Jiangsu Province, China
| | - Ying Yu
- Department of Ophthalmology, Affiliated Hospital and Medical School of Nantong University, Nantong City, Jiangsu Province, China
- * E-mail: (LCL); (YY); (AS)
| | - Long-Cheng Li
- Ractigen Therapeutics, Nantong City, Jiangsu Province, China
- Institute of Reproductive Medicine, Nantong University, Nantong City, Jiangsu Province, China
- * E-mail: (LCL); (YY); (AS)
| | - Aimin Sang
- Department of Ophthalmology, Affiliated Hospital and Medical School of Nantong University, Nantong City, Jiangsu Province, China
- * E-mail: (LCL); (YY); (AS)
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16
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Wang Y, Liu K, Zhou Y, Chen Y, Jin C, Hu Y. Integrated Analysis of microRNA and RNA-Seq Reveals Phenolic Acid Secretion Metabolism in Continuous Cropping of Polygonatum odoratum. PLANTS (BASEL, SWITZERLAND) 2023; 12:943. [PMID: 36840290 PMCID: PMC9962977 DOI: 10.3390/plants12040943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Polygonatum odoratum (Mill.) Druce is an essential Chinese herb, but continuous cropping (CC) often results in a serious root rot disease, reducing the yield and quality. Phenolic acids, released through plant root exudation, are typical autotoxic substances that easily cause root rot in CC. To better understand the phenolic acid biosynthesis of P. odoratum roots in response to CC, this study performed a combined microRNA (miRNA)-seq and RNA-seq analysis. The phenolic acid contents of the first cropping (FC) soil and CC soil were determined by HPLC analysis. The results showed that CC soils contained significantly higher levels of p-coumaric acid, phenylacetate, and caffeic acid than FC soil, except for cinnamic acid and sinapic acid. Transcriptome identification and miRNA sequencing revealed 15,788 differentially expressed genes (DEGs) and 142 differentially expressed miRNAs (DEMs) in roots from FC and CC plants. Among them, 28 DEGs and eight DEMs were involved in phenolic acid biosynthesis. Meanwhile, comparative transcriptome and microRNA-seq analysis demonstrated that eight miRNAs corresponding to five target DEGs related to phenolic acid synthesis were screened. Among them, ath-miR172a, ath-miR172c, novel_130, sbi-miR172f, and tcc-miR172d contributed to phenylalanine synthesis. Osa-miR528-5p and mtr-miR2673a were key miRNAs that regulate syringyl lignin biosynthesis. Nta-miR156f was closely related to the shikimate pathway. These results indicated that the key DEGs and DEMs involved in phenolic acid anabolism might play vital roles in phenolic acid secretion from roots of P. odoratum under the CC system. As a result of the study, we may have a better understanding of phenolic acid biosynthesis during CC of roots of P. odoratum.
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Affiliation(s)
- Yan Wang
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha 410082, China
| | - Kaitai Liu
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Yunyun Zhou
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Yong Chen
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Chenzhong Jin
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Yihong Hu
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
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17
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Roth C, Kilpinen H, Kurian MA, Barral S. Histone lysine methyltransferase-related neurodevelopmental disorders: current knowledge and saRNA future therapies. Front Cell Dev Biol 2023; 11:1090046. [PMID: 36923252 PMCID: PMC10009263 DOI: 10.3389/fcell.2023.1090046] [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: 12/07/2022] [Accepted: 02/06/2023] [Indexed: 03/02/2023] Open
Abstract
Neurodevelopmental disorders encompass a group of debilitating diseases presenting with motor and cognitive dysfunction, with variable age of onset and disease severity. Advances in genetic diagnostic tools have facilitated the identification of several monogenic chromatin remodeling diseases that cause Neurodevelopmental disorders. Chromatin remodelers play a key role in the neuro-epigenetic landscape and regulation of brain development; it is therefore not surprising that mutations, leading to loss of protein function, result in aberrant neurodevelopment. Heterozygous, usually de novo mutations in histone lysine methyltransferases have been described in patients leading to haploinsufficiency, dysregulated protein levels and impaired protein function. Studies in animal models and patient-derived cell lines, have highlighted the role of histone lysine methyltransferases in the regulation of cell self-renewal, cell fate specification and apoptosis. To date, in depth studies of histone lysine methyltransferases in oncology have provided strong evidence of histone lysine methyltransferase dysregulation as a determinant of cancer progression and drug resistance. As a result, histone lysine methyltransferases have become an important therapeutic target for the treatment of different cancer forms. Despite recent advances, we still lack knowledge about the role of histone lysine methyltransferases in neuronal development. This has hampered both the study and development of precision therapies for histone lysine methyltransferases-related Neurodevelopmental disorders. In this review, we will discuss the current knowledge of the role of histone lysine methyltransferases in neuronal development and disease progression. We will also discuss how RNA-based technologies using small-activating RNAs could potentially provide a novel therapeutic approach for the future treatment of histone lysine methyltransferase haploinsufficiency in these Neurodevelopmental disorders, and how they could be first tested in state-of-the-art patient-derived neuronal models.
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Affiliation(s)
- Charlotte Roth
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Helena Kilpinen
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Manju A Kurian
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Department of Neurology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Serena Barral
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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RNA therapeutics: updates and future potential. SCIENCE CHINA. LIFE SCIENCES 2023; 66:12-30. [PMID: 36100838 PMCID: PMC9470505 DOI: 10.1007/s11427-022-2171-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/17/2022] [Indexed: 02/04/2023]
Abstract
Recent advancements in the production, modification, and cellular delivery of RNA molecules facilitated the expansion of RNA-based therapeutics. The increasing understanding of RNA biology initiated a corresponding growth in RNA therapeutics. In this review, the general concepts of five classes of RNA-based therapeutics, including RNA interference-based therapies, antisense oligonucleotides, small activating RNA therapies, circular RNA therapies, and messenger RNA-based therapeutics, will be discussed. Moreover, we also provide an overview of RNA-based therapeutics that have already received regulatory approval or are currently being evaluated in clinical trials, along with challenges faced by these technologies. RNA-based drugs demonstrated positive clinical trial results and have the ability to address previously "undruggable" targets, which delivers great promise as a disruptive therapeutic technology to fulfill its full clinical potentiality.
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19
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Li Q, Huo Y, Wang S, Yang L, Li Q, Du X. TGF-β1 regulates the lncRNA transcriptome of ovarian granulosa cells in a transcription activity-dependent manner. Cell Prolif 2023; 56:e13336. [PMID: 36125095 DOI: 10.1111/cpr.13336] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVES Transforming growth factor β1 (TGF-β1), an essential cytokine belongs to TGF-β superfamily, is crucial for female fertility. Increasing evidence show that long noncoding RNAs (lncRNAs) influence the state of granulosa cells (GCs). This study aimed to detect the effects of TGF-β1 on the lncRNA transcriptome, and investigate whether lncRNAs mediate the functions of TGF-β1 in GCs. MATERIAL AND METHODS RNA-seq and bioinformatics analyses were performed to identify and characterize the differentially expressed lncRNAs (DElncRNAs). The regulatory mechanism of TGF-β1 to lncRNA transcriptome was analyzed by chromatin immunoprecipitation. The effects of lncRNAs on the antiapoptotic and proproliferative functions of TGF-β1 were examined by morphological analysis, fluorescence-activated cell sorting, Cell Counting Kit-8, and Western blot. RESULTS A total of 72 DElncRNAs highly sensitive to TGF-β1 were identified with the criteria of |log2 (fold chage)| ≥ 3 and false discovery rate < 0.05. Functional assessment showed that DElncRNAs were enriched in TGF-β, nuclear factor kappa B, p53, and Hippo pathways which are crucial for the normal state and function of GCs. Importantly, SMAD4 is essential for the regulation of TGF-β1 to lncRNA transcriptome. In vitro studies confirmed that TGF-β1 induced TEX14-IT1 transcription in a SMAD4-dependent manner, and TEX14-IT1 mediated the antiapoptotic and proproliferative effects of TGF-β1 in GCs. CONCLUSIONS Our findings demonstrate that TGF-β1 alters lncRNA transcriptome in a SMAD4-dependent manner, and highlight that lncRNAs mediate the functions of TGF-β1 in GCs, which contribute to a better understanding of the epigenetic regulation of female fertility.
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Affiliation(s)
- Qiqi Li
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yangan Huo
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Siqi Wang
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Liu Yang
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Qifa Li
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xing Du
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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20
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Gregory GL, Copple IM. Modulating the expression of tumor suppressor genes using activating oligonucleotide technologies as a therapeutic approach in cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 31:211-223. [PMID: 36700046 PMCID: PMC9840112 DOI: 10.1016/j.omtn.2022.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tumor suppressor genes (TSGs) are frequently downregulated in cancer, leading to dysregulation of the pathways that they control. The continuum model of tumor suppression suggests that even subtle changes in TSG expression, for example, driven by epigenetic modifications or copy number alterations, can lead to a loss of gene function and a phenotypic effect. This approach to exploring tumor suppression provides opportunities for alternative therapies that may be able to restore TSG expression toward normal levels, such as oligonucleotide therapies. Oligonucleotide therapies involve the administration of exogenous nucleic acids to modulate the expression of specific endogenous genes. This review focuses on two types of activating oligonucleotide therapies, small-activating RNAs and synthetic mRNAs, as novel methods to increase the expression of TSGs in cancer.
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Affiliation(s)
- Georgina L. Gregory
- Department of Pharmacology & Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool L69 3GE, UK
| | - Ian M. Copple
- Department of Pharmacology & Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool L69 3GE, UK
- Corresponding author: Department of Pharmacology & Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool L69 3GE, UK.
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21
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Wang F, Calvo-Roitberg E, Rembetsy-Brown JM, Fang M, Sousa J, Kartje Z, Krishnamurthy PM, Lee J, Green M, Pai A, Watts J. G-rich motifs within phosphorothioate-based antisense oligonucleotides (ASOs) drive activation of FXN expression through indirect effects. Nucleic Acids Res 2022; 50:12657-12673. [PMID: 36511872 PMCID: PMC9825156 DOI: 10.1093/nar/gkac1108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/11/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
Friedreich's ataxia is an incurable disease caused by frataxin (FXN) protein deficiency, which is mostly induced by GAA repeat expansion in intron 1 of the FXN gene. Here, we identified antisense oligonucleotides (ASOs), complementary to two regions within the first intron of FXN pre-mRNA, which could increase FXN mRNA by ∼2-fold in patient fibroblasts. The increase in FXN mRNA was confirmed by the identification of multiple overlapping FXN-activating ASOs at each region, two independent RNA quantification assays, and normalization by multiple housekeeping genes. Experiments on cells with the ASO-binding sites deleted indicate that the ASO-induced FXN activation was driven by indirect effects. RNA sequencing analyses showed that the two ASOs induced similar transcriptome-wide changes, which did not resemble the transcriptome of wild-type cells. This RNA-seq analysis did not identify directly base-paired off-target genes shared across ASOs. Mismatch studies identified two guanosine-rich motifs (CCGG and G4) within the ASOs that were required for FXN activation. The phosphorodiamidate morpholino oligomer analogs of our ASOs did not activate FXN, pointing to a PS-backbone-mediated effect. Our study demonstrates the importance of multiple, detailed control experiments and target validation in oligonucleotide studies employing novel mechanisms such as gene activation.
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Affiliation(s)
- Feng Wang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Ezequiel Calvo-Roitberg
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Julia M Rembetsy-Brown
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Minggang Fang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Zachary J Kartje
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | | | - Jonathan Lee
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Michael R Green
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Athma A Pai
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
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22
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Andrikakou P, Reebye V, Vasconcelos D, Yoon S, Voutila J, George AJT, Swiderski P, Habib R, Catley M, Blakey D, Habib NA, Rossi JJ, Huang KW. Enhancing SIRT1 Gene Expression Using Small Activating RNAs: A Novel Approach for Reversing Metabolic Syndrome. Nucleic Acid Ther 2022; 32:486-496. [PMID: 35895511 DOI: 10.1089/nat.2021.0115] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Metabolic syndrome (MetS) is a pathological condition characterized by abdominal obesity, insulin resistance, hypertension, and hyperlipidemia. Sirtuin 1 (SIRT1), a highly conserved histone deacetylase, is characterized as a key metabolic regulator and protector against aging-associated pathologies, including MetS. In this study, we investigate the therapeutic potential of activating SIRT1 using small activating RNAs (saRNA), thereby reducing inflammatory-like responses and re-establishing normal lipid metabolism. SIRT1 saRNA significantly increased SIRT1 messenger RNA (mRNA) and protein levels in both lipopolysaccharide-stimulated and nonstimulated macrophages. SIRT1 saRNA significantly decreased inflammatory-like responses, by reducing mRNA levels of key inflammatory cytokines, such as Tumor Necrosis Factor alpha, Interleukin 1 beta (IL-1β), Interleukin 6 (IL-6), and chemokines Monocyte Chemoattractant Protein-1 and keratinocyte chemoattractant. SIRT1 overexpression also significantly reduced phosphorylation of nuclear factor-κB and c-Jun N-terminal kinase, both key signaling molecules for the inflammatory pathway. To investigate the therapeutic effect of SIRT1 upregulation, we treated a high-fat diet model with SIRT1 saRNA conjugated to a transferrin receptor aptamer for delivery to the liver and cellular internalization. Animals in the SIRT1 saRNA treatment arm demonstrated significantly decreased weight gain with a significant reduction in white adipose tissue, triglycerides, fasting glucose levels, and intracellular lipid accumulation. These suggest treatment-induced changes to lipid and glucose metabolism in the animals. The results of this study demonstrate that targeted activation of SIRT1 by saRNAs is a potential strategy to reverse MetS.
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Affiliation(s)
- Pinelopi Andrikakou
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Vikash Reebye
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Daniel Vasconcelos
- MiNA Therapeutics Limited, London, United Kingdom.,Center for Drug Discovery and Innovative Medicines (MedInUP), University of Porto, Porto, Portugal
| | - Sorah Yoon
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Jon Voutila
- MiNA Therapeutics Limited, London, United Kingdom
| | | | - Piotr Swiderski
- DNA/RNA Synthesis Core Facility, Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Robert Habib
- MiNA Therapeutics Limited, London, United Kingdom
| | | | - David Blakey
- MiNA Therapeutics Limited, London, United Kingdom
| | - Nagy A Habib
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom.,MiNA Therapeutics Limited, London, United Kingdom
| | - John J Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Kai-Wen Huang
- Department of Surgery, Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan
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Xiong Y, Ke R, Zhang Q, Lan W, Yuan W, Chan KNI, Roussel T, Jiang Y, Wu J, Liu S, Wong AST, Shim JS, Zhang X, Xie R, Dusetti N, Iovanna J, Habib N, Peng L, Lee LTO. Small Activating RNA Modulation of the G Protein-Coupled Receptor for Cancer Treatment. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200562. [PMID: 35712764 PMCID: PMC9475523 DOI: 10.1002/advs.202200562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/23/2022] [Indexed: 06/15/2023]
Abstract
G protein-coupled receptors (GPCRs) are the most common and important drug targets. However, >70% of GPCRs are undruggable or difficult to target using conventional chemical agonists/antagonists. Small nucleic acid molecules, which can sequence-specifically modulate any gene, offer a unique opportunity to effectively expand drug targets, especially those that are undruggable or difficult to address, such as GPCRs. Here, the authors report for the first time that small activating RNAs (saRNAs) effectively modulate a GPCR for cancer treatment. Specifically, saRNAs promoting the expression of Mas receptor (MAS1), a GPCR that counteracts the classical angiotensin II pathway in cancer cell proliferation and migration, are identified. These saRNAs, delivered by an amphiphilic dendrimer vector, enhance MAS1 expression, counteracting the angiotensin II/angiotensin II Receptor Type 1 axis, and leading to significant suppression of tumorigenesis and the inhibition of tumor progression of multiple cancers in tumor-xenografted mouse models and patient-derived tumor models. This study provides not only a new strategy for cancer therapy by targeting the renin-angiotensin system, but also a new avenue to modulate GPCR signaling by RNA activation.
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Affiliation(s)
- Yunfang Xiong
- Cancer CentreFaculty of Health SciencesUniversity of MacauTaipaMacau999078China
| | - Ran Ke
- Cancer CentreFaculty of Health SciencesUniversity of MacauTaipaMacau999078China
| | - Qingyu Zhang
- Department of Obstetrics and GynaecologyAffiliated Hospital of Guangdong Medical UniversityZhanjiangGuangdong524001China
| | - Wenjun Lan
- Aix Marseille UniversitéCNRSCentre Interdisciplinaire de Nanoscience de Marseille (UMR 7325)Equipe Labellisée Ligue Contre le CancerMarseille13288France
- Centre de Recherche en Cancérologie de Marseille (CRCM)INSERM U1068CNRSAix‐Marseille Université and Institut Paoli‐CalmettesMarseille13288France
| | - Wanjun Yuan
- Cancer CentreFaculty of Health SciencesUniversity of MacauTaipaMacau999078China
| | - Karol Nga Ieng Chan
- Cancer CentreFaculty of Health SciencesUniversity of MacauTaipaMacau999078China
| | - Tom Roussel
- Aix Marseille UniversitéCNRSCentre Interdisciplinaire de Nanoscience de Marseille (UMR 7325)Equipe Labellisée Ligue Contre le CancerMarseille13288France
| | - Yifan Jiang
- Aix Marseille UniversitéCNRSCentre Interdisciplinaire de Nanoscience de Marseille (UMR 7325)Equipe Labellisée Ligue Contre le CancerMarseille13288France
| | - Jing Wu
- Aix Marseille UniversitéCNRSCentre Interdisciplinaire de Nanoscience de Marseille (UMR 7325)Equipe Labellisée Ligue Contre le CancerMarseille13288France
| | - Shuai Liu
- Cancer CentreFaculty of Health SciencesUniversity of MacauTaipaMacau999078China
| | - Alice Sze Tsai Wong
- School of Biological SciencesThe University of Hong KongPokfulam RoadHong KongChina
| | - Joong Sup Shim
- Cancer CentreFaculty of Health SciencesUniversity of MacauTaipaMacau999078China
- MOE Frontiers Science Center for Precision OncologyUniversity of MacauTaipaMacau999078China
| | - Xuanjun Zhang
- Cancer CentreFaculty of Health SciencesUniversity of MacauTaipaMacau999078China
- MOE Frontiers Science Center for Precision OncologyUniversity of MacauTaipaMacau999078China
| | - Ruiyu Xie
- Cancer CentreFaculty of Health SciencesUniversity of MacauTaipaMacau999078China
- MOE Frontiers Science Center for Precision OncologyUniversity of MacauTaipaMacau999078China
| | - Nelson Dusetti
- Centre de Recherche en Cancérologie de Marseille (CRCM)INSERM U1068CNRSAix‐Marseille Université and Institut Paoli‐CalmettesMarseille13288France
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM)INSERM U1068CNRSAix‐Marseille Université and Institut Paoli‐CalmettesMarseille13288France
| | - Nagy Habib
- Department of Surgery and CancerImperial College LondonLondonW12 0NNUK
- MiNA Therapeutics, Translation & Innovation Hub80 Wood LaneLondonW12 0BZUK
| | - Ling Peng
- Aix Marseille UniversitéCNRSCentre Interdisciplinaire de Nanoscience de Marseille (UMR 7325)Equipe Labellisée Ligue Contre le CancerMarseille13288France
| | - Leo Tsz On Lee
- Cancer CentreFaculty of Health SciencesUniversity of MacauTaipaMacau999078China
- MOE Frontiers Science Center for Precision OncologyUniversity of MacauTaipaMacau999078China
- Centre of Reproduction, Development, and AgingFaculty of Health SciencesUniversity of MacauTaipaMacau999078China
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24
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OXTR High stroma fibroblasts control the invasion pattern of oral squamous cell carcinoma via ERK5 signaling. Nat Commun 2022; 13:5124. [PMID: 36045118 PMCID: PMC9433374 DOI: 10.1038/s41467-022-32787-y] [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: 08/31/2021] [Accepted: 08/17/2022] [Indexed: 11/20/2022] Open
Abstract
The Pattern Of Invasion (POI) of tumor cells into adjacent normal tissues clinically predicts postoperative tumor metastasis/recurrence of early oral squamous cell carcinoma (OSCC), but the mechanisms underlying the development of these subtypes remain unclear. Focusing on the highest score of POIs (Worst POI, WPOI) present within each tumor, we observe a disease progression-driven shift of WPOI towards the high-risk type 4/5, associated with a mesenchymal phenotype in advanced OSCC. WPOI 4-5-derived cancer-associated fibroblasts (CAFsWPOI4-5), characterized by high oxytocin receptor expression (OXTRHigh), contribute to local-regional metastasis. OXTRHigh CAFs induce a desmoplastic stroma and CCL26 is required for the invasive phenotype of CCR3+ tumors. Mechanistically, OXTR activates nuclear ERK5 transcription signaling via Gαq and CDC37 to maintain high levels of OXTR and CCL26. ERK5 ablation reprograms the pro-invasive phenotype of OXTRHigh CAFs. Therefore, targeting ERK5 signaling in OXTRHigh CAFs is a potential therapeutic strategy for OSCC patients with WPOI 4-5. Worst pattern of invasion (WPOI) is a parameter used to quantify tumor invasiveness of oral squamous cell carcinoma (OSCC). Here the authors show that a fibroblast subset characterized by the expression of the oxytocin receptor is enriched in highly invasive WPOI 4-5 OSCC tumors and can be targeted to reduce the desmoplastic stroma and tumor metastasis.
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25
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Niu N, Li H, Du X, Wang C, Li J, Yang J, Liu C, Yang S, Zhu Y, Zhao W. Effects of NRF-1 and PGC-1α cooperation on HIF-1α and rat cardiomyocyte apoptosis under hypoxia. Gene 2022; 834:146565. [PMID: 35569770 DOI: 10.1016/j.gene.2022.146565] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/06/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Hypoxia is a primary inducer of cardiomyocyte injury, its significant marker being hypoxia-induced cardiomyocyte apoptosis. Nuclear respiratory factor-1 (NRF-1) and hypoxia-inducible factor-1α (HIF-1α) are transcriptional regulatory elements implicated in multiple biological functions, including oxidative stress response. However, their roles in hypoxia-induced cardiomyocyte apoptosis remain unknown. The effect HIF-1α, together with NRF-1, exerts on cardiomyocyte apoptosis also remains unclear. METHODS We established a myocardial hypoxia model and investigated the effects of these proteins on the proliferation and apoptosis of rat cardiomyocytes (H9C2) under hypoxia. Further, we examined the association between NRF-1 and HIF-1α to improve the current understanding of NRF-1 anti-apoptotic mechanisms. RESULTS The results show that NRF-1 and HIF-1α are important anti-apoptotic molecules in H9C2 cells under hypoxia, although their regulatory mechanisms differ. NRF-1 could bind to the promoter region of Hif1a and negatively regulate its expression. Additionally, HIF-1β exhibited competitive binding with NRF-1 and HIF-1α, demonstrating a synergism between NRF-1 and the peroxisome proliferator-activated receptor-gamma coactivator-1α. CONCLUSION These results indicate that cardiomyocytes can regulate different molecular patterns to tolerate hypoxia, providing a novel methodological framework for studying cardiomyocyte apoptosis under hypoxia.
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Affiliation(s)
- Nan Niu
- School of Basic Medicine, Ningxia Medical University, 1160 Shengli South Street, Xingqing District, Yinchuan City, Ningxia Hui Autonomous Region, China
| | - Hui Li
- School of Basic Medicine, Ningxia Medical University, 1160 Shengli South Street, Xingqing District, Yinchuan City, Ningxia Hui Autonomous Region, China
| | - Xiancai Du
- School of Basic Medicine, Ningxia Medical University, 1160 Shengli South Street, Xingqing District, Yinchuan City, Ningxia Hui Autonomous Region, China
| | - Chan Wang
- School of Basic Medicine, Ningxia Medical University, 1160 Shengli South Street, Xingqing District, Yinchuan City, Ningxia Hui Autonomous Region, China
| | - Junliang Li
- School of Basic Medicine, Ningxia Medical University, 1160 Shengli South Street, Xingqing District, Yinchuan City, Ningxia Hui Autonomous Region, China
| | - Jihui Yang
- School of Basic Medicine, Ningxia Medical University, 1160 Shengli South Street, Xingqing District, Yinchuan City, Ningxia Hui Autonomous Region, China
| | - Cheng Liu
- School of Basic Medicine, Ningxia Medical University, 1160 Shengli South Street, Xingqing District, Yinchuan City, Ningxia Hui Autonomous Region, China
| | - Songhao Yang
- School of Basic Medicine, Ningxia Medical University, 1160 Shengli South Street, Xingqing District, Yinchuan City, Ningxia Hui Autonomous Region, China
| | - Yazhou Zhu
- School of Basic Medicine, Ningxia Medical University, 1160 Shengli South Street, Xingqing District, Yinchuan City, Ningxia Hui Autonomous Region, China
| | - Wei Zhao
- School of Basic Medicine, Ningxia Medical University, 1160 Shengli South Street, Xingqing District, Yinchuan City, Ningxia Hui Autonomous Region, China.
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26
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Zhu Y, Zhu L, Wang X, Jin H. RNA-based therapeutics: an overview and prospectus. Cell Death Dis 2022; 13:644. [PMID: 35871216 PMCID: PMC9308039 DOI: 10.1038/s41419-022-05075-2] [Citation(s) in RCA: 172] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 01/21/2023]
Abstract
The growing understanding of RNA functions and their crucial roles in diseases promotes the application of various RNAs to selectively function on hitherto "undruggable" proteins, transcripts and genes, thus potentially broadening the therapeutic targets. Several RNA-based medications have been approved for clinical use, while others are still under investigation or preclinical trials. Various techniques have been explored to promote RNA intracellular trafficking and metabolic stability, despite significant challenges in developing RNA-based therapeutics. In this review, the mechanisms of action, challenges, solutions, and clinical application of RNA-based therapeutics have been comprehensively summarized.
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Affiliation(s)
- Yiran Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Liyuan Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Xian Wang
- grid.13402.340000 0004 1759 700XDepartment of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Hongchuan Jin
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
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27
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Müller M, Fäh T, Schaefer M, Hermes V, Luitz J, Stalder P, Arora R, Ngondo RP, Ciaudo C. AGO1 regulates pericentromeric regions in mouse embryonic stem cells. Life Sci Alliance 2022; 5:e202101277. [PMID: 35236760 PMCID: PMC8897595 DOI: 10.26508/lsa.202101277] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/17/2022] [Accepted: 02/17/2022] [Indexed: 01/09/2023] Open
Abstract
Argonaute proteins (AGOs), which play an essential role in cytosolic post-transcriptional gene silencing, have been also reported to function in nuclear processes like transcriptional activation or repression, alternative splicing and, chromatin organization. As most of these studies have been conducted in human cancer cell lines, the relevance of AGOs nuclear functions in the context of mouse early embryonic development remains uninvestigated. Here, we examined a possible role of the AGO1 protein on the distribution of constitutive heterochromatin in mouse embryonic stem cells (mESCs). We observed a specific redistribution of the repressive histone mark H3K9me3 and the heterochromatin protein HP1α, away from pericentromeric regions upon Ago1 depletion. Furthermore, we demonstrated that major satellite transcripts are strongly up-regulated in Ago1_KO mESCs and that their levels are partially restored upon AGO1 rescue. We also observed a similar redistribution of H3K9me3 and HP1α in Drosha_KO mESCs, suggesting a role for microRNAs (miRNAs) in the regulation of heterochromatin distribution in mESCs. Finally, we showed that specific miRNAs with complementarity to major satellites can partially regulate the expression of these transcripts.
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Affiliation(s)
- Madlen Müller
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
- Life Science Zurich Graduate School, University of Zürich, Zürich, Switzerland
| | - Tara Fäh
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Moritz Schaefer
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
- Life Science Zurich Graduate School, University of Zürich, Zürich, Switzerland
| | - Victoria Hermes
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Janina Luitz
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Patrick Stalder
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
- Life Science Zurich Graduate School, University of Zürich, Zürich, Switzerland
| | - Rajika Arora
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Richard Patryk Ngondo
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Constance Ciaudo
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
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Van Simaeys D, De La Fuente A, Zilio S, Zoso A, Kuznetsova V, Alcazar O, Buchwald P, Grilli A, Caroli J, Bicciato S, Serafini P. RNA aptamers specific for transmembrane p24 trafficking protein 6 and Clusterin for the targeted delivery of imaging reagents and RNA therapeutics to human β cells. Nat Commun 2022; 13:1815. [PMID: 35383192 PMCID: PMC8983715 DOI: 10.1038/s41467-022-29377-3] [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: 01/14/2020] [Accepted: 03/08/2022] [Indexed: 12/20/2022] Open
Abstract
The ability to detect and target β cells in vivo can substantially refine how diabetes is studied and treated. However, the lack of specific probes still hampers a precise characterization of human β cell mass and the delivery of therapeutics in clinical settings. Here, we report the identification of two RNA aptamers that specifically and selectively recognize mouse and human β cells. The putative targets of the two aptamers are transmembrane p24 trafficking protein 6 (TMED6) and clusterin (CLUS). When given systemically in immune deficient mice, these aptamers recognize the human islet graft producing a fluorescent signal proportional to the number of human islets transplanted. These aptamers cross-react with endogenous mouse β cells and allow monitoring the rejection of mouse islet allografts. Finally, once conjugated to saRNA specific for X-linked inhibitor of apoptosis (XIAP), they can efficiently transfect non-dissociated human islets, prevent early graft loss, and improve the efficacy of human islet transplantation in immunodeficient in mice.
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Affiliation(s)
- Dimitri Van Simaeys
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Adriana De La Fuente
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Serena Zilio
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Alessia Zoso
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Victoria Kuznetsova
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Oscar Alcazar
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Peter Buchwald
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Andrea Grilli
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Jimmy Caroli
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Silvio Bicciato
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Paolo Serafini
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA. .,Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA. .,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA.
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29
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La Rocca G, Cavalieri V. Roles of the Core Components of the Mammalian miRISC in Chromatin Biology. Genes (Basel) 2022; 13:414. [PMID: 35327968 PMCID: PMC8954937 DOI: 10.3390/genes13030414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/20/2022] [Accepted: 02/23/2022] [Indexed: 12/16/2022] Open
Abstract
The Argonaute (AGO) and the Trinucleotide Repeat Containing 6 (TNRC6) family proteins are the core components of the mammalian microRNA-induced silencing complex (miRISC), the machinery that mediates microRNA function in the cytoplasm. The cytoplasmic miRISC-mediated post-transcriptional gene repression has been established as the canonical mechanism through which AGO and TNRC6 proteins operate. However, growing evidence points towards an additional mechanism through which AGO and TNRC6 regulate gene expression in the nucleus. While several mechanisms through which miRISC components function in the nucleus have been described, in this review we aim to summarize the major findings that have shed light on the role of AGO and TNRC6 in mammalian chromatin biology and on the implications these novel mechanisms may have in our understanding of regulating gene expression.
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Affiliation(s)
- Gaspare La Rocca
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
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30
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Halloy F, Biscans A, Bujold KE, Debacker A, Hill AC, Lacroix A, Luige O, Strömberg R, Sundstrom L, Vogel J, Ghidini A. Innovative developments and emerging technologies in RNA therapeutics. RNA Biol 2022; 19:313-332. [PMID: 35188077 PMCID: PMC8865321 DOI: 10.1080/15476286.2022.2027150] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNA-based therapeutics are emerging as a powerful platform for the treatment of multiple diseases. Currently, the two main categories of nucleic acid therapeutics, antisense oligonucleotides and small interfering RNAs (siRNAs), achieve their therapeutic effect through either gene silencing, splicing modulation or microRNA binding, giving rise to versatile options to target pathogenic gene expression patterns. Moreover, ongoing research seeks to expand the scope of RNA-based drugs to include more complex nucleic acid templates, such as messenger RNA, as exemplified by the first approved mRNA-based vaccine in 2020. The increasing number of approved sequences and ongoing clinical trials has attracted considerable interest in the chemical development of oligonucleotides and nucleic acids as drugs, especially since the FDA approval of the first siRNA drug in 2018. As a result, a variety of innovative approaches is emerging, highlighting the potential of RNA as one of the most prominent therapeutic tools in the drug design and development pipeline. This review seeks to provide a comprehensive summary of current efforts in academia and industry aimed at fully realizing the potential of RNA-based therapeutics. Towards this, we introduce established and emerging RNA-based technologies, with a focus on their potential as biosensors and therapeutics. We then describe their mechanisms of action and their application in different disease contexts, along with the strengths and limitations of each strategy. Since the nucleic acid toolbox is rapidly expanding, we also introduce RNA minimal architectures, RNA/protein cleavers and viral RNA as promising modalities for new therapeutics and discuss future directions for the field.
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Affiliation(s)
- François Halloy
- Department of Paediatrics, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Annabelle Biscans
- Oligonucleotide Chemistry, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Katherine E. Bujold
- Department of Chemistry & Chemical Biology, McMaster University, (Ontario), Canada
| | | | - Alyssa C. Hill
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eth Zürich, Zürich, Switzerland
| | - Aurélie Lacroix
- Sixfold Bioscience, Translation & Innovation Hub, London, UK
| | - Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Linda Sundstrom
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (Hiri), Helmholtz Center for Infection Research (Hzi), Würzburg, Germany
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Alice Ghidini
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
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31
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Liu H, Chen S, Sun Q, Sha Q, Tang Y, Jia W, Chen L, Zhao J, Wang T, Sun X. Let-7c increases BACE2 expression by RNAa and decreases Aβ production. Am J Transl Res 2022; 14:899-908. [PMID: 35273693 PMCID: PMC8902526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 10/30/2021] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs) are highly conserved, non-coding transcripts that regulate gene expression in various ways. Evidence suggests that miRNAs may be a contributory factor in neurodegeneration, including Alzheimer's disease (AD), Parkinson's disease (PD), and triplet repeat disorders. In order to further understand the potential roles of miRNAs in the pathogenesis of AD, we analyzed Down syndrome (DS), a special model of AD, by using a TaqMan microRNA array and found that miRNA let-7c was up-regulated in both DS and AD. ELISA assay showed that let-7c reduced the expression level of Aβ significantly. Real-time quantitative-polymerase chain reaction (RT-qPCR) was conducted to reveal that the expression level of let-7c increased dramatically in DS cells, patients with DS and mice with AD compared with normal ones respectively. Additionally, western blotting illustrated that let-7c suppressed the expression of Aβ by inducing BACE2 to cut C99 and increase the content of C83/80. BACE2 expression was inhibited by let-7c and luciferase reporter gene assay revealed that let-7c increased the activity of wild-type BACE2 promoter but not 3'UTR. Furthermore, promoter analysis of BACE2 confirmed that let-7c could bind to BACE2 in the sequence between -1368 and -1347. In addition, immunoblotting assay demonstrated that let-7c induced BACE2 expression by RNAa. To the best of our knowledge, our study revealed for the first time that let-7c up-regulated BACE2 expression and decreased Aβ production.
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Affiliation(s)
- Heng Liu
- School of Medicine, Cheeloo College of Medicine, Shandong UniversityJinan 250012, Shandong, China
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
- Department of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Shuai Chen
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
- Department of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Qian Sun
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
- Department of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Qingquan Sha
- Department of Education, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Yu Tang
- Department of Neurology, Dezhou People’s HospitalDezhou 253000, Shandong, China
| | - Wenming Jia
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
- Department of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Long Chen
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
- Department of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Juan Zhao
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
- Department of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Tan Wang
- Department of Geriatric Medicine, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Xiulian Sun
- Brain Research Institute, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
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32
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Tan CP, Sinigaglia L, Gomez V, Nicholls J, Habib NA. RNA Activation-A Novel Approach to Therapeutically Upregulate Gene Transcription. Molecules 2021; 26:molecules26216530. [PMID: 34770939 PMCID: PMC8586927 DOI: 10.3390/molecules26216530] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/23/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022] Open
Abstract
RNA activation (RNAa) is a mechanism whereby RNA oligos complementary to genomic sequences around the promoter region of genes increase the transcription output of their target gene. Small activating RNA (saRNA) mediate RNAa through interaction with protein co-factors to facilitate RNA polymerase II activity and nucleosome remodeling. As saRNA are small, versatile and safe, they represent a new class of therapeutics that can rescue the downregulation of critical genes in disease settings. This review highlights our current understanding of saRNA biology and describes various examples of how saRNA are successfully used to treat various oncological, neurological and monogenic diseases. MTL-CEBPA, a first-in-class compound that reverses CEBPA downregulation in oncogenic processes using CEBPA-51 saRNA has entered clinical trial for the treatment of hepatocellular carcinoma (HCC). Preclinical models demonstrate that MTL-CEBPA reverses the immunosuppressive effects of myeloid cells and allows for the synergistic enhancement of other anticancer drugs. Encouraging results led to the initiation of a clinical trial combining MTL-CEBPA with a PD-1 inhibitor for treatment of solid tumors.
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Affiliation(s)
- Choon Ping Tan
- MiNA Therapeutics Ltd., Translation & Innovation Hub, 84 Wood Lane, London W12 0BZ, UK; (C.P.T.); (L.S.); (V.G.); (J.N.)
| | - Laura Sinigaglia
- MiNA Therapeutics Ltd., Translation & Innovation Hub, 84 Wood Lane, London W12 0BZ, UK; (C.P.T.); (L.S.); (V.G.); (J.N.)
| | - Valentí Gomez
- MiNA Therapeutics Ltd., Translation & Innovation Hub, 84 Wood Lane, London W12 0BZ, UK; (C.P.T.); (L.S.); (V.G.); (J.N.)
| | - Joanna Nicholls
- MiNA Therapeutics Ltd., Translation & Innovation Hub, 84 Wood Lane, London W12 0BZ, UK; (C.P.T.); (L.S.); (V.G.); (J.N.)
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN, UK
| | - Nagy A. Habib
- MiNA Therapeutics Ltd., Translation & Innovation Hub, 84 Wood Lane, London W12 0BZ, UK; (C.P.T.); (L.S.); (V.G.); (J.N.)
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN, UK
- Correspondence: ; Tel.: +44-(0)20-3313-8574
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33
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Chu Y, Yokota S, Liu J, Kilikevicius A, Johnson KC, Corey DR. Argonaute binding within human nuclear RNA and its impact on alternative splicing. RNA (NEW YORK, N.Y.) 2021; 27:991-1003. [PMID: 34108230 PMCID: PMC8370746 DOI: 10.1261/rna.078707.121] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/04/2021] [Indexed: 05/03/2023]
Abstract
Mammalian RNA interference (RNAi) is often linked to the regulation of gene expression in the cytoplasm. Synthetic RNAs, however, can also act through the RNAi pathway to regulate transcription and splicing. While nuclear regulation by synthetic RNAs can be robust, a critical unanswered question is whether endogenous functions for nuclear RNAi exist in mammalian cells. Using enhanced crosslinking immunoprecipitation (eCLIP) in combination with RNA sequencing (RNA-seq) and multiple AGO knockout cell lines, we mapped AGO2 protein binding sites within nuclear RNA. The strongest AGO2 binding sites were mapped to micro RNAs (miRNAs). The most abundant miRNAs were distributed similarly between the cytoplasm and nucleus, providing no evidence for mechanisms that facilitate localization of miRNAs in one compartment versus the other. Beyond miRNAs, most statistically significant AGO2 binding was within introns. Splicing changes were confirmed by RT-PCR and recapitulated by synthetic miRNA mimics complementary to the sites of AGO2 binding. These data support the hypothesis that miRNAs can control gene splicing. While nuclear RNAi proteins have the potential to be natural regulatory mechanisms, careful study will be necessary to identify critical RNA drivers of normal physiology and disease.
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Affiliation(s)
- Yongjun Chu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - Shinnichi Yokota
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - Jing Liu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - Audrius Kilikevicius
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - Krystal C Johnson
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - David R Corey
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
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34
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The regulatory impact of RNA-binding proteins on microRNA targeting. Nat Commun 2021; 12:5057. [PMID: 34417449 PMCID: PMC8379221 DOI: 10.1038/s41467-021-25078-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/20/2021] [Indexed: 12/31/2022] Open
Abstract
Argonaute is the primary mediator of metazoan miRNA targeting (MT). Among the currently identified >1,500 human RNA-binding proteins (RBPs), there are only a handful of RBPs known to enhance MT and several others reported to suppress MT, leaving the global impact of RBPs on MT elusive. In this study, we have systematically analyzed transcriptome-wide binding sites for 150 human RBPs and evaluated the quantitative effect of individual RBPs on MT efficacy. In contrast to previous studies, we show that most RBPs significantly affect MT and that all of those MT-regulating RBPs function as MT enhancers rather than suppressors, by making the local secondary structure of the target site accessible to Argonaute. Our findings illuminate the unappreciated regulatory impact of human RBPs on MT, and as these RBPs may play key roles in the gene regulatory network governed by metazoan miRNAs, MT should be understood in the context of co-regulating RBPs. miRNAs are loaded into Argonaute protein and repress complementary mRNA targets. Here the authors show the unappreciated role of RNA binding proteins for efficient miRNA targeting and expand the current understanding of miRNA targeting.
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35
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Zhu Y, Ma X, Zhang H, Wu Y, Kang M, Fang Y, Xue Y. Mechanism of circADD2 as ceRNA in Childhood Acute Lymphoblastic Leukemia. Front Cell Dev Biol 2021; 9:639910. [PMID: 34055775 PMCID: PMC8155473 DOI: 10.3389/fcell.2021.639910] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/21/2021] [Indexed: 12/23/2022] Open
Abstract
Background: Acute lymphocytic leukemia (ALL) is the most common malignant tumor in children. Increasing evidence suggests that circular RNAs (circRNAs) play critical regulatory roles in tumor biology. However, the expression patterns and roles of circRNAs in childhood acute lymphoblastic leukemia (ALL) remain largely unknown. Methods: circADD2 was selected by microarray assay and confirmed by qRT-PCR; in vitro effects of circADD2 were determined by CCK-8 and flow cytometry; while mice subcutaneous tumor model was designed for in vivo analysis. RNA immunoprecipitation and dual-luciferase assay were applied for mechanistic study. Protein levels were examined by Western blot assay. Results: circADD2 was down-regulated in ALL tissues and cell lines. Overexpression of circADD2 inhibited cell proliferation and promoted apoptosis both in vitro and in vivo. Briefly, circADD2 could directly sponge miR-149-5p, and the level of AKT2, a target gene of miR-149-5p, was downregulated by circADD2. Conclusion: circADD2, as a tumor suppressor in ALL, can sponge miR-149-5p, and may serve as a potential biomarker for the diagnosis or treatment of ALL.
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Affiliation(s)
- Yuting Zhu
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Xiaopeng Ma
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Heng Zhang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Yijun Wu
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Meiyun Kang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Yongjun Fang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Yao Xue
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
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36
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Földes-Papp Z, Baumann G, Li LC. Visualization of subdiffusive sites in a live single cell. J Biol Methods 2021; 8:e142. [PMID: 33604394 PMCID: PMC7884708 DOI: 10.14440/jbm.2021.348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/05/2020] [Accepted: 12/05/2020] [Indexed: 11/23/2022] Open
Abstract
We measured anomalous diffusion in human prostate cancer cells which were transfected with the Alexa633 fluorescent RNA probe and co-transfected with enhanced green fluorescent protein-labeled argonaute2 protein by laser scanning microscopy. The image analysis arose from diffusion based on a “two-level system”. A trap was an interaction site where the diffusive motion was slowed down. Anomalous subdiffusive spreading occurred at cellular traps. The cellular traps were not immobile. We showed how the novel analysis method of imaging data resulted in new information about the number of traps in the crowded and heterogeneous environment of a single human prostate cancer cell. The imaging data were consistent with and explained by our modern ideas of anomalous diffusion of mixed origins in live cells. Our original research presented in this study is significant as we obtained a complex diffusion mechanism in live single cells.
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Affiliation(s)
- Zeno Földes-Papp
- Head of the Department of Geriatrics, Asklepios Clinic Lindau, 88131 Lindau (at Lake Constance), Bavaria, Germany
| | - Gerd Baumann
- Head of the Mathematics Department, Faculty of Basic Sciences, German University in Cairo (GUC), 11835 New Cairo City, Egypt
| | - Long-Cheng Li
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong 226001, China
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37
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Fan J, Li H, Xie R, Zhang X, Nie X, Shi X, Zhan J, Yin Z, Zhao Y, Dai B, Yuan S, Wen Z, Chen C, Wang DW. LncRNA ZNF593-AS Alleviates Contractile Dysfunction in Dilated Cardiomyopathy. Circ Res 2021; 128:1708-1723. [PMID: 33550812 DOI: 10.1161/circresaha.120.318437] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Jiahui Fan
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Huaping Li
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Rong Xie
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Xudong Zhang
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Xiang Nie
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Xiaolu Shi
- Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China (X.S.)
| | - Jiabing Zhan
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Zhongwei Yin
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Yanru Zhao
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Beibei Dai
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Shuai Yuan
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Zheng Wen
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Chen Chen
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Dao Wen Wang
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
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38
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Jiang W, Zhu D, Wang C, Zhu Y. Tumor suppressing effects of tristetraprolin and its small double-stranded RNAs in bladder cancer. Cancer Med 2021; 10:269-285. [PMID: 33259133 PMCID: PMC7826468 DOI: 10.1002/cam4.3622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/20/2020] [Accepted: 10/25/2020] [Indexed: 12/23/2022] Open
Abstract
Bladder cancer (BCa) is a common malignant tumor of urinary system with few treatments, so more useful therapeutic targets are still needed. Antitumor effects of tristetraprolin (TTP) have been explored in many type tumors, but its roles in bladder cancer are still unknown until now. In this study, public expression profiles and tissue microarray analysis showed that TTP mRNA and protein levels decreased in BCa relative to the normal bladder tissue. To explore biological functions of TTP in BCa, 488 TTP target genes, which could be both suppressed and bound by TTP, were identified by comprehensively analyzing publicly available high-throughput data obtained from Gene Expression Omnibus (GEO). Gene enrichment analysis showed that these genes were enriched in pathways such as cell cycle, epithelial to mesenchymal transition (EMT), and Wnt signaling. Clustering analysis and gene set variation analysis indicated that patients with high expression of TTP target genes had poorer prognosis and stronger tumor proliferation ability relative to the BCa patients with low expression of TTP target genes. In vitro experiments validated that TTP could suppress proliferation, migration, and invasiveness of BCa cells. And TTP could suppress mRNA expression of cyclin-dependent kinase 1 (CDK1) in BCa cells by target its 3' UTR. Then, we identified a new small double-stranded RNA (dsRNA) named dsTTP-973 which could increase TTP expression in BCa cells, in vivo and in vitro experiments revealed that dsTTP-973 could suppress aggressiveness of BCa. In conclusion, TTP played a role of tumor suppressor gene in BCa like other tumors, and its dsRNA named dsTTP-973 could induce TTP expression in BCa and suppress aggressiveness of BCa. With the help of materials science, dsTTP-973 may become a potential treatment for BCa in the future.
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Affiliation(s)
- Wen Jiang
- Department of UrologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Dandan Zhu
- Department of UrologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Chenghe Wang
- Department of UrologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yu Zhu
- Department of UrologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
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39
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Argonaute 2 is a key regulator of maternal mRNA degradation in mouse early embryos. Cell Death Discov 2020; 6:133. [PMID: 33298889 PMCID: PMC7691497 DOI: 10.1038/s41420-020-00368-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/06/2020] [Accepted: 11/02/2020] [Indexed: 11/16/2022] Open
Abstract
In mammalian early embryos, the transition from maternal to embryonic control of gene expression requires timely degradation of a subset of maternal mRNAs (MRD). Recently, zygotic genome activation (ZGA)-dependent MRD has been characterized in mouse 2-cell embryo. However, in early embryos, the dynamics of MRD is still poorly understood, and the maternal factor-mediated MRD before and along with ZGA has not been investigated. Argonaute 2 (Ago2) is highly expressed in mouse oocyte and early embryos. In this study, we showed that Ago2-dependent degradation involving RNA interference (RNAi) and RNA activation (RNAa) pathways contributes to the decay of over half of the maternal mRNAs in mouse early embryos. We demonstrated that AGO2 guided by endogenous small interfering RNAs (endosiRNAs), generated from double-stranded RNAs (dsRNAs) formed by maternal mRNAs with their complementary long noncoding RNAs (CMR-lncRNAs), could target maternal mRNAs and cooperate with P-bodies to promote MRD. In addition, we also showed that AGO2 may interact with small activating RNAs (saRNAs) to activate Yap1 and Tead4, triggering ZGA-dependent MRD. Thus, Ago2-dependent degradation is required for timely elimination of subgroups of maternal mRNAs and facilitates the transition between developmental states.
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40
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Debacker AJ, Voutila J, Catley M, Blakey D, Habib N. Delivery of Oligonucleotides to the Liver with GalNAc: From Research to Registered Therapeutic Drug. Mol Ther 2020; 28:1759-1771. [PMID: 32592692 PMCID: PMC7403466 DOI: 10.1016/j.ymthe.2020.06.015] [Citation(s) in RCA: 170] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/08/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
Targeted delivery of oligonucleotides to liver hepatocytes using N-acetylgalactosamine (GalNAc) conjugates that bind to the asialoglycoprotein receptor has become a breakthrough approach in the therapeutic oligonucleotide field. This technology has led to the approval of givosiran for the treatment of acute hepatic porphyria, and there are another seven conjugates in registrational review or phase 3 trials and at least another 21 conjugates at earlier stages of clinical development. This review highlights some of the recent chemical and preclinical advances in this space, leading to a large number of clinical candidates against a diverse range of targets in liver hepatocytes. The review focuses on the use of this delivery system for small interfering RNAs (siRNAs) and antisense molecules that cause downregulation of target mRNA and protein. A number of other approaches such as anti-microRNAs and small activating RNAs are starting to exploit the technology, broadening the potential of this approach for therapeutic oligonucleotide intervention.
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Affiliation(s)
- Alexandre J Debacker
- MiNA Therapeutics, Translation & Innovation Hub, 80 Wood Lane, London W12 0BZ, UK
| | - Jon Voutila
- MiNA Therapeutics, Translation & Innovation Hub, 80 Wood Lane, London W12 0BZ, UK
| | - Matthew Catley
- MiNA Therapeutics, Translation & Innovation Hub, 80 Wood Lane, London W12 0BZ, UK
| | - David Blakey
- MiNA Therapeutics, Translation & Innovation Hub, 80 Wood Lane, London W12 0BZ, UK.
| | - Nagy Habib
- MiNA Therapeutics, Translation & Innovation Hub, 80 Wood Lane, London W12 0BZ, UK; Department of Surgery & Cancer, Hammersmith Hospital, Imperial College London, Du Cane Road, London W12 0NN, UK
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41
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Human Insulin Growth Factor 2 mRNA Binding Protein 2 Increases MicroRNA 33a/b Inhibition of Liver ABCA1 Expression and Alters Low-Density Apolipoprotein Levels in Mice. Mol Cell Biol 2020; 40:MCB.00058-20. [PMID: 32482798 DOI: 10.1128/mcb.00058-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/26/2020] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies (GWAS) have linked IGF2BP2 single-nucleotide polymorphisms (SNPs) with type 2 diabetes (T2D). Mice overexpressing mIGF2BP2 have elevated cholesterol levels when fed a diet that induces hepatic steatosis. These and other studies suggest an important role for insulin growth factor 2 mRNA binding protein 2 (IGF2BP2) in the initiation and progression of several metabolic disorders. The ATPase binding cassette protein ABCA1 initiates nascent high-density apolipoprotein (HDL) biogenesis by transferring phospholipid and cholesterol to delipidated apolipoprotein AI (ApoAI). Individuals with mutational ablation of ABCA1 have Tangier disease, which is characterized by a complete loss of HDL. MicroRNA 33a and 33b (miR-33a/b) bind to the 3' untranslated region (UTR) of ABCA1 and repress its posttranscriptional gene expression. Here, we show that IGF2BP2 works together with miR-33a/b in repressing ABCA1 expression. Our data suggest that IGF2BP2 is an accessory protein of the argonaute (AGO2)-miR-33a/b-RISC complex, as it directly binds to miR-33a/b, AGO2, and the 3' UTR of ABCA1 Finally, we show that mice overexpressing human IGF2BP2 have decreased ABCA1 expression, increased low-density lipoprotein-cholesterol (LDL-C) and cholesterol blood levels, and elevated SREBP-dependent signaling. Our data support the hypothesis that IGF2BP2 has an important role in maintaining lipid homeostasis through its modulation of ABCA1 expression, as its overexpression or loss leads to dyslipidemia.
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42
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Zhou LY, Qin Z, Zhu YH, He ZY, Xu T. Current RNA-based Therapeutics in Clinical Trials. Curr Gene Ther 2020; 19:172-196. [PMID: 31566126 DOI: 10.2174/1566523219666190719100526] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/26/2019] [Accepted: 07/09/2019] [Indexed: 02/08/2023]
Abstract
Long-term research on various types of RNAs has led to further understanding of diverse mechanisms, which eventually resulted in the rapid development of RNA-based therapeutics as powerful tools in clinical disease treatment. Some of the developing RNA drugs obey the antisense mechanisms including antisense oligonucleotides, small interfering RNAs, microRNAs, small activating RNAs, and ribozymes. These types of RNAs could be utilized to inhibit/activate gene expression or change splicing to provide functional proteins. In the meantime, some others based on different mechanisms like modified messenger RNAs could replace the dysfunctional endogenous genes to manage some genetic diseases, and aptamers with special three-dimensional structures could bind to specific targets in a high-affinity manner. In addition, the recent most popular CRISPR-Cas technology, consisting of a crucial single guide RNA, could edit DNA directly to generate therapeutic effects. The desired results from recent clinical trials indicated the great potential of RNA-based drugs in the treatment of various diseases, but further studies on improving delivery materials and RNA modifications are required for the novel RNA-based drugs to translate to the clinic. This review focused on the advances and clinical studies of current RNA-based therapeutics, analyzed their challenges and prospects.
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Affiliation(s)
- Ling-Yan Zhou
- Department of Pharmacy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
| | - Zhou Qin
- Department of Pharmacy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
| | - Yang-Hui Zhu
- Department of Pharmacy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China.,State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Zhi-Yao He
- Department of Pharmacy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China.,State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Ting Xu
- Department of Pharmacy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
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43
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Developing small activating RNA as a therapeutic: current challenges and promises. Ther Deliv 2020; 10:151-164. [PMID: 30909853 DOI: 10.4155/tde-2018-0061] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RNA activation (RNAa) allows specific gene upregulation mediated by a small activating RNA (saRNA). Harnessing this process would help in developing novel therapeutics for undruggable diseases. Since its discovery in mid 2000s, improvements of saRNA design, synthetic chemistry and understanding of the biology have matured the way to apply RNAa. Indeed, MiNA therapeutics Ltd has conducted the first RNAa clinical trial for advanced hepatocellular carcinoma patients with promising outcomes. However, to fully realize the RNAa potential better saRNA delivery strategies are needed to target other diseases. Currently, saRNA can be delivered in vivo by lipid nanoparticles, dendrimers, lipid and polymer hybrids and aptamers. Further developing these delivery technologies and novel application of RNAa will prove to be invaluable for new treatment development.
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Ickenstein LM, Garidel P. Lipid-based nanoparticle formulations for small molecules and RNA drugs. Expert Opin Drug Deliv 2020; 16:1205-1226. [PMID: 31530041 DOI: 10.1080/17425247.2019.1669558] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Introduction: Liposomes and lipid-based nanoparticles (LNPs) effectively deliver cargo molecules to specific tissues, cells, and cellular compartments. Patients benefit from these nanoparticle formulations by altered pharmacokinetic properties, higher efficacy, or reduced side effects. While liposomes are an established delivery option for small molecules, Onpattro® (Sanofi Genzyme, Cambridge, MA) is the first commercially available LNP formulation of a small interfering ribonucleic acid (siRNA). Areas covered: This review article summarizes key features of liposomal formulations for small molecule drugs and LNP formulations for RNA therapeutics. We describe liposomal formulations that are commercially available or in late-stage clinical development and the most promising LNP formulations for ASOs, siRNAs, saRNA, and mRNA therapeutics. Expert opinion: Similar to liposomes, LNPs for RNA therapeutics have matured but still possess a niche application status. RNA therapeutics, however, bear an immense hope for difficult to treat diseases and fuel the imagination for further applications of RNA drugs. LNPs face similar challenges as liposomes including limitations in biodistribution, the risk to provoke immune responses, and other toxicities. However, since properties of RNA molecules within the same group are very similar, the entire class of therapeutic molecules would benefit from improvements in a few key parameters of the delivery technology.
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Affiliation(s)
- Ludger M Ickenstein
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, Pharmaceutical Development Biologicals , Biberach an der Riss , Germany
| | - Patrick Garidel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, Pharmaceutical Development Biologicals , Biberach an der Riss , Germany
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45
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De Hayr L, Asad S, Hussain M, Asgari S. RNA activation in insects: The targeted activation of endogenous and exogenous genes. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 119:103325. [PMID: 31978586 DOI: 10.1016/j.ibmb.2020.103325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/10/2019] [Accepted: 01/15/2020] [Indexed: 06/10/2023]
Abstract
RNA activation (RNAa) is a newly emerging area of research in which dsRNA targeting promoter regions can induce the expression of the target gene. Although still in its infancy, it is already having significant impacts in several research areas in particular as cancer therapeutics. So far, the scope of RNAa has been limited to mammals and Caenorhabditis elegans with no indication of its prevalence in insects. In this study, we aimed to demonstrate the presence of RNAa in the insect dengue vector Aedes aegypti. Furthermore, we looked to uncover some details surrounding the involvement of host factors in order to present this as a new technique for insect research. The outcomes of this study provide new opportunities to further research into arthropod-borne diseases and insect biology in the same way as RNA interference.
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Affiliation(s)
- Lachlan De Hayr
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sultan Asad
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mazhar Hussain
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
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46
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Abstract
Cancer immunotherapy has shown great potential as witnessed by an increasing number of immuno-oncology drug approvals in the past few years. Meanwhile, the field of nucleic acid therapeutics has made significant advancement. Nucleic acid therapeutics, such as plasmids, antisense oligonucleotides (ASO), small interfering RNA (siRNA) and microRNA, messenger RNA (mRNA), immunomodulatory DNA/RNA, and gene-editing guide RNA (gRNA) are attractive due to their versatile abilities to alter the expression of target endogenous genes or even synthetic genes, and modulate the immune responses. These abilities can play vital roles in the development of novel immunotherapy strategies. However, limited by the intrinsic physicochemical properties such as negative charges, hydrophilicity, as well as susceptibility to enzymatic degradation, the delivery of nucleic acid therapeutics faces multiple challenges. It is therefore pivotal to develop drug delivery systems that can carry, protect, and specifically deliver and release nucleic acid therapeutics to target tissues and cells. In this review, we attempted to summarize recent advances in nucleic acid therapeutics and the delivery systems for these therapeutics in cancer immunotherapy.
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Affiliation(s)
- Shurong Zhou
- Department of Pharmaceutics, Center for Pharmaceutical Engineering and Sciences, Institute for Structural Biology, Drug Discovery and Development (ISB3D), School of Pharmacy, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23219, USA
| | - Wenjie Chen
- Department of Pharmaceutics, Center for Pharmaceutical Engineering and Sciences, Institute for Structural Biology, Drug Discovery and Development (ISB3D), School of Pharmacy, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23219, USA
| | - Janet Cole
- Department of Pharmaceutics, Center for Pharmaceutical Engineering and Sciences, Institute for Structural Biology, Drug Discovery and Development (ISB3D), School of Pharmacy, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23219, USA
| | - Guizhi Zhu
- Department of Pharmaceutics, Center for Pharmaceutical Engineering and Sciences, Institute for Structural Biology, Drug Discovery and Development (ISB3D), School of Pharmacy, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23219, USA
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47
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Li X, Wang X, Cheng Z, Zhu Q. AGO2 and its partners: a silencing complex, a chromatin modulator, and new features. Crit Rev Biochem Mol Biol 2020; 55:33-53. [DOI: 10.1080/10409238.2020.1738331] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Xiaojing Li
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Xueying Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Zeneng Cheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
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48
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Li H, Zhan J, Zhao Y, Fan J, Yuan S, Yin Z, Dai B, Chen C, Wang DW. Identification of ncRNA-Mediated Functions of Nucleus-Localized miR-320 in Cardiomyocytes. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 19:132-143. [PMID: 31837603 PMCID: PMC6920229 DOI: 10.1016/j.omtn.2019.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/16/2019] [Accepted: 11/08/2019] [Indexed: 01/31/2023]
Abstract
In recent years, systematic analyses of the subcellular distribution of microRNAs (miRNAs) suggest that the majority of miRNAs are present in both nuclear and cytoplasmic compartments. However, the full extent of nuclear miRNA function in cardiomyocytes is currently unknown. Here, subcellular fractionation, followed by the miRNA microarray, revealed that most miRNAs were detectable in both nuclear and cytoplasmic fractions of cardiomyocytes. We employed miR-320 as an example to explore the function of nucleus-localized miRNAs, finding that CRISPR-Cas9-mediated Ago2 knockdown abolished miR-320-induced transcriptional remodeling. Furthermore, nuclear Ago2 re-expression restored the effects of miR-320 in the nucleus. Moreover, liquid chromatography-mass spectrometry (LC-MS) analysis revealed the association of nuclear Ago2 with transcription factors YLP motif-containing protein 1 (Ylpm1) and single-stranded DNA binding protein 1 (Ssbp1). Intersection of the data of transcriptome-sequencing (seq) with Ago2-chromatin immunoprecipitation (ChIP)-seq revealed that the binding of Ago2 with the target promoter DNA may require promoter RNAs. Specifically, Cep57 was upregulated, whereas Fscn2 was downregulated by miR-320, and a similar effect was also observed by knockdown of their promoter RNA, respectively. Chromatin isolation by RNA purification (ChIRP) analysis showed decreased binding of the Cep57 and Fscn2 promoter RNA on their promoter DNA by miR-320 overexpression.Our work provided a preliminary idea that promoter RNA transcripts act as “pioneers” to disrupt chromatin that permits Ago2/miR-320 complexes to target Cep57 or Fscn2 promoter DNA for transcriptional regulation. miRNAs are naturally located in both cytoplasm and nucleus; however, their pathophysiological functions are largely unknown. Our work provided a theoretical basis for developing nuclear miRNA-based therapeutics against various diseases in the future.
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Affiliation(s)
- Huaping Li
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Jiabing Zhan
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Yanru Zhao
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Jiahui Fan
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Shuai Yuan
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Zhongwei Yin
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Beibei Dai
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Chen Chen
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China.
| | - Dao Wen Wang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China.
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Abstract
The RNA interference (RNAi) pathway regulates mRNA stability and translation in nearly all human cells. Small double-stranded RNA molecules can efficiently trigger RNAi silencing of specific genes, but their therapeutic use has faced numerous challenges involving safety and potency. However, August 2018 marked a new era for the field, with the US Food and Drug Administration approving patisiran, the first RNAi-based drug. In this Review, we discuss key advances in the design and development of RNAi drugs leading up to this landmark achievement, the state of the current clinical pipeline and prospects for future advances, including novel RNAi pathway agents utilizing mechanisms beyond post-translational RNAi silencing.
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50
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Li H, Fan J, Zhao Y, Zhang X, Dai B, Zhan J, Yin Z, Nie X, Fu XD, Chen C, Wang DW. Nuclear miR-320 Mediates Diabetes-Induced Cardiac Dysfunction by Activating Transcription of Fatty Acid Metabolic Genes to Cause Lipotoxicity in the Heart. Circ Res 2019; 125:1106-1120. [PMID: 31638474 PMCID: PMC6903355 DOI: 10.1161/circresaha.119.314898] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Supplemental Digital Content is available in the text. Diabetes mellitus is often associated with cardiovascular complications, which is the leading cause of morbidity and mortality among patients with diabetes mellitus, but little is known about the mechanism that connects diabetes mellitus to the development of cardiovascular dysfunction.
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Affiliation(s)
- Huaping Li
- From the Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., Z.Y., X.N., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., X.N., C.C., D.W.W.)
| | - Jiahui Fan
- From the Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., Z.Y., X.N., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., X.N., C.C., D.W.W.)
| | - Yanru Zhao
- From the Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., Z.Y., X.N., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., X.N., C.C., D.W.W.)
| | - Xiaorong Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing (X.Z.)
| | - Beibei Dai
- From the Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., Z.Y., X.N., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., X.N., C.C., D.W.W.)
| | - Jiabing Zhan
- From the Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., Z.Y., X.N., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., X.N., C.C., D.W.W.)
| | - Zhongwei Yin
- From the Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., Z.Y., X.N., C.C., D.W.W.)
| | - Xiang Nie
- From the Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., Z.Y., X.N., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., X.N., C.C., D.W.W.)
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, La Jolla, San Diego (X.-D.F.)
| | - Chen Chen
- From the Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., Z.Y., X.N., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., X.N., C.C., D.W.W.)
| | - Dao Wen Wang
- From the Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., Z.Y., X.N., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., X.N., C.C., D.W.W.)
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