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Li Q, Yuan H, Zhao G, Ou D, Zhang J, Li L, Li S, Feng T, Gu R, Kou Q, Wang Q, Li S, Wang G, Zhao M, Yu H, Qu J, Lin P, Li K. DDX39B protects against sorafenib-induced ferroptosis by facilitating the splicing and cytoplasmic export of GPX4 pre-mRNA in hepatocellular carcinoma. Biochem Pharmacol 2024; 225:116251. [PMID: 38701867 DOI: 10.1016/j.bcp.2024.116251] [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: 01/15/2024] [Revised: 04/16/2024] [Accepted: 04/30/2024] [Indexed: 05/05/2024]
Abstract
Hepatocellular carcinoma (HCC) is the main histological subtype of primary liver cancer and remains one of the most common solid malignancies globally. Ferroptosis was recently defined as an iron-catalyzed form of regulated necrosis. Because cancer cells exhibit higher iron requirements than noncancer cells, treatment with ferroptosis-inducing compounds may be a feasible strategy for cancer therapy. However, cancer cells develop acquired resistance to evade ferroptosis, and the mechanisms responsible for ferroptosis resistance are not fully clarified. In the current study, we reported that DDX39B was downregulated during sorafenib-induced ferroptosis in a dose- and time-dependent manner. Exogenous introduction of DDX39B ensured the survival of HCC cells upon exposure to sorafenib, while the opposite phenomenon was observed in DDX39B-silenced HCC cells. Mechanistically, we demonstrated that DDX39B increased GPX4 levels by promoting the splicing and cytoplasmic translocation of GPX4 pre-mRNA, which was sufficient to detoxify sorafenib-triggered excess lipid ROS production, lipid peroxidation accumulation, ferrous iron levels, and mitochondrial damage. Inhibition of DDX39B ATPase activity by CCT018159 repressed the splicing and cytoplasmic export of GPX4 pre-mRNA and synergistically assisted sorafenib-induced ferroptotic cell death in HCC cells. Taken together, our data uncover a novel role for DDX39B in ferroptosis resistance by modulating the maturation of GPX4 mRNA via a posttranscriptional approach and suggest that DDX39B inhibition may be a promising therapeutic strategy to enhance the sensitivity and vulnerability of HCC cells to sorafenib.
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Affiliation(s)
- Qin Li
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Hang Yuan
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Gang Zhao
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Deqiong Ou
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Jie Zhang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Liang Li
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Siqi Li
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Tianyu Feng
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Rui Gu
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Qiming Kou
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Qijing Wang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Shan Li
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Guanru Wang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Minghui Zhao
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Huayang Yu
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Jie Qu
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Ping Lin
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China.
| | - Kai Li
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China.
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2
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Iliopoulos F, Tu D, Pence IJ, Li X, Ghosh P, Luke MC, Raney SG, Rantou E, Evans CL. Determining topical product bioequivalence with stimulated Raman scattering microscopy. J Control Release 2024; 367:864-876. [PMID: 38346503 DOI: 10.1016/j.jconrel.2024.02.010] [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: 10/23/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/19/2024]
Abstract
Generic drugs are essential for affordable medicine and improving accessibility to treatments. Bioequivalence (BE) is typically demonstrated by assessing a generic product's pharmacokinetics (PK) relative to a reference-listed drug (RLD). Accurately estimating cutaneous PK (cPK) at or near the site of action can be challenging for locally acting topical products. Certain cPK approaches are available for assessing local bioavailability (BA) in the skin. Stimulated Raman scattering (SRS) microscopy has unique capabilities enabling continuous, high spatial and temporal resolution and quantitative imaging of drugs within the skin. In this paper, we developed an approach based on SRS and a polymer-based standard reference for the evaluation of topical product BA and BE in human skin ex vivo. BE assessment of tazarotene-containing formulations was achieved using cPK parameters obtained within different skin microstructures. The establishment of BE between the RLD and an approved generic product was successfully demonstrated. Interestingly, within the constraints of the current study design the results suggest similar BA between the tested gel formulation and the reference cream formulation, despite the differences in the formulation/dosage form. Another formulation containing polyethylene glycol as the vehicle was demonstrated to be not bioequivalent to the RLD. Compared to using the SRS approach without a standard reference, the developed approach enabled more consistent and reproducible results, which is crucial in BE assessment. The abundant information from the developed approach can help to systematically identify key areas of study design that will enable a better comparison of topical products and support an assessment of BE.
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Affiliation(s)
- Fotis Iliopoulos
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown 02129, MA, USA
| | - Dandan Tu
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown 02129, MA, USA
| | - Isaac J Pence
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown 02129, MA, USA
| | - Xiaolei Li
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown 02129, MA, USA
| | - Priyanka Ghosh
- Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring 20993, MD, USA
| | - Markham C Luke
- Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring 20993, MD, USA
| | - Sam G Raney
- Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring 20993, MD, USA
| | - Elena Rantou
- Office of Biostatistics, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring 20993, MD, USA
| | - Conor L Evans
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown 02129, MA, USA.
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3
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Zhu Y, Huang C, Zhang C, Zhou Y, Zhao E, Zhang Y, Pan X, Huang H, Liao W, Wang X. LncRNA MIR200CHG inhibits EMT in gastric cancer by stabilizing miR-200c from target-directed miRNA degradation. Nat Commun 2023; 14:8141. [PMID: 38065939 PMCID: PMC10709323 DOI: 10.1038/s41467-023-43974-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
Gastric cancer (GC) is a heterogeneous disease, threatening millions of lives worldwide, yet the functional roles of long non-coding RNAs (lncRNAs) in different GC subtypes remain poorly characterized. Microsatellite stable (MSS)/epithelial-mesenchymal transition (EMT) GC is the most aggressive subtype associated with a poor prognosis. Here, we apply integrated network analysis to uncover lncRNA heterogeneity between GC subtypes, and identify MIR200CHG as a master regulator mediating EMT specifically in MSS/EMT GC. The expression of MIR200CHG is silenced in MSS/EMT GC by promoter hypermethylation, associated with poor prognosis. MIR200CHG reverses the mesenchymal identity of GC cells in vitro and inhibits metastasis in vivo. Mechanistically, MIR200CHG not only facilitates the biogenesis of its intronic miRNAs miR-200c and miR-141, but also protects miR-200c from target-directed miRNA degradation (TDMD) through direct binding to miR-200c. Our studies reveal a landscape of a subtype-specific lncRNA regulatory network, providing clinically relevant biological insights towards MSS/EMT GC.
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Grants
- 2020N368 Shenzhen Science and Technology Innovation Commission
- C4024-22GF Research Grants Council, University Grants Committee (RGC, UGC)
- 14104223 Research Grants Council, University Grants Committee (RGC, UGC)
- 11103619 Research Grants Council, University Grants Committee (RGC, UGC)
- 14111522 Research Grants Council, University Grants Committee (RGC, UGC)
- R4017-18 Research Grants Council, University Grants Committee (RGC, UGC)
- 82173289 National Natural Science Foundation of China (National Science Foundation of China)
- 81872401 National Natural Science Foundation of China (National Science Foundation of China)
- Guangdong Basic and Applied Basic Research Foundation (Project No.2019B030302012), a startup grant (Project No. 4937084), direct grant (2021.077), Faculty Postdoctoral Fellowship Scheme 2021/22 (Project No. FPFS/2122/32), Shenzhen Bay Scholars Program.
- Guangdong Basic and Applied Basic Research Foundation (2021A1515010425)
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Affiliation(s)
- Yixiao Zhu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chengmei Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Chao Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yi Zhou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Enen Zhao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yaxin Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Xingyan Pan
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Huilin Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
| | - Wenting Liao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
| | - Xin Wang
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Guangdong, China.
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4
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Wang J, Horlacher M, Cheng L, Winther O. RNA trafficking and subcellular localization-a review of mechanisms, experimental and predictive methodologies. Brief Bioinform 2023; 24:bbad249. [PMID: 37466130 PMCID: PMC10516376 DOI: 10.1093/bib/bbad249] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/30/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
RNA localization is essential for regulating spatial translation, where RNAs are trafficked to their target locations via various biological mechanisms. In this review, we discuss RNA localization in the context of molecular mechanisms, experimental techniques and machine learning-based prediction tools. Three main types of molecular mechanisms that control the localization of RNA to distinct cellular compartments are reviewed, including directed transport, protection from mRNA degradation, as well as diffusion and local entrapment. Advances in experimental methods, both image and sequence based, provide substantial data resources, which allow for the design of powerful machine learning models to predict RNA localizations. We review the publicly available predictive tools to serve as a guide for users and inspire developers to build more effective prediction models. Finally, we provide an overview of multimodal learning, which may provide a new avenue for the prediction of RNA localization.
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Affiliation(s)
- Jun Wang
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
| | - Marc Horlacher
- Computational Health Center, Helmholtz Center, Munich, Germany
| | - Lixin Cheng
- Shenzhen People’s Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen 518020, China
| | - Ole Winther
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen 2100, Denmark
- Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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5
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Fasolo F, Winski G, Li Z, Wu Z, Winter H, Ritzer J, Glukha N, Roy J, Hultgren R, Pauli J, Busch A, Sachs N, Knappich C, Eckstein HH, Boon RA, Paloschi V, Maegdefessel L. The circular RNA Ataxia Telangiectasia Mutated regulates oxidative stress in smooth muscle cells in expanding abdominal aortic aneurysms. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:848-865. [PMID: 37680984 PMCID: PMC10481153 DOI: 10.1016/j.omtn.2023.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 08/14/2023] [Indexed: 09/09/2023]
Abstract
An abdominal aortic aneurysm (AAA) is a pathological widening of the aortic wall characterized by loss of smooth muscle cells (SMCs), extracellular matrix degradation, and local inflammation. This condition is often asymptomatic until rupture occurs, leading to high morbidity and mortality rates. Diagnosis is mostly accidental and the only currently available treatment option remains surgical intervention. Circular RNAs (circRNAs) represent a novel class of regulatory non-coding RNAs that originate from backsplicing. Their highly stable loop structure, combined with a remarkable enrichment in body fluids, make circRNAs promising disease biomarkers. We investigated the contribution of circRNAs to AAA pathogenesis and their potential application to improve AAA diagnostics. Gene expression analysis revealed the presence of deregulated circular transcripts stemming from AAA-relevant gene loci. Among these, the circRNA to the Ataxia Telangiectasia Mutated gene (cATM) was upregulated in human AAA specimens, in AAA-derived SMCs, and serum samples collected from aneurysm patients. In primary aortic SMCs, cATM increased upon angiotensin II and doxorubicin stimulation, while its silencing triggered apoptosis. Higher cATM levels made AAA-derived SMCs less vulnerable to oxidative stress, compared with control SMCs. These data suggest that cATM contributes to elicit an adaptive oxidative-stress response in SMCs and provides a reliable AAA disease signature.
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Affiliation(s)
- Francesca Fasolo
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 10785 Berlin, Germany
| | - Greg Winski
- Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Zhaolong Li
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 10785 Berlin, Germany
| | - Zhiyan Wu
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 10785 Berlin, Germany
- Department of Vascular Surgery, Beijing Hospital, National Center of Gerontology and Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing 100730, P.R. China
| | - Hanna Winter
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 10785 Berlin, Germany
| | - Julia Ritzer
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany
| | - Nadiya Glukha
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany
| | - Joy Roy
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden
- Department of Vascular Surgery, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Rebecka Hultgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden
- Department of Vascular Surgery, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Jessica Pauli
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 10785 Berlin, Germany
| | - Albert Busch
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany
- Division of Vascular and Endovascular Surgery, Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty, Carl Gustav Carus and University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Nadja Sachs
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany
| | - Christoph Knappich
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany
| | - Hans-Henning Eckstein
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany
| | - Reinier A. Boon
- German Center for Cardiovascular Research DZHK 10785 Berlin, Partner Site Frankfurt Rhine-Main, Frankfurt am Main, Germany
- Institute of Cardiovascular Regeneration, Goethe University, 60590 Frankfurt am Main, Germany
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Physiology, 1081 Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, 1081 Amsterdam, the Netherlands
| | - Valentina Paloschi
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 10785 Berlin, Germany
| | - Lars Maegdefessel
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 10785 Berlin, Germany
- Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
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6
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Xie Y, Gao S, Zhang K, Bhat P, Clarke BP, Batten K, Mei M, Gazzara M, Shay JW, Lynch KW, Angelos AE, Hill PS, Ivey AL, Fontoura BMA, Ren Y. Structural basis for high-order complex of SARNP and DDX39B to facilitate mRNP assembly. Cell Rep 2023; 42:112988. [PMID: 37578863 PMCID: PMC10508174 DOI: 10.1016/j.celrep.2023.112988] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/10/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023] Open
Abstract
mRNA in eukaryotic cells is packaged into highly compacted ribonucleoprotein particles (mRNPs) in the nucleus and exported to the cytoplasm for translation. mRNP packaging and export require the evolutionarily conserved transcription-export (TREX) complex. TREX facilitates loading of various RNA-binding proteins on mRNA through the action of its DDX39B subunit. SARNP (Tho1 [transcriptional defect of Hpr1 by overexpression 1] in yeast) is shown to interact with DDX39B and affect mRNA export. The molecular mechanism of how SARNP recognizes DDX39B and functions in mRNP assembly is unclear. Here, we determine the crystal structure of a Tho1/DDX39B/RNA complex, revealing a multivalent interaction mediated by tandem DDX39B interacting motifs in SARNP/Tho1. The high-order complex of SARNP and DDX39B is evolutionarily conserved, and human SARNP can engage with five DDX39B molecules. RNA sequencing (RNA-seq) from SARNP knockdown cells shows the most affected RNAs in export are GC rich. Our work suggests the role of the high-order SARNP/DDX39B/RNA complex in mRNP assembly and export.
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Affiliation(s)
- Yihu Xie
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Shengyan Gao
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Ke Zhang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Prasanna Bhat
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Bradley P Clarke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Kimberly Batten
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Menghan Mei
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Matthew Gazzara
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexia E Angelos
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Pate S Hill
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Austin L Ivey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Beatriz M A Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA.
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.
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7
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Maksimova V, Wilkie T, Smith S, Phelps C, Melvin C, Yu L, Niewiesk S, Green PL, Panfil AR. HTLV-1 Hbz protein, but not hbz mRNA secondary structure, is critical for viral persistence and disease development. PLoS Pathog 2023; 19:e1011459. [PMID: 37327244 DOI: 10.1371/journal.ppat.1011459] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/05/2023] [Indexed: 06/18/2023] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is the etiologic cause of adult T-cell leukemia/lymphoma (ATL) and encodes a viral oncoprotein (Hbz) that is consistently expressed in asymptomatic carriers and ATL patients, suggesting its importance in the development and maintenance of HTLV-1 leukemic cells. Our previous work found Hbz protein is dispensable for virus-mediated T-cell immortalization but enhances viral persistence. We and others have also shown that hbz mRNA promotes T-cell proliferation. In our current studies, we evaluated the role of hbz mRNA on HTLV-1-mediated immortalization in vitro as well as in vivo persistence and disease development. We generated mutant proviral clones to examine the individual contributions of hbz mRNA, hbz mRNA secondary structure (stem-loop), and Hbz protein. Wild-type (WT) and all mutant viruses produced virions and immortalized T-cells in vitro. Viral persistence and disease development were also evaluated in vivo by infection of a rabbit model and humanized immune system (HIS) mice, respectively. Proviral load and sense and antisense viral gene expression were significantly lower in rabbits infected with mutant viruses lacking Hbz protein compared to WT or virus with an altered hbz mRNA stem-loop (M3 mutant). HIS mice infected with Hbz protein-deficient viruses showed significantly increased survival times compared to animals infected with WT or M3 mutant virus. Altered hbz mRNA secondary structure, or loss of hbz mRNA or protein, has no significant effect on T-cell immortalization induced by HTLV-1 in vitro; however, the Hbz protein plays a critical role in establishing viral persistence and leukemogenesis in vivo.
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Affiliation(s)
- Victoria Maksimova
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Tasha Wilkie
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Susan Smith
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Cameron Phelps
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Corrine Melvin
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Lianbo Yu
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Stefan Niewiesk
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Patrick L Green
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States
- Comprehensive Cancer Center and Solove Research Institute, The Ohio State University, Columbus, Ohio, United States
| | - Amanda R Panfil
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States
- Comprehensive Cancer Center and Solove Research Institute, The Ohio State University, Columbus, Ohio, United States
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8
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Functional Relationships between Long Non-Coding RNAs and Estrogen Receptor Alpha: A New Frontier in Hormone-Responsive Breast Cancer Management. Int J Mol Sci 2023; 24:ijms24021145. [PMID: 36674656 PMCID: PMC9863308 DOI: 10.3390/ijms24021145] [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: 12/22/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
In the complex and articulated machinery of the human genome, less than 2% of the transcriptome encodes for proteins, while at least 75% is actively transcribed into non-coding RNAs (ncRNAs). Among the non-coding transcripts, those ≥200 nucleotides long (lncRNAs) are receiving growing attention for their involvement in human diseases, particularly cancer. Genomic studies have revealed the multiplicity of processes, including neoplastic transformation and tumor progression, in which lncRNAs are involved by regulating gene expression at epigenetic, transcriptional, and post-transcriptional levels by mechanism(s) that still need to be clarified. In breast cancer, several lncRNAs were identified and demonstrated to have either oncogenic or tumor-suppressive roles. The functional understanding of the mechanisms of lncRNA action in this disease could represent a potential for translational applications, as these molecules may serve as novel biomarkers of clinical use and potential therapeutic targets. This review highlights the relationship between lncRNAs and the principal hallmark of the luminal breast cancer phenotype, estrogen receptor α (ERα), providing an overview of new potential ways to inhibit estrogenic signaling via this nuclear receptor toward escaping resistance to endocrine therapy.
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9
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Wang J, Lai X, Peng X. CircLIFR Inhibits Non-small Cell Lung Cancer Progression by Acting as a miR-429 Sponge to Enhance CELF2 Expression. Biochem Genet 2022; 61:725-741. [PMID: 36104590 DOI: 10.1007/s10528-022-10285-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 09/01/2022] [Indexed: 11/27/2022]
Abstract
Lung cancer is the most commonly diagnosed cancer and the leading reason for tumor-related mortality, while non-small cell lung cancer (NSCLC) is the most usual type of lung cancer. Circular RNAs (circRNAs) have emerged as vital regulators in the development of human cancers, including NSCLC. We aimed to explore the functions of circRNA leukemia inhibitory factor receptor (circLIFR) in NSCLC progression. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to quantify the expression of circLIFR, microRNA-429 (miR-429), and Elav-like family member 2 (CELF2) in NSCLC tissues and cells. Cell proliferation capability of NSCLC cells was determined by Cell Counting Kit-8 (CCK-8) and colony formation assays. The flow cytometry assay was performed to evaluate cell-cycle distribution and apoptosis of NSCLC cells. The abilities of migration and invasion were measured by transwell assay. In addition, the activities of caspase 3 and caspase 9 were measured by the assay kits. The interaction relationship between miR-429 and circLIFR or CELF2 was analyzed by dual-luciferase reporter, RNA immunoprecipitation (RIP), and RNA pull-down assays. The expression levels of related proteins were examined by Western Blot assay. The xenograft experiment was established to explore the role of circLIFR in vivo. CircLIFR, circular, and stable transcript in NSCLC cells, was decreased more than 2 folds in NSCLC tissues and cells than controls (P < 0.0001). Importantly, overexpression of circLIFR impeded cell proliferation, migration, invasion, and inactivated protein kinase B (AKT)/phosphatase and tensin homolog (PTEN)-signaling pathways while enhanced apoptosis and cell-cycle arrest in NSCLC cells, which was overturned by upregulation of miR-429 or silencing of CELF2. Furthermore, the upregulation of circLIFR inhibited NSCLC tumor growth in vivo. Overexpression of circLIFR could suppress NSCLC progress by acting as a sponge of miR-429 to regulate the expression of CELF2 and PTEN/AKT-signaling pathways in NSCLC.
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Affiliation(s)
- Junbin Wang
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Beijing, China
| | - Xinyi Lai
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Beijing, China
| | - Xuxing Peng
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Beijing, China.
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10
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Gao S, Esparza M, Dehghan I, Aksenova V, Zhang K, Batten K, Ferretti MB, Begg BE, Cagatay T, Shay JW, García-Sastre A, Goldsmith EJ, Chen ZJ, Dasso M, Lynch KW, Cobb MH, Fontoura BMA. Nuclear speckle integrity and function require TAO2 kinase. Proc Natl Acad Sci U S A 2022; 119:e2206046119. [PMID: 35704758 PMCID: PMC9231605 DOI: 10.1073/pnas.2206046119] [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: 04/06/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022] Open
Abstract
Nuclear speckles are non-membrane-bound organelles known as storage sites for messenger RNA (mRNA) processing and splicing factors. More recently, nuclear speckles have also been implicated in splicing and export of a subset of mRNAs, including the influenza virus M mRNA that encodes proteins required for viral entry, trafficking, and budding. However, little is known about how nuclear speckles are assembled or regulated. Here, we uncovered a role for the cellular protein kinase TAO2 as a constituent of nuclear speckles and as a factor required for the integrity of these nuclear bodies and for their functions in pre-mRNA splicing and trafficking. We found that a nuclear pool of TAO2 is localized at nuclear speckles and interacts with nuclear speckle factors involved in RNA splicing and nuclear export, including SRSF1 and Aly/Ref. Depletion of TAO2 or inhibition of its kinase activity disrupts nuclear speckle structure, decreasing the levels of several proteins involved in nuclear speckle assembly and splicing, including SC35 and SON. Consequently, splicing and nuclear export of influenza virus M mRNA were severely compromised and caused a disruption in the virus life cycle. In fact, low levels of TAO2 led to a decrease in viral protein levels and inhibited viral replication. Additionally, depletion or inhibition of TAO2 resulted in abnormal expression of a subset of mRNAs with key roles in viral replication and immunity. Together, these findings uncovered a function of TAO2 in nuclear speckle formation and function and revealed host requirements and vulnerabilities for influenza infection.
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Affiliation(s)
- Shengyan Gao
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Matthew Esparza
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Ishmael Dehghan
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Vasilisa Aksenova
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892
| | - Ke Zhang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kimberly Batten
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Max B. Ferretti
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104
| | - Bridget E. Begg
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104
| | - Tolga Cagatay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jerry W. Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Elizabeth J. Goldsmith
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Zhijian J. Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892
| | - Kristen W. Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104
| | - Melanie H. Cobb
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Beatriz M. A. Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
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11
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Pakhomova T, Moshareva M, Vasilkova D, Zatsepin T, Dontsova O, Rubtsova M. Role of RNA Biogenesis Factors in the Processing and Transport of Human Telomerase RNA. Biomedicines 2022; 10:biomedicines10061275. [PMID: 35740297 PMCID: PMC9219725 DOI: 10.3390/biomedicines10061275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/21/2022] Open
Abstract
Telomerase RNA has long been considered to be a noncoding component of telomerase. However, the expression of the telomerase RNA gene is not always associated with telomerase activity. The existence of distinct TERC gene expression products possessing different functions were demonstrated recently. During biogenesis, hTR is processed by distinct pathways and localized in different cell compartments, depending on whether it functions as a telomerase complex component or facilitates antistress activities as a noncoding RNA, in which case it is either processed in the mitochondria or translated. In order to identify the factors responsible for the appearance and localization of the exact isoform of hTR, we investigated the roles of the factors regulating transcription DSIF (Spt5) and NELF-E; exosome-attracting factors ZCCHC7, ZCCHC8, and ZFC3H1; ARS2, which attracts processing and transport factors; and transport factor PHAX during the biogenesis of hTR. The data obtained revealed that ZFC3H1 participates in hTR biogenesis via pathways related to the polyadenylated RNA degradation mechanism. The data revealed essential differences that are important for understanding hTR biogenesis and that are interesting for further investigations of new, therapeutically significant targets.
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Affiliation(s)
- Tatiana Pakhomova
- Department of Chemistry, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (T.P.); (M.M.); (D.V.); (O.D.)
| | - Maria Moshareva
- Department of Chemistry, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (T.P.); (M.M.); (D.V.); (O.D.)
| | - Daria Vasilkova
- Department of Chemistry, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (T.P.); (M.M.); (D.V.); (O.D.)
| | - Timofey Zatsepin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia;
| | - Olga Dontsova
- Department of Chemistry, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (T.P.); (M.M.); (D.V.); (O.D.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia;
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow 121205, Russia
| | - Maria Rubtsova
- Department of Chemistry, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (T.P.); (M.M.); (D.V.); (O.D.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia;
- Correspondence:
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12
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Sgubin M, Pegoraro S, Pellarin I, Ros G, Sgarra R, Piazza S, Baldassarre G, Belletti B, Manfioletti G. HMGA1 positively regulates the microtubule-destabilizing protein stathmin promoting motility in TNBC cells and decreasing tumour sensitivity to paclitaxel. Cell Death Dis 2022; 13:429. [PMID: 35504904 PMCID: PMC9065117 DOI: 10.1038/s41419-022-04843-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 12/14/2022]
Abstract
High Mobility Group A1 (HMGA1) is an architectural chromatin factor involved in the regulation of gene expression and a master regulator in Triple Negative Breast Cancer (TNBC). In TNBC, HMGA1 is overexpressed and coordinates a gene network that controls cellular processes involved in tumour development, progression, and metastasis formation. Here, we find that the expression of HMGA1 and of the microtubule-destabilizing protein stathmin correlates in breast cancer (BC) patients. We demonstrate that HMGA1 depletion leads to a downregulation of stathmin expression and activity on microtubules resulting in decreased TNBC cell motility. We show that this pathway is mediated by the cyclin-dependent kinase inhibitor p27kip1 (p27). Indeed, the silencing of HMGA1 expression in TNBC cells results both in an increased p27 protein stability and p27-stathmin binding. When the expression of both HMGA1 and p27 is silenced, we observe a significant rescue in cell motility. These data, obtained in cellular models, were validated in BC patients. In fact, we find that patients with high levels of both HMGA1 and stathmin and low levels of p27 have a statistically significant lower survival probability in terms of relapse-free survival (RFS) and distant metastasis-free survival (DMFS) with respect to the patient group with low HMGA1, low stathmin, and high p27 expression levels. Finally, we show in an in vivo xenograft model that depletion of HMGA1 chemo-sensitizes tumour cells to paclitaxel, a drug that is commonly used in TNBC treatments. This study unveils a new interaction among HMGA1, p27, and stathmin that is critical in BC cell migration. Moreover, our data suggest that taxol-based treatments may be more effective in reducing the tumour burden when tumour cells express low levels of HMGA1.
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Affiliation(s)
- Michela Sgubin
- grid.5133.40000 0001 1941 4308Department of Life Sciences, University of Trieste, Trieste, Italy ,grid.418321.d0000 0004 1757 9741Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, Aviano, Italy
| | - Silvia Pegoraro
- grid.5133.40000 0001 1941 4308Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Ilenia Pellarin
- grid.418321.d0000 0004 1757 9741Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, Aviano, Italy
| | - Gloria Ros
- grid.5133.40000 0001 1941 4308Department of Life Sciences, University of Trieste, Trieste, Italy ,grid.5970.b0000 0004 1762 9868Present Address: International School for Advanced Studies (SISSA), Area of Neuroscience Trieste, Trieste, Italy
| | - Riccardo Sgarra
- grid.5133.40000 0001 1941 4308Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Silvano Piazza
- grid.425196.d0000 0004 1759 4810International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Trieste, Italy
| | - Gustavo Baldassarre
- grid.418321.d0000 0004 1757 9741Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, Aviano, Italy
| | - Barbara Belletti
- grid.418321.d0000 0004 1757 9741Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, Aviano, Italy
| | - Guidalberto Manfioletti
- grid.5133.40000 0001 1941 4308Department of Life Sciences, University of Trieste, Trieste, Italy
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13
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Reautschnig P, Wahn N, Wettengel J, Schulz AE, Latifi N, Vogel P, Kang TW, Pfeiffer LS, Zarges C, Naumann U, Zender L, Li JB, Stafforst T. CLUSTER guide RNAs enable precise and efficient RNA editing with endogenous ADAR enzymes in vivo. Nat Biotechnol 2022; 40:759-768. [PMID: 34980913 DOI: 10.1038/s41587-021-01105-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 09/23/2021] [Indexed: 11/09/2022]
Abstract
RNA base editing represents a promising alternative to genome editing. Recent approaches harness the endogenous RNA-editing enzyme adenosine deaminase acting on RNA (ADAR) to circumvent problems caused by ectopic expression of engineered editing enzymes, but suffer from sequence restriction, lack of efficiency and bystander editing. Here we present in silico-optimized CLUSTER guide RNAs that bind their target messenger RNAs in a multivalent fashion, achieve editing with high precision and efficiency and enable targeting of sequences that were not accessible using previous gRNA designs. CLUSTER gRNAs can be genetically encoded and delivered using viruses, and are active in a wide range of cell lines. In cell culture, CLUSTER gRNAs achieve on-target editing of endogenous transcripts with yields of up to 45% without bystander editing. In vivo, CLUSTER gRNAs delivered to mouse liver by hydrodynamic tail vein injection edited reporter constructs at rates of up to 10%. The CLUSTER approach opens avenues for drug development in the field of RNA base editing.
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Affiliation(s)
- Philipp Reautschnig
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | | | - Jacqueline Wettengel
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Annika E Schulz
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Ngadhnjim Latifi
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Paul Vogel
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Tae-Won Kang
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen, Germany
- German Cancer Research Consortium, Partner Site Tübingen, German Cancer Research Center, Heidelberg, Germany
| | - Laura S Pfeiffer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Christine Zarges
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Ulrike Naumann
- Hertie Institute for Clinical Brain Research, Center of Neurology, University Hospital Tübingen, University of Tübingen, Tübingen, Germany
| | - Lars Zender
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen, Germany
- German Cancer Research Consortium, Partner Site Tübingen, German Cancer Research Center, Heidelberg, Germany
- DFG Cluster of Excellence 2180 'Image-guided and Functional Instructed Tumor Therapy', University of Tübingen, Tübingen, Germany
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
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14
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Kim EJ, Kim JS, Lee S, Cheon I, Kim SR, Ko YH, Kang K, Tan X, Kurie JM, Ahn YH. ZEB1-regulated lnc-Nr2f1 promotes the migration and invasion of lung adenocarcinoma cells. Cancer Lett 2022; 533:215601. [PMID: 35176421 DOI: 10.1016/j.canlet.2022.215601] [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: 11/12/2021] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 11/25/2022]
Abstract
Numerous long non-coding RNAs (lncRNAs) are differentially expressed in cancer cells compared with normal cells and are involved in tumor progression and metastasis. Metastasis is initiated by the epithelial-to-mesenchymal transition (EMT) process, which can also be regulated by lncRNAs. Given that ZEB1 is an important transcription factor inducing EMT, we screened lncRNAs controlled by ZEB1 using RNA sequencing in murine lung adenocarcinoma cells. Among several lncRNAs regulated by ZEB1, we selected lnc-Nr2f1. Lnc-Nr2f1 is upregulated by ZEB1 and TGF-β, a potent EMT signal. Growth, migration, and invasion of lung adenocarcinoma cells were decreased after lnc-Nr2f1 knockdown and increased after lnc-Nr2f1 overexpression. Interestingly, lnc-Nr2f1 was transcriptionally controlled by NR2F1, a transcription factor that is transcribed in the antisense direction. NR2F1 was also upregulated and positively correlated with ZEB1, forming a ZEB1/NR2F1/lnc-Nr2f1 axis. Lnc-Nr2f1, in turn, promoted Twist2 transcription through direct binding to its genomic DNA region. Collectively, lnc-Nr2f1 was upregulated by ZEB1 and NR2F1, and promoted migration and invasion of lung adenocarcinoma cells via TWIST2 regulation.
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Affiliation(s)
- Eun Ju Kim
- Department of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul, 07804, South Korea
| | - Jeong Seon Kim
- Department of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul, 07804, South Korea; Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA
| | - Sieun Lee
- Department of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul, 07804, South Korea
| | - Inyoung Cheon
- Department of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul, 07804, South Korea
| | - Seo Ree Kim
- Division of Oncology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Yoon Ho Ko
- Division of Oncology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan, Chungnam, 31116, South Korea
| | - Xiaochao Tan
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jonathan M Kurie
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Young-Ho Ahn
- Department of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul, 07804, South Korea.
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15
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Culjkovic-Kraljacic B, Borden KLB. Subcellular Fractionation Suitable for Studies of RNA and Protein Trafficking. Methods Mol Biol 2022; 2502:91-104. [PMID: 35412233 DOI: 10.1007/978-1-0716-2337-4_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The nuclear pore complex is the major conduit for trafficking between the nucleus and cytoplasm. Nuclear import and export of both proteins and RNAs represent important functional steps for many biological processes. One of the major means to study NPC activity and the nuclear and cytoplasmic distribution of proteins and RNAs is through biochemical fractionation. Here, we describe detailed methods to generate high quality nuclear and cytoplasmic fractions simultaneously capturing RNA and proteins which can be used subsequently for a wide array of biochemical characterizations including proteomics and next generation sequencings.
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Affiliation(s)
- Biljana Culjkovic-Kraljacic
- Department of Pathology and Cell Biology, Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada.
| | - Katherine L B Borden
- Department of Pathology and Cell Biology, Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada.
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16
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Zhou Y, Li J, Yang X, Song Y, Li H. Rhophilin rho GTPase binding protein 1-antisense RNA 1 (RHPN1-AS1) promotes ovarian carcinogenesis by sponging microRNA-485-5p and releasing DNA topoisomerase II alpha ( TOP2A). Bioengineered 2021; 12:12003-12022. [PMID: 34787052 PMCID: PMC8810118 DOI: 10.1080/21655979.2021.2002494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/22/2021] [Accepted: 10/30/2021] [Indexed: 10/29/2022] Open
Abstract
Ovarian cancer (OC) is the most common and lethal gynecological cancer worldwide. Long non-coding RNAs (lncRNAs) and sponging microRNAs (miRNAs) serve as key regulators in the biological processes of OC. We sought to evaluate the effect of the RHPN1-AS1-miR-485-5p-DNA topoisomerase II alpha (TOP2A) axis in regulating OC progression. RHPN1-AS1, miR-485-5p, and TOP2A levels in OC tissues and cells were determined by RT-qPCR. The interaction of RHPN1-AS1/miR-485-5p/TOP2A was assessed using luciferase, RNA immunoprecipitation, and RNA pull-down assays. RHPN1-AS1 silencing allowed us to explore its biological function by measuring cell viability, proliferation, migration, invasion, and apoptosis in OC cells. In vivo experiments were performed to verify the in vitro findings. We found that the RHPN1-AS1 and TOP2A levels were significantly enhanced, whereas the miR-485-5p levels were reduced in OC tissues and cells. RHPN1-AS1 silencing attenuated cell growth, facilitated apoptosis in OC cells, and inhibited tumor growth in vivo. Notably, RHPN1-AS1 negatively regulating miR-485-5p promoted the TOP2A expression in OC cells. In conclusion, RHPN1-AS1 sponging miR-485-5p accelerated the progression of OC by elevating TOP2A expression, which makes it a promising target for the treatment of OC patients.
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Affiliation(s)
- Yi Zhou
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, Hunan, China
- Academician Workstation, Changsha Medical University, Changsha, Hunan, China
| | - Jing Li
- Department of Obstetrics and Gynecology, Wuhan Third Hospital, Wuhan, Hubei, China
| | - Xiaoxin Yang
- Department of Obstetrics and Gynecology, Wuhan Third Hospital, Wuhan, Hubei, China
| | - Yu Song
- Department of Obstetrics and Gynecology, Wuhan Third Hospital, Wuhan, Hubei, China
| | - Haigang Li
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, Hunan, China
- Academician Workstation, Changsha Medical University, Changsha, Hunan, China
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17
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Ghosh G, Samui S, Das S, Singh V, Pal D, Das S, Naskar J, Sinha Roy S, Basu U. Poly C Binding Protein 2 dependent nuclear retention of the utrophin-A mRNA in C2C12 cells. RNA Biol 2021; 18:612-622. [PMID: 34904931 PMCID: PMC8782177 DOI: 10.1080/15476286.2021.2004683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Upregulation of utrophin, the autosomal homologue of dystrophin, can compensate dystrophin deficiency in Duchenne Muscular Dystrophy (DMD) although the therapeutic success is yet to be achieved. The present study has identified Poly (C) binding protein 2 (PCBP2) as a post-transcriptional suppresser for the expression of utrophin-A, the muscle-specific utrophin isoform. This study confirms nuclear retention of utrophin-A mRNA in C2C12 cells, which is mediated by PCBP2. Further investigation demonstrates PCBP2-dependent nuclear retention of follistatin mRNA as well. Its involvement in nuclear retention of mRNA sheds light on a novel function of PCBP2 that makes utrophin-A mRNA less available in cytosol. PCBP2, therefore, may be a target to de-repress utrophin-A expression in DMD.
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Affiliation(s)
- Gargi Ghosh
- Department of Molecular Biology & Biotechnology, University of Kalyani, Kalyani, India
| | - Satyabrata Samui
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, India
| | - Santanu Das
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, India
| | - Vandana Singh
- CSIR-Institute of Genomics and Integrative Biology, Delhi University Campus, New Delhi, India
| | - Doel Pal
- Department of Molecular Biology & Biotechnology, University of Kalyani, Kalyani, India
| | - Subhanwita Das
- Department of Molecular Biology & Biotechnology, University of Kalyani, Kalyani, India
| | - Jishu Naskar
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, India
| | - Soumya Sinha Roy
- CSIR-Institute of Genomics and Integrative Biology, Delhi University Campus, New Delhi, India
| | - Utpal Basu
- Department of Molecular Biology & Biotechnology, University of Kalyani, Kalyani, India,CONTACT Utpal Basu Department of Molecular Biology & Biotechnology, University of Kalyani, Kalyani, West Bengal741235, India
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18
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Fasolo F, Jin H, Winski G, Chernogubova E, Pauli J, Winter H, Li DY, Glukha N, Bauer S, Metschl S, Wu Z, Koschinsky ML, Reilly M, Pelisek J, Kempf W, Eckstein HH, Soehnlein O, Matic L, Hedin U, Bäcklund A, Bergmark C, Paloschi V, Maegdefessel L. Long Noncoding RNA MIAT Controls Advanced Atherosclerotic Lesion Formation and Plaque Destabilization. Circulation 2021; 144:1567-1583. [PMID: 34647815 PMCID: PMC8570347 DOI: 10.1161/circulationaha.120.052023] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Supplemental Digital Content is available in the text. Long noncoding RNAs (lncRNAs) are important regulators of biological processes involved in vascular tissue homeostasis and disease development. The present study assessed the functional contribution of the lncRNA myocardial infarction-associated transcript (MIAT) to atherosclerosis and carotid artery disease.
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Affiliation(s)
- Francesca Fasolo
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (F.F., J. Pauli, H.W., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel).,German Center for Cardiovascular Research (DZHK), Berlin, Germany; partner site Munich Heart Alliance (F.F., J. Pauli, H.W., F.F., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel)
| | - Hong Jin
- Department of Medicine (H.J., G.W., E.C., A.B.), Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery (H.J., L. Matic, U.H., C.B., L. Maegdefessel), Karolinska Institutet, Stockholm, Sweden
| | - Greg Winski
- Department of Medicine (H.J., G.W., E.C., A.B.), Karolinska Institutet, Stockholm, Sweden
| | - Ekaterina Chernogubova
- Department of Medicine (H.J., G.W., E.C., A.B.), Karolinska Institutet, Stockholm, Sweden
| | - Jessica Pauli
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (F.F., J. Pauli, H.W., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel).,German Center for Cardiovascular Research (DZHK), Berlin, Germany; partner site Munich Heart Alliance (F.F., J. Pauli, H.W., F.F., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel)
| | - Hanna Winter
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (F.F., J. Pauli, H.W., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel).,German Center for Cardiovascular Research (DZHK), Berlin, Germany; partner site Munich Heart Alliance (F.F., J. Pauli, H.W., F.F., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel)
| | - Daniel Y Li
- Department of Cardiology, Columbia University Medical Center, New York, NY (D.Y.L., M.R.)
| | - Nadiya Glukha
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (F.F., J. Pauli, H.W., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel).,German Center for Cardiovascular Research (DZHK), Berlin, Germany; partner site Munich Heart Alliance (F.F., J. Pauli, H.W., F.F., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel)
| | - Sabine Bauer
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (F.F., J. Pauli, H.W., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel).,German Center for Cardiovascular Research (DZHK), Berlin, Germany; partner site Munich Heart Alliance (F.F., J. Pauli, H.W., F.F., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel)
| | - Susanne Metschl
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (F.F., J. Pauli, H.W., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel).,German Center for Cardiovascular Research (DZHK), Berlin, Germany; partner site Munich Heart Alliance (F.F., J. Pauli, H.W., F.F., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel)
| | - Zhiyuan Wu
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (F.F., J. Pauli, H.W., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel).,German Center for Cardiovascular Research (DZHK), Berlin, Germany; partner site Munich Heart Alliance (F.F., J. Pauli, H.W., F.F., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel)
| | | | - Muredach Reilly
- Department of Cardiology, Columbia University Medical Center, New York, NY (D.Y.L., M.R.)
| | - Jaroslav Pelisek
- Department of Vascular Surgery, University Hospital Zurich, Switzerland (J. Pelisek)
| | - Wolfgang Kempf
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (F.F., J. Pauli, H.W., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel).,German Center for Cardiovascular Research (DZHK), Berlin, Germany; partner site Munich Heart Alliance (F.F., J. Pauli, H.W., F.F., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel)
| | - Hans-Henning Eckstein
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (F.F., J. Pauli, H.W., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel).,German Center for Cardiovascular Research (DZHK), Berlin, Germany; partner site Munich Heart Alliance (F.F., J. Pauli, H.W., F.F., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel)
| | - Oliver Soehnlein
- Department of Experimental Pathology, Westphalian Wilhelms University, Munster, Germany (O.S.).,Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (O.S.).,Institute for Cardiovascular Prevention, Ludwig Maximilian University of Munich, Germany (O.S.)
| | - Ljubica Matic
- Department of Molecular Medicine and Surgery (H.J., L. Matic, U.H., C.B., L. Maegdefessel), Karolinska Institutet, Stockholm, Sweden
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery (H.J., L. Matic, U.H., C.B., L. Maegdefessel), Karolinska Institutet, Stockholm, Sweden
| | - Alexandra Bäcklund
- Department of Medicine (H.J., G.W., E.C., A.B.), Karolinska Institutet, Stockholm, Sweden
| | - Claes Bergmark
- Department of Molecular Medicine and Surgery (H.J., L. Matic, U.H., C.B., L. Maegdefessel), Karolinska Institutet, Stockholm, Sweden
| | - Valentina Paloschi
- German Center for Cardiovascular Research (DZHK), Berlin, Germany; partner site Munich Heart Alliance (F.F., J. Pauli, H.W., F.F., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel)
| | - Lars Maegdefessel
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (F.F., J. Pauli, H.W., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel).,German Center for Cardiovascular Research (DZHK), Berlin, Germany; partner site Munich Heart Alliance (F.F., J. Pauli, H.W., F.F., N.G., S.B., S.M., Z.W., W.K., H.-H.E., V.P., L. Maegdefessel).,Department of Molecular Medicine and Surgery (H.J., L. Matic, U.H., C.B., L. Maegdefessel), Karolinska Institutet, Stockholm, Sweden
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19
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Jing R, Ma B, Qi T, Hu C, Liao C, Wen C, Shao Y, Pei C. Long Noncoding RNA OIP5-AS1 Promotes Cell Apoptosis and Cataract Formation by Blocking POLG Expression Under Oxidative Stress. Invest Ophthalmol Vis Sci 2021; 61:3. [PMID: 33006594 PMCID: PMC7545078 DOI: 10.1167/iovs.61.12.3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Purpose Cataract, a clouding of the intraocular lens, is the leading cause of blindness. The lens-expressed long noncoding RNA OIP5-AS1 was upregulated in lens epithelial cells from patients with cataracts, suggesting its pathogenic role in cataracts. We investigated the regulatory role of OIP5-AS1 in the development of cataracts as well as potential RNA binding proteins, downstream target genes, and upstream transcription factors. Methods Clinical capsules and ex vivo and in vitro cataract models were used to test OIP5-AS1 expression. Cell apoptosis was detected using Western blots, JC-1 staining, and flow cytometry. Ribonucleoprotein immunoprecipitation-qPCR was performed to confirm the interaction of OIP5-AS1 and POLG. Chromatin immunoprecipitation-qPCR was used to determine the binding of TFAP2A and the OIP5-AS1 promoter region. Results OIP5-AS1 was upregulated in cataract lenses and B3 cells under oxidative stress. OIP5-AS1 knockdown protected B3 cells from H2O2-induced apoptosis and alleviated lens opacity in the ex vivo cataract model. HuR functioned as a scaffold carrying OIP5-AS1 and POLG mRNA and mediated the decay of POLG mRNA. POLG was downregulated in the cataract lens and oxidative-stressed B3 cells, and POLG depletion decreased the mtDNA copy number and MMP, increased reactive oxygen species production, and sensitized B3 cells to oxidative stress-induced apoptosis. POLG overexpression reversed these effects. TFAP2A bound the OIP5-AS1 promoter and contributed to OIP5-AS1 expression. Conclusions We demonstrated that OIP5-AS1, activated by TFAP2A, contributed to cataract formation by inhibiting POLG expression mediated by HuR, thus leading to increased apoptosis of lens epithelial cells and aggravated lens opacity, suggesting that OIP5-AS1 is a potential target for cataract treatment.
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Affiliation(s)
- Ruihua Jing
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Bo Ma
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Tiantian Qi
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Conghui Hu
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Chongbing Liao
- Center for Translational Medicine, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Chan Wen
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yongping Shao
- Center for Translational Medicine, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Cheng Pei
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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20
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Gao H, Lu X, Huang H, Ji H, Zhang L, Su Z. Thyroid-stimulating hormone level is negatively associated with fertilization rate in patients with polycystic ovary syndrome undergoing in vitro fertilization. Int J Gynaecol Obstet 2021; 155:138-145. [PMID: 33410141 DOI: 10.1002/ijgo.13581] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/21/2020] [Accepted: 01/04/2021] [Indexed: 12/15/2022]
Abstract
OBJECTIVE In this study, we investigated the effect of thyroid-stimulating hormone (TSH) level on the outcomes of in vitro fertilization (IVF) in patients with polycystic ovary syndrome (PCOS). METHODS Data pertaining to 60 patients who underwent IVF between May 2017 and May 2018 were included in the study. Thirty-two patients were diagnosed as PCOS (PCOS group) and 28 patients had tubal infertility (control group). Serum and follicular fluid TSH levels and follicular cyclic AMP (cAMP) level were detected by ELISA. TSH receptor (TSHR) expression level in granulosa cells was quantified by RT-PCR and Western blot. RESULTS In the PCOS group, oocyte maturation rate and fertilization rate were significantly lower than in the control group. Serum and follicular fluid TSH levels and ovarian cAMP level were higher in the PCOS group with an upregulation of ovarian TSHR. On multivariate linear regression analysis, fertilization rate showed a negative correlation with TSH levels in serum (B = -0.106, P = 0.005) and follicular fluid (B = -0.107, P = 0.001). CONCLUSION In PCOS patients, TSH levels, both in serum and follicular fluid, were negatively correlated with IVF oocyte maturation rate and fertilization rate. The effect of TSH on controlled ovarian hyperstimulated oocyte growth was likely mediated by the TSHR/cAMP signaling pathway.
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Affiliation(s)
- Haijie Gao
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Reproduction and Genetics, Xiamen, China
| | - Xiaohui Lu
- Department of Laboratory Medicine, The First Affiliated Hospital of Xiamen University, Xiamen Key Laboratory of Genetic Testing, Xiamen, China
| | - Hui Huang
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Reproduction and Genetics, Xiamen, China
| | - Hong Ji
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Reproduction and Genetics, Xiamen, China
| | - Ling Zhang
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Reproduction and Genetics, Xiamen, China
| | - Zhiying Su
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Reproduction and Genetics, Xiamen, China
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21
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Pinkney HR, Wright BM, Diermeier SD. The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis. Noncoding RNA 2020; 6:E49. [PMID: 33339309 PMCID: PMC7768357 DOI: 10.3390/ncrna6040049] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are a rapidly expanding field of research, with many new transcripts identified each year. However, only a small subset of lncRNAs has been characterized functionally thus far. To aid investigating the mechanisms of action by which new lncRNAs act, bioinformatic tools and databases are invaluable. Here, we review a selection of computational tools and databases for the in silico analysis of lncRNAs, including tissue-specific expression, protein coding potential, subcellular localization, structural conformation, and interaction partners. The assembled lncRNA toolkit is aimed primarily at experimental researchers as a useful starting point to guide wet-lab experiments, mainly containing multi-functional, user-friendly interfaces. With more and more new lncRNA analysis tools available, it will be essential to provide continuous updates and maintain the availability of key software in the future.
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Affiliation(s)
| | | | - Sarah D. Diermeier
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand; (H.R.P.); (B.M.W.)
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22
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Mordstein C, Savisaar R, Young RS, Bazile J, Talmane L, Luft J, Liss M, Taylor MS, Hurst LD, Kudla G. Codon Usage and Splicing Jointly Influence mRNA Localization. Cell Syst 2020; 10:351-362.e8. [PMID: 32275854 PMCID: PMC7181179 DOI: 10.1016/j.cels.2020.03.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 12/19/2019] [Accepted: 03/05/2020] [Indexed: 12/11/2022]
Abstract
In the human genome, most genes undergo splicing, and patterns of codon usage are splicing dependent: guanine and cytosine (GC) content is the highest within single-exon genes and within first exons of multi-exon genes. However, the effects of codon usage on gene expression are typically characterized in unspliced model genes. Here, we measured the effects of splicing on expression in a panel of synonymous reporter genes that varied in nucleotide composition. We found that high GC content increased protein yield, mRNA yield, cytoplasmic mRNA localization, and translation of unspliced reporters. Splicing did not affect the expression of GC-rich variants. However, splicing promoted the expression of AT-rich variants by increasing their steady-state protein and mRNA levels, in part through promoting cytoplasmic localization of mRNA. We propose that splicing promotes the nuclear export of AU-rich mRNAs and that codon- and splicing-dependent effects on expression are under evolutionary pressure in the human genome.
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Affiliation(s)
- Christine Mordstein
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK; Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Rosina Savisaar
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK; Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Robert S Young
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK; Centre for Global Health Research, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Jeanne Bazile
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Lana Talmane
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Juliet Luft
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Michael Liss
- Thermo Fisher Scientific, GENEART GmbH, Regensburg, Germany
| | - Martin S Taylor
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Laurence D Hurst
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK.
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23
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Cai P, Otten ABC, Cheng B, Ishii MA, Zhang W, Huang B, Qu K, Sun BK. A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis. Genome Res 2019; 30:22-34. [PMID: 31804951 PMCID: PMC6961571 DOI: 10.1101/gr.251561.119] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022]
Abstract
Genome-wide association studies indicate that many disease susceptibility regions reside in non-protein-coding regions of the genome. Long noncoding RNAs (lncRNAs) are a major component of the noncoding genome, but their biological impacts are not fully understood. Here, we performed a CRISPR interference (CRISPRi) screen on 2263 epidermis-expressed lncRNAs and identified nine novel candidate lncRNAs regulating keratinocyte proliferation. We further characterized a top hit from the screen, progenitor renewal associated non-coding RNA (PRANCR), using RNA interference–mediated knockdown and phenotypic analysis in organotypic human tissue. PRANCR regulates keratinocyte proliferation, cell cycle progression, and clonogenicity. PRANCR-deficient epidermis displayed impaired stratification with reduced expression of differentiation genes that are altered in human skin diseases, including keratins 1 and 10, filaggrin, and loricrin. Transcriptome analysis showed that PRANCR controls the expression of 1136 genes, with strong enrichment for late cell cycle genes containing a CHR promoter element. In addition, PRANCR depletion led to increased levels of both total and nuclear CDKN1A (also known as p21), which is known to govern both keratinocyte proliferation and differentiation. Collectively, these data show that PRANCR is a novel lncRNA regulating epidermal homeostasis and identify other lncRNA candidates that may have roles in this process as well.
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Affiliation(s)
- Pengfei Cai
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Auke B C Otten
- Department of Dermatology, University of California-San Diego, La Jolla, California 92109, USA
| | - Binbin Cheng
- Department of Dermatology, University of California-San Diego, La Jolla, California 92109, USA
| | - Mitsuhiro A Ishii
- Department of Dermatology, University of California-San Diego, La Jolla, California 92109, USA
| | - Wen Zhang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Beibei Huang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Kun Qu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.,CAS Center for Excellence in Molecular Cell Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Bryan K Sun
- Department of Dermatology, University of California-San Diego, La Jolla, California 92109, USA
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24
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Cui Y, Feng Q, Liu Q, Li H, Song X, Hu Z, Xu Z, Li J, Li M, Zheng W, Li Z, Pan H. Posttranscriptional regulation of MMP‐9 by HuR contributes to IL‐1β‐induced pterygium fibroblast migration and invasion. J Cell Physiol 2019; 235:5130-5140. [PMID: 31691974 DOI: 10.1002/jcp.29387] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 09/30/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Yu‐Hong Cui
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital, School of Basic Medical SciencesGuangzhou Medical University Guangzhou China
- Department of Histology and Embryology, School of Basic Medical SciencesGuangzhou Medical University Guangzhou China
| | - Qing‐Yang Feng
- Department of OphthalmologyGuangdong Women and Children Hospital Guangzhou China
- Institute of Ophthalmology, School of MedicineJinan University Guangzhou China
| | - Qun Liu
- Department of Histology and Embryology, School of Basic Medical SciencesGuangzhou Medical University Guangzhou China
| | - Hong‐Yang Li
- Department of OphthalmologyGuangdong No. 2 Provincial People's Hospital Guangzhou China
- Department of Ophthalmology, Guangzhou Red Cross HospitalThe Fourth Affiliated Hospital of Jinan University Guangzhou China
| | - Xi‐Ling Song
- Department of Public Health and Preventive MedicineJinan University Guangzhou China
| | - Zi‐Xuan Hu
- Department of Public Health and Preventive MedicineJinan University Guangzhou China
| | - Zhi‐Yi Xu
- Department of Ophthalmology, The First Affiliated HospitalJinan University Guangzhou China
- Institute of Ophthalmology, School of MedicineJinan University Guangzhou China
| | - Jia‐Hui Li
- Department of Public Health and Preventive MedicineJinan University Guangzhou China
| | - Mei‐Jun Li
- Department of Ophthalmology, The First Affiliated HospitalJinan University Guangzhou China
- Institute of Ophthalmology, School of MedicineJinan University Guangzhou China
| | - Wen‐Lin Zheng
- Department of Public Health and Preventive MedicineJinan University Guangzhou China
| | - Zhi‐Jie Li
- Institute of Ophthalmology, School of MedicineJinan University Guangzhou China
| | - Hong‐Wei Pan
- Department of Public Health and Preventive MedicineJinan University Guangzhou China
- Department of Ophthalmology, The First Affiliated HospitalJinan University Guangzhou China
- Institute of Ophthalmology, School of MedicineJinan University Guangzhou China
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25
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Poganik JR, Long MJC, Disare MT, Liu X, Chang SH, Hla T, Aye Y. Post-transcriptional regulation of Nrf2-mRNA by the mRNA-binding proteins HuR and AUF1. FASEB J 2019; 33:14636-14652. [PMID: 31665914 DOI: 10.1096/fj.201901930r] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The nuclear factor erythroid 2-related factor 2 (Nrf2) signaling axis is a target of covalent drugs and bioactive native electrophiles. However, much of our understanding of Nrf2 regulation has been focused at the protein level. Here we report a post-transcriptional modality to directly regulate Nrf2-mRNA. Our initial studies focused on the effects of the key mRNA-binding protein (mRBP) HuR on global transcriptomic changes incurred upon oxidant or electrophile stimulation. These RNA-sequencing data and subsequent mechanistic analyses led us to discover a novel role of HuR in regulating Nrf2 activity, and in the process, we further identified the related mRBP AUF1 as an additional novel Nrf2 regulator. Both mRBPs regulate Nrf2 activity by direct interaction with the Nrf2 transcript. Our data showed that HuR enhances Nrf2-mRNA maturation and promotes its nuclear export, whereas AUF1 stabilizes Nrf2-mRNA. Both mRBPs target the 3'-UTR of Nrf2-mRNA. Using a Nrf2 activity-reporter zebrafish strain, we document that this post-transcriptional control of Nrf2 activity is conserved at the whole-vertebrate level.-Poganik, J. R., Long, M. J. C., Disare, M. T., Liu, X., Chang, S.-H., Hla, T., Aye, Y. Post-transcriptional regulation of Nrf2-mRNA by the mRNA-binding proteins HuR and AUF1.
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Affiliation(s)
- Jesse R Poganik
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Marcus J C Long
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Michael T Disare
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Xuyu Liu
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Sung-Hee Chang
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Timothy Hla
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, USA; and.,Vascular Biology Program, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
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26
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Fasolo F, Patrucco L, Volpe M, Bon C, Peano C, Mignone F, Carninci P, Persichetti F, Santoro C, Zucchelli S, Sblattero D, Sanges R, Cotella D, Gustincich S. The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs. FASEB J 2019; 33:13572-13589. [PMID: 31570000 PMCID: PMC6894054 DOI: 10.1096/fj.201901618rr] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Transposable elements (TEs) compose about half of the mammalian genome and, as embedded sequences, up to 40% of long noncoding RNA (lncRNA) transcripts. Embedded TEs may represent functional domains within lncRNAs, providing a structured RNA platform for protein interaction. Here we show the interactome profile of the mouse inverted short interspersed nuclear element (SINE) of subfamily B2 (invSINEB2) alone and embedded in antisense (AS) ubiquitin C-terminal hydrolase L1 (Uchl1), an lncRNA that is AS to Uchl1 gene. AS Uchl1 is the representative member of a functional class of AS lncRNAs, named SINEUPs, in which the invSINEB2 acts as effector domain (ED)-enhancing translation of sense protein-coding mRNAs. By using RNA-interacting domainome technology, we identify the IL enhancer-binding factor 3 (ILF3) as a protein partner of AS Uchl1 RNA. We determine that this interaction is mediated by the RNA-binding motif 2 of ILF3 and the invSINEB2. Furthermore, we show that ILF3 is able to bind a free right Arthrobacter luteus (Alu) monomer sequence, the embedded TE acting as ED in human SINEUPs. Bioinformatic analysis of Encyclopedia of DNA Elements-enhanced cross-linking immunoprecipitation data reveals that ILF3 binds transcribed human SINE sequences at transcriptome-wide levels. We then demonstrate that the embedded TEs modulate AS Uchl1 RNA nuclear localization to an extent moderately influenced by ILF3. This work unveils the existence of a specific interaction between embedded TEs and an RNA-binding protein, strengthening the model of TEs as functional modules in lncRNAs.-Fasolo, F., Patrucco, L., Volpe, M., Bon, C., Peano, C., Mignone, F., Carninci, P., Persichetti, F., Santoro, C., Zucchelli, S., Sblattero, D., Sanges, R., Cotella, D., Gustincich, S. The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs.
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Affiliation(s)
- Francesca Fasolo
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Laura Patrucco
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Massimiliano Volpe
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Carlotta Bon
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Clelia Peano
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
| | - Flavio Mignone
- Department of Sciences and Innovation, Università del Piemonte Orientale, Alessandria, Italy
| | - Piero Carninci
- Division of Genomic Technologies, Riken Center for Life Science Technologies, Yokohama, Japan
| | | | - Claudio Santoro
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Silvia Zucchelli
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.,Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | | | - Remo Sanges
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Diego Cotella
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Stefano Gustincich
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
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27
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Zhang X, Xue C, Lin J, Ferguson JF, Weiner A, Liu W, Han Y, Hinkle C, Li W, Jiang H, Gosai S, Hachet M, Garcia BA, Gregory BD, Soccio RE, Hogenesch JB, Seale P, Li M, Reilly MP. Interrogation of nonconserved human adipose lincRNAs identifies a regulatory role of linc-ADAL in adipocyte metabolism. Sci Transl Med 2019; 10:10/446/eaar5987. [PMID: 29925637 DOI: 10.1126/scitranslmed.aar5987] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 11/27/2017] [Accepted: 05/04/2018] [Indexed: 12/16/2022]
Abstract
Long intergenic noncoding RNAs (lincRNAs) have emerged as important modulators of cellular functions. Most lincRNAs are not conserved among mammals, raising the fundamental question of whether nonconserved adipose-expressed lincRNAs are functional. To address this, we performed deep RNA sequencing of gluteal subcutaneous adipose tissue from 25 healthy humans. We identified 1001 putative lincRNAs expressed in all samples through de novo reconstruction of noncoding transcriptomes and integration with existing lincRNA annotations. One hundred twenty lincRNAs had adipose-enriched expression, and 54 of these exhibited peroxisome proliferator-activated receptor γ (PPARγ) or CCAAT/enhancer binding protein α (C/EBPα) binding at their loci. Most of these adipose-enriched lincRNAs (~85%) were not conserved in mice, yet on average, they showed degrees of expression and binding of PPARγ and C/EBPα similar to those displayed by conserved lincRNAs. Most adipose lincRNAs differentially expressed (n = 53) in patients after bariatric surgery were nonconserved. The most abundant adipose-enriched lincRNA in our subcutaneous adipose data set, linc-ADAL, was nonconserved, up-regulated in adipose depots of obese individuals, and markedly induced during in vitro human adipocyte differentiation. We demonstrated that linc-ADAL interacts with heterogeneous nuclear ribonucleoprotein U (hnRNPU) and insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) at distinct subcellular locations to regulate adipocyte differentiation and lipogenesis.
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Affiliation(s)
- Xuan Zhang
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Chenyi Xue
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Jennie Lin
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jane F Ferguson
- Division of Cardiovascular Medicine, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Amber Weiner
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wen Liu
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Yumiao Han
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christine Hinkle
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenjun Li
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hongfeng Jiang
- Key Laboratory of Remodeling-Related Cardiovascular Diseases, Beijing Collaborative Innovation Center for Cardiovascular Disorders, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China.,Beijing Institute of Heart, Lung and Blood Vessel Disease, Beijing 100029, China
| | - Sager Gosai
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Melanie Hachet
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raymond E Soccio
- The Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John B Hogenesch
- Divisions of Human Genetics and Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45267, USA
| | - Patrick Seale
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Muredach P Reilly
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA. .,Irving Institute for Clinical and Translational Research, Columbia University, New York, NY 10032, USA
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28
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The nuclear hypoxia-regulated NLUCAT1 long non-coding RNA contributes to an aggressive phenotype in lung adenocarcinoma through regulation of oxidative stress. Oncogene 2019; 38:7146-7165. [PMID: 31417181 DOI: 10.1038/s41388-019-0935-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 05/15/2019] [Accepted: 06/07/2019] [Indexed: 01/03/2023]
Abstract
Lung cancer is the leading cause of cancer death worldwide, with poor prognosis and a high rate of recurrence despite early surgical removal. Hypoxic regions within tumors represent sources of aggressiveness and resistance to therapy. Although long non-coding RNAs (lncRNAs) are increasingly recognized as major gene expression regulators, their regulation and function following hypoxic stress are still largely unexplored. Combining profiling studies on early-stage lung adenocarcinoma (LUAD) biopsies and on A549 LUAD cell lines cultured in normoxic or hypoxic conditions, we identified a subset of lncRNAs that are both correlated with the hypoxic status of tumors and regulated by hypoxia in vitro. We focused on a new transcript, NLUCAT1, which is strongly upregulated by hypoxia in vitro and correlated with hypoxic markers and poor prognosis in LUADs. Full molecular characterization showed that NLUCAT1 is a large nuclear transcript composed of six exons and mainly regulated by NF-κB and NRF2 transcription factors. CRISPR-Cas9-mediated invalidation of NLUCAT1 revealed a decrease in proliferative and invasive properties, an increase in oxidative stress and a higher sensitivity to cisplatin-induced apoptosis. Transcriptome analysis of NLUCAT1-deficient cells showed repressed genes within the antioxidant and/or cisplatin-response networks. We demonstrated that the concomitant knockdown of four of these genes products, GPX2, GLRX, ALDH3A1, and PDK4, significantly increased ROS-dependent caspase activation, thus partially mimicking the consequences of NLUCAT1 inactivation in LUAD cells. Overall, we demonstrate that NLUCAT1 contributes to an aggressive phenotype in early-stage hypoxic tumors, suggesting it may represent a new potential therapeutic target in LUADs.
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29
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Rubtsova M, Naraykina Y, Vasilkova D, Meerson M, Zvereva M, Prassolov V, Lazarev V, Manuvera V, Kovalchuk S, Anikanov N, Butenko I, Pobeguts O, Govorun V, Dontsova O. Protein encoded in human telomerase RNA is involved in cell protective pathways. Nucleic Acids Res 2019; 46:8966-8977. [PMID: 30102362 PMCID: PMC6158713 DOI: 10.1093/nar/gky705] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/23/2018] [Indexed: 01/06/2023] Open
Abstract
Several studies have described functional peptides encoded in RNA that are considered to be noncoding. Telomerase RNA together with telomerase reverse transcriptase and regulatory proteins make up the telomerase complex, the major component of the telomere length-maintaining machinery. In contrast to protein subunits, telomerase RNA is expressed constitutively in most somatic cells where telomerase reverse transcriptase is absent. We show here that the transcript of human telomerase RNA codes a 121 amino acid protein (hTERP). The existence of hTERP was shown by immunoblotting, immunofluorescence microscopy and mass spectroscopy. Gain-of-function and loss-of-function experiments showed that hTERP protects cells from drug-induced apoptosis and participates in the processing of autophagosome. We suggest that hTERP regulates crosstalk between autophagy and apoptosis and is involved in cellular adaptation under stress conditions.
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Affiliation(s)
- Maria Rubtsova
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Department of Chemistry, and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Yulia Naraykina
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Daria Vasilkova
- Department of Chemistry, and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Mark Meerson
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Maria Zvereva
- Department of Chemistry, and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Vladimir Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Vasily Lazarev
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow 119992, Russia
| | - Valentin Manuvera
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow 119992, Russia
| | - Sergey Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Nickolay Anikanov
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow 119992, Russia
| | - Ivan Butenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow 119992, Russia
| | - Olga Pobeguts
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow 119992, Russia
| | - Vadim Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow 119992, Russia
| | - Olga Dontsova
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Department of Chemistry, and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
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30
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Alessio E, Buson L, Chemello F, Peggion C, Grespi F, Martini P, Massimino ML, Pacchioni B, Millino C, Romualdi C, Bertoli A, Scorrano L, Lanfranchi G, Cagnin S. Single cell analysis reveals the involvement of the long non-coding RNA Pvt1 in the modulation of muscle atrophy and mitochondrial network. Nucleic Acids Res 2019; 47:1653-1670. [PMID: 30649422 PMCID: PMC6393313 DOI: 10.1093/nar/gkz007] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/05/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as important players in the regulation of several aspects of cellular biology. For a better comprehension of their function, it is fundamental to determine their tissue or cell specificity and to identify their subcellular localization. In fact, the activity of lncRNAs may vary according to cell and tissue specificity and subcellular compartmentalization. Myofibers are the smallest complete contractile system of skeletal muscle influencing its contraction velocity and metabolism. How lncRNAs are expressed in different myofibers, participate in metabolism regulation and muscle atrophy or how they are compartmentalized within a single myofiber is still unknown. We compiled a comprehensive catalog of lncRNAs expressed in skeletal muscle, associating the fiber-type specificity and subcellular location to each of them, and demonstrating that many lncRNAs can be involved in the biological processes de-regulated during muscle atrophy. We demonstrated that the lncRNA Pvt1, activated early during muscle atrophy, impacts mitochondrial respiration and morphology and affects mito/autophagy, apoptosis and myofiber size in vivo. This work corroborates the importance of lncRNAs in the regulation of metabolism and neuromuscular pathologies and offers a valuable resource to study the metabolism in single cells characterized by pronounced plasticity.
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Affiliation(s)
- Enrico Alessio
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Lisa Buson
- Department of Biology, University of Padova, 35131 Padova, Italy
| | | | - Caterina Peggion
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Francesca Grespi
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Paolo Martini
- Department of Biology, University of Padova, 35131 Padova, Italy
| | | | - Beniamina Pacchioni
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
| | - Caterina Millino
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
| | - Chiara Romualdi
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Alessandro Bertoli
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Padova Neuroscience Center, University of Padova, 35131 Padova, Italy
| | - Luca Scorrano
- Department of Biology, University of Padova, 35131 Padova, Italy
- Venetian Institute of Molecular Medicine, 35131 Padova, Italy
| | - Gerolamo Lanfranchi
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
- CIR-Myo Myology Center, University of Padova, 35131 Padova, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
- CIR-Myo Myology Center, University of Padova, 35131 Padova, Italy
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31
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Marié IJ, Chang HM, Levy DE. HDAC stimulates gene expression through BRD4 availability in response to IFN and in interferonopathies. J Exp Med 2018; 215:3194-3212. [PMID: 30463877 PMCID: PMC6279398 DOI: 10.1084/jem.20180520] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/15/2018] [Accepted: 10/19/2018] [Indexed: 01/12/2023] Open
Abstract
In contrast to the common role of histone deacetylases (HDACs) for gene repression, HDAC activity provides a required positive function for IFN-stimulated gene (ISG) expression. Here, we show that HDAC1/2 as components of the Sin3A complex are required for ISG transcriptional elongation but not for recruitment of RNA polymerase or transcriptional initiation. Transcriptional arrest by HDAC inhibition coincides with failure to recruit the epigenetic reader Brd4 and elongation factor P-TEFb due to sequestration of Brd4 on hyperacetylated chromatin. Brd4 availability is regulated by an equilibrium cycle between opposed acetyltransferase and deacetylase activities that maintains a steady-state pool of free Brd4 available for recruitment to inducible promoters. An ISG expression signature is a hallmark of interferonopathies and other autoimmune diseases. Combined inhibition of HDAC1/2 and Brd4 resolved the aberrant ISG expression detected in cells derived from patients with two inherited interferonopathies, ISG15 and USP18 deficiencies, defining a novel therapeutic approach to ISG-associated autoimmune diseases.
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Affiliation(s)
- Isabelle J Marié
- Departments of Pathology and Microbiology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY
| | - Hao-Ming Chang
- Departments of Pathology and Microbiology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY
| | - David E Levy
- Departments of Pathology and Microbiology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY
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32
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Chen Q, Xiong C, Jia K, Jin J, Li Z, Huang Y, Liu Y, Wang L, Luo H, Li H, Meng QH, Li W. Hepatic transcriptome analysis from HFD-fed mice defines a long noncoding RNA regulating cellular cholesterol levels. J Lipid Res 2018; 60:341-352. [PMID: 30504232 PMCID: PMC6358296 DOI: 10.1194/jlr.m086215] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 11/12/2018] [Indexed: 12/21/2022] Open
Abstract
To elucidate the transcriptomic changes of long noncoding RNAs (lncRNAs) in high-fat diet (HFD)-fed mice, we defined their hepatic transcriptome by RNA sequencing. Aberrant expression of 37 representative lncRNAs and 254 protein-coding RNAs was observed in the livers of HFD-fed mice with insulin resistance compared with the livers from control mice. Of these, 24 lncRNAs and 179 protein-coding RNAs were upregulated, whereas 13 lncRNAs and 75 protein-coding RNAs were downregulated. Functional analyses showed that the aberrantly expressed protein-coding RNAs were enriched in various lipid metabolic processes and in the insulin signaling pathway. Genomic juxtaposition and coexpression patterns identified six pairs of aberrantly expressed lncRNAs and protein-coding genes, consisting of five lncRNAs and five protein-coding genes. Four of these protein-coding genes are targeted genes upregulated by PPARα. As expected, the corresponding lncRNAs were significantly elevated in AML12 cells treated with palmitic acid or the PPARα agonist, WY14643. In Hepa1-6 cells, knockdown of NONMMUG027912 increased the cellular cholesterol level, the expression of cholesterol biosynthesis genes and proteins, and the HMG-CoA reductase activity. This genome-wide profiling of lncRNAs in HFD-fed mice reveals one lncRNA, NONMMUG027912, which is potentially regulated by PPARα and is implicated in the process of cholesterol biosynthesis.
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Affiliation(s)
- Qian Chen
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Chaoliang Xiong
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Kunyun Jia
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Jing Jin
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Ziyang Li
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Yazhou Huang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Yewen Liu
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Lingling Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Haitao Luo
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Haiyan Li
- Department of Rehabilitation Medicine, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, China
| | - Qing H Meng
- Department of Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Wei Li
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China .,Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
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33
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Farman FU, Haq F, Muhammad N, Ali N, Rahman H, Saeed M. Aberrant promoter methylation status is associated with upregulation of the E2F4 gene in breast cancer. Oncol Lett 2018; 15:8461-8469. [PMID: 29805583 PMCID: PMC5950537 DOI: 10.3892/ol.2018.8382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 01/11/2018] [Indexed: 12/30/2022] Open
Abstract
E2F4 is an important basal transcription factor with the potential to promote tumor growth. Its upregulation in various types of cancer has been linked to numerous genetic factors; however, the nature of the involvement of epigenetic mechanisms, including DNA methylation, remains elusive. In the present study, E2F4 expression profiles were determined in 100 paired breast tumor and control samples, through RT-qPCR using the SYBR® green method. Furthermore, the E2F4 promoter methylation status in each of these samples was assessed using methylation specific PCR, in order to evaluate its impact on gene expression. A two-fold increase in E2F4 gene expression was observed in the breast tumors compared with in their respective controls (P=0.022); of these tumors, ~72% were under-methylated. The change in methylation status was also significantly higher (P<0.001) in the tumor samples. Methylation status was negatively correlated (r=-30) with E2F4 expression profiles, indicating that a decrease in methylation may promote higher expression of E2F4. The two study cohorts (>45 and ≤45 years) had comparable methylation profiles, though they had significantly decreased methylation status compared with controls. Various histo-pathological types also have different methylation profiles, indicating the presence of a tissue specific methylation signature. The results of the present study demonstrated that E2F4 methylation status can have a notable influence on its expression, and that it may have prognostic value in breast carcinogenesis.
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Affiliation(s)
- Farman Ullah Farman
- Cancer Genetics and Epigenetics Laboratory, Department of Biosciences, COMSATS Institute of Information Technology, Chak Shahzad, Islamabad 45550, Pakistan
| | - Farhan Haq
- Cancer Genetics and Epigenetics Laboratory, Department of Biosciences, COMSATS Institute of Information Technology, Chak Shahzad, Islamabad 45550, Pakistan
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Nawab Ali
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Hazir Rahman
- Department of Microbiology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan
| | - Muhammad Saeed
- Cancer Genetics and Epigenetics Laboratory, Department of Biosciences, COMSATS Institute of Information Technology, Chak Shahzad, Islamabad 45550, Pakistan
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34
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Wang PH, Schulenberg G, Whitlock S, Worden A, Zhou N, Novak S, Chen W. RNase I f -treated quantitative PCR for dsRNA quantitation of RNAi trait in genetically modified crops. BMC Biotechnol 2018; 18:3. [PMID: 29343265 PMCID: PMC5773123 DOI: 10.1186/s12896-018-0413-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/02/2018] [Indexed: 01/08/2023] Open
Abstract
Background RNA interference (RNAi) technology has been widely used to knockdown target genes via post-transcriptional silencing. In plants, RNAi is used as an effective tool with diverse applications being developed such as resistance against insects, fungi, viruses, and metabolism manipulation. To develop genetically modified (GM) RNAi traits for insect control, a transgene is created and composed of an inversely-repeated sequence of the target gene with a spacer region inserted between the repeats. The transgene design is subject to form a self-complementary hairpin RNA (hpRNA) and the active molecules are > 60 bp doubled-stranded RNA (dsRNA) derived from the hpRNA. However, in some cases, an undesirable intermediate such as single-stranded RNA (ssRNA) may be formed, which is not an active molecule. The aforementioned characteristics of RNAi traits lead to increase the challenges for RNAi-derived dsRNA quantitation. Results To quantify the dsRNA and distinguish it from the ssRNA in transgenic maize, an analytical tool is required to be able to effectively quantify dsRNA which contains a strong secondary structure. Herein, we develop a modified qRT-PCR method (abbreviated as RNase If -qPCR) coupled with a ssRNA preferred endonuclease (i.e., RNase If). This method enables the precise measurement of the active molecules (i.e., dsRNA) derived from RNAi traits of GM crops and separately quantifies the dsRNA from ssRNA. Notably, we also demonstrate that the RNase If -qPCR is comparable to a hybridization-based method (Quantigene Plex 2.0). Conclusions To our best knowledge, this is the first report of a method combining RNase If with modified qRT-PCR protocol. The method represents a reliable analytical tool to quantify dsRNA for GM RNAi crops. It provides a cost-effective and feasible analytical tool for general molecular laboratory without using additional equipment for other methods. The RNase If -qPCR method demonstrates high sensitivity (to 0.001 pg/ μL of dsRNA), precision and accuracy. In this report, we demonstrated the deployment of this method to characterize the RNAi events carrying v-ATPase C in maize during trait development process. The method can be utilized in any application which requires the dsRNA quantification such as double-stranded RNA virus or sprayable dsRNA as herbicide. Electronic supplementary material The online version of this article (10.1186/s12896-018-0413-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Po-Hao Wang
- Dow AgroSciences LLC, 9330 Zionsville Rd, Indianapolis, IN, 46268, USA.
| | - Greg Schulenberg
- Dow AgroSciences LLC, 9330 Zionsville Rd, Indianapolis, IN, 46268, USA
| | - Shannon Whitlock
- Dow AgroSciences LLC, 9330 Zionsville Rd, Indianapolis, IN, 46268, USA
| | - Andrew Worden
- Dow AgroSciences LLC, 9330 Zionsville Rd, Indianapolis, IN, 46268, USA
| | - Ning Zhou
- Dow AgroSciences LLC, 9330 Zionsville Rd, Indianapolis, IN, 46268, USA
| | - Stephen Novak
- Dow AgroSciences LLC, 9330 Zionsville Rd, Indianapolis, IN, 46268, USA
| | - Wei Chen
- Dow AgroSciences LLC, 9330 Zionsville Rd, Indianapolis, IN, 46268, USA
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35
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Gong D, Kim YH, Xiao Y, Du Y, Xie Y, Lee KK, Feng J, Farhat N, Zhao D, Shu S, Dai X, Chanda SK, Rana TM, Krogan NJ, Sun R, Wu TT. A Herpesvirus Protein Selectively Inhibits Cellular mRNA Nuclear Export. Cell Host Microbe 2017; 20:642-653. [PMID: 27832591 DOI: 10.1016/j.chom.2016.10.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/06/2016] [Accepted: 10/05/2016] [Indexed: 11/19/2022]
Abstract
Nuclear mRNA export is highly regulated to ensure accurate cellular gene expression. Viral inhibition of cellular mRNA export can enhance viral access to the cellular translation machinery and prevent anti-viral protein production but is generally thought to be nonselective. We report that ORF10 of Kaposi's sarcoma-associated herpesvirus (KSHV), a nuclear DNA virus, inhibits mRNA export in a transcript-selective manner to control cellular gene expression. Nuclear export inhibition by ORF10 requires an interaction with an RNA export factor, Rae1. Genome-wide analysis reveals a subset of cellular mRNAs whose nuclear export is blocked by ORF10 with the 3' UTRs of ORF10-targeted transcripts conferring sensitivity to export inhibition. The ORF10-Rae1 interaction is important for the virus to express viral genes and produce infectious virions. These results suggest that a nuclear DNA virus can selectively interfere with RNA export to restrict host gene expression for optimal replication.
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Affiliation(s)
- Danyang Gong
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yong Hoon Kim
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yuchen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yushen Du
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yafang Xie
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin K Lee
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jun Feng
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nisar Farhat
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dawei Zhao
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sara Shu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xinghong Dai
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sumit K Chanda
- Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Tariq M Rana
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ting-Ting Wu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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36
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Goldie BJ, Fitzsimmons C, Weidenhofer J, Atkins JR, Wang DO, Cairns MJ. miRNA Enriched in Human Neuroblast Nuclei Bind the MAZ Transcription Factor and Their Precursors Contain the MAZ Consensus Motif. Front Mol Neurosci 2017; 10:259. [PMID: 28878619 PMCID: PMC5573442 DOI: 10.3389/fnmol.2017.00259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/31/2017] [Indexed: 12/31/2022] Open
Abstract
While the cytoplasmic function of microRNA (miRNA) as post-transcriptional regulators of mRNA has been the subject of significant research effort, their activity in the nucleus is less well characterized. Here we use a human neuronal cell model to show that some mature miRNA are preferentially enriched in the nucleus. These molecules were predominantly primate-specific and contained a sequence motif with homology to the consensus MAZ transcription factor binding element. Precursor miRNA containing this motif were shown to have affinity for MAZ protein in nuclear extract. We then used Ago1/2 RIP-Seq to explore nuclear miRNA-associated mRNA targets. Interestingly, the genes for Ago2-associated transcripts were also significantly enriched with MAZ binding sites and neural function, whereas Ago1-transcripts were associated with general metabolic processes and localized with SC35 spliceosomes. These findings suggest the MAZ transcription factor is associated with miRNA in the nucleus and may influence the regulation of neuronal development through Ago2-associated miRNA induced silencing complexes. The MAZ transcription factor may therefore be important for organizing higher order integration of transcriptional and post-transcriptional processes in primate neurons.
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Affiliation(s)
- Belinda J Goldie
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, CallaghanNSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, The University of Newcastle, CallaghanNSW, Australia.,World Premier International Research Center - Institute for Integrated Cell-Material Sciences, Kyoto UniversityKyoto, Japan
| | - Chantel Fitzsimmons
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, CallaghanNSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, The University of Newcastle, CallaghanNSW, Australia
| | - Judith Weidenhofer
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, CallaghanNSW, Australia
| | - Joshua R Atkins
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, CallaghanNSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, The University of Newcastle, CallaghanNSW, Australia
| | - Dan O Wang
- World Premier International Research Center - Institute for Integrated Cell-Material Sciences, Kyoto UniversityKyoto, Japan.,The Keihanshin Consortium for Fostering the Next Generation of Global Leaders in ResearchKyoto, Japan
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, CallaghanNSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, The University of Newcastle, CallaghanNSW, Australia
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Mas-Ponte D, Carlevaro-Fita J, Palumbo E, Hermoso Pulido T, Guigo R, Johnson R. LncATLAS database for subcellular localization of long noncoding RNAs. RNA (NEW YORK, N.Y.) 2017; 23:1080-1087. [PMID: 28386015 PMCID: PMC5473142 DOI: 10.1261/rna.060814.117] [Citation(s) in RCA: 204] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/31/2017] [Indexed: 05/04/2023]
Abstract
The subcellular localization of long noncoding RNAs (lncRNAs) holds valuable clues to their molecular function. However, measuring localization of newly discovered lncRNAs involves time-consuming and costly experimental methods. We have created "lncATLAS," a comprehensive resource of lncRNA localization in human cells based on RNA-sequencing data sets. Altogether, 6768 GENCODE-annotated lncRNAs are represented across various compartments of 15 cell lines. We introduce relative concentration index (RCI) as a useful measure of localization derived from ensemble RNA-seq measurements. LncATLAS is accessible through an intuitive and informative webserver, from which lncRNAs of interest are accessed using identifiers or names. Localization is presented across cell types and organelles, and may be compared to the distribution of all other genes. Publication-quality figures and raw data tables are automatically generated with each query, and the entire data set is also available to download. LncATLAS makes lncRNA subcellular localization data available to the widest possible number of researchers. It is available at lncatlas.crg.eu.
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Affiliation(s)
- David Mas-Ponte
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Joana Carlevaro-Fita
- Department of Clinical Research, University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
| | - Emilio Palumbo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Toni Hermoso Pulido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Catalonia, Spain
| | - Rory Johnson
- Department of Clinical Research, University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
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38
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Carvalho T, Martins S, Rino J, Marinho S, Carmo-Fonseca M. Pharmacological inhibition of the spliceosome subunit SF3b triggers exon junction complex-independent nonsense-mediated decay. J Cell Sci 2017; 130:1519-1531. [PMID: 28302904 DOI: 10.1242/jcs.202200] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/06/2017] [Indexed: 12/12/2022] Open
Abstract
Spliceostatin A, meayamycin, and pladienolide B are small molecules that target the SF3b subunit of the spliceosomal U2 small nuclear ribonucleoprotein (snRNP). These compounds are attracting much attention as tools to manipulate splicing and for use as potential anti-cancer drugs. We investigated the effects of these inhibitors on mRNA transport and stability in human cells. Upon splicing inhibition, unspliced pre-mRNAs accumulated in the nucleus, particularly within enlarged nuclear speckles. However, a small fraction of the pre-mRNA molecules were exported to the cytoplasm. We identified the export adaptor ALYREF as being associated with intron-containing transcripts and show its requirement for the nucleo-cytoplasmic transport of unspliced pre-mRNA. In contrast, the exon junction complex (EJC) core protein eIF4AIII failed to form a stable complex with intron-containing transcripts. Despite the absence of EJC, unspliced transcripts in the cytoplasm were degraded by nonsense-mediated decay (NMD), suggesting that unspliced transcripts are degraded by an EJC-independent NMD pathway. Collectively, our results indicate that although blocking the function of SF3b elicits a massive accumulation of unspliced pre-mRNAs in the nucleus, intron-containing transcripts can still bind the ALYREF export factor and be transported to the cytoplasm, where they trigger an alternative NMD pathway.
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Affiliation(s)
- Teresa Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Sandra Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - José Rino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Sérgio Marinho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
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Cristóbal HA, Poma HR, Abate CM, Rajal VB. Quantification of the Genetic Expression of bgl-A, bgl, and CspA and Enzymatic Characterization of β-Glucosidases from Shewanella sp. G5. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:396-408. [PMID: 27164864 DOI: 10.1007/s10126-016-9702-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 03/26/2016] [Indexed: 06/05/2023]
Abstract
Shewanella sp. G5, a psychrotolerant marine bacterium, has a cold-shock protein (CspA) and three β-glucosidases, two of which were classified in the glycosyl hydrolase families 1 and 3 and are encoded by bgl-A and bgl genes, respectively. Shewanella sp. G5 was cultured on Luria-Bertani (LB) and Mineral Medium Brunner (MMB) media with glucose and cellobiose at various temperatures and pH 6 and 8. Relative quantification of the expression levels of all three genes was studied by real-time PCR with the comparative Ct method (2(-ΔΔCt)) using the gyrB housekeeping gene as a normalizer. Results showed that the genes had remarkably different genetic expression levels under the conditions evaluated, with increased expression of all genes obtained on MMB with cellobiose at 30 °C. Specific growth rate and specific β-glucosidase activity were also determined for all the culture conditions. Shewanella sp. G5 was able to grow on both media at 4 °C, showing the maximum specific growth rate on LB with cellobiose at 37 °C. The specific β-glucosidase activity obtained on MMB with cellobiose at 30 °C was 25 to 50 % higher than for all other conditions. At pH 8, relative activity was 34, 60, and 63 % higher at 30 °C than at 10 °C, with three peaks at 10, 25, and 37 °C on both media. Enzyme activity increased by 61 and 47 % in the presence of Ca(2+) and by 24 and 31 % in the presence of Mg(2+) on LB and MMB at 30 °C, respectively, but it was totally inhibited by Hg(2+), Cu(2+), and EDTA. Moreover, this activity was slightly decreased by SDS, Zn(2+), and DTT, all at 5 mM. Ethanol (14 % v/v) and glucose (100 mM) also reduced the activity by 63 and 60 %, respectively.
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Affiliation(s)
- Héctor Antonio Cristóbal
- Instituto de Investigaciones para la Industria Química, Universidad Nacional de Salta (INIQUI - CONICET-UNSa), Av. Bolivia 5150, 4400, Salta, Argentina.
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI - CONICET), Av. Belgrano y Pje. Caseros, 4000, Tucumán, Argentina.
| | - Hugo Ramiro Poma
- Instituto de Investigaciones para la Industria Química, Universidad Nacional de Salta (INIQUI - CONICET-UNSa), Av. Bolivia 5150, 4400, Salta, Argentina
| | - Carlos Mauricio Abate
- Instituto de Investigaciones para la Industria Química, Universidad Nacional de Salta (INIQUI - CONICET-UNSa), Av. Bolivia 5150, 4400, Salta, Argentina
| | - Verónica Beatriz Rajal
- Instituto de Investigaciones para la Industria Química, Universidad Nacional de Salta (INIQUI - CONICET-UNSa), Av. Bolivia 5150, 4400, Salta, Argentina
- Facultad de Ingeniería, Universidad Nacional de Salta, Avda. Bolivia 5150, 4400, Salta, Argentina
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40
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Up-regulated extracellular matrix components and inflammatory chemokines may impair the regeneration of cholestatic liver. Sci Rep 2016; 6:26540. [PMID: 27226149 PMCID: PMC4880910 DOI: 10.1038/srep26540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 05/04/2016] [Indexed: 12/22/2022] Open
Abstract
Although the healthy liver is known to have high regenerative potential, poor liver regeneration under pathological conditions remains a substantial problem. We investigated the key molecules that impair the regeneration of cholestatic liver. C57BL/6 mice were randomly subjected to partial hepatectomy and bile duct ligation (PH+BDL group, n = 16), partial hepatectomy only (PH group, n = 16), or sham operation (Sham group, n = 16). The liver sizes and histological findings were similar in the PH and sham groups 14 days after operation. However, compared with those in the sham group, the livers in mice in the PH+BDL group had a smaller size, a lower cell proliferative activity, and more fibrotic tissue 14 days after the operation, suggesting the insufficient regeneration of the cholestatic liver. Pathway-focused array analysis showed that many genes were up- or down-regulated over 1.5-fold in both PH+BDL and PH groups at 1, 3, 7, and 14 days after treatment. Interestingly, more genes that were functionally related to the extracellular matrix and inflammatory chemokines were found in the PH+BDL group than in the PH group at 7 and 14 days after treatment. Our data suggest that up-regulated extracellular matrix components and inflammatory chemokines may impair the regeneration of cholestatic liver.
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41
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Zhou L, Sun K, Zhao Y, Zhang S, Wang X, Li Y, Lu L, Chen X, Chen F, Bao X, Zhu X, Wang L, Tang LY, Esteban MA, Wang CC, Jauch R, Sun H, Wang H. Linc-YY1 promotes myogenic differentiation and muscle regeneration through an interaction with the transcription factor YY1. Nat Commun 2015; 6:10026. [PMID: 26658965 DOI: 10.1038/ncomms10026] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 10/28/2015] [Indexed: 12/22/2022] Open
Abstract
Little is known how lincRNAs are involved in skeletal myogenesis. Here we describe the discovery of Linc-YY1 from the promoter of the transcription factor (TF) Yin Yang 1 (YY1) gene. We demonstrate that Linc-YY1 is dynamically regulated during myogenesis in vitro and in vivo. Gain or loss of function of Linc-YY1 in C2C12 myoblasts or muscle satellite cells alters myogenic differentiation and in injured muscles has an impact on the course of regeneration. Linc-YY1 interacts with YY1 through its middle domain, to evict YY1/Polycomb repressive complex (PRC2) from target promoters, thus activating the gene expression in trans. In addition, Linc-YY1 also regulates PRC2-independent function of YY1. Finally, we identify a human Linc-YY1 orthologue with conserved function and show that many human and mouse TF genes are associated with lincRNAs that may modulate their activity. Altogether, we show that Linc-YY1 regulates skeletal myogenesis and uncover a previously unappreciated mechanism of gene regulation by lincRNA.
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Affiliation(s)
- Liang Zhou
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kun Sun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Yu Zhao
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Suyang Zhang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Xuecong Wang
- Genome Regulation Laboratory, Drug Discovery Pipeline, Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Yuying Li
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Leina Lu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaona Chen
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Fengyuan Chen
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Xichen Bao
- Laboratory of Chromatin and Human Disease, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Xihua Zhu
- Laboratory of Chromatin and Human Disease, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Lijun Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ling-Yin Tang
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Miguel A Esteban
- Laboratory of Chromatin and Human Disease, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Chi-Chiu Wang
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Ralf Jauch
- Genome Regulation Laboratory, Drug Discovery Pipeline, Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Hao Sun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Orthopedics and Traumatology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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Veselenak RL, Miller AL, Milligan GN, Bourne N, Pyles RB. Development and utilization of a custom PCR array workflow: analysis of gene expression in mycoplasma genitalium and guinea pig (Cavia porcellus). Mol Biotechnol 2015; 57:172-83. [PMID: 25358686 PMCID: PMC4298676 DOI: 10.1007/s12033-014-9813-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Transcriptome analysis is a powerful tool for evaluating molecular pathways central to maturation of specific biological processes and disease states. Recently, PCR-based arrays have supplemented microarray and RNA-seq methodologies for studying changes in gene expression levels. PCR arrays are a more cost efficient alternative, however commercially available assemblies are generally limited to only a few more widely researched species (e.g., rat, human, and mouse). Consequently, the investigation of emerging or under-studied species is hindered until such assays are created. To address this need, we present data documenting the success of a developed workflow with enhanced potential to create and validate novel RT-PCR arrays for underrepresented species with whole or partial genome annotation. Utilizing this enhanced workflow, we have achieved a success rate of 80 % for first-round designs for over 400 primer pairs. Of these, ~160 distinct targets were sequence confirmed. Proof of concept studies using two unique arrays, one targeting the pathogenic bacterium Mycoplasma genitalium and the other specific for the guinea pig (Cavia porcellus), allowed us to identify significant (P < 0.05) changes in mRNA expression validated by subsequent qPCR. This flexible and adaptable platform provides a valuable and cost-effective alternative for gene expression analysis.
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Affiliation(s)
- Ronald L Veselenak
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-0436, USA
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Zucchelli S, Fasolo F, Russo R, Cimatti L, Patrucco L, Takahashi H, Jones MH, Santoro C, Sblattero D, Cotella D, Persichetti F, Carninci P, Gustincich S. SINEUPs are modular antisense long non-coding RNAs that increase synthesis of target proteins in cells. Front Cell Neurosci 2015; 9:174. [PMID: 26029048 PMCID: PMC4429562 DOI: 10.3389/fncel.2015.00174] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/20/2015] [Indexed: 12/02/2022] Open
Abstract
Despite recent efforts in discovering novel long non-coding RNAs (lncRNAs) and unveiling their functions in a wide range of biological processes their applications as biotechnological or therapeutic tools are still at their infancy. We have recently shown that AS Uchl1, a natural lncRNA antisense to the Parkinson's disease-associated gene Ubiquitin carboxyl-terminal esterase L1 (Uchl1), is able to increase UchL1 protein synthesis at post-transcriptional level. Its activity requires two RNA elements: an embedded inverted SINEB2 sequence to increase translation and the overlapping region to target its sense mRNA. This functional organization is shared with several mouse lncRNAs antisense to protein coding genes. The potential use of AS Uchl1-derived lncRNAs as enhancers of target mRNA translation remains unexplored. Here we define AS Uchl1 as the representative member of a new functional class of natural and synthetic antisense lncRNAs that activate translation. We named this class of RNAs SINEUPs for their requirement of the inverted SINEB2 sequence to UP-regulate translation in a gene-specific manner. The overlapping region is indicated as the Binding Doman (BD) while the embedded inverted SINEB2 element is the Effector Domain (ED). By swapping BD, synthetic SINEUPs are designed targeting mRNAs of interest. SINEUPs function in an array of cell lines and can be efficiently directed toward N-terminally tagged proteins. Their biological activity is retained in a miniaturized version within the range of small RNAs length. Its modular structure was exploited to successfully design synthetic SINEUPs targeting endogenous Parkinson's disease-associated DJ-1 and proved to be active in different neuronal cell lines. In summary, SINEUPs represent the first scalable tool to increase synthesis of proteins of interest. We propose SINEUPs as reagents for molecular biology experiments, in protein manufacturing as well as in therapy of haploinsufficiencies.
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Affiliation(s)
- Silvia Zucchelli
- Scuola Internazionale Superiore di Studi Avanzati, Area of Neuroscience Trieste, Italy ; Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy
| | - Francesca Fasolo
- Scuola Internazionale Superiore di Studi Avanzati, Area of Neuroscience Trieste, Italy
| | - Roberta Russo
- Scuola Internazionale Superiore di Studi Avanzati, Area of Neuroscience Trieste, Italy
| | - Laura Cimatti
- Scuola Internazionale Superiore di Studi Avanzati, Area of Neuroscience Trieste, Italy
| | - Laura Patrucco
- Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy
| | - Hazuki Takahashi
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies Yokohama, Japan
| | | | - Claudio Santoro
- Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy
| | - Daniele Sblattero
- Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy
| | - Diego Cotella
- Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy
| | - Francesca Persichetti
- Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies Yokohama, Japan
| | - Stefano Gustincich
- Scuola Internazionale Superiore di Studi Avanzati, Area of Neuroscience Trieste, Italy
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Regulated Intron Retention and Nuclear Pre-mRNA Decay Contribute to PABPN1 Autoregulation. Mol Cell Biol 2015; 35:2503-17. [PMID: 25963658 DOI: 10.1128/mcb.00070-15] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/02/2015] [Indexed: 11/20/2022] Open
Abstract
The poly(A)-binding protein nuclear 1 is encoded by the PABPN1 gene, whose mutations result in oculopharyngeal muscular dystrophy, a late-onset disorder for which the molecular basis remains unknown. Despite recent studies investigating the functional roles of PABPN1, little is known about its regulation. Here, we show that PABPN1 negatively controls its own expression to maintain homeostatic levels in human cells. Transcription from the PABPN1 gene results in the accumulation of two major isoforms: an unspliced nuclear transcript that retains the 3'-terminal intron and a fully spliced cytoplasmic mRNA. Increased dosage of PABPN1 protein causes a significant decrease in the spliced/unspliced ratio, reducing the levels of endogenous PABPN1 protein. We also show that PABPN1 autoregulation requires inefficient splicing of its 3'-terminal intron. Our data suggest that autoregulation occurs via the binding of PABPN1 to an adenosine (A)-rich region in its 3' untranslated region, which promotes retention of the 3'-terminal intron and clearance of intron-retained pre-mRNAs by the nuclear exosome. Our findings unveil a mechanism of regulated intron retention coupled to nuclear pre-mRNA decay that functions in the homeostatic control of PABPN1 expression.
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Vaz-Drago R, Pinheiro MT, Martins S, Enguita FJ, Carmo-Fonseca M, Custódio N. Transcription-coupled RNA surveillance in human genetic diseases caused by splice site mutations. Hum Mol Genet 2015; 24:2784-95. [PMID: 25652404 DOI: 10.1093/hmg/ddv039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 01/31/2015] [Indexed: 12/15/2022] Open
Abstract
Current estimates indicate that approximately one-third of all disease-causing mutations are expected to disrupt splicing. Abnormal splicing often leads to disruption of the reading frame with introduction of a premature termination codon (PTC) that targets the mRNA for degradation in the cytoplasm by nonsense mediated decay (NMD). In addition to NMD there are RNA surveillance mechanisms that act in the nucleus while transcripts are still associated with the chromatin template. However, the significance of nuclear RNA quality control in the context of human genetic diseases is unknown. Here we used patient-derived lymphoblastoid cell lines as disease models to address how biogenesis of mRNAs is affected by splice site mutations. We observed that most of the mutations analyzed introduce PTCs and trigger mRNA degradation in the cytoplasm. However, for some mutant transcripts, RNA levels associated with chromatin were found down-regulated. Quantification of nascent transcripts further revealed that a subset of genes containing splicing mutations (SM) have reduced transcriptional activity. Following treatment with the translation inhibitor cycloheximide the cytoplasmic levels of mutant RNAs increased, while the levels of chromatin-associated transcripts remained unaltered. These results suggest that transcription-coupled surveillance mechanisms operate independently from NMD to reduce cellular levels of abnormal RNAs caused by SM.
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Affiliation(s)
- Rita Vaz-Drago
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Marco T Pinheiro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Sandra Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Noélia Custódio
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
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Haggerty TJ, Dunn IS, Rose LB, Newton EE, Pandolfi F, Kurnick JT. Heat shock protein-90 inhibitors enhance antigen expression on melanomas and increase T cell recognition of tumor cells. PLoS One 2014; 9:e114506. [PMID: 25503774 PMCID: PMC4264751 DOI: 10.1371/journal.pone.0114506] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 11/10/2014] [Indexed: 12/23/2022] Open
Abstract
In an effort to enhance antigen-specific T cell recognition of cancer cells, we have examined numerous modulators of antigen-expression. In this report we demonstrate that twelve different Hsp90 inhibitors (iHsp90) share the ability to increase the expression of differentiation antigens and MHC Class I antigens. These iHsp90 are active in several molecular and cellular assays on a series of tumor cell lines, including eleven human melanomas, a murine B16 melanoma, and two human glioma-derived cell lines. Intra-cytoplasmic antibody staining showed that all of the tested iHsp90 increased expression of the melanocyte differentiation antigens Melan-A/MART-1, gp100, and TRP-2, as well as MHC Class I. The gliomas showed enhanced gp100 and MHC staining. Quantitative analysis of mRNA levels showed a parallel increase in message transcription, and a reporter assay shows induction of promoter activity for Melan-A/MART-1 gene. In addition, iHsp90 increased recognition of tumor cells by T cells specific for Melan-A/MART-1. In contrast to direct Hsp90 client proteins, the increased levels of full-length differentiation antigens that result from iHsp90 treatment are most likely the result of transcriptional activation of their encoding genes. In combination, these results suggest that iHsp90 improve recognition of tumor cells by T cells specific for a melanoma-associated antigen as a result of increasing the expressed intracellular antigen pool available for processing and presentation by MHC Class I, along with increased levels of MHC Class I itself. As these Hsp90 inhibitors do not interfere with T cell function, they could have potential for use in immunotherapy of cancer.
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Affiliation(s)
- Timothy J. Haggerty
- CytoCure LLC, Suite 430C, 100 Cummings Center, Beverly, MA, United States of America
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Ian S. Dunn
- CytoCure LLC, Suite 430C, 100 Cummings Center, Beverly, MA, United States of America
| | - Lenora B. Rose
- CytoCure LLC, Suite 430C, 100 Cummings Center, Beverly, MA, United States of America
| | - Estelle E. Newton
- CytoCure LLC, Suite 430C, 100 Cummings Center, Beverly, MA, United States of America
| | - Franco Pandolfi
- Department of Internal Medicine, Catholic University, Rome, Italy
- * E-mail:
| | - James T. Kurnick
- CytoCure LLC, Suite 430C, 100 Cummings Center, Beverly, MA, United States of America
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
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Cytoplasmic parafibromin/hCdc73 targets and destabilizes p53 mRNA to control p53-mediated apoptosis. Nat Commun 2014; 5:5433. [DOI: 10.1038/ncomms6433] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 10/01/2014] [Indexed: 01/20/2023] Open
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Bhunia RK, Chakraborty A, Kaur R, Gayatri T, Bhattacharyya J, Basu A, Maiti MK, Sen SK. Seed-specific increased expression of 2S albumin promoter of sesame qualifies it as a useful genetic tool for fatty acid metabolic engineering and related transgenic intervention in sesame and other oil seed crops. PLANT MOLECULAR BIOLOGY 2014; 86:351-65. [PMID: 25139230 DOI: 10.1007/s11103-014-0233-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 07/24/2014] [Indexed: 06/03/2023]
Abstract
The sesame 2S albumin (2Salb) promoter was evaluated for its capacity to express the reporter gusA gene encoding β-glucuronidase in transgenic tobacco seeds relative to the soybean fad3C gene promoter element. Results revealed increased expression of gusA gene in tobacco seed tissue when driven by sesame 2S albumin promoter. Prediction based deletion analysis of both the promoter elements confirmed the necessary cis-acting regulatory elements as well as the minimal promoter element for optimal expression in each case. The results also revealed that cis-regulatory elements might have been responsible for high level expression as well as spatio-temporal regulation of the sesame 2S albumin promoter. Transgenic over-expression of a fatty acid desaturase (fad3C) gene of soybean driven by 2S albumin promoter resulted in seed-specific enhanced level of α-linolenic acid in sesame. The present study, for the first time helped to identify that the sesame 2S albumin promoter is a promising endogenous genetic element in genetic engineering approaches requiring spatio-temporal regulation of gene(s) of interest in sesame and can also be useful as a heterologous genetic element in other important oil seed crop plants in general for which seed oil is the harvested product. The study also established the feasibility of fatty acid metabolic engineering strategy undertaken to improve quality of edible seed oil in sesame using the 2S albumin promoter as regulatory element.
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Affiliation(s)
- Rupam Kumar Bhunia
- Advanced Laboratory for Plant Genetic Engineering, Indian Institute of Technology, Kharagpur, 721302, India
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Liu G, Guo J, Liu J, Wang Z, Liang D. Toll-like receptor signaling directly increases functional IL-17RA expression in neuroglial cells. Clin Immunol 2014; 154:127-40. [PMID: 25076485 DOI: 10.1016/j.clim.2014.07.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 07/18/2014] [Accepted: 07/19/2014] [Indexed: 11/26/2022]
Abstract
IL-17, the hallmark cytokine of Th17 cells, plays a pivotal role in the pathogenesis of autoimmune diseases, including encephalomyelitis. In the central nervous system, neuroglial cells are the main residents that express IL-17R and respond to IL-17 by producing chemokines/cytokines and boosting local inflammation. Factors that influence the IL-17R expression in neuroglial cells can also exert their impacts on the outbreak, progression and outcome of encephalomyelitis. Here, we reported that Toll-like receptor signaling has its bias for promoting the IL-17RA, but not the IL-17RC, expression in mouse neuroglial cells in a T cell infiltration independent manner. Elevated IL-17R functionally responded to IL-17 by secreting more chemokines and accelerating CD4 cell migration. First, real-time PCR confirmed that the expression of Il-17ra, but not Il-17rc, was significantly increased in the brain and spinal cord of EAE-induced mice. This effect was elicited by something in complete Freund's adjuvant (CFA), because markedly increased IL-17R was detected in mice immunized with CFA only, even though no evidence of EAE was found. Furthermore, in Rag1(-/-) mice, it was confirmed that CFA could augment the IL-17RA expression in the CNS in the absence of T cell infiltration. In vivo immunization with TLR ligands and in vitro treatment of purified neuroglial cells demonstrated that TLR ligands directly and effectively evoke the IL-17RA expression in the CNS and in cultured astrocytes, microglia and oligodendrocytes. LPS was the most effective inducer of the IL-17RA expression in astrocytes, and polyIC was superior to LPS for microglia and oligodendrocytes. Activated CD4 cells can also promote the secretion of chemokines by LPS pre-treated astrocytes, and hence accelerate the migration of CD4 cells, which was blocked by the neutralization of IL-17RA on the surface of the astrocyte. Taken together, we concluded that TLR signaling can directly stimulate the expression of IL-17RA, but not IL-17RC, in neuroglial cells, which functionally respond to IL-17A by secreting chemokines, accelerating CD4 cell migration, and contributing to the pathogenesis of encephalomyelitis.
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Affiliation(s)
- Guoping Liu
- Department of Neurology, Tianjin First Central Hospital, Tianjin 300192, China
| | - Jie Guo
- Department of Neurology, Tianjin First Central Hospital, Tianjin 300192, China
| | - Jin Liu
- Department of Neurology, Tianjin First Central Hospital, Tianjin 300192, China
| | - Zhiyun Wang
- Department of Neurology, Tianjin First Central Hospital, Tianjin 300192, China
| | - Dongchun Liang
- Doheny Eye Institute, University of Southern California, CA 90033, USA.
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50
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Safdar M, Abasıyanık M. Development of fast multiplex real-time PCR assays based on EvaGreen fluorescence dye for identification of beef and soybean origins in processed sausages. Food Res Int 2013. [DOI: 10.1016/j.foodres.2013.09.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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