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Yang L, Wang M, Wang Y, Zhu Y, Wang J, Wu M, Guo Q, Han X, Pandey V, Wu Z, Lobie PE, Zhu T. LINC00460-FUS-MYC feedback loop drives breast cancer metastasis and doxorubicin resistance. Oncogene 2024; 43:1249-1262. [PMID: 38418543 DOI: 10.1038/s41388-024-02972-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 02/03/2024] [Accepted: 02/07/2024] [Indexed: 03/01/2024]
Abstract
Therapeutic resistance and metastasis largely contribute to mortality from breast cancer and therefore understanding the underlying mechanisms of such remains an urgent challenge. By cross-analysis of TCGA and GEO databases, LINC00460 was identified as an oncogenic long non-coding RNA, highly expressed in Doxorubicin resistant breast cancer. LINC00460 was further demonstrated to promote stem cell-like and epithelial-mesenchymal transition (EMT) characteristics in breast cancer cells. LINC00460 interacts with FUS protein with consequent enhanced stabilization, which further promotes MYC mRNA maturation. LINC00460 expression was transcriptionally enhanced by c-MYC protein, forming a positive feedback loop to promote metastasis and Doxorubicin resistance. LINC00460 depletion in Doxorubicin-resistant breast cancer cells restored sensitivity to Doxorubicin and increased the efficacy of c-MYC inhibitor therapy. Collectively, these findings implicate LINC00460 as a promising prognostic biomarker and potential therapeutic target to overcome Doxorubicin resistance in breast cancer.
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Affiliation(s)
- Leiyan Yang
- Department of Oncology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
- Key Laboratory of Immune Response and Immunotherapy, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Miaomiao Wang
- Department of Oncology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
- Key Laboratory of Immune Response and Immunotherapy, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Ya Wang
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, 310000, Zhejiang, China
| | - Yong Zhu
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, 230032, Hefei, Anhui, China
| | - Jiarui Wang
- Department of Oncology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
- Key Laboratory of Immune Response and Immunotherapy, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Mingming Wu
- Department of Oncology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
- Key Laboratory of Immune Response and Immunotherapy, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Qianying Guo
- Department of Pathology, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Xinghua Han
- Department of Oncology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Vijay Pandey
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Zhengsheng Wu
- Department of Pathology, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Peter E Lobie
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
- Shenzhen Bay Laboratory, Shenzhen, 518055, China.
| | - Tao Zhu
- Department of Oncology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China.
- Key Laboratory of Immune Response and Immunotherapy, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China.
- Shenzhen Bay Laboratory, Shenzhen, 518055, China.
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2
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Khalifah BA, Alghamdi SA, Alhasan AH. Unleashing the potential of catalytic RNAs to combat mis-spliced transcripts. Front Bioeng Biotechnol 2023; 11:1244377. [PMID: 38047291 PMCID: PMC10690607 DOI: 10.3389/fbioe.2023.1244377] [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: 06/22/2023] [Accepted: 10/23/2023] [Indexed: 12/05/2023] Open
Abstract
Human transcriptome can undergo RNA mis-splicing due to spliceopathies contributing to the increasing number of genetic diseases including muscular dystrophy (MD), Alzheimer disease (AD), Huntington disease (HD), myelodysplastic syndromes (MDS). Intron retention (IR) is a major inducer of spliceopathies where two or more introns remain in the final mature mRNA and account for many intronic expansion diseases. Potential removal of such introns for therapeutic purposes can be feasible when utilizing bioinformatics, catalytic RNAs, and nano-drug delivery systems. Overcoming delivery challenges of catalytic RNAs was discussed in this review as a future perspective highlighting the significance of utilizing synthetic biology in addition to high throughput deep sequencing and computational approaches for the treatment of mis-spliced transcripts.
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Affiliation(s)
- Bashayer A. Khalifah
- Institute for Bioengineering, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Ali H. Alhasan
- Institute for Bioengineering, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- College of Science and General Studies, Alfaisal University, Riyadh, Saudi Arabia
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3
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Shi X, Won M, Tang C, Ding Q, Sharma A, Wang F, Kim JS. RNA splicing based on reporter genes system: Detection, imaging and applications. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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4
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Hsu KW, Lai JCY, Chang JS, Peng PH, Huang CH, Lee DY, Tsai YC, Chung CJ, Chang H, Chang CH, Chen JL, Pang ST, Hao Z, Cui XL, He C, Wu KJ. METTL4-mediated nuclear N6-deoxyadenosine methylation promotes metastasis through activating multiple metastasis-inducing targets. Genome Biol 2022; 23:249. [PMID: 36461076 PMCID: PMC9716733 DOI: 10.1186/s13059-022-02819-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND DNA N6-methyldeoxyadenosine (6mA) is rarely present in mammalian cells and its nuclear role remains elusive. RESULTS Here we show that hypoxia induces nuclear 6mA modification through a DNA methyltransferase, METTL4, in hypoxia-induced epithelial-mesenchymal transition (EMT) and tumor metastasis. Co-expression of METTL4 and 6mA represents a prognosis marker for upper tract urothelial cancer patients. By RNA sequencing and 6mA chromatin immunoprecipitation-exonuclease digestion followed by sequencing, we identify lncRNA RP11-390F4.3 and one novel HIF-1α co-activator, ZMIZ1, that are co-regulated by hypoxia and METTL4. Other genes involved in hypoxia-mediated phenotypes are also regulated by 6mA modification. Quantitative chromatin isolation by RNA purification assay shows the occupancy of lncRNA RP11-390F4.3 on the promoters of multiple EMT regulators, indicating lncRNA-chromatin interaction. Knockdown of lncRNA RP11-390F4.3 abolishes METTL4-mediated tumor metastasis. We demonstrate that ZMIZ1 is an essential co-activator of HIF-1α. CONCLUSIONS We show that hypoxia results in enriched 6mA levels in mammalian tumor cells through METTL4. This METTL4-mediated nuclear 6mA deposition induces tumor metastasis through activating multiple metastasis-inducing genes. METTL4 is characterized as a potential therapeutic target in hypoxic tumors.
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Affiliation(s)
- Kai-Wen Hsu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, No. 15, Wenhua 1st Road, Gueishan Dist., Taoyuan, 333 Taiwan ,Research Center for Cancer Biology, Taipei, Taiwan ,grid.254145.30000 0001 0083 6092Institute of Translational Medicine and New Drug Development, China Medical University, Taichung, 404 Taiwan
| | - Joseph Chieh-Yu Lai
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, No. 15, Wenhua 1st Road, Gueishan Dist., Taoyuan, 333 Taiwan ,grid.254145.30000 0001 0083 6092Institute of Biomedical Sciences, China Medical University, Taichung, 404 Taiwan
| | - Jeng-Shou Chang
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, No. 15, Wenhua 1st Road, Gueishan Dist., Taoyuan, 333 Taiwan
| | - Pei-Hua Peng
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, No. 15, Wenhua 1st Road, Gueishan Dist., Taoyuan, 333 Taiwan
| | - Ching-Hui Huang
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, No. 15, Wenhua 1st Road, Gueishan Dist., Taoyuan, 333 Taiwan
| | - Der-Yen Lee
- grid.254145.30000 0001 0083 6092Institute of Integrated Medicine, China Medical University, Taichung, 404 Taiwan
| | | | - Chi-Jung Chung
- grid.254145.30000 0001 0083 6092Department of Health Risk Management, College of Public Health, China Medical University, Taichung, 404 Taiwan
| | - Han Chang
- grid.411508.90000 0004 0572 9415Department of Pathology, China Medical University Hospital, Taichung, 404 Taiwan
| | - Chao-Hsiang Chang
- grid.411508.90000 0004 0572 9415Department of Urology, China Medical University Hospital, Taichung, 404 Taiwan
| | - Ji-Lin Chen
- grid.278247.c0000 0004 0604 5314Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, 112 Taiwan
| | - See-Tong Pang
- Division of Urology, Department of Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, 333 Taiwan
| | - Ziyang Hao
- grid.170205.10000 0004 1936 7822Departments of Chemistry & Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th St., Chicago, IL 60637 USA ,grid.24696.3f0000 0004 0369 153XSchool of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069 China
| | - Xiao-Long Cui
- grid.170205.10000 0004 1936 7822Departments of Chemistry & Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th St., Chicago, IL 60637 USA
| | - Chuan He
- grid.170205.10000 0004 1936 7822Departments of Chemistry & Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th St., Chicago, IL 60637 USA ,grid.170205.10000 0004 1936 7822Howard Hughes Medical Institute, The University of Chicago, 929 E. 57th St., Chicago, IL 60637 USA
| | - Kou-Juey Wu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, No. 15, Wenhua 1st Road, Gueishan Dist., Taoyuan, 333 Taiwan
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5
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Herring B, Jang S, Whitt J, Goliwas K, Aburjania Z, Dudeja V, Ren B, Berry J, Bibb J, Frost A, Chen H, Rose JB, Jaskula-Sztul R. Ex Vivo Modeling of Human Neuroendocrine Tumors in Tissue Surrogates. Front Endocrinol (Lausanne) 2021; 12:710009. [PMID: 35002949 PMCID: PMC8734644 DOI: 10.3389/fendo.2021.710009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 11/10/2021] [Indexed: 12/24/2022] Open
Abstract
Few models exist for studying neuroendocrine tumors (NETs), and there are mounting concerns that the currently available array of cell lines is not representative of NET biology. The lack of stable patient-derived NET xenograft models further limits the scientific community's ability to make conclusions about NETs and their response to therapy in patients. To address these limitations, we propose the use of an ex vivo 3D flow-perfusion bioreactor system for culturing and studying patient-derived NET surrogates. Herein, we demonstrate the utility of the bioreactor system for culturing NET surrogates and provide methods for evaluating the efficacy of therapeutic agents on human NET cell line xenograft constructs and patient-derived NET surrogates. We also demonstrate that patient-derived NET tissues can be propagated using the bioreactor system and investigate the near-infrared (NIR) dye IR-783 for its use in monitoring their status within the bioreactor. The results indicate that the bioreactor system and similar 3D culture models may be valuable tools for culturing patient-derived NETs and monitoring their response to therapy ex vivo.
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Affiliation(s)
- Brendon Herring
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Samuel Jang
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jason Whitt
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kayla Goliwas
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Zviadi Aburjania
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Vikas Dudeja
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Bin Ren
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Joel Berry
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
| | - James Bibb
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Andra Frost
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Herbert Chen
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - John Bart Rose
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Renata Jaskula-Sztul
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
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6
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Zhu J, Wang J, Wang X, Gao M, Guo B, Gao M, Liu J, Yu Y, Wang L, Kong W, An Y, Liu Z, Sun X, Huang Z, Zhou H, Zhang N, Zheng R, Xie Z. Prediction of drug efficacy from transcriptional profiles with deep learning. Nat Biotechnol 2021; 39:1444-1452. [PMID: 34140681 DOI: 10.1038/s41587-021-00946-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 05/06/2021] [Indexed: 02/05/2023]
Abstract
Drug discovery focused on target proteins has been a successful strategy, but many diseases and biological processes lack obvious targets to enable such approaches. Here, to overcome this challenge, we describe a deep learning-based efficacy prediction system (DLEPS) that identifies drug candidates using a change in the gene expression profile in the diseased state as input. DLEPS was trained using chemically induced changes in transcriptional profiles from the L1000 project. We found that the changes in transcriptional profiles for previously unexamined molecules were predicted with a Pearson correlation coefficient of 0.74. We examined three disorders and experimentally tested the top drug candidates in mouse disease models. Validation showed that perillen, chikusetsusaponin IV and trametinib confer disease-relevant impacts against obesity, hyperuricemia and nonalcoholic steatohepatitis, respectively. DLEPS can generate insights into pathogenic mechanisms, and we demonstrate that the MEK-ERK signaling pathway is a target for developing agents against nonalcoholic steatohepatitis. Our findings suggest that DLEPS is an effective tool for drug repurposing and discovery.
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Affiliation(s)
- Jie Zhu
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, China.,Department of Pharmacology, School of Basic Medical Sciences, Health Science Center, Peking University, Beijing, China
| | - Jingxiang Wang
- Beijing & Qingdao Langu Pharmaceutical R&D Platform, Beijing Gigaceuticals Tech. Co. Ltd., Beijing, China
| | - Xin Wang
- Department of Pharmacology, School of Basic Medical Sciences, Health Science Center, Peking University, Beijing, China
| | - Mingjing Gao
- Beijing & Qingdao Langu Pharmaceutical R&D Platform, Beijing Gigaceuticals Tech. Co. Ltd., Beijing, China
| | - Bingbing Guo
- Department of Anatomy, Histology and Embryology, Neuroscience Research Institute, Health Science Center, Peking University, Beijing, China
| | - Miaomiao Gao
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, China
| | - Jiarui Liu
- Department of Anatomy, Histology and Embryology, Neuroscience Research Institute, Health Science Center, Peking University, Beijing, China
| | - Yanqiu Yu
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, China
| | - Liang Wang
- Department of Pharmacology, School of Basic Medical Sciences, Health Science Center, Peking University, Beijing, China
| | - Weikaixin Kong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Health Science Center, Peking University, Beijing, China
| | - Yongpan An
- Department of Pharmacology, School of Basic Medical Sciences, Health Science Center, Peking University, Beijing, China
| | - Zurui Liu
- Beijing & Qingdao Langu Pharmaceutical R&D Platform, Beijing Gigaceuticals Tech. Co. Ltd., Beijing, China
| | - Xinpei Sun
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, China
| | - Zhuo Huang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Health Science Center, Peking University, Beijing, China
| | - Hong Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Health Science Center, Peking University, Beijing, China.
| | - Ning Zhang
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, China.
| | - Ruimao Zheng
- Department of Anatomy, Histology and Embryology, Neuroscience Research Institute, Health Science Center, Peking University, Beijing, China.
| | - Zhengwei Xie
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, China. .,Beijing & Qingdao Langu Pharmaceutical R&D Platform, Beijing Gigaceuticals Tech. Co. Ltd., Beijing, China.
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7
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Chen S, Shu W, Zheng H, Ma Z, Li M, Wang F. Dynamic visualization of mRNA splicing variants with a transactivating reporter. Chem Commun (Camb) 2021; 57:9594-9597. [PMID: 34546238 DOI: 10.1039/d1cc02439f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynamic changes in intron sequences, with their loss and gain, are poorly detected due to the limited methods for the non-invasive monitoring of the pre-mRNA splicing process. Here, we describe the design of a two-step transcriptional activation (TSTA) reporter for the real-time imaging of the splicing process in living subjects. By taking advantage of the strong transactivating properties of the GAL4-VP16 fusion protein, which can target upstream activation sequence (UAS) elements to boost subsequent firefly luciferase reporter gene expression, we successfully and consistently detected the dynamic pre-mRNA splicing activity in response to exogenous splicing modulators in living cells and animals. Our findings provide a valuable tool for the high-throughput screening of splicing modulators, which could speed up the development of new drugs for the treatment of disordered splicing diseases.
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Affiliation(s)
- Si Chen
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Wenjie Shu
- Institute of Medical Engineering, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China
| | - Haifeng Zheng
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Zhe Ma
- Institute of Medical Engineering, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China.,School of Pharmacy, Shaanxi Institute of International Trade & Commerce, Xi'an 712046, China.,Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an Jiaotong University, Xi'an 710061, China
| | - Miao Li
- Department of Radiology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Fu Wang
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an 710071, China.,Institute of Medical Engineering, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China.,School of Pharmacy, Shaanxi Institute of International Trade & Commerce, Xi'an 712046, China.,Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an Jiaotong University, Xi'an 710061, China
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8
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Guo B, Shi X, Ma Z, Ji M, Tang C, Wang F. A ratiometric dual luciferase reporter for quantitative monitoring of pre-mRNA splicing efficiency in vivo. J Biol Chem 2021; 297:100933. [PMID: 34216622 PMCID: PMC8322121 DOI: 10.1016/j.jbc.2021.100933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/08/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022] Open
Abstract
Precursor messenger RNA (pre-mRNA) splicing is critical for cell growth and development, and errors in RNA splicing frequently cause cellular dysfunction, abnormal gene expression, and a variety of human diseases. However, there is currently a lack of reliable systems to noninvasively monitor the mRNA splicing efficiency in cells and animals. Here, we described the design of a genetically engineered ratiometric dual luciferase reporter to continuously quantify the changes in mRNA splice variants in vivo. This reporter system is encoded within a single polypeptide but on separate exons, thus generating two distinct luciferase signals derived from spliced and unspliced mRNAs. With this reporter, the two kinds of luciferase in the same individual can minimize the influence of indirect factors on splicing, and the ratio of these two luciferase intensities represents the dynamic splicing efficiency of pre-mRNA. Our study offers a convenient and robust tool for the screening and identification of small molecules or trans-acting factors that affect the efficiency of specific splicing reactions.
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Affiliation(s)
- Bin Guo
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, China
| | - Xiaorui Shi
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, China
| | - Zhe Ma
- Institute of Medical Engineering, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Moxuan Ji
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, China
| | - Chu Tang
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, China
| | - Fu Wang
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, China; Institute of Medical Engineering, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China; School of Pharmacy, Shaanxi Institute of International Trade & Commerce, Xi'an, China.
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9
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Rational Design of an Activatable Reporter for Quantitative Imaging of RNA Aberrant Splicing In Vivo. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:904-911. [PMID: 32405512 PMCID: PMC7210378 DOI: 10.1016/j.omtm.2020.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 04/13/2020] [Indexed: 02/02/2023]
Abstract
Pre-mRNA splicing, the process of removing introns from pre-mRNA and the arrangement of exons to produce mature transcripts, is a crucial step in the expression of most eukaryote genes. However, the splicing kinetics remain poorly characterized in living cells, mainly because current methods cannot provide the dynamic information of splicing events. Here, we developed a genetically encoded bioluminescence reporter for real-time imaging of the pre-mRNA splicing process in living subjects. We showed that the bioluminescence reporter is able to visualize the pre-mRNA aberrant splicing process in living cells in a dose- and time-dependent manner. Moreover, this reporter could provide quantitative and longitudinal information of splicing activity in response to exogenous splicing inhibitors in living animals. Our data suggest that this activatable reporter could serve as a promising tool for the high-throughput screening of splicing modulators, which would facilitate the drug development for human diseases caused by the abnormal splicing of mRNA.
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10
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Zheng H, Chen S, Wang X, Xie J, Tian J, Wang F. Intron Retained Bioluminescence Reporter for Real-Time Imaging of Pre-mRNA Splicing in Living Subjects. Anal Chem 2019; 91:12392-12398. [DOI: 10.1021/acs.analchem.9b02935] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Haifeng Zheng
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi’an 710071, China
- Institute of Medical Research, Northwestern Polytechnical University, Xi’an 710072, China
| | - Si Chen
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi’an 710071, China
| | - Xinan Wang
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi’an 710071, China
| | - Jinrong Xie
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi’an 710071, China
| | - Jie Tian
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi’an 710071, China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation Chinese Academy of Sciences, Beijing 100190, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine, Beihang University, Beijing 100190, China
| | - Fu Wang
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi’an 710071, China
- Institute of Medical Research, Northwestern Polytechnical University, Xi’an 710072, China
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