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Ren QS, Sun Q, Cheng SQ, Du LM, Guo PX. Hepatocellular carcinoma: An analysis of the expression status of stress granules and their prognostic value. World J Gastrointest Oncol 2024; 16:2559-2579. [DOI: 10.4251/wjgo.v16.i6.2559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/24/2024] [Accepted: 04/01/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a global popular malignant tumor, which is difficult to cure, and the current treatment is limited.
AIM To analyze the impacts of stress granule (SG) genes on overall survival (OS), survival time, and prognosis in HCC.
METHODS The combined The Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC), GSE25097, and GSE36376 datasets were utilized to obtain genetic and clinical information. Optimal hub gene numbers and corresponding coefficients were determined using the Least absolute shrinkage and selection operator model approach, and genes for constructing risk scores and corresponding correlation coefficients were calculated according to multivariate Cox regression, respectively. The prognostic model’s receiver operating characteristic (ROC) curve was produced and plotted utilizing the time ROC software package. Nomogram models were constructed to predict the outcomes at 1, 3, and 5-year OS prognostications with good prediction accuracy.
RESULTS We identified seven SG genes (DDX1, DKC1, BICC1, HNRNPUL1, CNOT6, DYRK3, CCDC124) having a prognostic significance and developed a risk score model. The findings of Kaplan-Meier analysis indicated that the group with a high risk exhibited significantly reduced OS in comparison with those of the low-risk group (P < 0.001). The nomogram model’s findings indicate a significant enhancement in the accuracy of OS prediction for individuals with HCC in the TCGA-HCC cohort. Gene Ontology and Gene Set Enrichment Analysis suggested that these SGs might be involved in the cell cycle, RNA editing, and other biological processes.
CONCLUSION Based on the impact of SG genes on HCC prognosis, in the future, it will be used as a biomarker as well as a unique therapeutic target for the identification and treatment of HCC.
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Affiliation(s)
- Qing-Shuai Ren
- Department of Cardiovascular Surgery, North China University of Science and Technology Affiliated Hospital, Tangshan 063000, Hebei Province, China
| | - Qiu Sun
- Department of Hepatobiliary, Kailuan General Hospital, Tangshan 063000, Hebei Province, China
| | - Shu-Qin Cheng
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin 300000, China
| | - Li-Ming Du
- Department of Traditional Chinese Medicine, Kailuan General Hospital, Tangshan 063000, Hebei Province, China
| | - Ping-Xuan Guo
- Department of Anesthesiology, Kailuan General Hospital, North China University of Science and Technology, Tangshan 063000, Hebei Province, China
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Ren QS, Sun Q, Cheng SQ, Du LM, Guo PX. Hepatocellular carcinoma: An analysis of the expression status of stress granules and their prognostic value. World J Gastrointest Oncol 2024; 16:2571-2591. [DOI: 10.4251/wjgo.v16.i6.2571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/24/2024] [Accepted: 04/01/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a global popular malignant tumor, which is difficult to cure, and the current treatment is limited.
AIM To analyze the impacts of stress granule (SG) genes on overall survival (OS), survival time, and prognosis in HCC.
METHODS The combined The Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC), GSE25097, and GSE36376 datasets were utilized to obtain genetic and clinical information. Optimal hub gene numbers and corresponding coefficients were determined using the Least absolute shrinkage and selection operator model approach, and genes for constructing risk scores and corresponding correlation coefficients were calculated according to multivariate Cox regression, respectively. The prognostic model’s receiver operating characteristic (ROC) curve was produced and plotted utilizing the time ROC software package. Nomogram models were constructed to predict the outcomes at 1, 3, and 5-year OS prognostications with good prediction accuracy.
RESULTS We identified seven SG genes (DDX1, DKC1, BICC1, HNRNPUL1, CNOT6, DYRK3, CCDC124) having a prognostic significance and developed a risk score model. The findings of Kaplan-Meier analysis indicated that the group with a high risk exhibited significantly reduced OS in comparison with those of the low-risk group (P < 0.001). The nomogram model’s findings indicate a significant enhancement in the accuracy of OS prediction for individuals with HCC in the TCGA-HCC cohort. Gene Ontology and Gene Set Enrichment Analysis suggested that these SGs might be involved in the cell cycle, RNA editing, and other biological processes.
CONCLUSION Based on the impact of SG genes on HCC prognosis, in the future, it will be used as a biomarker as well as a unique therapeutic target for the identification and treatment of HCC.
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Affiliation(s)
- Qing-Shuai Ren
- Department of Cardiovascular Surgery, North China University of Science and Technology Affiliated Hospital, Tangshan 063000, Hebei Province, China
| | - Qiu Sun
- Department of Hepatobiliary, Kailuan General Hospital, Tangshan 063000, Hebei Province, China
| | - Shu-Qin Cheng
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin 300000, China
| | - Li-Ming Du
- Department of Traditional Chinese Medicine, Kailuan General Hospital, Tangshan 063000, Hebei Province, China
| | - Ping-Xuan Guo
- Department of Anesthesiology, Kailuan General Hospital, North China University of Science and Technology, Tangshan 063000, Hebei Province, China
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3
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Tao Y, Gong Z, Shen S, Ding Y, Zan R, Zheng B, Sun W, Ma C, Shu M, Lu X, Liu H, Ni X, Liu H, Suo T. Fasting-induced RNF152 resensitizes gallbladder cancer cells to gemcitabine by inhibiting mTORC1-mediated glycolysis. iScience 2024; 27:109659. [PMID: 38706841 PMCID: PMC11068552 DOI: 10.1016/j.isci.2024.109659] [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: 10/17/2023] [Revised: 01/05/2024] [Accepted: 04/01/2024] [Indexed: 05/07/2024] Open
Abstract
Abnormal mTORC1 activation by the lysosomal Ragulator complex has been implicated in cancer and glycolytic metabolism associated with drug resistance. Fasting upregulates RNF152 and mediates the metabolic status of cells. We report that RNF152 regulates mTORC1 signaling by targeting a Ragulator subunit, p18, and attenuates gemcitabine resistance in gallbladder cancer (GBC). We detected levels of RNF152 and p18 in tissues and undertook mechanistic studies using activators, inhibitors, and lentivirus transfections. RNF152 levels were significantly lower in GBC than in adjacent non-cancer tissues. Fasting impairs glycolysis, induces gemcitabine sensitivity, and upregulates RNF152 expression. RNF152 overexpression increases the sensitivity of GBC cells to gemcitabine, whereas silencing RNF152 has the opposite effect. Fasting-induced RNF152 ubiquitinates p18, resulting in proteasomal degradation. RNF152 deficiency increases the lysosomal localization of p18 and increases mTORC1 activity, to promote glycolysis and decrease gemcitabine sensitivity. RNF152 suppresses mTORC1 activity to inhibit glycolysis and enhance gemcitabine sensitivity in GBC.
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Affiliation(s)
- Ying Tao
- Department of General Surgery, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, China
| | - Zijun Gong
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
- Biliary Tract Disease Institute, Fudan University, Shanghai, China
- The Center of Biliary Disease Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sheng Shen
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
- Biliary Tract Disease Institute, Fudan University, Shanghai, China
- The Center of Biliary Disease Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yaqi Ding
- Ruijin Hospital LuWan Branch, Shanghai Jiao Tong University School of Medicine Central Laboratory, Shanghai, China
| | - Rui Zan
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
- Biliary Tract Disease Institute, Fudan University, Shanghai, China
- The Center of Biliary Disease Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bohao Zheng
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
- Biliary Tract Disease Institute, Fudan University, Shanghai, China
- The Center of Biliary Disease Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wentao Sun
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
- Biliary Tract Disease Institute, Fudan University, Shanghai, China
- The Center of Biliary Disease Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chaolin Ma
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
- Biliary Tract Disease Institute, Fudan University, Shanghai, China
- The Center of Biliary Disease Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Mengxuan Shu
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
- Biliary Tract Disease Institute, Fudan University, Shanghai, China
- The Center of Biliary Disease Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiao Lu
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
- Biliary Tract Disease Institute, Fudan University, Shanghai, China
- The Center of Biliary Disease Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Han Liu
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
- Biliary Tract Disease Institute, Fudan University, Shanghai, China
- The Center of Biliary Disease Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaoling Ni
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
- Biliary Tract Disease Institute, Fudan University, Shanghai, China
- The Center of Biliary Disease Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Houbao Liu
- Department of General Surgery, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, China
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
- Biliary Tract Disease Institute, Fudan University, Shanghai, China
- The Center of Biliary Disease Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tao Suo
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
- Biliary Tract Disease Institute, Fudan University, Shanghai, China
- The Center of Biliary Disease Center, Zhongshan Hospital, Fudan University, Shanghai, China
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Zheng B, Chen X, Ling Q, Cheng Q, Ye S. Role and therapeutic potential of DEAD-box RNA helicase family in colorectal cancer. Front Oncol 2023; 13:1278282. [PMID: 38023215 PMCID: PMC10654640 DOI: 10.3389/fonc.2023.1278282] [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: 08/16/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed and the second cancer-related death worldwide, leading to more than 0.9 million deaths every year. Unfortunately, this disease is changing rapidly to a younger age, and in a more advanced stage when diagnosed. The DEAD-box RNA helicase proteins are the largest family of RNA helicases so far. They regulate almost every aspect of RNA physiological processes, including RNA transcription, editing, splicing and transport. Aberrant expression and critical roles of the DEAD-box RNA helicase proteins have been found in CRC. In this review, we first summarize the protein structure, cellular distribution, and diverse biological functions of DEAD-box RNA helicases. Then, we discuss the distinct roles of DEAD-box RNA helicase family in CRC and describe the cellular mechanism of actions based on recent studies, with an aim to provide future strategies for the treatment of CRC.
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Affiliation(s)
- Bichun Zheng
- Department of Anorectal Surgery, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
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García-Cárdenas JM, Armendáriz-Castillo I, García-Cárdenas N, Pesantez-Coronel D, López-Cortés A, Indacochea A, Guerrero S. Data mining identifies novel RNA-binding proteins involved in colon and rectal carcinomas. Front Cell Dev Biol 2023; 11:1088057. [PMID: 37384253 PMCID: PMC10293682 DOI: 10.3389/fcell.2023.1088057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/13/2023] [Indexed: 06/30/2023] Open
Abstract
Colorectal adenocarcinoma (COREAD) is the second most deadly cancer and third most frequently encountered malignancy worldwide. Despite efforts in molecular subtyping and subsequent personalized COREAD treatments, multidisciplinary evidence suggests separating COREAD into colon cancer (COAD) and rectal cancer (READ). This new perspective could improve diagnosis and treatment of both carcinomas. RNA-binding proteins (RBPs), as critical regulators of every hallmark of cancer, could fulfill the need to identify sensitive biomarkers for COAD and READ separately. To detect new RBPs involved in COAD and READ progression, here we used a multidata integration strategy to prioritize tumorigenic RBPs. We analyzed and integrated 1) RBPs genomic and transcriptomic alterations from 488 COAD and 155 READ patients, 2) ∼ 10,000 raw associations between RBPs and cancer genes, 3) ∼ 15,000 immunostainings, and 4) loss-of-function screens performed in 102 COREAD cell lines. Thus, we unraveled new putative roles of NOP56, RBM12, NAT10, FKBP1A, EMG1, and CSE1L in COAD and READ progression. Interestingly, FKBP1A and EMG1 have never been related with any of these carcinomas but presented tumorigenic features in other cancer types. Subsequent survival analyses highlighted the clinical relevance of FKBP1A, NOP56, and NAT10 mRNA expression to predict poor prognosis in COREAD and COAD patients. Further research should be performed to validate their clinical potential and to elucidate their molecular mechanisms underlying these malignancies.
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Affiliation(s)
- Jennyfer M. García-Cárdenas
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Isaac Armendáriz-Castillo
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
- Facultad de Ingenierías y Ciencias Aplicadas, Universidad Internacional SEK, Quito, Ecuador
| | | | - David Pesantez-Coronel
- Medical Oncology Department Hospital Clinic and Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Andrés López-Cortés
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Alberto Indacochea
- Medical Oncology Department Hospital Clinic and Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Santiago Guerrero
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
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Gencel-Augusto J, Su X, Qi Y, Whitley EM, Pant V, Xiong S, Shah V, Lin J, Perez E, Fiorotto ML, Mahmud I, Jain AK, Lorenzi PL, Navin NE, Richie ER, Lozano G. Dimeric p53 Mutant Elicits Unique Tumor-Suppressive Activities through an Altered Metabolic Program. Cancer Discov 2023; 13:1230-1249. [PMID: 37067911 PMCID: PMC10164062 DOI: 10.1158/2159-8290.cd-22-0872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/20/2022] [Accepted: 02/27/2023] [Indexed: 04/18/2023]
Abstract
Cancer-related alterations of the p53 tetramerization domain (TD) abrogate wild-type (WT) p53 function. They result in a protein that preferentially forms monomers or dimers, which are also normal p53 states under basal cellular conditions. However, their physiologic relevance is not well understood. We have established in vivo models for monomeric and dimeric p53, which model Li-Fraumeni syndrome patients with germline p53 TD alterations. p53 monomers are inactive forms of the protein. Unexpectedly, p53 dimers conferred some tumor suppression that is not mediated by canonical WT p53 activities. p53 dimers upregulate the PPAR pathway. These activities are associated with lower prevalence of thymic lymphomas and increased CD8+ T-cell differentiation. Lymphomas derived from dimeric p53 mice show cooperating alterations in the PPAR pathway, further implicating a role for these activities in tumor suppression. Our data reveal novel functions for p53 dimers and support the exploration of PPAR agonists as therapies. SIGNIFICANCE New mouse models with TP53R342P (monomer) or TP53A347D (dimer) mutations mimic Li-Fraumeni syndrome. Although p53 monomers lack function, p53 dimers conferred noncanonical tumor-suppressive activities. We describe novel activities for p53 dimers facilitated by PPARs and propose these are "basal" p53 activities. See related commentary by Stieg et al., p. 1046. See related article by Choe et al., p. 1250. This article is highlighted in the In This Issue feature, p. 1027.
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Affiliation(s)
- Jovanka Gencel-Augusto
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences
- Department of Genetics, The University of Texas MD Anderson Cancer Center (MDACC)
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, MDACC
| | - Yuan Qi
- Department of Bioinformatics and Computational Biology, MDACC
| | | | - Vinod Pant
- Department of Genetics, The University of Texas MD Anderson Cancer Center (MDACC)
| | - Shunbin Xiong
- Department of Genetics, The University of Texas MD Anderson Cancer Center (MDACC)
| | - Vrutant Shah
- Department of Genetics, The University of Texas MD Anderson Cancer Center (MDACC)
| | - Jerome Lin
- Department of Genetics, The University of Texas MD Anderson Cancer Center (MDACC)
| | | | - Marta L. Fiorotto
- USDA/Agricultural Research Service Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine
| | - Iqbal Mahmud
- Department of Bioinformatics and Computational Biology, MDACC
- Metabolomics Core Facility, MDACC
| | - Abhinav K. Jain
- Department of Epigenetics and Molecular Carcinogenesis, MDACC
| | - Philip L. Lorenzi
- Department of Bioinformatics and Computational Biology, MDACC
- Metabolomics Core Facility, MDACC
| | - Nicholas E. Navin
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences
- Department of Genetics, The University of Texas MD Anderson Cancer Center (MDACC)
| | - Ellen R. Richie
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences
- Department of Epigenetics and Molecular Carcinogenesis, MDACC
| | - Guillermina Lozano
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences
- Department of Genetics, The University of Texas MD Anderson Cancer Center (MDACC)
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Yang Q, Xu P, Liu Q, Hu F, Xie X, Jiang L, Bi R, Wang L, Ding F, Xiao H. Depleting DDX1 sensitizes non-small cell lung cancer cells to chemotherapy by attenuating cancer stem cell traits. Life Sci 2023; 323:121592. [PMID: 36934972 DOI: 10.1016/j.lfs.2023.121592] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023]
Abstract
AIMS DEAD-box helicase 1 (DDX1) has oncogenic properties in several human cancers. However, the clinical significance and biological role of DDX1 in non-small cell lung cancer (NSCLC) remain elusive. Here, we examined the chemotherapeutic relevance of DDX1 in NSCLC. MAIN METHODS We used the UALCAN database, Western blot analysis, and immunohistochemical and RT-qPCR assays to assess DDX1 expression in NSCLC cell lines (H1650 and A549) and patient tissues. The role of DDX1 in the chemosensitivity of NSCLC cells and the underlying mechanisms were determined using colony formation, CCK-8, flow cytometry, wound healing, Transwell, tumor sphere formation, and immunostaining assays, together with a xenograft tumor model in nude mice. KEY FINDINGS Our study revealed that DDX1 was overexpressed in NSCLC cell lines and tissues. We further found that depleting DDX1 increased the sensitivity of NSCLC cells to the chemotherapy drug cisplatin, increased cell apoptosis, and inhibited cell migration and invasion. Co-immunoprecipitation assays revealed that DDX1 bound to ADAR1, and increased ADAR1 protein expression. Furthermore, we found that ADAR1 mediated cancer-promoting effects, independent of deaminase activity, by binding to RAC3 mRNA. Our findings not only show that DDX1 mediates chemosensitivity to cisplatin via the ADAR1/RAC3 axis but also highlight the importance of ADARs as essential RNA-binding proteins for cell homeostasis, as well as cancer progression. SIGNIFICANCE Our results suggest that DDX1 plays an important role in the development and progression of human NSCLC and that DDX1 may serve as a therapeutic target in NSCLC patients.
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Affiliation(s)
- Qi Yang
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China
| | - Pei Xu
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China
| | - Qingtao Liu
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China
| | - Fengqing Hu
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China
| | - Xiao Xie
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China
| | - Lianyong Jiang
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China
| | - Rui Bi
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China
| | - Lei Wang
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China.
| | - Fangbao Ding
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China.
| | - Haibo Xiao
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China.
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8
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King CM, Marx OM, Ding W, Koltun WA, Yochum GS. TCF7L1 Regulates LGR5 Expression in Colorectal Cancer Cells. Genes (Basel) 2023; 14:481. [PMID: 36833408 PMCID: PMC9956233 DOI: 10.3390/genes14020481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/06/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023] Open
Abstract
Mutations in components of the Wnt/β-catenin signaling pathway drive colorectal cancer (CRC), in part, by deregulating expression of genes controlled by the T-cell factor (TCF) family of transcription factors. TCFs contain a conserved DNA binding domain that mediates association with TCF binding elements (TBEs) within Wnt-responsive DNA elements (WREs). Intestinal stem cell marker, leucine-rich-repeat containing G-protein-coupled receptor 5 (LGR5), is a Wnt target gene that has been implicated in CRC stem cell plasticity. However, the WREs at the LGR5 gene locus and how TCF factors directly regulate LGR5 gene expression in CRC have not been fully defined. Here, we report that TCF family member, TCF7L1, plays a significant role in regulating LGR5 expression in CRC cells. We demonstrate that TCF7L1 binds to a novel promoter-proximal WRE through association with a consensus TBE at the LGR5 locus to repress LGR5 expression. Using CRISPR activation and interference (CRISPRa/i) technologies to direct epigenetic modulation, we demonstrate that this WRE is a critical regulator of LGR5 expression and spheroid formation capacity of CRC cells. Furthermore, we found that restoring LGR5 expression rescues the TCF7L1-mediated reduction in spheroid formation efficiency. These results demonstrate a role for TCF7L1 in repressing LGR5 gene expression to govern the spheroid formation potential of CRC cells.
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Affiliation(s)
- Carli M. King
- Department of Biochemistry & Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA 17036, USA
- Department of Surgery, Division of Colon & Rectal Surgery, Milton S. Hershey Medical Center, The Pennsylvania State University, Hershey, PA 17036, USA
| | - Olivia M. Marx
- Department of Biochemistry & Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA 17036, USA
- Department of Surgery, Division of Colon & Rectal Surgery, Milton S. Hershey Medical Center, The Pennsylvania State University, Hershey, PA 17036, USA
| | - Wei Ding
- Department of Surgery, Division of Colon & Rectal Surgery, Milton S. Hershey Medical Center, The Pennsylvania State University, Hershey, PA 17036, USA
| | - Walter A. Koltun
- Department of Surgery, Division of Colon & Rectal Surgery, Milton S. Hershey Medical Center, The Pennsylvania State University, Hershey, PA 17036, USA
| | - Gregory S. Yochum
- Department of Biochemistry & Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA 17036, USA
- Department of Surgery, Division of Colon & Rectal Surgery, Milton S. Hershey Medical Center, The Pennsylvania State University, Hershey, PA 17036, USA
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9
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Yuan M, Xu J, Cao S, Sun S. DDX1 is a prognostic biomarker and correlates with immune infiltrations in hepatocellular carcinoma. BMC Immunol 2022; 23:59. [PMID: 36451087 PMCID: PMC9710136 DOI: 10.1186/s12865-022-00533-0] [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: 08/03/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading lethal malignant tumors worldwide. DEAD-box (DDX) family helicases are implicated in numerous human cancers. However, the role of DDX1 in HCC has not yet been fully elucidated. We downloaded gene expression data and clinical information data of HCC from The Cancer Genome Atlas and International Cancer Genome Consortium (ICGC) database and conducted subsequent analyses using the R package and online portal. The results revealed that HCC tissues had higher DDX1 expression compared with either paired or unpaired normal tissues. The increased DDX1 expression was closely related to the advanced pathological grade and histologic grade of HCC. Further analysis suggested that patients with high DDX1 expression contributed to poor prognosis The Cox regression analysis revealed that the expression level of DDX1 was an independent prognostic factor for HCC. In addition, an ICGC cohort was used for external validation. The cBio-Portal, MethSurv, and UALCAN database were used for evaluating the genomic mechanism. Moreover, the Tumor Immune Estimation Resource dataset and QUANTISEQ algorithm revealed that DDX1 expression positively correlates with immune infiltrating cells. We also identified the DDX1-related differentially expressed genes (DEGs) and explored their biological functions by GO, KEGG, and GSEA analyses, which indicated that DDX1 may regulate the progression of HCC. In general, increased DDX1 expression predicts a poor prognosis and drives the progression of HCC.
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Affiliation(s)
- Mengping Yuan
- grid.417384.d0000 0004 1764 2632Department of Gastroenterology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, 325000 People’s Republic of China
| | - Jinyong Xu
- Department of Pathology, Shenzhen Hyzen Hospital, Shenzhen, 518038 People’s Republic of China
| | - Shuguang Cao
- grid.417384.d0000 0004 1764 2632Department of Gastroenterology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, 325000 People’s Republic of China
| | - Shuangshuang Sun
- grid.417384.d0000 0004 1764 2632Department of Oncology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, 325000 People’s Republic of China
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10
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Chen L, Liu Z, Tang H, Zhou Z, Chen J, Ma Z, Deng M, Li X, Wu Y, Zheng L, Zhou L, Zheng X, Liu Z. Knockdown of ZBTB11 impedes R‐loop elimination and increases the sensitivity to cisplatin by inhibiting DDX1 transcription in bladder cancer. Cell Prolif 2022; 55:e13325. [DOI: 10.1111/cpr.13325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/28/2022] [Accepted: 07/26/2022] [Indexed: 11/26/2022] Open
Affiliation(s)
- Lei Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Zefu Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Huancheng Tang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Zhaohui Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Jiawei Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Zikun Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Minhua Deng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Xiangdong Li
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Yuanzhong Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
| | - Lisi Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
| | - Liwen Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
| | - Xianchong Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Zhuowei Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
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11
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Zhou X, Liu Z, He T, Zhang C, Jiang M, Jin Y, Wu Z, Gu C, Zhang W, Yang X. DDX10 promotes the proliferation and metastasis of colorectal cancer cells via splicing RPL35. Cancer Cell Int 2022; 22:58. [PMID: 35109823 PMCID: PMC8812018 DOI: 10.1186/s12935-022-02478-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/19/2022] [Indexed: 12/24/2022] Open
Abstract
Background Colorectal cancer (CRC) has become the second deadliest cancer in the world and severely threatens human health. An increasing number of studies have focused on the role of the RNA helicase DEAD-box (DDX) family in CRC. However, the mechanism of DDX10 in CRC has not been elucidated. Methods In our study, we analysed the expression data of CRC samples from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Subsequently, we performed cytological experiments and animal experiments to explore the role of DDX10 in CRC cells. Furthermore, we performed Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and protein–protein interaction (PPI) network analyses. Finally, we predicted the interacting protein of DDX10 by LC–MS/MS and verified it by coimmunoprecipitation (Co-IP) and qPCR. Results In the present study, we identified that DDX10 mRNA was extremely highly expressed in CRC tissues compared with normal colon tissues in the TCGA and GEO databases. The protein expression of DDX10 was measured by immunochemistry (IHC) in 17 CRC patients. The biological roles of DDX10 were explored via cell and molecular biology experiments in vitro and in vivo and cell cycle assays. We found that DDX10 knockdown markedly reduced CRC cell proliferation, migration and invasion. Then, we constructed a PPI network with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING). GO and KEGG enrichment analysis and gene set enrichment analysis (GSEA) showed that DDX10 was closely related to RNA splicing and E2F targets. Using LC–MS/MS and Co-IP assays, we discovered that RPL35 is the interacting protein of DDX10. In addition, we hypothesize that RPL35 is related to the E2F pathway and the immune response in CRC. Conclusions In conclusion, provides a better understanding of the molecular mechanisms of DDX10 in CRC and provides a potential biomarker for the diagnosis and treatment of CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02478-1.
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Affiliation(s)
- Xin Zhou
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China
| | - Zhihong Liu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China
| | - Tengfei He
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China
| | - Cuifeng Zhang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China
| | - Manman Jiang
- Soochow University, 1 Shizi Street, Suzhou, China
| | - Yuxiao Jin
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China
| | - Ziyu Wu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China
| | - Changji Gu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China
| | - Wei Zhang
- Department of Radiotherapy, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China.
| | - Xiaodong Yang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China.
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12
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Gao B, Li X, Li S, Wang S, Wu J, Li J. Pan-cancer analysis identifies RNA helicase DDX1 as a prognostic marker. PHENOMICS (CHAM, SWITZERLAND) 2022; 2:33-49. [PMID: 36939765 PMCID: PMC9590584 DOI: 10.1007/s43657-021-00034-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
Abstract
The DEAD-box RNA helicase (DDX) family plays a critical role in the growth and development of multiple organisms. DDX1 is involved in mRNA/rRNA processing and mature, virus replication and transcription, hormone metabolism, tumorigenesis, and tumor development. However, how DDX1 functions in various cancers remains unclear. Here, we explored the potential oncogenic roles of DDX1 across 33 tumors with The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases. DDX1 is highly expressed in breast cancer (BRCA), cholangiocarcinoma (CHOL), and colon adenocarcinoma (COAD), but it is lowly expressed in renal cancers, including kidney renal clear cell carcinoma (KIRC), kidney chromophobe (KICH), and kidney renal papillary cell carcinoma (KIRP). Low expression of DDX1 in KIRC is correlated with a good prognosis of overall survival (OS) and disease-free survival (DFS). Highly expressed DDX1 is linked to a poor prognosis of OS for adrenocortical carcinoma (ACC), bladder urothelial carcinoma (BLCA), KICH, and liver hepatocellular carcinoma (LIHC). Also, the residue Ser481 of DDX1 had an enhanced phosphorylation level in BRCA and ovarian cancer (OV) but decreased in KIRC. Immune infiltration analysis exhibited that DDX1 expression affected CD8+ T cells, and it was significantly associated with MSI (microsatellite instability), TMB (tumor mutational burden), and ICT (immune checkpoint blockade therapy) in tumors. In addition, the depletion of DDX1 dramatically affected the cell viability of human tumor-derived cell lines. DDX1 could affect the DNA repair pathway and the RNA transport/DNA replication processes during tumorigenesis by analyzing the CancerSEA database. Thus, our pan-cancer analysis revealed that DDX1 had complicated impacts on different cancers and might act as a prognostic marker for cancers such as renal cancer. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-021-00034-x.
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Affiliation(s)
- Baocai Gao
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Xiangnan Li
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Shujie Li
- Kunming Institute of Physics, Kunming, 650223 China
| | - Sen Wang
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Jiaxue Wu
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Jixi Li
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
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13
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Wang F, He J, Liu S, Gao A, Yang L, Sun G, Ding W, Li CY, Gou F, He M, Wang F, Wang X, Zhao X, Zhu P, Hao S, Ma Y, Cheng H, Yu J, Cheng T. A comprehensive RNA editome reveals that edited Azin1 partners with DDX1 to enable hematopoietic stem cell differentiation. Blood 2021; 138:1939-1952. [PMID: 34388251 PMCID: PMC8602937 DOI: 10.1182/blood.2021011314] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/06/2021] [Indexed: 11/20/2022] Open
Abstract
Adenosine-to-inosine RNA editing and the catalyzing enzyme adenosine deaminase are both essential for hematopoietic development and differentiation. However, the RNA editome during hematopoiesis and the underlying mechanisms are poorly defined. Here, we sorted 12 murine adult hematopoietic cell populations at different stages and identified 30 796 editing sites through RNA sequencing. The dynamic landscape of the RNA editome comprises stage- and group-specific and stable editing patterns, but undergoes significant changes during lineage commitment. Notably, we found that antizyme inhibitor 1 (Azin1) was highly edited in hematopoietic stem and progenitor cells (HSPCs). Azin1 editing results in an amino acid change to induce Azin1 protein (AZI) translocation to the nucleus, enhanced AZI binding affinity for DEAD box polypeptide 1 to alter the chromatin distribution of the latter, and altered expression of multiple hematopoietic regulators that ultimately promote HSPC differentiation. Our findings have delineated an essential role for Azin1 RNA editing in hematopoietic cells, and our data set is a valuable resource for studying RNA editing on a more general basis.
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Affiliation(s)
- Fengjiao Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Tianjin, China
| | - Jiahuan He
- State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, CAMS and Peking Union Medical College, Beijing, China
| | - Siqi Liu
- State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, CAMS and Peking Union Medical College, Beijing, China
| | - Ai Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Tianjin, China
| | - Liu Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Tianjin, China
| | - Guohuan Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Tianjin, China
| | - Wanqiu Ding
- Institute of Molecular Medicine, Peking University, Beijing, China; and
| | - Chuan-Yun Li
- Institute of Molecular Medicine, Peking University, Beijing, China; and
| | - Fanglin Gou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Tianjin, China
| | - Manman He
- State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, CAMS and Peking Union Medical College, Beijing, China
| | - Fang Wang
- State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, CAMS and Peking Union Medical College, Beijing, China
| | - Xiaoshuang Wang
- State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, CAMS and Peking Union Medical College, Beijing, China
| | - Xiangnan Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Tianjin, China
| | - Ping Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Tianjin, China
- Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, CAMS and Peking Union Medical College, Tianjin, China
| | - Sha Hao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Tianjin, China
- Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, CAMS and Peking Union Medical College, Tianjin, China
| | - Yanni Ma
- State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, CAMS and Peking Union Medical College, Beijing, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Tianjin, China
- Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, CAMS and Peking Union Medical College, Tianjin, China
| | - Jia Yu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Tianjin, China
- State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, CAMS and Peking Union Medical College, Beijing, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Tianjin, China
- Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, CAMS and Peking Union Medical College, Tianjin, China
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14
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Lin Z, Wang J, Zhu W, Yu X, Wang Z, Ma J, Wang H, Yan Y, Sun J, Cheng Y. Chicken DDX1 Acts as an RNA Sensor to Mediate IFN-β Signaling Pathway Activation in Antiviral Innate Immunity. Front Immunol 2021; 12:742074. [PMID: 34630423 PMCID: PMC8494776 DOI: 10.3389/fimmu.2021.742074] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/06/2021] [Indexed: 12/25/2022] Open
Abstract
Chickens are the natural host of Newcastle disease virus (NDV) and avian influenza virus (AIV). The discovery that the RIG-I gene, the primary RNA virus pattern recognition receptor (PRR) in mammals, is naturally absent in chickens has directed attention to studies of chicken RNA PRRs and their functions in antiviral immune responses. Here, we identified Asp-Glu-Ala-Asp (DEAD)-box helicase 1 (DDX1) as an essential RNA virus PRR in chickens and investigated its functions in anti-RNA viral infections. The chDDX1 gene was cloned, and cross-species sequence alignment and phylogenetic tree analyses revealed high conservation of DDX1 among vertebrates. A quantitative RT-PCR showed that chDDX1 mRNA are widely expressed in different tissues in healthy chickens. In addition, chDDX1 was significantly upregulated after infection with AIV, NDV, or GFP-expressing vesicular stomatitis virus (VSV-GFP). Overexpression of chDDX1 in DF-1 cells induced the expression of IFN-β, IFN-stimulated genes (ISGs), and proinflammatory cytokines; it also inhibited NDV and VSV replications. The knockdown of chDDX1 increased the viral yield of NDV and VSV and decreased the production of IFN-β, which was induced by RNA analog polyinosinic-polycytidylic acid (poly[I:C]), by AIV, and by NDV. We used a chicken IRF7 (chIRF7) knockout DF-1 cell line in a series of experiments to demonstrate that chDDX1 activates IFN signaling via the chIRF7 pathway. Finally, an in-vitro pulldown assay showed a strong and direct interaction between poly(I:C) and the chDDX1 protein, indicating that chDDX1 may act as an RNA PRR during IFN activation. In brief, our results suggest that chDDX1 is an important mediator of IFN-β and is involved in RNA- and RNA virus-mediated chDDX1-IRF7-IFN-β signaling pathways.
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Affiliation(s)
- Zhenyu Lin
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Agriculture Ministry Key Laboratory of Urban Agriculture (South), Shanghai, China
| | - Jie Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Agriculture Ministry Key Laboratory of Urban Agriculture (South), Shanghai, China
| | - Wenxian Zhu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Agriculture Ministry Key Laboratory of Urban Agriculture (South), Shanghai, China
| | - Xiangyu Yu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Agriculture Ministry Key Laboratory of Urban Agriculture (South), Shanghai, China
| | - Zhaofei Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Agriculture Ministry Key Laboratory of Urban Agriculture (South), Shanghai, China
| | - Jingjiao Ma
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Agriculture Ministry Key Laboratory of Urban Agriculture (South), Shanghai, China
| | - Hengan Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Agriculture Ministry Key Laboratory of Urban Agriculture (South), Shanghai, China
| | - Yaxian Yan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Agriculture Ministry Key Laboratory of Urban Agriculture (South), Shanghai, China
| | - Jianhe Sun
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Agriculture Ministry Key Laboratory of Urban Agriculture (South), Shanghai, China
| | - Yuqiang Cheng
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Agriculture Ministry Key Laboratory of Urban Agriculture (South), Shanghai, China
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15
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Caterino M, Paeschke K. Action and function of helicases on RNA G-quadruplexes. Methods 2021; 204:110-125. [PMID: 34509630 PMCID: PMC9236196 DOI: 10.1016/j.ymeth.2021.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Methodological progresses and piling evidence prove the rG4 biology in vivo. rG4s step in virtually every aspect of RNA biology. Helicases unwinding of rG4s is a fine regulatory layer to the downstream processes and general cell homeostasis. The current knowledge is however limited to a few cell lines. The regulation of helicases themselves is delineating as a important question. Non-helicase rG4-processing proteins likely play a role.
The nucleic acid structure called G-quadruplex (G4) is currently discussed to function in nucleic acid-based mechanisms that influence several cellular processes. They can modulate the cellular machinery either positively or negatively, both at the DNA and RNA level. The majority of what we know about G4 biology comes from DNA G4 (dG4) research. RNA G4s (rG4), on the other hand, are gaining interest as researchers become more aware of their role in several aspects of cellular homeostasis. In either case, the correct regulation of G4 structures within cells is essential and demands specialized proteins able to resolve them. Small changes in the formation and unfolding of G4 structures can have severe consequences for the cells that could even stimulate genome instability, apoptosis or proliferation. Helicases are the most relevant negative G4 regulators, which prevent and unfold G4 formation within cells during different pathways. Yet, and despite their importance only a handful of rG4 unwinding helicases have been identified and characterized thus far. This review addresses the current knowledge on rG4s-processing helicases with a focus on methodological approaches. An example of a non-helicase rG4s-unwinding protein is also briefly described.
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Affiliation(s)
- Marco Caterino
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany.
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16
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Suzuki T, Katada E, Mizuoka Y, Takagi S, Kazuki Y, Oshimura M, Shindo M, Hara T. A novel all-in-one conditional knockout system uncovered an essential role of DDX1 in ribosomal RNA processing. Nucleic Acids Res 2021; 49:e40. [PMID: 33503245 PMCID: PMC8053084 DOI: 10.1093/nar/gkaa1296] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/09/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
Generation of conditional knockout (cKO) and various gene-modified cells is laborious and time-consuming. Here, we established an all-in-one cKO system, which enables highly efficient generation of cKO cells and simultaneous gene modifications, including epitope tagging and reporter gene knock-in. We applied this system to mouse embryonic stem cells (ESCs) and generated RNA helicase Ddx1 cKO ESCs. The targeted cells displayed endogenous promoter-driven EGFP and FLAG-tagged DDX1 expression, and they were converted to Ddx1 KO via FLP recombinase. We further established TetFE ESCs, which carried a reverse tetracycline transactivator (rtTA) expression cassette and a tetracycline response element (TRE)-regulated FLPERT2 cassette in the Gt(ROSA26)Sor locus for instant and tightly regulated induction of gene KO. By utilizing TetFE Ddx1F/F ESCs, we isolated highly pure Ddx1F/F and Ddx1−/− ESCs and found that loss of Ddx1 caused rRNA processing defects, thereby activating the ribosome stress–p53 pathway. We also demonstrated cKO of various genes in ESCs and homologous recombination-non-proficient human HT1080 cells. The frequency of cKO clones was remarkably high for both cell types and reached up to 96% when EGFP-positive clones were analyzed. This all-in-one cKO system will be a powerful tool for rapid and precise analyses of gene functions.
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Affiliation(s)
- Teruhiko Suzuki
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Eiji Katada
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yuki Mizuoka
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Satoko Takagi
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yasuhiro Kazuki
- Chromosome Engineering Research Center (CERC), Tottori University, 86 Nishicho, Yonago 683-8503, Japan.,Division of Genome and Cellular Functions, Department of Molecular and Cellular Biology, School of Life Science, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan
| | - Mitsuo Oshimura
- Chromosome Engineering Research Center (CERC), Tottori University, 86 Nishicho, Yonago 683-8503, Japan
| | - Mayumi Shindo
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Takahiko Hara
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.,Graduate School of Science, Department of Biological Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji-shi, Tokyo 192-0397, Japan
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17
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Yu Y, Wang JL, Meng LL, Hu CT, Yan ZW, He ZP, Shi XQ, Fu GH, Zu LD. DDX54 Plays a Cancerous Role Through Activating P65 and AKT Signaling Pathway in Colorectal Cancer. Front Oncol 2021; 11:650360. [PMID: 33968751 PMCID: PMC8097168 DOI: 10.3389/fonc.2021.650360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/17/2021] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most malignant cancers, and its incidence is still steadily increasing. The DDX RNA helicase family members have been found to play a role in various cancers; however, the role of DDX54 in colorectal cancer is still unclear and needed to be defined. Here, we found DDX54 was overexpressed in CRC tissues by the label-free mass spectrum, which was also verified in tissue microarray of colon cancer, as well as the CRC cell lines and TCGA database. High DDX54 level was correlated with tumor stage and distant metastasis, which always indicated a poor prognosis to the CRC patients. DDX54 could promote the proliferation and mobility of CRC cells through increasing the phosphorylation level p65 and AKT leading to the tumorigenesis. Here, we have preliminarily studied the function of DDX54 in CRC, which would improve our understanding of the underlying biology of CRC and provide the new insight that could be translated into novel therapeutic approaches.
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Affiliation(s)
- Yi Yu
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jing-Long Wang
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li-Li Meng
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chun-Ting Hu
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhao-Wen Yan
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi-Ping He
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao-Qin Shi
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Guo-Hui Fu
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li-Dong Zu
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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18
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Moulin AP, Stathopoulos C, Marcelli F, Schoumans Pouw J, Beck-Popovic M, Munier FL. Secondary enucleated retinoblastoma with MYCN amplification. Ophthalmic Genet 2021; 42:354-359. [PMID: 33870828 DOI: 10.1080/13816810.2021.1897847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Background: Absence of RB1 mutation is rare in retinoblastoma and MYCN amplifications were recently identified in a subset of aggressive retinoblastomas occurring in infants. Here we describe not only the clinical phenotype of MYCN retinoblastoma at presentation, but also the tumor response to the first attempt of conservative management in this context.Methods: Interventional retrospective case reportResults: A 6-month-old boy was referred with right leukocoria. Examination under anesthesia revealed a group D unilateral retinoblastoma with an extensive whitish mass and total retinal detachment. Despite partial response following combined sequential intravenous and intra-arterial chemotherapy, tumor relapse in the aqueous humor occurred with posterior chamber involvement over 360°, this transiently controlled by intracameral and intravitreal melphalan injections. Eleven months post-diagnosis the eye was enucleated due to diffuse retinal recurrence invading the ciliary body and obscuring the optic nerve, associated with neovascular glaucoma. Histopathology revealed a poorly differentiated retinoblastoma with diffuse retinal invasion, extending from the superior ciliary body to the inferior equatorial choroid. There was post laminar optic nerve extension without involvement of the surgical margin. RB1 and diffuse MYCN nuclear expression were identified. FISH and SNP-array confirmed MYCN amplification. At 65 months follow-up the patient remained in good health without local recurrence or metastasis.Conclusions: To the best of our knowledge, this study is the first to attempt conservative management of an MYCN retinoblastoma, although secondary enucleation could not be avoided due to highly aggressive recurrence resisting all targeted modalities of chemotherapy.
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Affiliation(s)
| | | | | | | | | | - Francis L Munier
- Jules-Gonin Eye Hospital, Lausanne University, Lausanne, Switzerland
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19
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Wang J, Li T, Deng S, Ma E, Zhang J, Xing S. DDX6 Is Essential for Oocyte Development and Maturation in Locusta migratoria. INSECTS 2021; 12:70. [PMID: 33466820 PMCID: PMC7830464 DOI: 10.3390/insects12010070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 11/16/2022]
Abstract
DEAD-box protein 6 (DDX6) is a member of the DDX RNA helicase family that exists in all eukaryotes. It has been extensively studied in yeast and mammals and has been shown to be involved in messenger ribonucleoprotein assembly, mRNA storage, and decay, as well as in miRNA-mediated gene silencing. DDX6 participates in many developmental processes but the biological function of DDX6 in insects has not yet been adequately addressed. Herein, we characterized the LmDDX6 gene that encodes the LmDDX6 protein in Locusta migratoria, a global, destructive pest. LmDDX6 possesses five motifs unique to the DDX6 subfamily. In the phylogenetic tree, LmDDX6 was closely related to its orthologs in Apis dorsata and Zootermopsis nevadensis. RT-qPCR data revealed high expression of LmDDX6 in the ovary, muscle, and fat body, with a declining trend in the ovary after adult ecdysis. LmDDX6 knockdown downregulated the expression levels of the juvenile hormone receptor Met, and genes encoding Met downstream targeted Grp78-1 and Grp78-2, reduced LmVg expression, and impaired ovary development and oocyte maturation. These results demonstrate that LmDDX6 plays an essential role in locust female reproduction and, thus, could be a novel target for locust biological control.
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Affiliation(s)
- Junxiu Wang
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China; (J.W.); (T.L.); (S.D.); (E.M.); (J.Z.)
- College of Life Science, Shanxi University, Taiyuan 030006, Shanxi, China
| | - Tingting Li
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China; (J.W.); (T.L.); (S.D.); (E.M.); (J.Z.)
- College of Life Science, Shanxi University, Taiyuan 030006, Shanxi, China
| | - Sufang Deng
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China; (J.W.); (T.L.); (S.D.); (E.M.); (J.Z.)
- College of Life Science, Shanxi University, Taiyuan 030006, Shanxi, China
- College of Biological Sciences and Technology, Jinzhong University, Jinzhong 030600, Shanxi, China
| | - Enbo Ma
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China; (J.W.); (T.L.); (S.D.); (E.M.); (J.Z.)
- Shanxi Provincial Key Laboratory of Agricultural Integrated Pest Management, Taiyuan 030006, Shanxi, China
| | - Jianzhen Zhang
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China; (J.W.); (T.L.); (S.D.); (E.M.); (J.Z.)
- Shanxi Provincial Key Laboratory of Agricultural Integrated Pest Management, Taiyuan 030006, Shanxi, China
| | - Shuping Xing
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China; (J.W.); (T.L.); (S.D.); (E.M.); (J.Z.)
- Shanxi Provincial Key Laboratory of Agricultural Integrated Pest Management, Taiyuan 030006, Shanxi, China
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20
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Zhou YT, Zheng LY, Wang YJ, Yang L, Xie YT, Panda I, Tian XX, Fang WG. Effect of functional variant rs11466313 on breast cancer susceptibility and TGFB1 promoter activity. Breast Cancer Res Treat 2020; 184:237-248. [PMID: 32757134 DOI: 10.1007/s10549-020-05841-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 07/28/2020] [Indexed: 12/19/2022]
Abstract
PURPOSE This study aimed to investigate whether genetic polymorphisms in TGFB1 contribute to breast cancer (BC) susceptibility, and explore the mechanism of action. METHODS A total of 7 tagging SNPs (tSNPs) were genotyped in 1161 BC cases and 1337 age-matched controls among Chinese Han population. Bioinformatics analysis was used to predict functional SNP closely linked to tSNPs. Luciferase gene reporter assay was performed to determine the effect of genetic variants on promoter activity. DNA pull-down assay and mass spectrometry were used to identify the differentially binding proteins to genetic variants. RESULTS Genotyping analysis showed that rs1800469 (C>T) in the 5' regulatory region of TGFB1 was associated with reduced BC risk. Bioinformatics analysis predicted that rs11466313 (-2389_-2391 Del/AGG) in the 5' regulatory region of TGFB1, was closely linked to tSNP rs1800469 and could be functional. The genotyping of rs11466313 by PCR-SSCP showed that rs11466313 also conferred decreased BC risk. Luciferase assays demonstrated that rs11466313 minor allele reduced over ninefold of promoter activity compared with its major allele (p < 0.001). DNA pull-down assay and mass spectrometry revealed that rs11466313 minor allele lost the binding ability with FAM98B and HSP90B. Knocking down FAM98B but not HSP90B, the enhanced promoter activity driven by TGFB1 rs11466313 major allele was attenuated. CONCLUSIONS This study elucidates the impact of functional polymorphism rs11466313 in the regulatory region of TGFB1 on breast cancer susceptibility and gene expression, and could be helpful for future research to determine the value of this TGFB1 variant in the clinical setting.
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Affiliation(s)
- Yan-Ting Zhou
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, 100191, China
| | - Li-Yuan Zheng
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, 100191, China
| | - Ya-Jun Wang
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, 100191, China
| | - Li Yang
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, 100191, China
| | - Yun-Tao Xie
- Breast Center, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, 100142, China
| | - Ipsita Panda
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, 100191, China
| | - Xin-Xia Tian
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, 100191, China.
| | - Wei-Gang Fang
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, 100191, China.
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21
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Wang J, Zhang X, Deng S, Ma E, Zhang J, Xing S. Molecular characterization and RNA interference analysis of the DEAD-box gene family in Locusta migratoria. Gene 2020; 728:144297. [DOI: 10.1016/j.gene.2019.144297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 12/17/2022]
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22
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Kouyama Y, Masuda T, Fujii A, Ogawa Y, Sato K, Tobo T, Wakiyama H, Yoshikawa Y, Noda M, Tsuruda Y, Kuroda Y, Eguchi H, Ishida F, Kudo SE, Mimori K. Oncogenic splicing abnormalities induced by DEAD-Box Helicase 56 amplification in colorectal cancer. Cancer Sci 2019; 110:3132-3144. [PMID: 31390121 PMCID: PMC6778637 DOI: 10.1111/cas.14163] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing, regulated by DEAD‐Box Helicase (DDX) families, plays an important role in cancer. However, the relationship between the DDX family and cancer has not been fully elucidated. In the present study, we identified a candidate oncogene DDX56 on Ch.7p by a bioinformatics approach using The Cancer Genome Atlas (TCGA) dataset of colorectal cancer (CRC). DDX56 expression was measured by RT‐qPCR and immunochemical staining in 108 CRC patients. Clinicopathological and survival analyses were carried out using three CRC datasets. Biological roles of DDX56 were explored by gene set enrichment analysis (GSEA), and cell proliferation in vitro and in vivo, cell cycle assays, and using DDX56‐knockdown or overexpressed CRC cells. RNA sequencing was carried out to elucidate the effect of DDX56 on mRNA splicing. We found that DDX56 expression was positively correlated with the amplification of DDX56 and was upregulated in CRC cells. High DDX56 expression was associated with lymphatic invasion and distant metastasis and was an independent poor prognostic factor. In vitro analysis, in vivo analysis and GSEA showed that DDX56 promoted proliferation ability through regulating the cell cycle. DDX56 knockdown reduced intron retention and tumor suppressor WEE1 expression, which functions as a G2‐M DNA damage checkpoint. We have identified DDX56 as a novel oncogene and prognostic biomarker of CRC that promotes alternative splicing of WEE1.
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Affiliation(s)
- Yuta Kouyama
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan.,Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Atsushi Fujii
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Yushi Ogawa
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Kuniaki Sato
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Taro Tobo
- Department of Clinical Laboratory Medicine, Kyushu University Beppu Hospital, Oita, Japan
| | - Hiroaki Wakiyama
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | | | - Miwa Noda
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Yusuke Tsuruda
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Yousuke Kuroda
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Hidetoshi Eguchi
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Fumio Ishida
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Shin-Ei Kudo
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
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23
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Shen R, Wu T, Huang P, Shao Q, Chen M. The clinicopathological significance of ubiquitin-conjugating enzyme E2C, leucine-rich repeated-containing G protein-coupled receptor, WW domain-containing oxidoreductase, and vasculogenic mimicry in invasive breast carcinoma. Medicine (Baltimore) 2019; 98:e15232. [PMID: 31008954 PMCID: PMC6494285 DOI: 10.1097/md.0000000000015232] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Ubiquitin-conjugating enzyme E2C (UBE2C), a crucial part of the ubiquitin-conjugating enzyme complex, is reported to promote progression of various cancers. Leucine-rich repeated-containing G protein-coupled receptor (LGR5), a biomarker of cancer stem cells, is reported to be responsible for the initiation and progression of cancers. WW domain-containing oxidoreductase (WWOX), a suppressor of tumor, is reported to inhibit initiation and progression of cancers. Vasculogenic mimicry (VM), a new blood supply pattern, is associated with progression of cancers. However, the clinicopathological significance of UBE2C, LGR5, WWOX, and VM in invasive breast carcinoma (IBC) remains elusive. The aim of this study is to investigate the positive rate of UBE2C, LGR5, WWOX, and VM in IBC and their clinical significance.Positive rates of UBE2C, LGR5, WWOX, and VM in 247 whole IBC samples were detected through immunohistochemistry. Patients data (including clinical, demography, follow-up) were collected.Levels of UBE2C, LGR5, VM, and microvessel density (MVD) were significantly higher, and level of WWOX was significantly lower in IBC specimens when compared with normal mammary gland tissues. Levels of UBE2C, LGR5, VM, and MVD were all positively associated with tumor stages, lymph node metastasis (LNM) stages, tumor grades, and tumor-node-metastasis (TNM) stages, and unfavorably with patients' overall survival (OS) and disease-free survival (DFS). Level of WWOX was negatively associated with tumor stages, LNM stages, grades, and TNM stages, and favorably with patients' OS and DFS. Multivariate analysis indicated that levels of UBE2C, LGR5, VM, MVD, and WWOX, as well as TNM stages were independently prognostic factors for OS and DFS in patients with IBC.UBE2C, LGR5, VM, MVD, and WWOX may be considered as promising indicator of IBC prognosis.
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Affiliation(s)
- Rong Shen
- Department of Pathology, Zhenjiang First People's Hospital, Affiliated to Jiangsu University
- Department of Pathology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ting Wu
- Department of Pathology, Zhenjiang First People's Hospital, Affiliated to Jiangsu University
| | - Pan Huang
- Department of Pathology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qixiang Shao
- Department of Pathology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Miao Chen
- Department of Pathology, Zhenjiang First People's Hospital, Affiliated to Jiangsu University
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24
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Tanaka K, Ikeda N, Miyashita K, Nuriya H, Hara T. DEAD box protein DDX1 promotes colorectal tumorigenesis through transcriptional activation of the LGR5 gene. Cancer Sci 2018; 109:2479-2489. [PMID: 29869821 PMCID: PMC6113447 DOI: 10.1111/cas.13661] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/01/2018] [Indexed: 02/02/2023] Open
Abstract
DDX1, a member of the DEAD box RNA helicase family, plays a critical role in testicular tumors. However, it remains to be clarified whether DDX1 is involved in other types of malignant tumors such as colorectal cancer. We disrupted the DDX1 gene in a human colorectal cancer cell line LoVo using the CRISPR/Cas9‐mediated gene‐targeting system. DDX1‐KO LoVo cells exhibited a much slower growth rate, produced fewer colonies in soft agar medium, and generated smaller solid tumors in nude mice than parental LoVo cells. Such phenotypes of the DDX1‐KO cells were mostly reversed by exogenous expression of DDX1. These results indicate that DDX1 is required for tumorigenicity of colorectal cancer cells. In the DDX1‐KO cells, the cancer stem cell marker genes LGR5, CD133, ALDH1 and SOX2 were markedly suppressed. Among them, expression of LGR5, which is essential for tumorigenicity of colorectal cancer cells, was restored in the DDX1‐transfected DDX1‐KO cells. Consistently, the DDX1‐KO cells lost sphere‐forming capacity in a DDX1‐dependent fashion. Reporter and chromatin immunoprecipitation assays revealed that DDX1 directly bound to the −1837 to −1662 region of the enhancer/promoter region of the human LGR5 gene and enhanced its transcription in LoVo cells. Repression of LGR5 by DDX1 knockdown was observed in 2 other human colorectal cancer cell lines, Colo320 and SW837. These results suggest that LGR5 is a critical effector of DDX1 in colorectal cancer cells. The DDX1‐LGR5 axis could be a new drug target for this type of malignant cancer.
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Affiliation(s)
- Kiyoko Tanaka
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Narumi Ikeda
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Setagaya-ku, Tokyo, Japan
| | - Kazuya Miyashita
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Division of Cell Therapy, The Institute of Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hideko Nuriya
- Core Technology and Research Center, Tokyo Metropolitan Institute of Medical Science, Minato-ku, Tokyo, Japan
| | - Takahiko Hara
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Setagaya-ku, Tokyo, Japan
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