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Fan J, Li Z, Pei L, Hou Y. Post-transcriptional regulation of DEAD-box RNA helicases in hematopoietic malignancies. Genes Dis 2024; 11:101252. [PMID: 38993792 PMCID: PMC11237855 DOI: 10.1016/j.gendis.2024.101252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 02/01/2024] [Accepted: 02/11/2024] [Indexed: 07/13/2024] Open
Abstract
Hematopoiesis represents a meticulously regulated and dynamic biological process. Genetic aberrations affecting blood cells, induced by various factors, frequently give rise to hematological tumors. These instances are often accompanied by a multitude of abnormal post-transcriptional regulatory events, including RNA alternative splicing, RNA localization, RNA degradation, and storage. Notably, post-transcriptional regulation plays a pivotal role in preserving hematopoietic homeostasis. The DEAD-Box RNA helicase genes emerge as crucial post-transcriptional regulatory factors, intricately involved in sustaining normal hematopoiesis through diverse mechanisms such as RNA alternative splicing, RNA modification, and ribosome assembly. This review consolidates the existing knowledge on the role of DEAD-box RNA helicases in regulating normal hematopoiesis and underscores the pathogenicity of mutant DEAD-Box RNA helicases in malignant hematopoiesis. Emphasis is placed on elucidating both the positive and negative contributions of DEAD-box RNA helicases within the hematopoietic system.
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Affiliation(s)
- Jiankun Fan
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Zhigang Li
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Li Pei
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yu Hou
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
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2
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Han X, Li C, Qin G, Wang X, Zhang B, Lin Q. Growth increase and gonadal dysfunction of the lined seahorse triggered by zinc exposure. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 272:106947. [PMID: 38776607 DOI: 10.1016/j.aquatox.2024.106947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/10/2024] [Accepted: 05/12/2024] [Indexed: 05/25/2024]
Abstract
Seahorses are characterized by unique characteristics such as a male pregnancy reproductive strategy and grasping preferences, which make these species vulnerable to various environmental risks. Zinc (Zn) is one of the most frequently occurring toxic elements in coastal waters; however, little is known about the effect of Zn exposure on seahorses. In the present study, line seahorses (Hippocampus erectus) were exposed to waterborne Zn (0.2 and 1.0 mg/L) and the impact on growth and gonadal development was investigated. Zn exposure induced growth improvement, but also led to gonadal dysfunction in the lined seahorse. Female seahorses exhibited high testosterone levels, immature follicles, and weight increase after Zn exposure, which is the typical characteristics of a polycystic ovary syndrome (PCOS)-like phenotype. Transcriptomic data suggested that the Zn-induced growth promotion resulted from the dysregulated expression of fat accumulation genes. Further investigation of gene expression profiles in the brain, ovaries, and testes indicated that Zn affected the expression of genes involved in growth, immunity, tissue remodeling, and gonadal development by regulating serum steroid hormone levels and androgen receptor expression. This study not only clarifies the complex impact of Zn on seahorses using physiological, histological, and molecular evidence but can also provide new insights into the mechanism underlying PCOS in reproductive-aged women. Moreover, this work demonstrates the risk of the common practice of Zn supplementation in the aquaculture industry as the consequent growth yield may not represent a healthy condition.
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Affiliation(s)
- Xue Han
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Chunyan Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100101, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Bo Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100101, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
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3
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Lin J, Liu C, Hu E. Elucidating sleep disorders: a comprehensive bioinformatics analysis of functional gene sets and hub genes. Front Immunol 2024; 15:1381765. [PMID: 38919616 PMCID: PMC11196417 DOI: 10.3389/fimmu.2024.1381765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Background Sleep disorders (SD) are known to have a profound impact on human health and quality of life although their exact pathogenic mechanisms remain poorly understood. Methods The study first accessed SD datasets from the GEO and identified DEGs. These DEGs were then subjected to gene set enrichment analysis. Several advanced techniques, including the RF, SVM-RFE, PPI networks, and LASSO methodologies, were utilized to identify hub genes closely associated with SD. Additionally, the ssGSEA approach was employed to analyze immune cell infiltration and functional gene set scores in SD. DEGs were also scrutinized in relation to miRNA, and the DGIdb database was used to explore potential pharmacological treatments for SD. Furthermore, in an SD murine model, the expression levels of these hub genes were confirmed through RT-qPCR and Western Blot analyses. Results The findings of the study indicate that DEGs are significantly enriched in functions and pathways related to immune cell activity, stress response, and neural system regulation. The analysis of immunoinfiltration demonstrated a marked elevation in the levels of Activated CD4+ T cells and CD8+ T cells in the SD cohort, accompanied by a notable rise in Central memory CD4 T cells, Central memory CD8 T cells, and Natural killer T cells. Using machine learning algorithms, the study also identified hub genes closely associated with SD, including IPO9, RAP2A, DDX17, MBNL2, PIK3AP1, and ZNF385A. Based on these genes, an SD diagnostic model was constructed and its efficacy validated across multiple datasets. In the SD murine model, the mRNA and protein expressions of these 6 hub genes were found to be consistent with the results of the bioinformatics analysis. Conclusion In conclusion, this study identified 6 genes closely linked to SD, which may play pivotal roles in neural system development, the immune microenvironment, and inflammatory responses. Additionally, the key gene-based SD diagnostic model constructed in this study, validated on multiple datasets showed a high degree of reliability and accuracy, predicting its wide potential for clinical applications. However, limited by the range of data sources and sample size, this may affect the generalizability of the results.
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Affiliation(s)
- Junhan Lin
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, China
| | - Changyuan Liu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, China
| | - Ende Hu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, China
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Hang C, Zu L, Luo X, Wang Y, Yan L, Zhang Z, Le K, Huang Y, Ye L, Ying Y, Chen K, Xu X, Lv Q, Du L. Ddx5 Targeted Epigenetic Modification of Pericytes in Pulmonary Hypertension After Intrauterine Growth Restriction. Am J Respir Cell Mol Biol 2024; 70:400-413. [PMID: 38301267 DOI: 10.1165/rcmb.2023-0244oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 02/01/2024] [Indexed: 02/03/2024] Open
Abstract
Newborns with intrauterine growth restriction (IUGR) have a higher likelihood of developing pulmonary arterial hypertension (PAH) in adulthood. Although there is increasing evidence suggesting that pericytes play a role in regulating myofibroblast transdifferentiation and angiogenesis in malignant and cardiovascular diseases, their involvement in the pathogenesis of IUGR-related pulmonary hypertension and the underlying mechanisms remain incompletely understood. To address this issue, a study was conducted using a Sprague-Dawley rat model of IUGR-related pulmonary hypertension. Our investigation revealed increased proliferation and migration of pulmonary microvascular pericytes in IUGR-related pulmonary hypertension, accompanied by weakened endothelial-pericyte interactions. Through whole-transcriptome sequencing, Ddx5 (DEAD-box protein 5) was identified as one of the hub genes in pericytes. DDX5, a member of the RNA helicase family, plays a role in the regulation of ATP-dependent RNA helicase activities and cellular function. MicroRNAs have been implicated in the pathogenesis of PAH, and microRNA-205 (miR-205) regulates cell proliferation, migration, and angiogenesis. The results of dual-luciferase reporter assays confirmed the specific binding of miR-205 to Ddx5. Mechanistically, miR-205 negatively regulates Ddx5, leading to the degradation of β-catenin by inhibiting the phosphorylation of Gsk3β at serine 9. In vitro experiments showed the addition of miR-205 effectively ameliorated pericyte dysfunction. Furthermore, in vivo experiments demonstrated that miR-205 agomir could ameliorate pulmonary hypertension. Our findings indicated that the downregulation of miR-205 expression mediates pericyte dysfunction through the activation of Ddx5. Therefore, targeting the miR-205/Ddx5/p-Gsk3β/β-catenin axis could be a promising therapeutic approach for IUGR-related pulmonary hypertension.
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Affiliation(s)
| | - Lu Zu
- Department of Neonatology and
| | - Xiaofei Luo
- Department of Pediatrics, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, People's Republic of China; and
| | - Yu Wang
- Department of Neonatology and
| | - Lingling Yan
- Department of Pediatrics, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, People's Republic of China; and
| | | | - Kaixing Le
- Academy of Pediatrics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, People's Republic of China
| | | | | | | | | | - Xuefeng Xu
- Department of Rheumatology, Immunology, and Allergy, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang Province, People's Republic of China
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Ning D, Jin J, Fang Y, Du P, Yuan C, Chen J, Huang Q, Cheng K, Mo J, Xu L, Guo H, Yang MJ, Chen X, Liang H, Zhang B, Zhang W. DEAD-Box Helicase 17 exacerbates non-alcoholic steatohepatitis via transcriptional repression of cyp2c29, inducing hepatic lipid metabolism disorder and eliciting the activation of M1 macrophages. Clin Transl Med 2024; 14:e1529. [PMID: 38303609 PMCID: PMC10835191 DOI: 10.1002/ctm2.1529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 02/03/2024] Open
Abstract
OBJECTIVE Our study was to elucidate the role of RNA helicase DEAD-Box Helicase 17 (DDX17) in NAFLD and to explore its underlying mechanisms. METHODS We created hepatocyte-specific Ddx17-deficient mice aim to investigate the impact of Ddx17 on NAFLD induced by a high-fat diet (HFD) as well as methionine and choline-deficient l-amino acid diet (MCD) in adult male mice. RNA-seq and lipidomic analyses were conducted to depict the metabolic landscape, and CUT&Tag combined with chromatin immunoprecipitation (ChIP) and luciferase reporter assays were conducted. RESULTS In this work, we observed a notable increase in DDX17 expression in the livers of patients with NASH and in murine models of NASH induced by HFD or MCD. After introducing lentiviruses into hepatocyte L02 for DDX17 knockdown or overexpression, we found that lipid accumulation induced by palmitic acid/oleic acid (PAOA) in L02 cells was noticeably weakened by DDX17 knockdown but augmented by DDX17 overexpression. Furthermore, hepatocyte-specific DDX17 knockout significantly alleviated hepatic steatosis, inflammatory response and fibrosis in mice after the administration of MCD and HFD. Mechanistically, our analysis of RNA-seq and CUT&Tag results combined with ChIP and luciferase reporter assays indicated that DDX17 transcriptionally represses Cyp2c29 gene expression by cooperating with CCCTC binding factor (CTCF) and DEAD-Box Helicase 5 (DDX5). Using absolute quantitative lipidomics analysis, we identified a hepatocyte-specific DDX17 deficiency that decreased lipid accumulation and altered lipid composition in the livers of mice after MCD administration. Based on the RNA-seq analysis, our findings suggest that DDX17 could potentially have an impact on the modulation of lipid metabolism and the activation of M1 macrophages in murine NASH models. CONCLUSION These results imply that DDX17 is involved in NASH development by promoting lipid accumulation in hepatocytes, inducing the activation of M1 macrophages, subsequent inflammatory responses and fibrosis through the transcriptional repression of Cyp2c29 in mice. Therefore, DDX17 holds promise as a potential drug target for the treatment of NASH.
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Affiliation(s)
- Deng Ning
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
- Department of Hepatobiliary SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Jie Jin
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Yuanyuan Fang
- Department of NeurologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Pengcheng Du
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Chaoyi Yuan
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Jin Chen
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Qibo Huang
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Kun Cheng
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Jie Mo
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Lei Xu
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Hui Guo
- Institute of Organ TransplantationTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Mia Jiming Yang
- Institute for Management in Medicine and Health SciencesUniversity of BayreuthBayreuthGermany
| | - Xiaoping Chen
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
- Key Laboratory of Organ TransplantationMinistry of Education and Ministry of HealthWuhanChina
| | - Huifang Liang
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
- Key Laboratory of Organ TransplantationMinistry of Education and Ministry of HealthWuhanChina
| | - Bixiang Zhang
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
- Key Laboratory of Organ TransplantationMinistry of Education and Ministry of HealthWuhanChina
| | - Wanguang Zhang
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
- Key Laboratory of Organ TransplantationMinistry of Education and Ministry of HealthWuhanChina
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6
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Taylor K, Piasecka A, Kajdasz A, Brzęk A, Polay Espinoza M, Bourgeois CF, Jankowski A, Borowiak M, Raczyńska KD, Sznajder ŁJ, Sobczak K. Modulatory role of RNA helicases in MBNL-dependent alternative splicing regulation. Cell Mol Life Sci 2023; 80:335. [PMID: 37882878 PMCID: PMC10602967 DOI: 10.1007/s00018-023-04927-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/14/2023] [Accepted: 08/17/2023] [Indexed: 10/27/2023]
Abstract
Muscleblind-like splicing regulators (MBNLs) activate or repress the inclusion of alternative splicing (AS) events, enabling the developmental transition of fetal mRNA splicing isoforms to their adult forms. Herein, we sought to elaborate the mechanism by which MBNLs mediate AS related to biological processes. We evaluated the functional role of DEAD-box (DDX) RNA helicases, DDX5 and DDX17 in MBNL-dependent AS regulation. Whole-transcriptome analysis and validation approaches revealed a handful of MBNLs-dependent AS events to be affected by DDX5 and DDX17 in mostly an opposite manner. The opposite expression patterns of these two groups of factors during muscle development and coordination of fetal-to-adult splicing transition indicate the importance of these proteins at early stages of development. The identified pathways of how the helicases modulate MBNL splicing activity include DDX5 and DDX17-dependent changes in the ratio of MBNL splicing isoforms and most likely changes in accessibility of MBNL-binding sites. Another pathway involves the mode of action of the helicases independent of MBNL activity. These findings lead to a deeper understanding of the network of interdependencies between RNA-binding proteins and constitute a valuable element in the discussion on developmental homeostasis and pathological states in which the studied protein factors play a significant role.
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Affiliation(s)
- Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
| | - Agnieszka Piasecka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Arkadiusz Kajdasz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Aleksandra Brzęk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Micaela Polay Espinoza
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 Allee d'Italie, 69364, Lyon, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 Allee d'Italie, 69364, Lyon, France
| | - Artur Jankowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Małgorzata Borowiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Katarzyna D Raczyńska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Łukasz J Sznajder
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV, 89154, USA
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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7
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Habault J, Schneider JA, Ha S, Ruoff R, Pereira LD, Puccini J, Ranieri M, Ayasun R, Deng J, Kasper AC, Bar-Sagi D, Wong KK, Zoubeidi A, Claessens F, Wise DR, Logan SK, Kirshenbaum K, Garabedian MJ. A Multivalent Peptoid Conjugate Modulates Androgen Receptor Transcriptional Activity to Inhibit Therapy-resistant Prostate Cancer. Mol Cancer Ther 2023; 22:1166-1181. [PMID: 37486978 PMCID: PMC10592247 DOI: 10.1158/1535-7163.mct-23-0196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/07/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
Prostate cancers adapt to androgen receptor (AR) pathway inhibitors and progress to castration resistance due to ongoing AR expression and function. To counter this, we developed a new approach to modulate the AR and inhibit castration-resistant prostate cancer (CRPC) using multivalent peptoid conjugates (MPC) that contain multiple copies of the AR-targeting ligand ethisterone attached to a peptidomimetic scaffold. Here, we investigated the antitumor effects of compound MPC309, a trivalent display of ethisterone conjugated to a peptoid oligomer backbone that binds to the AR with nanomolar affinity. MPC309 exhibited potent antiproliferative effects on various enzalutamide-resistant prostate cancer models, including those with AR splice variants, ligand-binding mutations, and noncanonical AR gene expression programs, as well as mouse prostate organoids harboring defined genetic alterations that mimic lethal human prostate cancer subtypes. MPC309 is taken up by cells through macropinocytosis, an endocytic process more prevalent in cancer cells than in normal ones, thus providing an opportunity to target tumors selectively. MPC309 triggers a distinct AR transcriptome compared with DHT and enzalutamide, a clinically used antiandrogen. Specifically, MPC309 enhances the expression of differentiation genes while reducing the expression of genes needed for cell division and metabolism. Mechanistically, MPC309 increases AR chromatin occupancy and alters AR interactions with coregulatory proteins in a pattern distinct from DHT. In xenograft studies, MPC309 produced significantly greater tumor suppression than enzalutamide. Altogether, MPC309 represents a promising new AR modulator that can combat resistant disease by promoting an AR antiproliferative gene expression program.
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Affiliation(s)
- Justine Habault
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Jeffrey A. Schneider
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Susan Ha
- Department of Urology, NYU Grossman School of Medicine, New York, NY, USA
| | - Rachel Ruoff
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Luiza D. Pereira
- Department of Medicine, Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Joseph Puccini
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Michela Ranieri
- Department of Medicine, Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Ruveyda Ayasun
- Department of Medicine, Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Jiehui Deng
- Department of Medicine, Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Dafna Bar-Sagi
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Kwok-Kin Wong
- Department of Medicine, Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Amina Zoubeidi
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - David R. Wise
- Department of Medicine, Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Susan K. Logan
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Urology, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Michael J. Garabedian
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Urology, NYU Grossman School of Medicine, New York, NY, USA
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8
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Wang J, Han C, Wang J, Peng Q. RNA helicase DDX5-induced circPHF14 promotes gastric cancer cell progression. Aging (Albany NY) 2023; 15:2525-2540. [PMID: 36996491 PMCID: PMC10120908 DOI: 10.18632/aging.204623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/21/2023] [Indexed: 04/01/2023]
Abstract
As a well-established member of a strongly conserved protein family, DDX5 binds to RNA helicase in a specific manner, which can regulate mRNA transcription, protein translation and synthesis and precursor messenger RNA processing or alternative splicing. The effects of DDX5 on carcinogenesis and cancer progression are increasingly evident. Circular RNAs (circRNAs), a novel group of functionally non-coding RNAs (ncRNAs) with disordered expression, are associated with various pathological processes (e.g., tumors). circRNA pattern and its function regulated by DDX5 have not yet been determined. According to our findings, DDX5 was dramatically upregulated for stomach cancer tissues, and its overexpression contributed to the cell growth and invasion of GC cells. Based on the analysis of genome-wide circRNAs conducted with circRNA sequencing, DDX5 induces a large number of circRNAs. Further to screen several circRNAs from PHF14 for function, it was found that circPHF14 was essential for the growth and tumorigenesis of DDX5-positive gastric cancer cells. These findings suggest that in addition to the messenger RNA and microRNA patterns, DDX5 also effects a circRNA pattern, as demonstrated by circPHF14. DDX5-induced circRNAs have been found to be of crucial importance for the growth of DDX5-positive gastric cancer cells, providing a new therapeutic target.
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Affiliation(s)
- Jia Wang
- Department of Immunology, Changzhi Medical College, Changzhi 046000, Shanxi, China
- Collaborative Innovation Center for Aging Mechanism Research and Transformation, Center for Healthy Aging, Changzhi Medical College, Changzhi 046000, Shanxi, China
| | - Chunjie Han
- Department of Orthopaedics, Heji Hospital Affiliated to Changzhi Medical College, Changzhi 046000, Shanxi, China
| | - Jinsheng Wang
- Key Laboratory of Esophageal Cancer Basic Research and Clinical Transformation, Heping Hospital Affiliated to Changzhi Medical College, Changzhi 046000, Shanxi, China
- Department of Pathology, Changzhi Medical College, Changzhi 046000, Shanxi, China
| | - Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
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Han M, Liang C, Liu Y, He X, Chu M. Integrated Transcriptome Analysis Reveals the Crucial mRNAs and miRNAs Related to Fecundity in the Hypothalamus of Yunshang Black Goats during the Luteal Phase. Animals (Basel) 2022; 12:ani12233397. [PMID: 36496918 PMCID: PMC9738480 DOI: 10.3390/ani12233397] [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: 10/20/2022] [Revised: 11/27/2022] [Accepted: 11/30/2022] [Indexed: 12/07/2022] Open
Abstract
A normal estrus cycle is essential for the breeding of goats, and the luteal phase accounts for most of the estrus cycle. The corpus luteum (CL) formed during the luteal phase is a transient endocrine gland that is crucial for the reproductive cycle and pregnancy maintenance, and is controlled by many regulatory factors. However, the molecular mechanism of the hypothalamus effect on the reproductive performance of different litter sizes during the luteal phase of goats has not been elucidated. In this study, RNA-sequencing was used to analyze the mRNA and miRNA expression profiles of the hypothalamic tissues with the high-fecundity goats during the luteal phase (LP-HF) and low-fecundity goats during the luteal phase (LP-LF). The RNA-seq results found that there were 1963 differentially expressed genes (DEGs) (890 up-regulated and 1073 down-regulated). The miRNA-seq identified 57 differentially expressed miRNAs (DEMs), including 11 up-regulated and 46 down-regulated, of which 199 DEGs were predicted to be potential target genes of DEMs. Meanwhile, the functional enrichment analysis identified several mRNA-miRNA pairs involved in the regulation of the hypothalamic activity, such as the common target gene MEA1 of novel-miR-972, novel-miR-125 and novel-miR-403, which can play a certain role as a related gene of the reproductive development in the hypothalamic-pituitary-gonadal (HPG) axis and its regulated network, by regulating the androgen secretion. While another target gene ADIPOR2 of the novel-miR-403, is distributed in the hypothalamus and affects the reproductive system through a central role on the HPG axis and a peripheral role in the gonadal tissue. An annotation analysis of the DE miRNA-mRNA pairs identified targets related to biological processes, such as anion binding (GO:0043168) and small molecule binding (GO: 0036094). Subsequently, the KEGG(Kyoto Encyclopedia of Genes and Genomes) pathways were performed to analyze the miRNA-mRNA pairs with negatively correlated miRNAs. We found that the GnRH signaling pathway (ko04912), the estrogen signaling pathway (ko04915), the Fc gamma R-mediated phagocytosis (ko04666), and the IL-17 signaling pathway (ko04657), etc., were directly and indirectly associated with the reproductive process. These targeting interactions may be closely related to the reproductive performance of goats. The results of this study provide a reference for further research on the molecular regulation mechanism for the high fertility in goats.
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Affiliation(s)
- Miaoceng Han
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China
| | - Chen Liang
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China
| | - Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: ; Tel.: +86-010-62819850
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10
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DDX17 promotes the growth and metastasis of lung adenocarcinoma. Cell Death Dis 2022; 8:425. [PMID: 36273228 PMCID: PMC9588018 DOI: 10.1038/s41420-022-01215-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 11/08/2022]
Abstract
DEAD box RNA helicase 17 (DDX17) has been shown to be an RNA binding protein involved in RNA metabolism and associated with cancer progression. However, the biological role of DDX17 in the pathogenesis of lung adenocarcinoma (LUAD) has not been well characterized. Here, we demonstrated that DDX17 promoted the proliferation, migration and invasion of H1299 and A549 lung adenocarcinoma cells. Analyses of public datasets showed that DDX17 is upregulated in LUAD specimens. Our tumor xenograft models confirmed the in vivo promoting role of DDX17 in the growth and metastasis of LUAD. Mechanistic analyses further revealed that DDX17 protein interacts with the mRNA of MYL9 and MAGEA6 and upregulates their levels. MYL9 could mediate the function of DDX17 to regulate the actin cytoskeleton rearrangement and cell adhesion, particularly by modulating the stress fiber and focal adhesion formation, whereas DDX17 might inhibit the autophagy process through MAGEA6/AMPKα1 axis in LUAD cells. Collectively, our study revealed the oncogenic role and pathways of DDX17 in LUAD.
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11
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Xu K, Sun S, Yan M, Cui J, Yang Y, Li W, Huang X, Dou L, Chen B, Tang W, Lan M, Li J, Shen T. DDX5 and DDX17—multifaceted proteins in the regulation of tumorigenesis and tumor progression. Front Oncol 2022; 12:943032. [PMID: 35992805 PMCID: PMC9382309 DOI: 10.3389/fonc.2022.943032] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/07/2022] [Indexed: 12/15/2022] Open
Abstract
DEAD-box (DDX)5 and DDX17, which belong to the DEAD-box RNA helicase family, are nuclear and cytoplasmic shuttle proteins. These proteins are expressed in most tissues and cells and participate in the regulation of normal physiological functions; their abnormal expression is closely related to tumorigenesis and tumor progression. DDX5/DDX17 participate in almost all processes of RNA metabolism, such as the alternative splicing of mRNA, biogenesis of microRNAs (miRNAs) and ribosomes, degradation of mRNA, interaction with long noncoding RNAs (lncRNAs) and coregulation of transcriptional activity. Moreover, different posttranslational modifications, such as phosphorylation, acetylation, ubiquitination, and sumoylation, endow DDX5/DDX17 with different functions in tumorigenesis and tumor progression. Indeed, DDX5 and DDX17 also interact with multiple key tumor-promoting molecules and participate in tumorigenesis and tumor progression signaling pathways. When DDX5/DDX17 expression or their posttranslational modification is dysregulated, the normal cellular signaling network collapses, leading to many pathological states, including tumorigenesis and tumor development. This review mainly discusses the molecular structure features and biological functions of DDX5/DDX17 and their effects on tumorigenesis and tumor progression, as well as their potential clinical application for tumor treatment.
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Affiliation(s)
- Kun Xu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Shenghui Sun
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Mingjing Yan
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
- Peking University Fifth School of Clinical Medicine, Beijing, China
| | - Ju Cui
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Yao Yang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Wenlin Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Xiuqing Huang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Lin Dou
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Beidong Chen
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Weiqing Tang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Ming Lan
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Jian Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Tao Shen
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
- *Correspondence: Tao Shen,
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12
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Zhang X, An T, Zhang X, Shen T, Li H, Dou L, Huang X, Man Y, Tang W, Li J. DDX17 protects hepatocytes against oleic acid/palmitic acid-induced lipid accumulation. Biochem Biophys Res Commun 2022; 612:169-175. [DOI: 10.1016/j.bbrc.2022.04.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 04/27/2022] [Indexed: 11/26/2022]
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13
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Liu Z, Ye Y, Liu Y, Liu Y, Chen H, Shen M, Wang Z, Huang S, Han L, Chen Z, He X. RNA Helicase DHX37 Facilitates Liver Cancer Progression by Cooperating with PLRG1 to Drive Superenhancer-Mediated Transcription of Cyclin D1. Cancer Res 2022; 82:1937-1952. [PMID: 35290436 PMCID: PMC9359749 DOI: 10.1158/0008-5472.can-21-3038] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/11/2022] [Accepted: 03/09/2022] [Indexed: 01/07/2023]
Abstract
RNA helicases are dysregulated in tumors. Here, we identified DHX37 as one of the top RNA helicase genes with upregulated expression in hepatocellular carcinoma (HCC). DHX37 promoted proliferation of liver cancer cells in vitro and in vivo. Epigenomic profiling of DHX37-knockdown and control HCC cells revealed that DHX37 is associated with superenhancer activity. Mechanistically, DHX37 interacted with pleiotropic regulator 1 (PLRG1) to transcriptionally activate cyclin D1 (CCND1) expression via co-occupation of its promoter and superenhancer elements. DHX37 and PLRG1 promoted liver cancer cell proliferation and contributed to the poor prognosis of patients with HCC. Importantly, CCND1 inhibitors were effective as antiproliferative agents for liver cancer. These results together demonstrate a cooperative mechanistic interaction between DHX37 and PLRG1 that regulates CCND1 expression and promotes liver cancer progression, advancing our understanding of the epigenetic and transcriptional dysregulations mediated by RNA helicases and superenhancers in HCC. SIGNIFICANCE This work characterizes a novel mechanism of superenhancer-driven cyclin D1 upregulation by DHX37 and PLRG1, implicating this pathway as a potential therapeutic target in hepatocellular carcinoma.
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Affiliation(s)
- Zhen Liu
- Department of Oncology, Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Youqiong Ye
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Yizhe Liu
- Department of Oncology, Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Yanfang Liu
- Department of Oncology, Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Huifang Chen
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Mengting Shen
- Department of Oncology, Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Zhen Wang
- Department of Oncology, Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Shenglin Huang
- Department of Oncology, Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P.R. China.,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, P.R. China
| | - Leng Han
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas
| | - Zhiao Chen
- Department of Oncology, Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P.R. China.,Corresponding Authors: Xianghuo He, Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Bldg. 7, Room 302, 270 Dong An Rd., Shanghai 200032, P.R. China. Phone: 8621-3477-7329; Fax: 8621-6417-2585; E-mail: ; and Zhiao Chen,
| | - Xianghuo He
- Department of Oncology, Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P.R. China.,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, P.R. China.,Corresponding Authors: Xianghuo He, Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Bldg. 7, Room 302, 270 Dong An Rd., Shanghai 200032, P.R. China. Phone: 8621-3477-7329; Fax: 8621-6417-2585; E-mail: ; and Zhiao Chen,
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14
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Zhou HZ, Li F, Cheng ST, Xu Y, Deng HJ, Gu DY, Wang J, Chen WX, Zhou YJ, Yang ML, Ren JH, Zheng L, Huang AL, Chen J. DDX17-regulated alternative splicing that produced an oncogenic isoform of PXN-AS1 to promote HCC metastasis. Hepatology 2022; 75:847-865. [PMID: 34626132 PMCID: PMC9304246 DOI: 10.1002/hep.32195] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 09/09/2021] [Accepted: 10/01/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS The mechanism underlying HCC metastasis remains unclear, many oncogenes are known to regulate this process. However, the role of alternative splicing (AS) in pro-metastatic HCC is poorly understood. APPROACH AND RESULTS By performing RNA sequencing on nine pairs of primary HCC tissues with extrahepatic metastasis (EHMH) and nine pairs of metastasis-free HCC (MFH) tissues, we depicted the AS landscape in HCC and found a higher frequency of AS events in EHMH compared with MFH. Moreover, 28 differentially expressed splicing regulators were identified in EHMH compared with MFH. Among these, DEAD-box RNA helicase 17 (DDX17) was significantly up-regulated in EHMH and was strongly associated with patient outcome. Functional studies indicated that DDX17 knockout inhibited the degradation of the extracellular matrix, and diminished the invasive ability of HCC cells. A significant reduction in lung metastasis induced by DDX17 deficiency was also demonstrated in a diethylnitrosamine-induced DDX17HKO mouse model. Mechanistically, high DDX17 induced intron 3 retention of PXN-AS1 and produced a transcript (termed PXN-AS1-IR3). The transcript PXN-AS1-IR3 acted as an important promoter of HCC metastasis by inducing MYC transcription activation via recruiting the complex of testis expressed 10 and p300 to the MYC enhancer region, which led to transcriptional activation of several metastasis-associated downstream genes. Finally, the PXN-AS1-IR3 level was significantly higher in serum and HCC tissues with extrahepatic metastasis. CONCLUSIONS DDX17 and PXN-AS1-IR3 act as important metastatic promoters by modulating MYC signaling, suggesting that DDX17 and PXN-AS1-IR3 may be potential prognostic markers for metastatic HCC.
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Affiliation(s)
- Hong-Zhong Zhou
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of EducationChongqing Medical UniversityChongqingChina.,Department of Clinical LaboratoryInstitute of Translational MedicineThe First Affiliated Hospital of Shenzhen University, Shenzhen Second People's HospitalShenzhenChina
| | - Fan Li
- Department of Endocrine and Breast SurgeryThe First Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Sheng-Tao Cheng
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of EducationChongqing Medical UniversityChongqingChina
| | - Yong Xu
- Department of Clinical LaboratoryInstitute of Translational MedicineThe First Affiliated Hospital of Shenzhen University, Shenzhen Second People's HospitalShenzhenChina
| | - Hai-Jun Deng
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of EducationChongqing Medical UniversityChongqingChina
| | - Da-Yong Gu
- Department of Clinical LaboratoryInstitute of Translational MedicineThe First Affiliated Hospital of Shenzhen University, Shenzhen Second People's HospitalShenzhenChina
| | - Jin Wang
- Department of Clinical LaboratoryInstitute of Translational MedicineThe First Affiliated Hospital of Shenzhen University, Shenzhen Second People's HospitalShenzhenChina
| | - Wei-Xian Chen
- Department of Clinical LaboratoryThe Second Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Yu-Jiao Zhou
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of EducationChongqing Medical UniversityChongqingChina
| | - Min-Li Yang
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of EducationChongqing Medical UniversityChongqingChina
| | - Ji-Hua Ren
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of EducationChongqing Medical UniversityChongqingChina
| | - Lu Zheng
- Department of Hepatobiliary Surgerythe Second Affiliated Hospital of Army Medical UniversityChongqingChina
| | - Ai-Long Huang
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of EducationChongqing Medical UniversityChongqingChina
| | - Juan Chen
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of EducationChongqing Medical UniversityChongqingChina
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15
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Identification of early and intermediate biomarkers for ARDS mortality by multi-omic approaches. Sci Rep 2021; 11:18874. [PMID: 34556700 PMCID: PMC8460799 DOI: 10.1038/s41598-021-98053-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/26/2021] [Indexed: 12/29/2022] Open
Abstract
The lack of successful clinical trials in acute respiratory distress syndrome (ARDS) has highlighted the unmet need for biomarkers predicting ARDS mortality and for novel therapeutics to reduce ARDS mortality. We utilized a systems biology multi-“omics” approach to identify predictive biomarkers for ARDS mortality. Integrating analyses were designed to differentiate ARDS non-survivors and survivors (568 subjects, 27% overall 28-day mortality) using datasets derived from multiple ‘omics’ studies in a multi-institution ARDS cohort (54% European descent, 40% African descent). ‘Omics’ data was available for each subject and included genome-wide association studies (GWAS, n = 297), RNA sequencing (n = 93), DNA methylation data (n = 61), and selective proteomic network analysis (n = 240). Integration of available “omic” data identified a 9-gene set (TNPO1, NUP214, HDAC1, HNRNPA1, GATAD2A, FOSB, DDX17, PHF20, CREBBP) that differentiated ARDS survivors/non-survivors, results that were validated utilizing a longitudinal transcription dataset. Pathway analysis identified TP53-, HDAC1-, TGF-β-, and IL-6-signaling pathways to be associated with ARDS mortality. Predictive biomarker discovery identified transcription levels of the 9-gene set (AUC-0.83) and Day 7 angiopoietin 2 protein levels as potential candidate predictors of ARDS mortality (AUC-0.70). These results underscore the value of utilizing integrated “multi-omics” approaches in underpowered datasets from racially diverse ARDS subjects.
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16
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Yu W, Ma H, Li J, Ge J, Wang P, Zhou Y, Zhang J, Shi G. DDX52 knockdown inhibits the growth of prostate cancer cells by regulating c-Myc signaling. Cancer Cell Int 2021; 21:430. [PMID: 34399732 PMCID: PMC8365980 DOI: 10.1186/s12935-021-02128-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/30/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND DDX52 is a type of DEAD/H box RNA helicase that was identified as a novel prostate cancer (PCa) genetic locus and possible causal gene in a European large-scale transcriptome-wide association study. However, the functions of DDX52 in PCa remain undetermined. The c-Myc oncogene plays a crucial role in the development of PCa, but the factors that regulate the activity of c-Myc in PCa are still unknown. METHODS We determined DDX52 protein levels in PCa tissues using immunohistochemistry (IHC). DDX52 expression and survival outcomes in other PCa cohorts were examined using bioinformatics analysis. The inhibition of DDX52 via RNA interference with shRNA was used to clarify the effects of DDX52 on PCa cell growth in vitro and in vivo. Gene set enrichment analysis and RNA sequencing were used to explore the signaling regulated by DDX52 in PCa. Western blotting and IHC were used to determine the possible DDX52 signaling mechanism in PCa. RESULTS DDX52 expression was upregulated in PCa tissues. Bioinformatics analysis showed that the level of DDX52 further increased in advanced PCa, with a high DDX52 level indicating a poor outcome. In vitro and in vivo experiments showed that downregulating DDX52 impeded the growth of PCa cells. High DDX52 levels contributed to activating c-Myc signaling in PCa patients and PCa cells. Furthermore, DDX52 expression was regulated by c-Myc and positively correlated with c-Myc expression in PCa. CONCLUSION DDX52 was overexpressed in PCa tissues in contrast to normal prostate tissues. DDX52 knockdown repressed the growth of PCa cells in vitro and in vivo. Deleting c-Myc inhibited DDX52 expression, which affected the activation of c-Myc signaling.
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Affiliation(s)
- Wandong Yu
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, 801 Heqing Road, Minhang District, Shanghai, 200240, People's Republic of China
| | - Hangbin Ma
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, 801 Heqing Road, Minhang District, Shanghai, 200240, People's Republic of China
| | - Junhong Li
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, 801 Heqing Road, Minhang District, Shanghai, 200240, People's Republic of China
| | - Jinchao Ge
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, 801 Heqing Road, Minhang District, Shanghai, 200240, People's Republic of China
| | - Pengyu Wang
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, 801 Heqing Road, Minhang District, Shanghai, 200240, People's Republic of China
| | - Yinghao Zhou
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, 801 Heqing Road, Minhang District, Shanghai, 200240, People's Republic of China
| | - Jun Zhang
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, 801 Heqing Road, Minhang District, Shanghai, 200240, People's Republic of China.
| | - Guowei Shi
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, 801 Heqing Road, Minhang District, Shanghai, 200240, People's Republic of China.
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17
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RNA Helicase DDX17 inhibits Hepatitis B Virus Replication by Blocking Viral Pregenomic RNA Encapsidation. J Virol 2021; 95:e0044421. [PMID: 34287051 DOI: 10.1128/jvi.00444-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
DDX17 is a member of the DEAD-Box helicase family proteins involved in cellular RNA folding, splicing, and translation. It has been reported that DDX17 serves as a co-factor of host zinc finger antiviral protein (ZAP)-mediated retroviral RNA degradation and exerts direct antiviral function against Raft Valley Fever Virus though binding to specific stem-loop structures of viral RNA. Intriguingly, we have previously shown that ZAP inhibits Hepatitis B virus (HBV) replication through promoting viral RNA decay, and the ZAP-responsive element (ZRE) of HBV pregenomic RNA (pgRNA) contains a stem-loop structure, specifically epsilon, which serves as the packaging signal for pgRNA encapsidation. In this study, we demonstrated that the endogenous DDX17 is constitutively expressed in human hepatocyte-derived cells but dispensable for ZAP-mediated HBV RNA degradation. However, DDX17 was found to inhibit HBV replication primarily by reducing the level of cytoplasmic encapsidated pgRNA in a helicase-dependent manner. Immunofluorescence assay revealed that DDX17 could gain access to cytoplasm from nucleus in the presence of HBV RNA. In addition, RNA immunoprecipitation and electrophoretic mobility shift assays demonstrated that the enzymatically active DDX17 competes with HBV polymerase to bind to pgRNA at the 5' epsilon motif. In summary, our study suggests that DDX17 serves as an intrinsic host restriction factor against HBV through interfering with pgRNA encapsidation. IMPORTANCE Hepatitis B virus (HBV) chronic infection, a long-studied but yet incurable disease, remains a major public health concern worldwide. Given that HBV replication cycle highly depends on host factors, deepening our understanding of the host-virus interaction is thus of great significance in the journey of finding a cure. In eukaryotic cells, RNA helicases of DEAD-box family are highly conserved enzymes involved in diverse processes of cellular RNA metabolism. Emerging data have shown that DDX17, a typical member of DEAD box family, functions as an antiviral factor through interacting with viral RNA. In this study, we, for the first time, demonstrate that DDX17 inhibits HBV through blocking the formation of viral replication complex, which not only broadens the antiviral spectrum of DDX17, but also provides new insight into the molecular mechanism of DDX17-mediated virus-host interaction.
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18
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The DEAD-box protein family of RNA helicases: sentinels for a myriad of cellular functions with emerging roles in tumorigenesis. Int J Clin Oncol 2021; 26:795-825. [PMID: 33656655 DOI: 10.1007/s10147-021-01892-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/20/2021] [Indexed: 02/06/2023]
Abstract
DEAD-box RNA helicases comprise a family within helicase superfamily 2 and make up the largest group of RNA helicases. They are a profoundly conserved family of RNA-binding proteins, carrying a generic Asp-Glu-Ala-Asp (D-E-A-D) motif that gives the family its name. Members of the DEAD-box family of RNA helicases are engaged in all facets of RNA metabolism from biogenesis to decay. DEAD-box proteins ordinarily function as constituents of enormous multi-protein complexes and it is believed that interactions with other components in the complexes might be answerable for the various capacities ascribed to these proteins. Therefore, their exact function is probably impacted by their interacting partners and to be profoundly context dependent. This may give a clarification to the occasionally inconsistent reports proposing that DEAD-box proteins have both pro- and anti-proliferative functions in cancer. There is emerging evidence that DEAD-box family of RNA helicases play pivotal functions in various cellular processes and in numerous cases have been embroiled in cellular proliferation and/or neoplastic transformation. In various malignancy types, DEAD-box RNA helicases have been reported to possess pro-proliferation or even oncogenic roles as well as anti-proliferative or tumor suppressor functions. Clarifying the exact function of DEAD-box helicases in cancer is probably intricate, and relies upon the cellular milieu and interacting factors. This review aims to summarize the current data on the numerous capacities that have been ascribed to DEAD-box RNA helicases. It also highlights their diverse actions upon malignant transformation in the various tumor types.
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Wu XC, Yan WG, Ji ZG, Zheng GY, Liu GH. Long noncoding RNA SNHG20 promotes prostate cancer progression via upregulating DDX17. Arch Med Sci 2021; 17:1752-1765. [PMID: 34900057 PMCID: PMC8641522 DOI: 10.5114/aoms.2019.85653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 04/20/2019] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Accumulating evidence has revealed the critical roles of long noncoding RNAs (lncRNAs) in various cancers. LncRNA SNHG20 has been shown to be a cancer-associated lncRNA in several cancers with diverse mechanisms. However, the clinical references, biological roles, and mechanisms of action of SNHG20 in prostate cancer (PCa) are still unclear. MATERIAL AND METHODS The expression of SNHG20 in PCa tissues and cell lines was detected by RT-qPCR. The correlations between SNHG20 expression and clinicopathological features were analyzed by χ2 test. The roles of SNHG20 in PCa cell proliferation and migration were detected by CCK-8, EdU incorporation, and transwell assays. The regulatory mechanisms of SNHG20 on DDX17 were detected by dual luciferase reporter assay, RT-qPCR, and western blot. RESULTS SNHG20 is highly expressed in PCa tissues and cell lines. High expression of SNHG20 is positively correlated with high Gleason score and advanced tumor stage. Functional experiments revealed that overexpression of SNHG20 promotes PCa cell proliferation and migration. SNHG20 knockdown represses PCa cell proliferation and migration. Mechanistically, SNHG20 was verified to act as a competing endogenous RNA (ceRNA) to upregulate DDX17. DDX17 is also highly expressed and has oncogenic roles in PCa. Furthermore, the expression of DDX17 is significantly positively correlated with that of SNHG20 in PCa tissues. Depletion of DDX17 reverses the oncogenic roles of SNHG20 in PCa. CONCLUSIONS These data showed that SNHG20 promotes PCa cell proliferation and migration via acting as a ceRNA to upregulate DDX17. This study also suggested that SNHG20 may be a potential novel therapeutic target for PCa.
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Affiliation(s)
- Xing-Cheng Wu
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking, China
| | - Wei-Gang Yan
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking, China
| | - Zhi-Gang Ji
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking, China
| | - Guo-Yang Zheng
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking, China
| | - Guang-Hua Liu
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking, China
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Ricciardi L, Giurato G, Memoli D, Pietrafesa M, Dal Col J, Salvato I, Nigro A, Vatrella A, Caramori G, Casolaro V, Stellato C. Posttranscriptional Gene Regulatory Networks in Chronic Airway Inflammatory Diseases: In silico Mapping of RNA-Binding Protein Expression in Airway Epithelium. Front Immunol 2020; 11:579889. [PMID: 33178205 PMCID: PMC7596416 DOI: 10.3389/fimmu.2020.579889] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/19/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Posttranscriptional gene regulation (PTGR) contributes to inflammation through alterations in messenger RNA (mRNA) turnover and translation rates. RNA-binding proteins (RBPs) coordinate these processes but their role in lung inflammatory diseases is ill-defined. We evaluated the expression of a curated list of mRNA-binding RBPs (mRBPs) in selected Gene Expression Omnibus (GEO) transcriptomic databases of airway epithelium isolated from chronic obstructive pulmonary disease (COPD), severe asthma (SA) and matched control subjects, hypothesizing that global changes in mRBPs expression could be used to infer their pathogenetic roles and identify novel disease-related regulatory networks. Methods: A published list of 692 mRBPs [Nat Rev Genet 2014] was searched in GEO datasets originated from bronchial brushings of stable COPD patients (C), smokers (S), non-smokers (NS) controls with normal lung function (n = 6/12/12) (GEO ID: GSE5058) and of (SA) and healthy control (HC) (n = 6/12) (GSE63142). Fluorescence intensity data were extracted and normalized on the medians for fold change (FC) comparisons. FCs were set at ≥ |1.5| with a false discovery rate (FDR) of ≤ 0.05. Pearson correlation maps and heatmaps were generated using tMEV tools v4_9_0.45. DNA sequence motifs were searched using PScan-ChIP. Gene Ontology (GO) was performed with Ingenuity Pathway Analysis (IPA) tool. Results: Significant mRBP expression changes were detected for S/NS, COPD/NS and COPD/S (n = 41, 391, 382, respectively). Of those, 32% of genes changed by FC ≥ |1.5| in S/NS but more than 60% in COPD/NS and COPD/S (n = 13, 267, 257, respectively). Genes were predominantly downregulated in COPD/NS (n = 194, 73%) and COPD/S (n = 202, 79%), less so in S/NS (n = 4, 31%). Unsupervised cluster analysis identified in 4 out of 12 S the same mRBP pattern seen in C, postulating subclinical COPD. Significant DNA motifs enrichment for transcriptional regulation was found for downregulated RBPs. Correlation analysis identified five clusters of co-expressed mRBPs. GO analysis revealed significant enrichments in canonical pathways both specific and shared among comparisons. Unexpectedly, no significant mRBPs modulation was found in SA compared to controls. Conclusions: Airway epithelial mRBPs profiling reveals a COPD-specific global downregulation of RBPs shared by a subset of control smokers, the potential of functional cooperation by coexpressed RBPs and significant impact on relevant pathogenetic pathways in COPD. Elucidation of PTGR in COPD could identify disease biomarkers or pathways for therapeutic targeting.
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Affiliation(s)
- Luca Ricciardi
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Domenico Memoli
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Mariagrazia Pietrafesa
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Jessica Dal Col
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Ilaria Salvato
- Pulmonology, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Annunziata Nigro
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Alessandro Vatrella
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Gaetano Caramori
- Pulmonology, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Vincenzo Casolaro
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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Liu H, Perumal N, Manicam C, Mercieca K, Prokosch V. Proteomics Reveals the Potential Protective Mechanism of Hydrogen Sulfide on Retinal Ganglion Cells in an Ischemia/Reperfusion Injury Animal Model. Pharmaceuticals (Basel) 2020; 13:ph13090213. [PMID: 32867129 PMCID: PMC7557839 DOI: 10.3390/ph13090213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
Glaucoma is the leading cause of irreversible blindness and is characterized by progressive retinal ganglion cell (RGC) degeneration. Hydrogen sulfide (H2S) is a potent neurotransmitter and has been proven to protect RGCs against glaucomatous injury in vitro and in vivo. This study is to provide an overall insight of H2S’s role in glaucoma pathophysiology. Ischemia-reperfusion injury (I/R) was induced in Sprague-Dawley rats (n = 12) by elevating intraocular pressure to 55 mmHg for 60 min. Six of the animals received intravitreal injection of H2S precursor prior to the procedure and the retina was harvested 24 h later. Contralateral eyes were assigned as control. RGCs were quantified and compared within the groups. Retinal proteins were analyzed via label-free mass spectrometry based quantitative proteomics approach. The pathways of the differentially expressed proteins were identified by ingenuity pathway analysis (IPA). H2S significantly improved RGC survival against I/R in vivo (p < 0.001). In total 1115 proteins were identified, 18 key proteins were significantly differentially expressed due to I/R and restored by H2S. Another 11 proteins were differentially expressed following H2S. IPA revealed a significant H2S-mediated activation of pathways related to mitochondrial function, iron homeostasis and vasodilation. This study provides first evidence of the complex role that H2S plays in protecting RGC against I/R.
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Affiliation(s)
- Hanhan Liu
- Experimental and Translational Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (H.L.); (N.P.); (C.M.)
| | - Natarajan Perumal
- Experimental and Translational Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (H.L.); (N.P.); (C.M.)
| | - Caroline Manicam
- Experimental and Translational Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (H.L.); (N.P.); (C.M.)
| | - Karl Mercieca
- Royal Eye Hospital, School of Medicine, University of Manchester, Manchester M13 9WH, UK;
| | - Verena Prokosch
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
- Correspondence: ; Tel.: +49-1703862250
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Sithole N, Williams CA, Abbink TEM, Lever AML. DDX5 potentiates HIV-1 transcription as a co-factor of Tat. Retrovirology 2020; 17:6. [PMID: 32228614 PMCID: PMC7106839 DOI: 10.1186/s12977-020-00514-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 03/16/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND HIV-1 does not encode a helicase and hijacks those of the cell for efficient replication. We and others previously showed that the DEAD box helicase, DDX5, is an essential HIV dependency factor. DDX5 was recently shown to be associated with the 7SK snRNP. Cellular positive transcription elongation factor b (P-TEFb) is bound in an inactive form with HEXIM1/2 on 7SK snRNP. The Tat/P-TEFb complex is essential for efficient processivity of Pol II in HIV-1 transcription elongation and Tat competes with HEXIM1/2 for P-TEFb. We investigated the precise role of DDX5 in HIV replication using siRNA mediated knockdown and rescue with DDX5 mutants which prevent protein-protein interactions and RNA and ATP binding. RESULTS We demonstrate a critical role for DDX5 in the Tat/HEXIM1 interaction. DDX5 acts to potentiate Tat activity and can bind both Tat and HEXIM1 suggesting it may facilitate the dissociation of HEXIM1/2 from the 7SK-snRNP complex, enhancing Tat/P-TEFb availability. We show knockdown of DDX5 in a T cell line significantly reduces HIV-1 infectivity and viral protein production. This activity is unique to DDX5 and cannot be substituted by its close paralog DDX17. Overexpression of DDX5 stimulates the Tat/LTR promoter but suppresses other cellular and viral promoters. Individual mutations of conserved ATP binding, RNA binding, helicase related or protein binding motifs within DDX5 show that the N terminal RNA binding motifs, the Walker B and the glycine doublet motifs are essential for this function. The Walker A and RNA binding motifs situated on the transactivation domain are however dispensable. CONCLUSION DDX5 is an essential cellular factor for efficient HIV transcription elongation. It interacts with Tat and may potentiate the availability of P-TEFb through sequestering HEXIM1.
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Affiliation(s)
- Nyaradzai Sithole
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Claire A Williams
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
- Department of Microbiology, Specialist Virology Centre, Norfolk and Norwich University Hospitals, Norwich, UK
| | - Truus E M Abbink
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
- Department of Paediatrics, Child Neurology, Centre for Childhood White Matter Disorders, VU University Medical Centre, Amsterdam, The Netherlands
| | - Andrew M L Lever
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK.
- Department of Medicine, National University of Singapore, Singapore, 119228, Singapore.
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GSK3: A Kinase Balancing Promotion and Resolution of Inflammation. Cells 2020; 9:cells9040820. [PMID: 32231133 PMCID: PMC7226814 DOI: 10.3390/cells9040820] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/11/2022] Open
Abstract
GSK3 has been implicated for years in the regulation of inflammation and addressed in a plethora of scientific reports using a variety of experimental (disease) models and approaches. However, the specific role of GSK3 in the inflammatory process is still not fully understood and controversially discussed. Following a detailed overview of structure, function, and various regulatory levels, this review focusses on the immunoregulatory functions of GSK3, including the current knowledge obtained from animal models. Its impact on pro-inflammatory cytokine/chemokine profiles, bacterial/viral infections, and the modulation of associated pro-inflammatory transcriptional and signaling pathways is discussed. Moreover, GSK3 contributes to the resolution of inflammation on multiple levels, e.g., via the regulation of pro-resolving mediators, the clearance of apoptotic immune cells, and tissue repair processes. The influence of GSK3 on the development of different forms of stimulation tolerance is also addressed. Collectively, the role of GSK3 as a kinase balancing the initiation/perpetuation and the amelioration/resolution of inflammation is highlighted.
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24
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Ngo TD, Partin AC, Nam Y. RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis. Cell Rep 2019; 29:4024-4035.e5. [PMID: 31851931 PMCID: PMC6953907 DOI: 10.1016/j.celrep.2019.11.059] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/03/2019] [Accepted: 11/14/2019] [Indexed: 11/23/2022] Open
Abstract
DDX17, a DEAD-box ATPase, is a multifunctional helicase important for various RNA functions, including microRNA maturation. Key questions for DDX17 include how it recognizes target RNAs and influences their structures, as well as how its ATPase activity may be regulated. Through crystal structures and biochemical assays, we show the ability of the core catalytic domains of DDX17 to recognize specific sequences in target RNAs. The RNA sequence preference of the catalytic core is critical for DDX17 to directly bind and remodel a specific region of primary microRNAs 3' to the mature sequence, and consequently enhance processing by Drosha. Furthermore, we identify an intramolecular interaction between the N-terminal tail and the DEAD domain of DDX17 to have an autoregulatory role in controlling the ATPase activity. Thus, we provide the molecular basis for how cognate RNA recognition and functional outcomes are linked for DDX17.
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Affiliation(s)
- Tri D Ngo
- Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Alexander C Partin
- Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yunsun Nam
- Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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25
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Nassa G, Giurato G, Salvati A, Gigantino V, Pecoraro G, Lamberti J, Rizzo F, Nyman TA, Tarallo R, Weisz A. The RNA-mediated estrogen receptor α interactome of hormone-dependent human breast cancer cell nuclei. Sci Data 2019; 6:173. [PMID: 31527615 PMCID: PMC6746822 DOI: 10.1038/s41597-019-0179-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/25/2019] [Indexed: 01/11/2023] Open
Abstract
Estrogen Receptor alpha (ERα) is a ligand-inducible transcription factor that mediates estrogen signaling in hormone-responsive cells, where it controls key cellular functions by assembling in gene-regulatory multiprotein complexes. For this reason, interaction proteomics has been shown to represent a useful tool to investigate the molecular mechanisms underlying ERα action in target cells. RNAs have emerged as bridging molecules, involved in both assembly and activity of transcription regulatory protein complexes. By applying Tandem Affinity Purification (TAP) coupled to mass spectrometry (MS) before and after RNase digestion in vitro, we generated a dataset of nuclear ERα molecular partners whose association with the receptor involves RNAs. These data provide a useful resource to elucidate the combined role of nuclear RNAs and the proteins identified here in ERα signaling to the genome in breast cancer and other cell types.
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Affiliation(s)
- Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Valerio Gigantino
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Giovanni Pecoraro
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Jessica Lamberti
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Tuula A Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo, 0372, Oslo, Norway
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy.
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy.
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Lambert MP, Terrone S, Giraud G, Benoit-Pilven C, Cluet D, Combaret V, Mortreux F, Auboeuf D, Bourgeois CF. The RNA helicase DDX17 controls the transcriptional activity of REST and the expression of proneural microRNAs in neuronal differentiation. Nucleic Acids Res 2019; 46:7686-7700. [PMID: 29931089 PMCID: PMC6125624 DOI: 10.1093/nar/gky545] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/04/2018] [Indexed: 12/22/2022] Open
Abstract
The Repressor Element 1-silencing transcription factor (REST) represses a number of neuronal genes in non-neuronal cells or in undifferentiated neural progenitors. Here, we report that the DEAD box RNA helicase DDX17 controls important REST-related processes that are critical during the early phases of neuronal differentiation. First, DDX17 associates with REST, promotes its binding to the promoter of a subset of REST-targeted genes and co-regulates REST transcriptional repression activity. During neuronal differentiation, we observed a downregulation of DDX17 along with that of the REST complex that contributes to the activation of neuronal genes. Second, DDX17 and its paralog DDX5 regulate the expression of several proneural microRNAs that are known to target the REST complex during neurogenesis, including miR-26a/b that are also direct regulators of DDX17 expression. In this context, we propose a new mechanism by which RNA helicases can control the biogenesis of intronic miRNAs. We show that the processing of the miR-26a2 precursor is dependent on RNA helicases, owing to an intronic regulatory region that negatively impacts on both miRNA processing and splicing of its host intron. Our work places DDX17 in the heart of a pathway involving REST and miRNAs that allows neuronal gene repression.
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Affiliation(s)
- Marie-Pierre Lambert
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Sophie Terrone
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Guillaume Giraud
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Clara Benoit-Pilven
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - David Cluet
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Valérie Combaret
- Laboratoire de Recherche Translationnelle, Centre Léon Bérard, F-69008 Lyon, France
| | - Franck Mortreux
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Didier Auboeuf
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
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27
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Jiménez-González V, Ogalla-García E, García-Quintanilla M, García-Quintanilla A. Deciphering GRINA/Lifeguard1: Nuclear Location, Ca 2+ Homeostasis and Vesicle Transport. Int J Mol Sci 2019; 20:ijms20164005. [PMID: 31426446 PMCID: PMC6719933 DOI: 10.3390/ijms20164005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/31/2019] [Accepted: 08/12/2019] [Indexed: 01/31/2023] Open
Abstract
The Glutamate Receptor Ionotropic NMDA-Associated Protein 1 (GRINA) belongs to the Lifeguard family and is involved in calcium homeostasis, which governs key processes, such as cell survival or the release of neurotransmitters. GRINA is mainly associated with membranes of the endoplasmic reticulum, Golgi, endosome, and the cell surface, but its presence in the nucleus has not been explained yet. Here we dissect, with the help of different software tools, the potential roles of GRINA in the cell and how they may be altered in diseases, such as schizophrenia or celiac disease. We describe for the first time that the cytoplasmic N-terminal half of GRINA (which spans a Proline-rich domain) contains a potential DNA-binding sequence, in addition to cleavage target sites and probable PY-nuclear localization sequences, that may enable it to be released from the rest of the protein and enter the nucleus under suitable conditions, where it could participate in the transcription, alternative splicing, and mRNA export of a subset of genes likely involved in lipid and sterol synthesis, ribosome biogenesis, or cell cycle progression. To support these findings, we include additional evidence based on an exhaustive review of the literature and our preliminary data of the protein–protein interaction network of GRINA.
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Affiliation(s)
| | - Elena Ogalla-García
- Department of Pharmacology, School of Pharmacy, University of Seville, 41012 Seville, Spain
| | - Meritxell García-Quintanilla
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
| | - Albert García-Quintanilla
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Seville, 41012 Seville, Spain.
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28
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Giraud G, Terrone S, Bourgeois CF. Functions of DEAD box RNA helicases DDX5 and DDX17 in chromatin organization and transcriptional regulation. BMB Rep 2019. [PMID: 30293550 PMCID: PMC6330936 DOI: 10.5483/bmbrep.2018.51.12.234] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA helicases DDX5 and DDX17 are multitasking proteins that regulate gene expression in different biological contexts through diverse activities. Special attention has long been paid to their function as coregulators of transcription factors, providing insight about their functional association with a number of chromatin modifiers and remodelers. However, to date, the variety of described mechanisms has made it difficult to understand precisely how these proteins work at the molecular level, and the contribution of their ATPase domain to these mechanisms remains unclear as well. In light of their association with long noncoding RNAs that are key epigenetic regulators, an emerging view is that DDX5 and DDX17 may act through modulating the activity of various ribonucleoprotein complexes that could ensure their targeting to specific chromatin loci. This review will comprehensively describe the current knowledge on these different mechanisms. We will also discuss the potential roles of DDX5 and DDX17 on the 3D chromatin organization and how these could impact gene expression at the transcriptional and post-transcriptional levels.
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Affiliation(s)
- Guillaume Giraud
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, CNRS UMR 5239, INSERM U1210, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Sophie Terrone
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, CNRS UMR 5239, INSERM U1210, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, CNRS UMR 5239, INSERM U1210, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
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Kao SH, Cheng WC, Wang YT, Wu HT, Yeh HY, Chen YJ, Tsai MH, Wu KJ. Regulation of miRNA Biogenesis and Histone Modification by K63-Polyubiquitinated DDX17 Controls Cancer Stem-like Features. Cancer Res 2019; 79:2549-2563. [PMID: 30877109 DOI: 10.1158/0008-5472.can-18-2376] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/17/2019] [Accepted: 03/12/2019] [Indexed: 11/16/2022]
Abstract
Markers of cancer stemness predispose patients to tumor aggressiveness, drug and immunotherapy resistance, relapse, and metastasis. DDX17 is a cofactor of the Drosha-DGCR8 complex in miRNA biogenesis and transcriptional coactivator and has been associated with cancer stem-like properties. However, the precise mechanism by which DDX17 controls cancer stem-like features remains elusive. Here, we show that the E3 ligase HectH9 mediated K63-polyubiquitination of DDX17 under hypoxia to control stem-like properties and tumor-initiating capabilities. Polyubiquitinated DDX17 disassociated from the Drosha-DGCR8 complex, leading to decreased biogenesis of anti-stemness miRNAs. Increased association of polyubiquitinated DDX17 with p300-YAP resulted in histone 3 lysine 56 (H3K56) acetylation proximal to stemness-related genes and their subsequent transcriptional activation. High expression of HectH9 and six stemness-related genes (BMI1, SOX2, OCT4, NANOG, NOTCH1, and NOTCH2) predicted poor survival in patients with head and neck squamous cell carcinoma and lung adenocarcinoma. Our findings demonstrate that concerted regulation of miRNA biogenesis and histone modifications through posttranslational modification of DDX17 underlies many cancer stem-like features. Inhibition of DDX17 ubiquitination may serve as a new therapeutic venue for cancer treatment. SIGNIFICANCE: Hypoxia-induced polyubiquitination of DDX17 controls its dissociation from the pri-miRNA-Drosha-DCGR8 complex to reduce anti-stemness miRNA biogenesis and association with YAP and p300 to enhance transcription of stemness-related genes.
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Affiliation(s)
- Shih-Han Kao
- Research Center for Tumor Medical Science, China Medical University, Taichung, Taiwan.,Drug Development Center, China Medical University, Taichung, Taiwan
| | - Wei-Chung Cheng
- Research Center for Tumor Medical Science, China Medical University, Taichung, Taiwan.,Drug Development Center, China Medical University, Taichung, Taiwan.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Yi-Ting Wang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Han-Tsang Wu
- Department of Cell and Tissue Engineering, Changhua Christian Hospital, Changhua City, Taiwan
| | - Han-Yu Yeh
- Research Center for Tumor Medical Science, China Medical University, Taichung, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Ming-Hsui Tsai
- Department of Otolaryngology, China Medical University Hospital, Taichung, Taiwan
| | - Kou-Juey Wu
- Research Center for Tumor Medical Science, China Medical University, Taichung, Taiwan. .,Drug Development Center, China Medical University, Taichung, Taiwan.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.,Institute of New Drug Development, China Medical University, Taichung, Taiwan.,Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.,Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
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30
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Chen Y, Wang Q, Wang Q, Liu J, Jiang X, Zhang Y, Liu Y, Zhou F, Liu H. DEAD-Box Helicase 5 Interacts With Transcription Factor 12 and Promotes the Progression of Osteosarcoma by Stimulating Cell Cycle Progression. Front Pharmacol 2019; 9:1558. [PMID: 30733679 PMCID: PMC6353832 DOI: 10.3389/fphar.2018.01558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/21/2018] [Indexed: 12/13/2022] Open
Abstract
Osteosarcoma (OS) is a common malignant primary bone tumor. Its mechanism of development and progression is poorly understood. Currently, there is no effective therapeutic regimens available for the treatment of OS. DEAD-box helicase 5 (DDX5) is involved in oncogenic processes. This study aimed to explore the role of DDX5 in the development and progression of OS and its relationship with transcription factor 12 (TCF12), which is as an important molecule of Wnt signaling pathway. We found that the expressions of DDX5 and TCF12 protein were significantly higher in OS patients tissues and in the MG63 cells than in the corresponding normal tissues and human osteoblast cell hFOB 1.19. Overexpressions of both DDX5 and TCF12 were associated with clinicopathological features and poor prognosis of OS patients. siRNA based knockdown of DDX5 inhibited the proliferation of MG63 cells as demonstrated by an in vitro MTS assay and 5-ethynyl-2-deoxyuridine DNA proliferation detection, and promoted apoptosis of MG63 cells measured by flow cytometry. In addition, DDX5 knockdown inhibited the MG63 cell migration and invasion on transwell assays. Further experiments showed that DDX5 knockdown not only inhibited the expression of TCF12 but also decreased the mRNA and protein levels of Cyclin E1, an important regulator of G1–S phase progression, suggesting that DDX5 was required for the entry of cells into S phase. Overexpression of TCF12 reversed the cell proliferation, migration and invasion in MG63 cells induced by DDX5 knockdown accompanied by the upregulation of Cyclin E1. Additionally, we observed that DDX5 interacted with TCF12 in both OS tissues and MG63 cells by Co-immunoprecipitation assays. Taken together, our study revealed that DDX5 interacts with TCF12 and promotes the progression of OS by stimulating cell cycle progression. Our results suggest that DDX5 and TCF12 could be potential biomarkers for the diagnosis and treatment of OS.
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Affiliation(s)
- Yanchun Chen
- Department of Histology and Embryology, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Qiaozhen Wang
- Department of Human Anatomy, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Qing Wang
- Department of Human Anatomy, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Jinmeng Liu
- Department of Histology and Embryology, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Xin Jiang
- Department of Histology and Embryology, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Yawen Zhang
- Department of Histology and Embryology, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Yongxin Liu
- Department of Anesthesiology, Weifang Medical University, Weifang, China
| | - Fenghua Zhou
- Department of Pathology, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Huancai Liu
- Department of Joint Surgery, Affiliated Hospital, Weifang Medical University, Weifang, China
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31
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Roles of DDX5 in the tumorigenesis, proliferation, differentiation, metastasis and pathway regulation of human malignancies. Biochim Biophys Acta Rev Cancer 2019; 1871:85-98. [DOI: 10.1016/j.bbcan.2018.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/02/2018] [Accepted: 11/03/2018] [Indexed: 02/07/2023]
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32
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Hashemi V, Masjedi A, Hazhir-Karzar B, Tanomand A, Shotorbani SS, Hojjat-Farsangi M, Ghalamfarsa G, Azizi G, Anvari E, Baradaran B, Jadidi-Niaragh F. The role of DEAD-box RNA helicase p68 (DDX5) in the development and treatment of breast cancer. J Cell Physiol 2018; 234:5478-5487. [PMID: 30417346 DOI: 10.1002/jcp.26912] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/13/2018] [Indexed: 12/13/2022]
Abstract
RNA helicase p68 or DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5) is a unique member of the highly conserved protein family, which is involved in a broad spectrum of biological processes, including transcription, translation, precursor messenger RNA processing or alternative splicing, and microRNA (miRNA) processing. It has been shown that p68 is necessary for cell growth and participates in the early development and maturation of some organs. Interestingly, p68 is a transcriptional coactivator of numerous oncogenic transcription factors, including nuclear factor-κβ (NF-κβ), estrogen receptor α (ERα), β-catenin, androgen receptor, Notch transcriptional activation complex, p53 and signal transducer, and activator of transcription 3 (STAT3). Recent studies on the role of p68 (DDX5) in multiple dysregulated cellular processes in various cancers and its abnormal expression indicate the importance of this factor in tumor development. Discussion of the precise role of p68 in cancer is complex and depends on the cellular microenvironment and interacting factors. In terms of the deregulated expression of p68 in breast cancer and the high prevalence of this cancer among women, it can be informative to review the precise function of this factor in the breast cancer. Therefore, an attempt will be made in this review to clarify the tumorigenic function of p68 in association with its targeting potential for the treatment of breast cancer.
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Affiliation(s)
- Vida Hashemi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Basic Sciences, Faculty of Medicine, Maragheh University of Medical Science, Maragheh, Iran
| | - Ali Masjedi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bita Hazhir-Karzar
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Asghar Tanomand
- Department of Basic Sciences, Faculty of Medicine, Maragheh University of Medical Science, Maragheh, Iran
| | | | - Mohammad Hojjat-Farsangi
- Department of Oncology-Pathology, Immune and Gene therapy Lab, Cancer Center Karolinska (CCK), Karolinska University Hospital Solna and Karolinska Institute, Stockholm, Sweden.,Department of Immunology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Ghasem Ghalamfarsa
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Gholamreza Azizi
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Enayat Anvari
- Department of Physiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farhad Jadidi-Niaragh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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33
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Cellular RNA Helicases Support Early and Late Events in Retroviral Replication. RETROVIRUS-CELL INTERACTIONS 2018. [PMCID: PMC7149973 DOI: 10.1016/b978-0-12-811185-7.00007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Retroviruses commandeer cell RNA helicases (RHs). Cell RHs are necessary for early and late events in retrovirus replication. The provirus is adopted by the cell-endogenous nuclear and cytoplasmic gene expression types of machinery. Whereas retroviruses engender the supportive activity of cell RHs, other RNA viruses provoke theantiviral role of this superfamily of conserved proteins. In this chapter, we contrast retrovirus reliance on host RNA helicases to support their replication cycle, with the virus-encoded helicaseactivity utilized by RNA viruses in cytoplasmic factories. Ironically, RHs are agonists to retroviruses and antagonists to other RNA viruses.
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34
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Hoch-Kraft P, White R, Tenzer S, Krämer-Albers EM, Trotter J, Gonsior C. Dual role of the RNA helicase DDX5 in post-transcriptional regulation of Myelin Basic Protein in oligodendrocytes. J Cell Sci 2018; 131:jcs.204750. [DOI: 10.1242/jcs.204750] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 03/28/2018] [Indexed: 01/11/2023] Open
Abstract
In the central nervous system, oligodendroglial expression of Myelin Basic Protein (MBP) is crucial for the assembly and structure of the myelin sheath. MBP synthesis is tightly regulated in space and time, particularly on the post-transcriptional level. We have identified the DEAD-box RNA helicase DDX5 (alias p68) in a complex with Mbp mRNA in oligodendroglial cells. Expression of DDX5 is highest in progenitor cells and immature oligodendrocytes, where it localizes to heterogeneous populations of cytoplasmic ribonucleoprotein (RNP) complexes associated with Mbp mRNA in the cell body and processes. Manipulation of DDX5 protein amounts inversely affects levels of MBP protein. We present evidence that DDX5 is involved in post-transcriptional regulation of MBP protein synthesis, with implications for oligodendroglial development. In addition, DDX5 knockdown results in an increased abundance of MBP exon 2-positive isoforms in immature oligodendrocytes, most likely by regulating alternative splicing of Mbp. Our findings contribute to the understanding of the complex nature of MBP post-transcriptional control in immature oligodendrocytes where DDX5 appears to affect the abundance of MBP proteins via distinct but converging mechanisms.
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Affiliation(s)
- Peter Hoch-Kraft
- Molecular Cell Biology, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg-University of Mainz, Anselm-Franz-von-Bentzelweg 3, 55128 Mainz, Germany
| | - Robin White
- Molecular Cell Biology, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg-University of Mainz, Anselm-Franz-von-Bentzelweg 3, 55128 Mainz, Germany
- Institute of Physiology and Pathophysiology, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128 Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Eva-Maria Krämer-Albers
- Molecular Cell Biology, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg-University of Mainz, Anselm-Franz-von-Bentzelweg 3, 55128 Mainz, Germany
| | - Jacqueline Trotter
- Molecular Cell Biology, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg-University of Mainz, Anselm-Franz-von-Bentzelweg 3, 55128 Mainz, Germany
| | - Constantin Gonsior
- Molecular Cell Biology, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg-University of Mainz, Anselm-Franz-von-Bentzelweg 3, 55128 Mainz, Germany
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35
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Tranchevent LC, Aubé F, Dulaurier L, Benoit-Pilven C, Rey A, Poret A, Chautard E, Mortada H, Desmet FO, Chakrama FZ, Moreno-Garcia MA, Goillot E, Janczarski S, Mortreux F, Bourgeois CF, Auboeuf D. Identification of protein features encoded by alternative exons using Exon Ontology. Genome Res 2017; 27:1087-1097. [PMID: 28420690 PMCID: PMC5453322 DOI: 10.1101/gr.212696.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 03/28/2017] [Indexed: 12/16/2022]
Abstract
Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named “Exon Ontology,” based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encoded protein features instead of gene level functional annotations. Exon Ontology describes the protein features encoded by a selected list of exons and looks for potential Exon Ontology term enrichment. By applying this strategy to exons that are differentially spliced between epithelial and mesenchymal cells and after extensive experimental validation, we demonstrate that Exon Ontology provides support to discover specific protein features regulated by alternative splicing. We also show that Exon Ontology helps to unravel biological processes that depend on suites of coregulated alternative exons, as we uncovered a role of epithelial cell-enriched splicing factors in the AKT signaling pathway and of mesenchymal cell-enriched splicing factors in driving splicing events impacting on autophagy. Freely available on the web, Exon Ontology is the first computational resource that allows getting a quick insight into the protein features encoded by alternative exons and investigating whether coregulated exons contain the same biological information.
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Affiliation(s)
- Léon-Charles Tranchevent
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Fabien Aubé
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Louis Dulaurier
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Clara Benoit-Pilven
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Amandine Rey
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Arnaud Poret
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Emilie Chautard
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, UMR CNRS 5558, INRIA Erable, Villeurbanne, F-69622, France
| | - Hussein Mortada
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - François-Olivier Desmet
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Fatima Zahra Chakrama
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Maira Alejandra Moreno-Garcia
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Evelyne Goillot
- Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, F-69007 France
| | - Stéphane Janczarski
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Franck Mortreux
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Cyril F Bourgeois
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Didier Auboeuf
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
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36
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Fletcher CE, Godfrey JD, Shibakawa A, Bushell M, Bevan CL. A novel role for GSK3β as a modulator of Drosha microprocessor activity and MicroRNA biogenesis. Nucleic Acids Res 2017; 45:2809-2828. [PMID: 27907888 PMCID: PMC5389555 DOI: 10.1093/nar/gkw938] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 09/13/2016] [Accepted: 10/19/2016] [Indexed: 01/13/2023] Open
Abstract
Regulation of microRNA (miR) biogenesis is complex and stringently controlled. Here, we identify the kinase GSK3β as an important modulator of miR biogenesis at Microprocessor level. Repression of GSK3β activity reduces Drosha activity toward pri-miRs, leading to accumulation of unprocessed pri-miRs and reduction of pre-miRs and mature miRs without altering levels or cellular localisation of miR biogenesis proteins. Conversely, GSK3β activation increases Drosha activity and mature miR accumulation. GSK3β achieves this through promoting Drosha:cofactor and Drosha:pri-miR interactions: it binds to DGCR8 and p72 in the Microprocessor, an effect dependent upon presence of RNA. Indeed, GSK3β itself can immunoprecipitate pri-miRs, suggesting possible RNA-binding capacity. Kinase assays identify the mechanism for GSK3β-enhanced Drosha activity, which requires GSK3β nuclear localisation, as phosphorylation of Drosha at S300 and/or S302; confirmed by enhanced Drosha activity and association with cofactors, and increased abundance of mature miRs in the presence of phospho-mimic Drosha. Functional implications of GSK3β-enhanced miR biogenesis are illustrated by increased levels of GSK3β-upregulated miR targets following GSK3β inhibition. These data, the first to link GSK3β with the miR cascade in humans, highlight a novel pro-biogenesis role for GSK3β in increasing miR biogenesis as a component of the Microprocessor complex with wide-ranging functional consequences.
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Affiliation(s)
- Claire E Fletcher
- Imperial Centre for Translational and Experimental Medicine, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Jack D Godfrey
- Medical Research Council Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester, LE1 9HN, UK
| | - Akifumi Shibakawa
- Imperial Centre for Translational and Experimental Medicine, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Martin Bushell
- Medical Research Council Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester, LE1 9HN, UK
| | - Charlotte L Bevan
- Imperial Centre for Translational and Experimental Medicine, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
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37
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Du C, Li DQ, Li N, Chen L, Li SS, Yang Y, Hou MX, Xie MJ, Zheng ZD. DDX5 promotes gastric cancer cell proliferation in vitro and in vivo through mTOR signaling pathway. Sci Rep 2017; 7:42876. [PMID: 28216662 PMCID: PMC5316961 DOI: 10.1038/srep42876] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 01/16/2017] [Indexed: 12/11/2022] Open
Abstract
DEAD (Asp-Glu-Ala-Asp) box helicase 5 (DDX5) is an ATP-dependent RNA helicase that is overexpressed in various malignancies. Increasing evidence suggests that DDX5 participates in carcinogenesis and cancer progression via promoting cell proliferation and metastasis. However, the functional role of DDX5 in gastric cancer is largely unknown. In this study, we observed that DDX5 was significantly up-regulated in gastric cancer tissues compared with the paired adjacent normal tissues. The expression of DDX5 correlated strongly with Ki67 index and pathological stage of gastric cancer. In vitro and in vivo studies suggested that knockdown of DDX5 inhibited gastric cancer cell proliferation, colony formation and xenografts growth, whereas ectopic expression of DDX5 promoted these cellular functions. Mechanically, DDX5 induced gastric cancer cell growth by activating mTOR/S6K1. Treatment of everolimus, the specific mTOR inhibitor, significantly attenuated DDX5-mediated cell proliferation. Interestingly, the expression of DDX5 and p-mTOR in gastric cancer tissues demonstrated a positive correlation. Taken together, these results revealed a novel role of DDX5 in gastric cancer cell proliferation via the mTOR pathway. Therefore, DDX5 may serve as a therapeutic target in gastric cancer.
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Affiliation(s)
- Cheng Du
- Department of Oncology, General Hospital of Shenyang Military Area Command, Shenyang 110840, P. R. China
| | - Dan-Qi Li
- Institute of Functional Molecules, Shenyang University of Chemical Technology, Shenyang 110142, P. R. China
| | - Na Li
- Department of Gynaecology and Obstetrics, First Affiliated Hospital, Jilin University, Jilin 130021, P. R. China
| | - Li Chen
- Department of Aerospace Medicine, The Fourth Military Medical University, Xi'an 710032, P. R. China
| | - Shi-Sen Li
- Department of Digestive Surgery, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi'an 710032, China
| | - Yang Yang
- Department of Oncology, Xijing Hospital, The Fourth Military Medical University, Xi'an 710032, P. R. China
| | - Ming-Xiao Hou
- Rescue Center of Severe Wound and Trauma of PLA, General Hospital of Shenyang Military Area Command, Shenyang 110840, P. R. China
| | - Man-Jiang Xie
- Department of Aerospace Medicine, The Fourth Military Medical University, Xi'an 710032, P. R. China
| | - Zhen-Dong Zheng
- Department of Oncology, General Hospital of Shenyang Military Area Command, Shenyang 110840, P. R. China
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38
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Shkreta L, Chabot B. The RNA Splicing Response to DNA Damage. Biomolecules 2015; 5:2935-77. [PMID: 26529031 PMCID: PMC4693264 DOI: 10.3390/biom5042935] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/20/2015] [Accepted: 10/16/2015] [Indexed: 12/29/2022] Open
Abstract
The number of factors known to participate in the DNA damage response (DDR) has expanded considerably in recent years to include splicing and alternative splicing factors. While the binding of splicing proteins and ribonucleoprotein complexes to nascent transcripts prevents genomic instability by deterring the formation of RNA/DNA duplexes, splicing factors are also recruited to, or removed from, sites of DNA damage. The first steps of the DDR promote the post-translational modification of splicing factors to affect their localization and activity, while more downstream DDR events alter their expression. Although descriptions of molecular mechanisms remain limited, an emerging trend is that DNA damage disrupts the coupling of constitutive and alternative splicing with the transcription of genes involved in DNA repair, cell-cycle control and apoptosis. A better understanding of how changes in splice site selection are integrated into the DDR may provide new avenues to combat cancer and delay aging.
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Affiliation(s)
- Lulzim Shkreta
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
| | - Benoit Chabot
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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39
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Moy RH, Cole BS, Yasunaga A, Gold B, Shankarling G, Varble A, Molleston JM, tenOever BR, Lynch KW, Cherry S. Stem-loop recognition by DDX17 facilitates miRNA processing and antiviral defense. Cell 2014; 158:764-777. [PMID: 25126784 DOI: 10.1016/j.cell.2014.06.023] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/20/2014] [Accepted: 06/06/2014] [Indexed: 12/18/2022]
Abstract
DEAD-box helicases play essential roles in RNA metabolism across species, but emerging data suggest that they have additional functions in immunity. Through RNAi screening, we identify an evolutionarily conserved and interferon-independent role for the DEAD-box helicase DDX17 in restricting Rift Valley fever virus (RVFV), a mosquito-transmitted virus in the bunyavirus family that causes severe morbidity and mortality in humans and livestock. Loss of Drosophila DDX17 (Rm62) in cells and flies enhanced RVFV infection. Similarly, depletion of DDX17 but not the related helicase DDX5 increased RVFV replication in human cells. Using crosslinking immunoprecipitation high-throughput sequencing (CLIP-seq), we show that DDX17 binds the stem loops of host pri-miRNA to facilitate their processing and also an essential stem loop in bunyaviral RNA to restrict infection. Thus, DDX17 has dual roles in the recognition of stem loops: in the nucleus for endogenous microRNA (miRNA) biogenesis and in the cytoplasm for surveillance against structured non-self-elements.
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Affiliation(s)
- Ryan H Moy
- Department of Microbiology, Penn Genome Frontiers Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brian S Cole
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ari Yasunaga
- Department of Microbiology, Penn Genome Frontiers Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beth Gold
- Department of Microbiology, Penn Genome Frontiers Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ganesh Shankarling
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew Varble
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jerome M Molleston
- Department of Microbiology, Penn Genome Frontiers Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sara Cherry
- Department of Microbiology, Penn Genome Frontiers Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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40
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Beurel E, Grieco SF, Jope RS. Glycogen synthase kinase-3 (GSK3): regulation, actions, and diseases. Pharmacol Ther 2014; 148:114-31. [PMID: 25435019 DOI: 10.1016/j.pharmthera.2014.11.016] [Citation(s) in RCA: 1129] [Impact Index Per Article: 112.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 11/18/2014] [Indexed: 12/23/2022]
Abstract
Glycogen synthase kinase-3 (GSK3) may be the busiest kinase in most cells, with over 100 known substrates to deal with. How does GSK3 maintain control to selectively phosphorylate each substrate, and why was it evolutionarily favorable for GSK3 to assume such a large responsibility? GSK3 must be particularly adaptable for incorporating new substrates into its repertoire, and we discuss the distinct properties of GSK3 that may contribute to its capacity to fulfill its roles in multiple signaling pathways. The mechanisms regulating GSK3 (predominantly post-translational modifications, substrate priming, cellular trafficking, protein complexes) have been reviewed previously, so here we focus on newly identified complexities in these mechanisms, how each of these regulatory mechanism contributes to the ability of GSK3 to select which substrates to phosphorylate, and how these mechanisms may have contributed to its adaptability as new substrates evolved. The current understanding of the mechanisms regulating GSK3 is reviewed, as are emerging topics in the actions of GSK3, particularly its interactions with receptors and receptor-coupled signal transduction events, and differential actions and regulation of the two GSK3 isoforms, GSK3α and GSK3β. Another remarkable characteristic of GSK3 is its involvement in many prevalent disorders, including psychiatric and neurological diseases, inflammatory diseases, cancer, and others. We address the feasibility of targeting GSK3 therapeutically, and provide an update of its involvement in the etiology and treatment of several disorders.
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Affiliation(s)
- Eleonore Beurel
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States; Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, United States
| | - Steven F Grieco
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States; Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, United States
| | - Richard S Jope
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States; Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, United States.
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41
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Dardenne E, Polay Espinoza M, Fattet L, Germann S, Lambert MP, Neil H, Zonta E, Mortada H, Gratadou L, Deygas M, Chakrama FZ, Samaan S, Desmet FO, Tranchevent LC, Dutertre M, Rimokh R, Bourgeois CF, Auboeuf D. RNA helicases DDX5 and DDX17 dynamically orchestrate transcription, miRNA, and splicing programs in cell differentiation. Cell Rep 2014; 7:1900-13. [PMID: 24910439 DOI: 10.1016/j.celrep.2014.05.010] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 04/08/2014] [Accepted: 05/05/2014] [Indexed: 02/07/2023] Open
Abstract
The RNA helicases DDX5 and DDX17 are members of a large family of highly conserved proteins that are involved in gene-expression regulation; however, their in vivo targets and activities in biological processes such as cell differentiation, which requires reprogramming of gene-expression programs at multiple levels, are not well characterized. Here, we uncovered a mechanism by which DDX5 and DDX17 cooperate with heterogeneous nuclear ribonucleoprotein (hnRNP) H/F splicing factors to define epithelial- and myoblast-specific splicing subprograms. We then observed that downregulation of DDX5 and DDX17 protein expression during myogenesis and epithelial-to-mesenchymal transdifferentiation contributes to the switching of splicing programs during these processes. Remarkably, this downregulation is mediated by the production of miRNAs induced upon differentiation in a DDX5/DDX17-dependent manner. Since DDX5 and DDX17 also function as coregulators of master transcriptional regulators of differentiation, we propose to name these proteins "master orchestrators" of differentiation that dynamically orchestrate several layers of gene expression.
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Affiliation(s)
- Etienne Dardenne
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Micaela Polay Espinoza
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Laurent Fattet
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Sophie Germann
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Marie-Pierre Lambert
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Helen Neil
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Eleonora Zonta
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Hussein Mortada
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Lise Gratadou
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Mathieu Deygas
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Fatima Zahra Chakrama
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Samaan Samaan
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - François-Olivier Desmet
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Léon-Charles Tranchevent
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Martin Dutertre
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Ruth Rimokh
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Cyril F Bourgeois
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France.
| | - Didier Auboeuf
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France.
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