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Choi WS, Liu RZ, Mak C, Maadi H, Godbout R. Overcoming retinoic acid resistance in HER2-enriched breast cancers: role of MYC. FEBS J 2024; 291:3521-3538. [PMID: 38708519 DOI: 10.1111/febs.17151] [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: 09/06/2023] [Revised: 02/12/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024]
Abstract
HER2-enriched (HER2+) breast cancers express high levels of the growth-promoting HER2 protein. Although these cancers are treated with the HER2-targeted drug, trastuzumab, resistance to treatment is common. Retinoic acid (RA) is an anti-cancer agent that has been successfully used for the treatment of leukemia and holds promise for the treatment of solid cancers, including breast cancer. The HER2 gene is frequently co-amplified with RARA, a key determinant of RA sensitivity in breast cancers. It seems surprising, therefore, that HER2+ breast cancers are refractory to RA treatment. Here, we show that MYC mediates RA resistance by suppressing the expression of cellular retinoic acid binding protein 2 (CRABP2), resulting in RARα inactivation. CRABP2 is an intracellular RA transporter that delivers RA to the nuclear receptor RARα for its activation. Our results indicate that response to RA is enhanced by MYC depletion in HER2+ breast cancer cells and that RA treatment enhances trastuzumab responsiveness. Our findings support the use of RA and trastuzumab for the treatment of subsets of patients with breast cancers that are HER2-RARα co-amplified and have low levels of MYC.
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Affiliation(s)
- Won-Shik Choi
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Canada
| | - Rong-Zong Liu
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Canada
| | - Caitlin Mak
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Canada
| | - Hamid Maadi
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Iran
| | - Roseline Godbout
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Canada
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2
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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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3
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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. [PMID: 38994142 PMCID: PMC11236250 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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Garg M, Li L, Godbout R. Role of DDX1 in the oxidative response of ataxia telangiectasia patient-derived fibroblasts. Redox Biol 2024; 69:102988. [PMID: 38096740 PMCID: PMC10761787 DOI: 10.1016/j.redox.2023.102988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/25/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
Ataxia Telangiectasia (A-T) is an inherited autosomal recessive disorder characterized by cerebellar neurodegeneration, radiosensitivity, immunodeficiency and a high incidence of lymphomas. A-T is caused by mutations in the ATM gene. While loss of ATM function in DNA repair explains some aspects of A-T pathophysiology such as radiosensitivity and cancer predisposition, other A-T features such as neurodegeneration imply additional roles for ATM outside the nucleus. Emerging evidence suggests that ATM participates in cellular response to oxidative stress, failure of which contributes to the neurodegeneration associated with A-T. Here, we use fibroblasts derived from A-T patients to investigate whether DEAD Box 1 (DDX1), an RNA binding/unwinding protein that functions downstream of ATM in DNA double strand break repair, also plays a role in ATM-dependent cellular response to oxidative stress. Focusing on DDX1 target RNAs that are associated with neurological disorders and oxidative stress response, we show that ATM is required for increased binding of DDX1 to its target RNAs in the presence of arsenite-induced oxidative stress. Our results indicate that DDX1 functions downstream of ATM by protecting specific mRNAs in the cytoplasm of arsenite-treated cells. In keeping with a role for ATM and DDX1 in oxidative stress, levels of reactive oxygen species (ROS) are increased in ATM-deficient as well as DDX1-depleted cells. We propose that reduced levels of cytoplasmic DDX1 RNA targets sensitizes ATM-deficient cells to oxidative stress resulting in increased cell death. This sensitization would be especially detrimental to long-lived highly metabolically active cells such as neurons providing a possible explanation for the neurodegenerative defects associated with A-T.
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Affiliation(s)
- Mansi Garg
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada
| | - Lei Li
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada
| | - Roseline Godbout
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada.
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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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Alromema N, Syed AH, Khan T. A Hybrid Machine Learning Approach to Screen Optimal Predictors for the Classification of Primary Breast Tumors from Gene Expression Microarray Data. Diagnostics (Basel) 2023; 13:diagnostics13040708. [PMID: 36832196 PMCID: PMC9955903 DOI: 10.3390/diagnostics13040708] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
The high dimensionality and sparsity of the microarray gene expression data make it challenging to analyze and screen the optimal subset of genes as predictors of breast cancer (BC). The authors in the present study propose a novel hybrid Feature Selection (FS) sequential framework involving minimum Redundancy-Maximum Relevance (mRMR), a two-tailed unpaired t-test, and meta-heuristics to screen the most optimal set of gene biomarkers as predictors for BC. The proposed framework identified a set of three most optimal gene biomarkers, namely, MAPK 1, APOBEC3B, and ENAH. In addition, the state-of-the-art supervised Machine Learning (ML) algorithms, namely Support Vector Machine (SVM), K-Nearest Neighbors (KNN), Neural Net (NN), Naïve Bayes (NB), Decision Tree (DT), eXtreme Gradient Boosting (XGBoost), and Logistic Regression (LR) were used to test the predictive capability of the selected gene biomarkers and select the most effective breast cancer diagnostic model with higher values of performance matrices. Our study found that the XGBoost-based model was the superior performer with an accuracy of 0.976 ± 0.027, an F1-Score of 0.974 ± 0.030, and an AUC value of 0.961 ± 0.035 when tested on an independent test dataset. The screened gene biomarkers-based classification system efficiently detects primary breast tumors from normal breast samples.
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Affiliation(s)
- Nashwan Alromema
- Department of Computer Science, Faculty of Computing and Information Technology Rabigh (FCITR), King Abdulaziz University, Jeddah 22254, Saudi Arabia
- Correspondence:
| | - Asif Hassan Syed
- Department of Computer Science, Faculty of Computing and Information Technology Rabigh (FCITR), King Abdulaziz University, Jeddah 22254, Saudi Arabia
| | - Tabrej Khan
- Department of Information Systems, Faculty of Computing and Information Technology Rabigh (FCITR), King Abdulaziz University, Jeddah 22254, Saudi Arabia
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Arna AB, Patel H, Singh RS, Vizeacoumar FS, Kusalik A, Freywald A, Vizeacoumar FJ, Wu Y. Synthetic lethal interactions of DEAD/H-box helicases as targets for cancer therapy. Front Oncol 2023; 12:1087989. [PMID: 36761420 PMCID: PMC9905851 DOI: 10.3389/fonc.2022.1087989] [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: 11/02/2022] [Accepted: 12/28/2022] [Indexed: 01/26/2023] Open
Abstract
DEAD/H-box helicases are implicated in virtually every aspect of RNA metabolism, including transcription, pre-mRNA splicing, ribosomes biogenesis, nuclear export, translation initiation, RNA degradation, and mRNA editing. Most of these helicases are upregulated in various cancers and mutations in some of them are associated with several malignancies. Lately, synthetic lethality (SL) and synthetic dosage lethality (SDL) approaches, where genetic interactions of cancer-related genes are exploited as therapeutic targets, are emerging as a leading area of cancer research. Several DEAD/H-box helicases, including DDX3, DDX9 (Dbp9), DDX10 (Dbp4), DDX11 (ChlR1), and DDX41 (Sacy-1), have been subjected to SL analyses in humans and different model organisms. It remains to be explored whether SDL can be utilized to identity druggable targets in DEAD/H-box helicase overexpressing cancers. In this review, we analyze gene expression data of a subset of DEAD/H-box helicases in multiple cancer types and discuss how their SL/SDL interactions can be used for therapeutic purposes. We also summarize the latest developments in clinical applications, apart from discussing some of the challenges in drug discovery in the context of targeting DEAD/H-box helicases.
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Affiliation(s)
- Ananna Bhadra Arna
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Hardikkumar Patel
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ravi Shankar Singh
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Franco J. Vizeacoumar
- Division of Oncology, College of Medicine, University of Saskatchewan and Saskatchewan Cancer Agency, Saskatoon, SK, Canada,*Correspondence: Yuliang Wu, ; Franco J. Vizeacoumar,
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada,*Correspondence: Yuliang Wu, ; Franco J. Vizeacoumar,
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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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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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Yin Y, Xu ZY, Liu YJ, Huang W, Zhang Q, Li JP, Zou X. Identification and Validation in a Novel Classification of Helicase Patterns for the Prediction of Tumor Proliferation and Prognosis. J Hepatocell Carcinoma 2022; 9:885-900. [PMID: 36061235 PMCID: PMC9432388 DOI: 10.2147/jhc.s378175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022] Open
Abstract
Background Helicases have been classified as a class of enzymes that determine the stability of the cellular genome. There is growing evidence that helicases can help tumor cells resist drug killing by repairing Deoxyribose Nucleic Acid (DNA) or stabilizing transcription, which may contribute to the understanding of drug resistance. Currently, identifying cancer biomarkers among helicases and stratifying patients according to helicase activity will be able to guide treatment well. Methods We clustered 371 hepatocellular carcinoma (HCC) patients from The Cancer Genome Atlas (TCGA) by consensus clustering based on helicase expression profiles to identify potential molecular subtypes. The Multiscale Embedded Gene Co-Expression Network Analysis (MEGENA) algorithm was used to find core differential gene modules between different molecular subtypes, and single-cell analysis was utlized to explore the potential function of hub gene. Immunohistochemical (IHC) staining was used to verify the diagnostic value of DDX56 and its ability to reflect the proliferation efficiency of cancer cells. Results We identified two subtypes associated with helicase. High helicase subtype was associated with poor clinical outcome, massive M0 macrophage infiltration, and highly active cell proliferation features. In addition, we identified a new biomarker, DDX56, which has not been reported in HCC, was highly expressed in HCC tissues, associated with poor prognosis, and was also shown to be associated with high cell proliferative activity. Conclusion In conclusion, based on helicase expression profiles, we have developed a new classification system for HCC, which is a proliferation-related system, and has clinical significance in evaluating prognosis and treating HCC patients, including immunotherapy and chemotherapy. In addition, we identified a new biomarker, DDX 56, which is overexpressed in HCC tissues, predicts a poor prognosis and is a validated index of tumor cell proliferation.
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Affiliation(s)
- Yi Yin
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
| | - Zi-Yuan Xu
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
| | - Yuan-jie Liu
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
| | - Wei Huang
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
| | - Qian Zhang
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
| | - Jie-pin Li
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
- Department of Oncology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, 215600, People’s Republic of China
| | - Xi Zou
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing, Jiangsu, 210029, People’s Republic of China
- Correspondence: Xi Zou; Jie-pin Li, Email ;
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11
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Li L, Garg M, Wang Y, Wang W, Godbout R. DEAD Box 1 (DDX1) protein binds to and protects cytoplasmic stress response mRNAs in cells exposed to oxidative stress. J Biol Chem 2022; 298:102180. [PMID: 35752363 PMCID: PMC9293777 DOI: 10.1016/j.jbc.2022.102180] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/28/2022] Open
Abstract
The integrated stress response is a network of highly orchestrated pathways activated when cells are exposed to environmental stressors. While global repression of translation is a well-recognized hallmark of the integrated stress response, less is known about the regulation of mRNA stability during stress. DEAD box proteins are a family of RNA unwinding/remodeling enzymes involved in every aspect of RNA metabolism. We previously showed that DEAD box 1 (DDX1) protein accumulates at DNA double-strand breaks during genotoxic stress and promotes DNA double-strand break repair via homologous recombination. Here, we examine the role of DDX1 in response to environmental stress. We show that DDX1 is recruited to stress granules (SGs) in cells exposed to a variety of environmental stressors, including arsenite, hydrogen peroxide, and thapsigargin. We also show that DDX1 depletion delays resolution of arsenite-induced SGs. Using RNA immunoprecipitation sequencing, we identify RNA targets bound to endogenous DDX1, including RNAs transcribed from genes previously implicated in stress responses. We show the amount of target RNAs bound to DDX1 increases when cells are exposed to stress, and the overall levels of these RNAs are increased during stress in a DDX1-dependent manner. Even though DDX1’s RNA-binding property is critical for maintenance of its target mRNA levels, we found RNA binding is not required for localization of DDX1 to SGs. Furthermore, DDX1 knockdown does not appear to affect RNA localization to SGs. Taken together, our results reveal a novel role for DDX1 in maintaining cytoplasmic mRNA levels in cells exposed to oxidative stress.
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Affiliation(s)
- Lei Li
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - Mansi Garg
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - Yixiong Wang
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - Weiwei Wang
- Department of Medicine, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Roseline Godbout
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada.
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Min Y, Feng Y, Luo H, Hu D, Wei X, He D, Yin G, Fan S. Identifying and Validating of an Autophagy-Related Gene Signature for the Prediction of Early Relapse in Breast Cancer. Front Endocrinol (Lausanne) 2022; 13:824362. [PMID: 35250881 PMCID: PMC8888901 DOI: 10.3389/fendo.2022.824362] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/26/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Compelling evidence has demonstrated the pivotal role of autophagy in the prognosis of breast cancer. Breast cancer (BC) patients with early relapse consistently exhibited worse survival. METHODS The autophagy-related genes were derived from the Human Autophagy Database (HADb) and high-sequencing data were obtained from The Cancer Genome Atlas (TCGA). Discrepantly expressed autophagy genes (DEAGs) between early relapse and long-term survival groups were performed using the Linear Models for Microarray data (LIMMA) method. Lasso Cox regression analysis was conducted for the selection of the 4-gene autophagy-related gene signature. GSE42568 and GSE21653 databases were enrolled in this study for the external validation of the signature. Then patients were divided into high and low-risk groups based on the specific score formula. GSEA was used to discover the related signaling pathway. The Kaplan-Meier curves and the receiver operating characteristic (ROC) curves were used to evaluate the discrimination and accuracy of the 4-gene signature. RESULTS A signature composed of four autophagy-related mRNA including APOL1, HSPA8, SIRT1, and TP73, was identified as significantly associated with the early relapse in BC patients. Time-dependent receiver-operating characteristic at 1 year suggested remarkable accuracy of the signature [area under the curve (AUC = 0.748)]. The risk score model based on the autophagy-related signature showed favorable predicting value in 1-, 2-, and 3-year relapse-free survival (RFS) in training and two validating cohorts. The GSEA displayed gene sets were remarkably enriched in carcinogenic activation pathways and autophagy-related pathways. The nomogram involving three variables (progesterone receptor status, T stage, and 4-gene signature) exhibited relatively good discrimination with a C-index of 0.766. CONCLUSIONS Our study establishes an autophagy-related 4-gene signature that can effectively stratify the high-risk and low-risk BC patients for early relapse. Combined with the clinicopathological variables, the signature could significantly help oncologists tailor more efficient treatment strategies for BC patients.
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Affiliation(s)
- Yu Min
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yang Feng
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Haojun Luo
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Daixing Hu
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaoyuan Wei
- Department of Cardiology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Danshuang He
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guobing Yin
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shenghao Fan
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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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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Hu DX, Sun QF, Xu L, Lu HD, Zhang F, Li ZM, Zhang MY. Knockdown of DEAD-box 51 inhibits tumor growth of esophageal squamous cell carcinoma via the PI3K/AKT pathway. World J Gastroenterol 2022; 28:464-478. [PMID: 35125830 PMCID: PMC8790558 DOI: 10.3748/wjg.v28.i4.464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 11/15/2021] [Accepted: 01/06/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent malignancies that seriously threaten people’s health worldwide. DEAD-box helicase 51 (DDX51) is a member of the DEAD-box (DDX) RNA helicase family, and drives or inhibits tumor progression in multiple cancer types.
AIM To determine whether DDX51 affects the biological behavior of ESCC.
METHODS The expression of DDX51 in ESCC tumor tissues and adjacent normal tissues was detected by Immunohistochemistry (IHC) analyses and quantitative PCR (qPCR). We knocked down DDX51 in ESCC cell lines by using a small interfering RNA (siRNA) transfection. The proliferation, apoptosis, and mobility of DDX51 siRNA-transfected cells were detected. The effect of DDX51 on the phosphoinositide 3-kinase (PI3K)/AKT pathway was investigated by western blot analysis. A mouse xenograft model was established to investigate the effects of DDX51 knockdown on ESCC tumor growth.
RESULTS DDX51 exhibited high expression in ESCC tissues compared with normal tissues and represented a poor prognosis in patients with ESCC. Knockdown of DDX51 induced inhibition of ESCC cell proliferation and promoted apoptosis. Moreover, DDX51 siRNA-expressing cells also exhibited lower migration and invasion rates. Investigations into the underlying mechanisms suggested that DDX51 knockdown induced inactivation of the PI3K/AKT pathway, including decreased phosphorylation levels of phosphate and tensin homolog, PI3K, AKT, and mammalian target of rapamycin. Rescue experiments demonstrated that the AKT activator insulin-like growth factor 1 could reverse the inhibitory effects of DDX51 on ESCC malignant development. Finally, we injected DDX51 siRNA-transfected TE-1 cells into an animal model, which resulted in slower tumor growth.
CONCLUSION Our study suggests for the first time that DDX51 promotes cancer cell proliferation by regulating the PI3K/AKT pathway; thus, DDX51 might be a therapeutic target for ESCC.
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Affiliation(s)
- Dong-Xin Hu
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong Province, China
| | - Qi-Feng Sun
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong Province, China
| | - Lin Xu
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong Province, China
| | - Hong-Da Lu
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong Province, China
| | - Fan Zhang
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong Province, China
| | - Zhen-Miao Li
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong Province, China
| | - Ming-Yan Zhang
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong Province, China
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15
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Qi Y, Wu H, Liu C, Zheng D, Yan C, Hu W, Zhang X, Dai X. Downstream Neighbor of Son Overexpression is Associated With Breast Cancer Progression and a Poor Prognosis. J Breast Cancer 2022; 25:327-343. [PMID: 35914745 PMCID: PMC9411031 DOI: 10.4048/jbc.2022.25.e26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/19/2022] [Accepted: 06/03/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Yufeng Qi
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Haodong Wu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Conghui Liu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Danni Zheng
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Congzhi Yan
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Wenjing Hu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Xiaohua Zhang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Xuanxuan Dai
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
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16
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Wu Q, Luo X, Terp MG, Li Q, Li Y, Shen L, Chen Y, Jacobsen K, Bivona TG, Chen H, Zeng R, Ditzel HJ. DDX56 modulates post-transcriptional Wnt signaling through miRNAs and is associated with early recurrence in squamous cell lung carcinoma. Mol Cancer 2021; 20:108. [PMID: 34446021 PMCID: PMC8393456 DOI: 10.1186/s12943-021-01403-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 08/10/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Early recurrence is a major obstacle to prolonged postoperative survival in squamous cell lung carcinoma (SqCLC). The molecular mechanisms underlying early SqCLC recurrence remain unclear, and effective prognostic biomarkers for predicting early recurrence are needed. METHODS We analyzed primary tumor samples of 20 SqCLC patients using quantitative proteomics to identify differentially-expressed proteins in patients who experienced early versus late disease recurrence. The expression and prognostic significance of DDX56 was evaluated using a SqCLC tumor tissue microarray and further verified using different online databases. We performed in vitro and in vivo experiments to obtain detailed molecular insight into the functional role of DDX56 in SqCLC. RESULTS We found that DDX56 exhibited increased expression in tumors of patients who experienced early versus late disease recurrence. Increased DDX56 expression in SqCLC tumors was subsequently confirmed as an independent prognostic factor of poor recurrence-free survival in independent SqCLC cohorts. Functionally, DDX56 promotes SqCLC cell growth and migration in vitro, and xenograft tumor progression in vivo. Mechanistically, DDX56 post-transcriptionally promotes expression of multiple Wnt signaling pathway-related genes, including CTNNB1, WNT2B, and represses a subset of miRNAs, including miR-378a-3p, a known suppressor of Wnt signaling. Detailed analysis revealed that DDX56 facilitated degradation of primary miR-378a, leading to down-regulation of mature miR-378a-3p and thus derepression of the target gene WNT2B. CONCLUSION We identified DDX56 as a novel independent prognostic biomarker that exerts its oncogenic effects through miRNA-mediated post-transcriptional regulation of Wnt signaling genes to promote early SqCLC recurrence. DDX56 may assist in identifying SqCLC patients at increased risk of early recurrence and who could benefit from Wnt signaling-targeted therapies.
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Affiliation(s)
- Qingqing Wu
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, J.B. Winsløwsvej 25, 5000, Odense C, Denmark
| | - Xiaoyang Luo
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Mikkel G Terp
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, J.B. Winsløwsvej 25, 5000, Odense C, Denmark
| | - Qingrun Li
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yuan Li
- Department of Oncology, Fudan University Shanghai Medical College, Shanghai, 200032, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Lei Shen
- Department of Oncology, Fudan University Shanghai Medical College, Shanghai, 200032, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Ying Chen
- Department of Oncology, Fudan University Shanghai Medical College, Shanghai, 200032, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Kirstine Jacobsen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, J.B. Winsløwsvej 25, 5000, Odense C, Denmark
| | - Trever G Bivona
- Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Haiquan Chen
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Fudan University Shanghai Medical College, Shanghai, 200032, China.
| | - Rong Zeng
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Henrik J Ditzel
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, J.B. Winsløwsvej 25, 5000, Odense C, Denmark.
- Department of Oncology, Odense University Hospital, 5000, Odense, Denmark.
- Department of Clinical Research, University of Southern Denmark, 5000, Odense, Denmark.
- Academy of Geriatric Cancer Research (AgeCare), Odense University Hospital, 5000, Odense, Denmark.
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Transcription/Replication Conflicts in Tumorigenesis and Their Potential Role as Novel Therapeutic Targets in Multiple Myeloma. Cancers (Basel) 2021; 13:cancers13153755. [PMID: 34359660 PMCID: PMC8345052 DOI: 10.3390/cancers13153755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/13/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Multiple myeloma is a hematologic cancer characterized by the accumulation of malignant plasma cells in the bone marrow. It remains a mostly incurable disease due to the inability to overcome refractory disease and drug-resistant relapse. Oncogenic transformation of PC in multiple myeloma is thought to occur within the secondary lymphoid organs. However, the precise molecular events leading to myelomagenesis remain obscure. Here, we identified genes involved in the prevention and the resolution of conflicts between the replication and transcription significantly overexpressed during the plasma cell differentiation process and in multiple myeloma cells. We discussed the potential role of these factors in myelomagenesis and myeloma biology. The specific targeting of these factors might constitute a new therapeutic strategy in multiple myeloma. Abstract Plasma cells (PCs) have an essential role in humoral immune response by secretion of antibodies, and represent the final stage of B lymphocytes differentiation. During this differentiation, the pre-plasmablastic stage is characterized by highly proliferative cells that start to secrete immunoglobulins (Igs). Thus, replication and transcription must be tightly regulated in these cells to avoid transcription/replication conflicts (TRCs), which could increase replication stress and lead to genomic instability. In this review, we analyzed expression of genes involved in TRCs resolution during B to PC differentiation and identified 41 genes significantly overexpressed in the pre-plasmablastic stage. This illustrates the importance of mechanisms required for adequate processing of TRCs during PCs differentiation. Furthermore, we identified that several of these factors were also found overexpressed in purified PCs from patients with multiple myeloma (MM) compared to normal PCs. Malignant PCs produce high levels of Igs concomitantly with cell cycle deregulation. Therefore, increasing the TRCs occurring in MM cells could represent a potent therapeutic strategy for MM patients. Here, we describe the potential roles of TRCs resolution factors in myelomagenesis and discuss the therapeutic interest of targeting the TRCs resolution machinery in MM.
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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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Asberger J, Erbes T, Jaeger M, Rücker G, Nöthling C, Ritter A, Berner K, Juhasz-Böss I, Hirschfeld M. Endoxifen and fulvestrant regulate estrogen-receptor α and related DEADbox proteins. Endocr Connect 2020; 9:1156-1167. [PMID: 33112831 PMCID: PMC7774761 DOI: 10.1530/ec-20-0281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 10/12/2020] [Indexed: 12/24/2022]
Abstract
Breast cancer (BC) represents the most common type of cancer in females worldwide. Endocrine therapy evolved as one of the main concepts in treatment of hormone-receptor positive BC. Current research focuses on the elucidation of tumour resistance mechanisms against endocrine therapy. In a translational in vitro approach, potential regulatory effects of clinically implemented BC anti-oestrogens on ERα, its coactivators DDX5, DDX17 and other DEADbox proteins as well as on the proliferation markers cyclin D1 and Ki67 were investigated on both the RNA and protein level. BC in vitro models for hormone-receptor positive (MCF-7, T-47D) and hormone-receptor negative cells (BT-20) were subjected to endocrine therapy. Anti-oestrogen-dependent expression regulation of target genes on the transcriptional and translational level was quantified and statistically assessed. Endocrine therapy decreases the expression levels of Ki67, cyclin D1 and ERα in hormone-receptor positive cells. In the hormone-receptor negative cells, the three parameters remained stable after endocrine therapy. Endoxifen triggers a downregulation of DDX5 and DDX23 in MCF-7 cells. Fulvestrant treatment downregulates the expression levels of all investigated DEADbox proteins in MCF-7 cells. In T-47D cells, endoxifen and fulvestrant lead to a decrease of all target gene expression levels. Interestingly, endocrine therapy affects DEADbox RNA expression levels in BT-20 cells, too. However, this result could only be confirmed for DDX1, immunocytologically. The investigated DEADbox proteins appear to correlate with the oestrogen-dependent tumourigenesis in hormone-receptor positive BC and show expression alterations after endocrine treatment.
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Affiliation(s)
- Jasmin Asberger
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Correspondence should be addressed to J Asberger:
| | - Thalia Erbes
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Markus Jaeger
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gerta Rücker
- Institute of Medical Biometry and Statistics, Medical Center – University of Freiburg, Freiburg, Germany
| | - Claudia Nöthling
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andrea Ritter
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kai Berner
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ingolf Juhasz-Böss
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marc Hirschfeld
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Veterinary Medicine, Georg-August-University Goettingen, Goettingen, Germany
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Low Expression of DDX60 Gene Might Associate with the Radiosensitivity for Patients with Breast Cancer. JOURNAL OF ONCOLOGY 2020; 2020:8309492. [PMID: 32765606 PMCID: PMC7387961 DOI: 10.1155/2020/8309492] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/26/2020] [Indexed: 12/24/2022]
Abstract
DEXD/H box helicase 60 (DDX60) is a new type of DEAD-box RNA helicase, which is induced to express after virus infection. It might involve in antiviral immunity by promoting RIG-I-like receptor-mediated signal transduction. In addition, previous studies had shown that the expression of DDX60 is related to cancer, but there was still a lack of relevant research in breast cancer. In this study, we used the information of patients with breast cancer in the TCGA database for statistical analysis and found that the breast cancer patients with low expression of DDX60 exhibited radiosensitivity. Comparing the radiotherapy groups with the nonradiotherapy groups, for patients with low expression of DDX60, the adjusted hazard ratio (HR) values for radiotherapy were 0.244 (0.064–0.921) and 0.199 (0.062–0.646) in the training and validation datasets, with the p values 0.040 and 0.007, respectively. However, for patients with high expression of DDX60, the adjusted hazard ratio (HR) values were 3.582 (0.627–20.467) and 2.421 (0.460–12.773), with the p values 0.054 and 0.297, respectively. These results suggested that the expression of DDX60 might strongly associate with individualized radiosensitivity in patients with breast cancer.
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21
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Hildebrandt MR, Wang Y, Li L, Yasmin L, Glubrecht DD, Godbout R. Cytoplasmic aggregation of DDX1 in developing embryos: Early embryonic lethality associated with Ddx1 knockout. Dev Biol 2019; 455:420-433. [DOI: 10.1016/j.ydbio.2019.07.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/04/2019] [Accepted: 07/19/2019] [Indexed: 01/12/2023]
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22
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Lewis CW, Bukhari AB, Xiao EJ, Choi WS, Smith JD, Homola E, Mackey JR, Campbell SD, Gamper AM, Chan GK. Upregulation of Myt1 Promotes Acquired Resistance of Cancer Cells to Wee1 Inhibition. Cancer Res 2019; 79:5971-5985. [PMID: 31594837 DOI: 10.1158/0008-5472.can-19-1961] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/04/2019] [Accepted: 10/04/2019] [Indexed: 11/16/2022]
Abstract
Adavosertib (also known as AZD1775 or MK1775) is a small-molecule inhibitor of the protein kinase Wee1, with single-agent activity in multiple solid tumors, including sarcoma, glioblastoma, and head and neck cancer. Adavosertib also shows promising results in combination with genotoxic agents such as ionizing radiation or chemotherapy. Previous studies have investigated molecular mechanisms of primary resistance to Wee1 inhibition. Here, we investigated mechanisms of acquired resistance to Wee1 inhibition, focusing on the role of the Wee1-related kinase Myt1. Myt1 and Wee1 kinases were both capable of phosphorylating and inhibiting Cdk1/cyclin B, the key enzymatic complex required for mitosis, demonstrating their functional redundancy. Ectopic activation of Cdk1 induced aberrant mitosis and cell death by mitotic catastrophe. Cancer cells with intrinsic adavosertib resistance had higher levels of Myt1 compared with sensitive cells. Furthermore, cancer cells that acquired resistance following short-term adavosertib treatment had higher levels of Myt1 compared with mock-treated cells. Downregulating Myt1 enhanced ectopic Cdk1 activity and restored sensitivity to adavosertib. These data demonstrate that upregulating Myt1 is a mechanism by which cancer cells acquire resistance to adavosertib. SIGNIFICANCE: Myt1 is a candidate predictive biomarker of acquired resistance to the Wee1 kinase inhibitor adavosertib.
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Affiliation(s)
- Cody W Lewis
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada.,Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, Alberta, Canada
| | - Amirali B Bukhari
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada.,Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, Alberta, Canada
| | - Edric J Xiao
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, Alberta, Canada
| | - Won-Shik Choi
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada.,Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, Alberta, Canada
| | - Joanne D Smith
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada.,Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, Alberta, Canada
| | - Ellen Homola
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - John R Mackey
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Medical Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Shelagh D Campbell
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Armin M Gamper
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada.,Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, Alberta, Canada
| | - Gordon K Chan
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada. .,Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada.,Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, Alberta, Canada
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23
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Li Z, Zhou M, Cai Z, Liu H, Zhong W, Hao Q, Cheng D, Hu X, Hou J, Xu P, Xue Y, Zhou Y, Xu T. RNA-binding protein DDX1 is responsible for fatty acid-mediated repression of insulin translation. Nucleic Acids Res 2019; 46:12052-12066. [PMID: 30295850 PMCID: PMC6294501 DOI: 10.1093/nar/gky867] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 09/14/2018] [Indexed: 01/13/2023] Open
Abstract
The molecular mechanism in pancreatic β cells underlying hyperlipidemia and insulin insufficiency remains unclear. Here, we find that the fatty acid-induced decrease in insulin levels occurs due to a decrease in insulin translation. Since regulation at the translational level is generally mediated through RNA-binding proteins, using RNA antisense purification coupled with mass spectrometry, we identify a novel insulin mRNA-binding protein, namely, DDX1, that is sensitive to palmitate treatment. Notably, the knockdown or overexpression of DDX1 affects insulin translation, and the knockdown of DDX1 eliminates the palmitate-induced repression of insulin translation. Molecular mechanism studies show that palmitate treatment causes DDX1 phosphorylation at S295 and dissociates DDX1 from insulin mRNA, thereby leading to the suppression of insulin translation. In addition, DDX1 may interact with the translation initiation factors eIF3A and eIF4B to regulate translation. In high-fat diet mice, the inhibition of insulin translation happens at an early prediabetic stage before the elevation of glucose levels. We speculate that the DDX1-mediated repression of insulin translation worsens the situation of insulin resistance and contributes to the elevation of blood glucose levels in obese animals.
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Affiliation(s)
- Zonghong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China.,Jilin Province Key Laboratory on Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Maoge Zhou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhaokui Cai
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongyang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen Zhong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Hao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Dongwan Cheng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Xihao Hu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Junjie Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingyong Xu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yifa Zhou
- Jilin Province Key Laboratory on Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Tao Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
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24
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Liu RZ, Vo TM, Jain S, Choi WS, Garcia E, Monckton EA, Mackey JR, Godbout R. NFIB promotes cell survival by directly suppressing p21 transcription in TP53-mutated triple-negative breast cancer. J Pathol 2018; 247:186-198. [PMID: 30350349 DOI: 10.1002/path.5182] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 09/21/2018] [Accepted: 10/10/2018] [Indexed: 12/27/2022]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with limited treatment options and poor prognosis. There is an urgent need to identify and understand the key factors and signalling pathways driving TNBC tumour progression, relapse, and treatment resistance. In this study, we report that gene copy numbers and expression levels of nuclear factor IB (NFIB), a recently identified oncogene in small cell lung cancer, are preferentially increased in TNBC compared to other breast cancer subtypes. Furthermore, increased levels of NFIB are significantly associated with high tumour grade, poor prognosis, and reduced chemotherapy response. Concurrent TP53 mutations and NFIB overexpression (z-scores > 0) were observed in 77.9% of TNBCs, in contrast to 28.5% in non-TNBCs. Depletion of NFIB in TP53-mutated TNBC cell lines promotes cell death, cell cycle arrest, and enhances sensitivity to docetaxel, a first-line chemotherapeutic drug in breast cancer treatment. Importantly, these alterations in growth properties were accompanied by induction of CDKN1A, the gene encoding p21, a downstream effector of p53. We show that NFIB directly interacts with the CDKN1A promoter in TNBC cells. Furthermore, knockdown of combined p21 and NFIB reverses the docetaxel-induced cell growth inhibition observed upon NFIB knockdown, indicating that NFIB's effect on chemotherapeutic drug response is mediated through p21. Our results indicate that NFIB is an important TNBC factor that drives tumour cell growth and drug resistance, leading to poor clinical outcomes. Thus, targeting NFIB in TP53-mutated TNBC may reverse oncogenic properties associated with mutant p53 by restoring p21 activity. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Rong-Zong Liu
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - The M Vo
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - Saket Jain
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - Won-Shik Choi
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - Elizabeth Garcia
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - Elizabeth A Monckton
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - John R Mackey
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - Roseline Godbout
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
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25
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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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26
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Meier-Stephenson V, Mrozowich T, Pham M, Patel TR. DEAD-box helicases: the Yin and Yang roles in viral infections. Biotechnol Genet Eng Rev 2018; 34:3-32. [PMID: 29742983 DOI: 10.1080/02648725.2018.1467146] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Viruses hijack the host cell machinery and recruit host proteins to aid their replication. Several host proteins also play vital roles in inhibiting viral replication. Emerging class of host proteins central to both of these processes are the DEAD-box helicases: a highly conserved family of ATP-dependent RNA helicases, bearing a common D-E-A-D (Asp-Glu-Ala-Asp) motif. They play key roles in numerous cellular processes, including transcription, splicing, miRNA biogenesis and translation. Though their sequences are highly conserved, these helicases have quite diverse roles in the cell. Interestingly, often these helicases display contradictory actions in terms of the support and/or clearance of invading viruses. Increasing evidence highlights the importance of these enzymes, however, little is known about the structural basis of viral RNA recognition by the members of the DEAD-box family. This review summarizes the current knowledge in the field for selected DEAD-box helicases and highlights their diverse actions upon viral invasion of the host cell. We anticipate that through a better understanding of how these helicases are being utilized by viral RNAs and proteins to aid viral replication, it will be possible to address the urgent need to develop novel therapeutic approaches to combat viral infections.
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Affiliation(s)
- Vanessa Meier-Stephenson
- a Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute , University of Lethbridge , Lethbridge , Canada.,b Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine , University of Calgary , Calgary , Canada
| | - Tyler Mrozowich
- a Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute , University of Lethbridge , Lethbridge , Canada
| | - Mimi Pham
- a Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute , University of Lethbridge , Lethbridge , Canada
| | - Trushar R Patel
- a Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute , University of Lethbridge , Lethbridge , Canada.,b Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine , University of Calgary , Calgary , Canada.,c Faculty of Medicine & Dentistry, DiscoveryLab , University of Alberta , Edmonton , Canada
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27
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High Myc expression and transcription activity underlies intra-tumoral heterogeneity in triple-negative breast cancer. Oncotarget 2018; 8:28101-28115. [PMID: 28427212 PMCID: PMC5438634 DOI: 10.18632/oncotarget.15891] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 02/21/2017] [Indexed: 01/11/2023] Open
Abstract
We have previously identified a novel intra-tumoral dichotomy in triple-negative breast cancer (TNBC) based on the differential responsiveness to a reporter containing the Sox2 regulatory region-2 (SRR2), with reporter responsive (RR) cells being more stem-like than reporter unresponsive (RU) cells. Using bioinformatics, we profiled the protein-DNA binding motifs of SRR2 and identified Myc as one of the potential transcription factors driving SRR2 activity. In support of its role, Myc was found to be highly expressed in RR cells as compared to RU cells. Enforced expression of MYC in RU cells resulted in a significant increase in SRR2 activity, Myc-DNA binding, proportion of cellsexpressing CD44+/CD24-, chemoresistance and mammosphere formation. Knockdown of Myc using siRNA in RR cells led to the opposite effects. We also found evidence that the relatively high ERK activation in RR cells contributes to their high expression of Myc and stem-like features. Using confocal microscopy and patient samples, we found a co-localization between Myc and CD44 in the same cell population. Lastly, a high proportion of Myc-positive cells in tumors significantly correlated with a short patient survival. In conclusion, inhibition of the MAPK/ERK/Myc axis may be an effective approach in eliminating stem-like cells in TNBC.
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28
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Fu TY, Wu CN, Sie HC, Cheng JT, Lin YS, Liou HH, Tseng YK, Shu CW, Tsai KW, Yen LM, Tseng HW, Tseng CJ, Ger LP, Liu PF. Subsite-specific association of DEAD box RNA helicase DDX60 with the development and prognosis of oral squamous cell carcinoma. Oncotarget 2018; 7:85097-85108. [PMID: 27835882 PMCID: PMC5356722 DOI: 10.18632/oncotarget.13197] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 10/28/2016] [Indexed: 01/05/2023] Open
Abstract
The clinical significance and biological function of DEXD/H box helicase 60 (DDX60) in oral cancer remains unknown. Herein, we evaluated the association of DDX60 expression with tumorigenesis and the prognosis of oral squamous cell carcinoma (OSCC). DDX60 expression was examined by immunohistochemistry on tissue microarray slides of 494 OSCC patients, including 180 buccal mucosal SCC (BMSCC), 241 tongue SCC (TSCC), and 73 lip SCC (LSCC) patients. DDX60 expression was significantly increased in all three subsites of OSCC compared to its expression in tumor adjacent normal tissues. However, its association with tumorigenesis was specific to the oral cavity subsite after the stratification of betel quid chewing, smoking, and drinking. Among OSCC patients, higher levels of DDX60 expression were associated with the male gender, a well-differentiated tumor, advanced stage of disease, and a large tumor size with subsite specific features. LSCC patients with high DDX60 expression levels showed shorter disease-specific survival, particularly those with moderately or poorly differentiated tumors. Additionally, TSCC or OSCC patients with high DDX60 expression showed a poor disease-free survival (DFS), particularly those with moderately or poorly differentiated tumors. Therefore, DDX60 is a novel and unfavorable biomarker for tumorigenesis and prognosis of OSCC in a subsite-specific manner.
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Affiliation(s)
- Ting-Ying Fu
- Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Optometry, Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan
| | - Chao-Nan Wu
- Department of Stomatology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Dental Technology, Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan
| | - Huei-Cin Sie
- Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Jiin-Tsuey Cheng
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Yaoh-Shiang Lin
- Department of Otorhinolaryngology-Head & Neck Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Huei-Han Liou
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Yu-Kai Tseng
- Department of Orthopedics, Show Chwan Memorial Hospital, Changhua, Taiwan.,Department of Orthopedics, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Chih-Wen Shu
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Kuo-Wang Tsai
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Chemical Biology, National Pingtung University of Education, Pingtung, Taiwan
| | - Leing-Ming Yen
- Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Hui-Wen Tseng
- Department of Dermatology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Nursing, Meiho University, Pingtung, Taiwan
| | - Ching-Jiunn Tseng
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Pharmacology, National Defense Medical Center, Taipei, Taiwan.,Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Luo-Ping Ger
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Pei-Feng Liu
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Biotechnology, Fooyin University, Kaohsiung, Taiwan
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29
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The pro-apoptotic paradox: the BH3-only protein Bcl-2 interacting killer (Bik) is prognostic for unfavorable outcomes in breast cancer. Oncotarget 2017; 7:33272-85. [PMID: 27120789 PMCID: PMC5078093 DOI: 10.18632/oncotarget.8924] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/10/2016] [Indexed: 01/24/2023] Open
Abstract
Breast cancer is the leading cause of cancer-associated deaths in women worldwide. Clinical biomarkers give information on disease progression and identify relevant biological pathways. A confounding factor that uncouples markers from disease outcome is the ability of tumor cells to mutate and evade clinical intervention. Therefore, we focussed on apoptotic genes that modulate tumor regression. Using gene and tissue microarray analyses, we identified an association of Bcl-2 interacting killer (Bik) with poor breast cancer prognosis. Bik prognostic ability was independent of Estrogen Receptor/Progesterone Receptor and Her2 status. Additionally, Bik was independent of anti-apoptotic Bcl-2, Bcl-xL, Mcl-1 and Bcl-w suggesting a complex mechanism of tumor promotion identified by Bik high tumors. Bik also stimulates autophagy, which can contribute to enhanced tumor fitness. We found a significant association between the autophagy marker ATG5 and Bik. Combined high expression level of ATG5 and Bik was a stronger predictor of outcome than either alone. Thus, our study identifies Bik as a novel, independent prognostic biomarker for poor outcomes in breast cancer and suggests that Bik-mediated autophagy contributes to disease recurrence.
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30
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Wang C, Kar S, Lai X, Cai W, Arfuso F, Sethi G, Lobie PE, Goh BC, Lim LHK, Hartman M, Chan CW, Lee SC, Tan SH, Kumar AP. Triple negative breast cancer in Asia: An insider's view. Cancer Treat Rev 2017; 62:29-38. [PMID: 29154023 DOI: 10.1016/j.ctrv.2017.10.014] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/29/2017] [Accepted: 10/31/2017] [Indexed: 12/31/2022]
Abstract
While tremendous improvement has been made for the treatment of breast cancers, the treatment of triple negative breast cancer (TNBC) still remains a challenge due to its aggressive characteristics and limited treatment options. Most of the studies on TNBC were conducted in Western population and TNBC is reported to be more frequent in the African women. This review encapsulates the studies conducted on TNBC patients in Asian population and elucidates the similarities and differences between these two regions. The current treatment of TNBC includes surgery, radiotherapy and chemotherapy. In addition to the current chemotherapies, which mainly include cytotoxic agents, such as taxanes and anthracyclines, many clinical trials are investigating the potential use of other chemotherapy drugs, targeted therapeutics and combinational therapies to treat TNBC. Moreover, this review also integrates the studies involving novel markers, which will help us to dissect the pathologic process of TNBC and in turn facilitate the development of better treatment strategies to combat TNBC.
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Affiliation(s)
- Chao Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shreya Kar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Xianning Lai
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Wanpei Cai
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Frank Arfuso
- Stem Cell and Cancer Biology Laboratory, School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Peter E Lobie
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Tsinghua Berkeley Shenzhen Institute, Tsinghua University Graduate School at Shenzhen, Shenzhen, China
| | - Boon C Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Haematology-Oncology, National University Hospital, National University Health System, Singapore; National University Cancer Institute, National University Health System, Singapore
| | - Lina H K Lim
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore; NUS Immunology Program, National University of Singapore, Singapore
| | - Mikael Hartman
- Department of Haematology-Oncology, National University Hospital, National University Health System, Singapore; Department of Surgery, National University Cancer Institute, National University Health System, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Ching W Chan
- Department of Surgery, National University Cancer Institute, National University Health System, Singapore
| | - Soo C Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Haematology-Oncology, National University Hospital, National University Health System, Singapore; National University Cancer Institute, National University Health System, Singapore
| | - Sing H Tan
- Department of Haematology-Oncology, National University Hospital, National University Health System, Singapore; National University Cancer Institute, National University Health System, Singapore; OncoCare Cancer Centre, Gleneagles Medical Centre, Singapore.
| | - Alan P Kumar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; National University Cancer Institute, National University Health System, Singapore; Curtin Medical School, Faculty of Health Sciences, Curtin University, Perth, WA, Australia; Medical Science Cluster, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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31
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Li L, Poon HY, Hildebrandt MR, Monckton EA, Germain DR, Fahlman RP, Godbout R. Role for RIF1-interacting partner DDX1 in BLM recruitment to DNA double-strand breaks. DNA Repair (Amst) 2017; 55:47-63. [DOI: 10.1016/j.dnarep.2017.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/01/2017] [Accepted: 05/02/2017] [Indexed: 01/13/2023]
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32
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Wang M, Zhang G, Wang Y, Ma R, Zhang L, Lv H, Fang F, Kang X. DHX32 expression is an indicator of poor breast cancer prognosis. Oncol Lett 2016; 13:942-948. [PMID: 28356982 DOI: 10.3892/ol.2016.5503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/26/2016] [Indexed: 02/06/2023] Open
Abstract
Emerging evidence suggests that DEAH-box polypeptide 32 (DHX32) serves an important role in the progression and metastasis of cancer. However, the role of DHX32 in breast cancer remains to be completely elucidated. The aim of the present study was to evaluate the expression and clinical significance of DHX32 in breast cancer. The reverse transcription-quantitative polymerase chain reaction was performed to analyze DHX32 messenger (m)RNA expression, and western blotting and immunohistochemistry were performed to examine DHX32 protein expression in breast cancer and adjacent non-cancerous tissues. The association in breast cancer between DHX32 expression, clinicopathological features and prognosis was analyzed using 193 breast cancer tissue samples. The results of the present study demonstrated that breast cancer tissues exhibited increased DHX32 mRNA and protein expression compared with adjacent non-cancerous tissues (P<0.001). In addition, DHX32 expression was significantly associated with breast cancer clinical stage (P=0.006), histological grade (P=0.029), lymph node metastasis (P<0.001) and expression of the proliferation marker Ki-67 (P=0.004). Kaplan-Meier estimator analysis indicated that increased DHX32 expression is associated with poor prognosis in patients with breast cancer. Furthermore, the Cox proportional hazards model indicated that DHX32 expression is an independent prognostic factor for decreased overall survival and disease-free survival in patients with breast cancer. In conclusion, the results of the present study suggest that DHX32 overexpression is an unfavorable prognostic biomarker in breast cancer and a potential therapeutic target of future breast cancer treatments.
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Affiliation(s)
- Meng Wang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Guojun Zhang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China; Beijing Engineering Research Center of Immunological Reagents and Clinical Research, Beijing 100050, P.R. China
| | - Yajie Wang
- Core Laboratory for Clinical Medical Research, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Ruimin Ma
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Limin Zhang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Hong Lv
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Fang Fang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Xixiong Kang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China; Beijing Engineering Research Center of Immunological Reagents and Clinical Research, Beijing 100050, P.R. China
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33
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DEAD Box 1 Facilitates Removal of RNA and Homologous Recombination at DNA Double-Strand Breaks. Mol Cell Biol 2016; 36:2794-2810. [PMID: 27550810 DOI: 10.1128/mcb.00415-16] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 08/17/2016] [Indexed: 12/16/2022] Open
Abstract
Although RNA and RNA-binding proteins have been linked to double-strand breaks (DSBs), little is known regarding their roles in the cellular response to DSBs and, if any, in the repair process. Here, we provide direct evidence for the presence of RNA-DNA hybrids at DSBs and suggest that binding of RNA to DNA at DSBs may impact repair efficiency. Our data indicate that the RNA-unwinding protein DEAD box 1 (DDX1) is required for efficient DSB repair and cell survival after ionizing radiation (IR), with depletion of DDX1 resulting in reduced DSB repair by homologous recombination (HR). While DDX1 is not essential for end resection, a key step in homology-directed DSB repair, DDX1 is required for maintenance of the single-stranded DNA once generated by end resection. We show that transcription deregulation has a significant effect on DSB repair by HR in DDX1-depleted cells and that RNA-DNA duplexes are elevated at DSBs in DDX1-depleted cells. Based on our combined data, we propose a role for DDX1 in resolving RNA-DNA structures that accumulate at DSBs located at sites of active transcription. Our findings point to a previously uncharacterized requirement for clearing RNA at DSBs for efficient repair by HR.
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34
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Krishnan P, Ghosh S, Wang B, Heyns M, Graham K, Mackey JR, Kovalchuk O, Damaraju S. Profiling of Small Nucleolar RNAs by Next Generation Sequencing: Potential New Players for Breast Cancer Prognosis. PLoS One 2016; 11:e0162622. [PMID: 27631501 PMCID: PMC5025248 DOI: 10.1371/journal.pone.0162622] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 08/25/2016] [Indexed: 01/09/2023] Open
Abstract
One of the most abundant, yet least explored, classes of RNA is the small nucleolar RNAs (snoRNAs), which are well known for their involvement in post-transcriptional modifications of other RNAs. Although snoRNAs were only considered to perform housekeeping functions for a long time, recent studies have highlighted their importance as regulators of gene expression and as diagnostic/prognostic markers. However, the prognostic potential of these RNAs has not been interrogated for breast cancer (BC). The objective of the current study was to identify snoRNAs as prognostic markers for BC. Small RNA sequencing (Illumina Genome Analyzer IIx) was performed for 104 BC cases and 11 normal breast tissues. Partek Genomics Suite was used for analyzing the sequencing files. Two independent and proven approaches were used to identify prognostic markers: case-control (CC) and case-only (CO). For both approaches, snoRNAs significant in the permutation test, following univariate Cox proportional hazards regression model were used for constructing risk scores. Risk scores were subsequently adjusted for potential confounders in a multivariate Cox model. For both approaches, thirteen snoRNAs were associated with overall survival and/or recurrence free survival. Patients belonging to the high-risk group were associated with poor outcomes, and the risk score was significant after adjusting for confounders. Validation of representative snoRNAs (SNORD46 and SNORD89) using qRT-PCR confirmed the observations from sequencing experiments. We also observed 64 snoRNAs harboring piwi-interacting RNAs and/or microRNAs that were predicted to target genes (mRNAs) involved in tumorigenesis. Our results demonstrate the potential of snoRNAs to serve (i) as novel prognostic markers for BC and (ii) as indirect regulators of gene expression.
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Affiliation(s)
- Preethi Krishnan
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Sunita Ghosh
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
| | - Bo Wang
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Mieke Heyns
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Kathryn Graham
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
| | - John R Mackey
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Sambasivarao Damaraju
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.,Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
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35
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Genome-wide profiling of transfer RNAs and their role as novel prognostic markers for breast cancer. Sci Rep 2016; 6:32843. [PMID: 27604545 PMCID: PMC5015097 DOI: 10.1038/srep32843] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/11/2016] [Indexed: 11/25/2022] Open
Abstract
Transfer RNAs (tRNAs, key molecules in protein synthesis) have not been investigated as potential prognostic markers in breast cancer (BC), despite early findings of their dysregulation and diagnostic potential. We aim to comprehensively profile tRNAs from breast tissues and to evaluate their role as prognostic markers (Overall Survival, OS and Recurrence Free Survival, RFS). tRNAs were profiled from 11 normal breast and 104 breast tumor tissues using next generation sequencing. We adopted a Case-control (CC) and Case-Only (CO) association study designs. Risk scores constructed from tRNAs were subjected to univariate and multivariate Cox-proportional hazards regression to investigate their prognostic value. Of the 571 tRNAs profiled, 76 were differentially expressed (DE) and three were significant for OS in the CC approach. We identified an additional 11 tRNAs associated with OS and 14 tRNAs as significant for RFS in the CO approach, indicating that CC alone may not capture all discriminatory tRNAs in prognoses. In both the approaches, the risk scores were significant in the multivariate analysis as independent prognostic factors, and patients belonging to high-risk group were associated with poor prognosis. Our results confirmed global up-regulation of tRNAs in BC and identified tRNAs as potential novel prognostic markers for BC.
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36
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Li B, Li YM, He WT, Chen H, Zhu HW, Liu T, Zhang JH, Song TN, Zhou YL. Knockdown of DDX46 inhibits proliferation and induces apoptosis in esophageal squamous cell carcinoma cells. Oncol Rep 2016; 36:223-30. [PMID: 27176873 DOI: 10.3892/or.2016.4803] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 02/24/2016] [Indexed: 11/05/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is the most common type of esophageal carcinoma and remains the leading cause of cancer-related death worldwide. DEAD-box RNA helicases play critical roles in cellular metabolism and in many cases have been implicated in cellular proliferation and neoplastic transformation. DDX46 belongs to DEAD-box helicase family, the expression pattern of DDX46 in ESCC tissues and the biologic role in ESCC progression have not been implicated previously. In this study, DDX46 expression in human ESCC and adjacent normal tissues were explored using immunohistochemistry, and ESCC cell lines compared with normal esophageal epithelium cell were quantified using real‑time PCR. Next, lentivirus-mediated RNA interference was applied to silence DDX46 in TE-1 and Eca-109 cells. Cell growth was monitored using high content screening. Cell viability was measured by MTT assay. Cell colony-forming capacity was measured by colony formation assay. Cell cycle progression and apoptosis were determined by flow cytometry. Further, the stress and apoptosis signaling antibody array kit was used to detect the changes of signaling molecules in TE-1 cells after DDX46 knockdown. We found that DDX46 was significantly upregulated in ESCC tissues and cells compared with normal tissues and cells. DDX46 knockdown led to decreased proliferation and increased apoptosis in TE-1 and Eca-109 cells. Moreover, DDX46 silencing resulted in apoptotic induction via decreased phosphorylation of Akt and IκBα, as well as negative regulation of NF-κB signaling. In conclusion, these results demonstrate that DDX46 knockdown inhibited cell growth, and induced apoptosis, suggest that DDX46 is critical for ESCC cells proliferation. In addition, this study provides a foundation for further study into the clinical potential diagnosis and novel therapeutic target for ESCC.
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Affiliation(s)
- Bin Li
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou 730030, P.R. China
| | - Yu-Min Li
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou 730030, P.R. China
| | - Wen-Ting He
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou 730030, P.R. China
| | - Hao Chen
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou 730030, P.R. China
| | - Hong-Wen Zhu
- Gansu Provincial Key Laboratory of Digestive System Tumors, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou 730030, P.R. China
| | - Tao Liu
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou 730030, P.R. China
| | - Jian-Hua Zhang
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou 730030, P.R. China
| | - Tie-Niu Song
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou 730030, P.R. China
| | - Ya-Li Zhou
- Gansu Provincial Key Laboratory of Digestive System Tumors, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou 730030, P.R. China
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37
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Loss of the Drosophila melanogaster DEAD box protein Ddx1 leads to reduced size and aberrant gametogenesis. Dev Biol 2015; 407:232-45. [PMID: 26433063 PMCID: PMC7094483 DOI: 10.1016/j.ydbio.2015.09.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/31/2015] [Accepted: 09/24/2015] [Indexed: 02/07/2023]
Abstract
Mammalian DDX1 has been implicated in RNA trafficking, DNA double-strand break repair and RNA processing; however, little is known about its role during animal development. Here, we report phenotypes associated with a null Ddx1 (Ddx1AX) mutation generated in Drosophila melanogaster. Ddx1 null flies are viable but significantly smaller than control and Ddx1 heterozygous flies. Female Ddx1 null flies have reduced fertility with egg chambers undergoing autophagy, whereas males are sterile due to disrupted spermatogenesis. Comparative RNA sequencing of control and Ddx1 null third instars identified several transcripts affected by Ddx1 inactivation. One of these, Sirup mRNA, was previously shown to be overexpressed under starvation conditions and implicated in mitochondrial function. We demonstrate that Sirup is a direct binding target of Ddx1 and that Sirup mRNA is differentially spliced in the presence or absence of Ddx1. Combining Ddx1 null mutation with Sirup dsRNA-mediated knock-down causes epistatic lethality not observed in either single mutant. Our data suggest a role for Drosophila Ddx1 in stress-induced regulation of splicing. We describe a new Ddx1 null Drosophila line. Ddx1 null flies are smaller in size and display aberrant gametogenesis. Sirup splicing is altered in Ddx1 null flies. We show both a physical and a genetic interaction between Ddx1 and Sirup.
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38
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Benesch MGK, Tang X, Dewald J, Dong WF, Mackey JR, Hemmings DG, McMullen TPW, Brindley DN. Tumor-induced inflammation in mammary adipose tissue stimulates a vicious cycle of autotaxin expression and breast cancer progression. FASEB J 2015; 29:3990-4000. [DOI: 10.1096/fj.15-274480] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/26/2015] [Indexed: 02/06/2023]
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39
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Law J, Salla M, Zare A, Wong Y, Luong L, Volodko N, Svystun O, Flood K, Lim J, Sung M, Dyck JRB, Tan CT, Su YC, Yu VC, Mackey J, Baksh S. Modulator of apoptosis 1 (MOAP-1) is a tumor suppressor protein linked to the RASSF1A protein. J Biol Chem 2015; 290:24100-18. [PMID: 26269600 PMCID: PMC4591801 DOI: 10.1074/jbc.m115.648345] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 01/21/2023] Open
Abstract
Modulator of apoptosis 1 (MOAP-1) is a BH3-like protein that plays key roles in cell death or apoptosis. It is an integral partner to the tumor suppressor protein, Ras association domain family 1A (RASSF1A), and functions to activate the Bcl-2 family pro-apoptotic protein Bax. Although RASSF1A is now considered a bona fide tumor suppressor protein, the role of MOAP-1 as a tumor suppressor protein has yet to be determined. In this study, we present several lines of evidence from cancer databases, immunoblotting of cancer cells, proliferation, and xenograft assays as well as DNA microarray analysis to demonstrate the role of MOAP-1 as a tumor suppressor protein. Frequent loss of MOAP-1 expression, in at least some cancers, appears to be attributed to mRNA down-regulation and the rapid proteasomal degradation of MOAP-1 that could be reversed utilizing the proteasome inhibitor MG132. Overexpression of MOAP-1 in several cancer cell lines resulted in reduced tumorigenesis and up-regulation of genes involved in cancer regulatory pathways that include apoptosis (p53, Fas, and MST1), DNA damage control (poly(ADP)-ribose polymerase and ataxia telangiectasia mutated), those within the cell metabolism (IR-α, IR-β, and AMP-activated protein kinase), and a stabilizing effect on microtubules. The loss of RASSF1A (an upstream regulator of MOAP-1) is one of the earliest detectable epigenetically silenced tumor suppressor proteins in cancer, and we speculate that the additional loss of function of MOAP-1 may be a second hit to functionally compromise the RASSF1A/MOAP-1 death receptor-dependent pathway and drive tumorigenesis.
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Affiliation(s)
| | | | | | - Yoke Wong
- From the Departments of Biochemistry and
| | - Le Luong
- From the Departments of Biochemistry and
| | | | | | | | | | - Miranda Sung
- Pediatrics, Cardiovascular Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jason R B Dyck
- Pediatrics, Cardiovascular Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Chong Teik Tan
- the Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
| | - Yu-Chin Su
- the Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
| | - Victor C Yu
- the Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
| | - John Mackey
- the Department of Experimental Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada, and
| | - Shairaz Baksh
- From the Departments of Biochemistry and Pediatrics, the Department of Experimental Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada, and the Cancer Research Institute of Northern Alberta, Edmonton, Alberta T6G 1Z2, Canada, the Alberta IBD Consortium, Edmonton, Alberta T6G 2X8, Canada, and the Women and Children's Health Research Institute, Edmonton, Alberta T6G 1C9, Canada
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40
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Liu RZ, Garcia E, Glubrecht DD, Poon HY, Mackey JR, Godbout R. CRABP1 is associated with a poor prognosis in breast cancer: adding to the complexity of breast cancer cell response to retinoic acid. Mol Cancer 2015; 14:129. [PMID: 26142905 PMCID: PMC4491424 DOI: 10.1186/s12943-015-0380-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 05/07/2015] [Indexed: 12/31/2022] Open
Abstract
Background Clinical trials designed to test the efficacy of retinoic acid (RA) as an adjuvant for the treatment of solid cancers have been disappointing, primarily due to RA resistance. Estrogen receptor (ER)-negative breast cancer cells are more resistant to RA than ER-positive cells. The expression and subcellular distribution of two RA-binding proteins, FABP5 and CRABP2, has already been shown to play critical roles in breast cancer cell response to RA. CRABP1, a third member of the RA-binding protein family, has not previously been investigated as a possible mediator of RA action in breast cancer. Methods CRABP1 and CRABP2 expression in primary breast tumor tissues was analyzed using gene expression and tissue microarrays. CRABP1 levels were manipulated using siRNAs and by transient overexpression. RA-induced subcellular translocation of CRABPs was examined by immunofluorescence microscopy and immunoblotting. RA-induced transactivation of RAR was analyzed using a RA response element (RARE)-driven luciferase reporter system. Effects of CRABP1 expression and RA treatment on downstream gene expression were investigated by semi-quantitative RT-PCR analysis. Results Compared to normal mammary tissues, CRABP1 expression is significantly down-regulated in ER+ breast tumors, but maintained in triple-negative breast cancers. Elevated CRABP1 levels are associated with poor patient prognosis, high Ki67 immunoreactivity and high tumor grade in breast cancer. The prognostic significance of CRABP1 is attributed to its cytoplasmic localization. We demonstrate that CRABP1 expression attenuates RA-induced cell growth arrest and inhibits RA signalling in breast cancer cells by sequestering RA in the cytoplasm. We also show that CRABP1 affects the expression of genes involved in RA biosynthesis, trafficking and metabolism. Conclusions CRABP1 is an adverse factor for clinical outcome in triple-negative breast cancer and a potent inhibitor of RA signalling in breast cancer cells. Our data indicate that CRABP1, in conjunction with previously identified CRABP2 and FABP5, plays a key role in breast cancer cell response to RA. We propose that these three RA-binding proteins can serve as biomarkers for predicting triple-negative breast cancer response to RA, with elevated levels of either cytoplasmic CRABP1 or FABP5 associated with RA resistance, and elevated levels of nuclear CRABP2 associated with sensitivity to RA. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0380-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rong-Zong Liu
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, T6G 1Z2, AB, Canada
| | - Elizabeth Garcia
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, T6G 1Z2, AB, Canada
| | - Darryl D Glubrecht
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, T6G 1Z2, AB, Canada
| | - Ho Yin Poon
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, T6G 1Z2, AB, Canada
| | - John R Mackey
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, T6G 1Z2, AB, Canada
| | - Roseline Godbout
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, T6G 1Z2, AB, Canada.
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41
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Yin J, Park G, Lee JE, Choi EY, Park JY, Kim TH, Park N, Jin X, Jung JE, Shin D, Hong JH, Kim H, Yoo H, Lee SH, Kim YJ, Park JB, Kim JH. DEAD-box RNA helicase DDX23 modulates glioma malignancy via elevating miR-21 biogenesis. Brain 2015; 138:2553-70. [DOI: 10.1093/brain/awv167] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 04/17/2015] [Indexed: 01/01/2023] Open
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42
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Hildebrandt MR, Germain DR, Monckton EA, Brun M, Godbout R. Ddx1 knockout results in transgenerational wild-type lethality in mice. Sci Rep 2015; 5:9829. [PMID: 25909345 PMCID: PMC4408975 DOI: 10.1038/srep09829] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/20/2015] [Indexed: 12/21/2022] Open
Abstract
DEAD box 1 (DDX1) is a member of the DEAD box family of RNA helicases which are
involved in all aspects of RNA metabolism. DDX1 has been implicated in a variety of
biological processes, including 3’-end processing of mRNA, DNA repair,
microRNA processing, tRNA maturation and mRNA transport. To study the role of DDX1
during development, we have generated mice carrying a constitutive Ddx1
knock-out allele. Ddx1+/− mice have no obvious
phenotype and express similar levels of DDX1 as wild-type mice indicating
compensation from the intact Ddx1 allele. Heterozygote matings produce no
viable Ddx1−/− progeny, with
Ddx1−/− embryos dying prior to
embryonic day (E) 3.5. Intriguingly, the number of wild-type progeny is
significantly decreased in heterozygote crosses, with two different heterozygote
populations identified based on parental genotype: (i) normal
Ddx1+/− mice which generate the expected number
of wild-type progeny and (ii) Ddx1*/− mice (with *
signifying a non-genetically altered allele) which generate a significantly reduced
number of wild-type mice. The transgenerational inheritance of wild-type lethality
observed upon crossing Ddx1*/− mice is independent
of parental sex and occurs in cis through a mechanism that is different from
other types of previously reported transgenerational epigenetic inheritance.
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Affiliation(s)
- Matthew R Hildebrandt
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Devon R Germain
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Elizabeth A Monckton
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Miranda Brun
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Roseline Godbout
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
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43
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Lentiviral DDX46 knockdown inhibits growth and induces apoptosis in human colorectal cancer cells. Gene 2015; 560:237-44. [DOI: 10.1016/j.gene.2015.02.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 01/26/2015] [Accepted: 02/08/2015] [Indexed: 12/11/2022]
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44
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Pavlou MP, Dimitromanolakis A, Martinez-Morillo E, Smid M, Foekens JA, Diamandis EP. Integrating Meta-Analysis of Microarray Data and Targeted Proteomics for Biomarker Identification: Application in Breast Cancer. J Proteome Res 2014; 13:2897-909. [DOI: 10.1021/pr500352e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Maria P. Pavlou
- Department
of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Department
of Pathology and Laboratory Medicine, Mount Sinai Hospital, 60 Murray
Street, Toronto, ON M5T 3L9, Canada
| | - Apostolos Dimitromanolakis
- Department
of Pathology and Laboratory Medicine, Mount Sinai Hospital, 60 Murray
Street, Toronto, ON M5T 3L9, Canada
| | - Eduardo Martinez-Morillo
- Lunenfeld-Tanenbaum
Research Institute, Joseph and Wolf Lebovic Health Complex, Mount Sinai Hospital, 60 Murray Street, Toronto, ON M5T 3L9, Canada
| | - Marcel Smid
- Department
of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Groene Hilledijk 301, 3075 EA Rotterdam, The Netherlands
| | - John A. Foekens
- Department
of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Groene Hilledijk 301, 3075 EA Rotterdam, The Netherlands
| | - Eleftherios P. Diamandis
- Department
of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Department
of Pathology and Laboratory Medicine, Mount Sinai Hospital, 60 Murray
Street, Toronto, ON M5T 3L9, Canada
- Lunenfeld-Tanenbaum
Research Institute, Joseph and Wolf Lebovic Health Complex, Mount Sinai Hospital, 60 Murray Street, Toronto, ON M5T 3L9, Canada
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HAGE (DDX43) is a biomarker for poor prognosis and a predictor of chemotherapy response in breast cancer. Br J Cancer 2014; 110:2450-61. [PMID: 24755885 PMCID: PMC4021517 DOI: 10.1038/bjc.2014.168] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/28/2014] [Accepted: 03/05/2014] [Indexed: 01/10/2023] Open
Abstract
Background: HAGE protein is a known immunogenic cancer-specific antigen. Methods: The biological, prognostic and predictive values of HAGE expression was studied using immunohistochemistry in three cohorts of patients with BC (n=2147): early primary (EP-BC; n=1676); primary oestrogen receptor-negative (PER-BC; n=275) treated with adjuvant anthracycline-combination therapies (Adjuvant-ACT); and primary locally advanced disease (PLA-BC) who received neo-adjuvant anthracycline-combination therapies (Neo-adjuvant-ACT; n=196). The relationship between HAGE expression and the tumour-infiltrating lymphocytes (TILs) in matched prechemotherapy and postchemotherapy samples were investigated. Results: Eight percent of patients with EP-BC exhibited high HAGE expression (HAGE+) and was associated with aggressive clinico-pathological features (Ps<0.01). Furthermore, HAGE+expression was associated with poor prognosis in both univariate and multivariate analysis (Ps<0.001). Patients with HAGE+did not benefit from hormonal therapy in high-risk ER-positive disease. HAGE+and TILs were found to be independent predictors for pathological complete response to neoadjuvant-ACT; P<0.001. A statistically significant loss of HAGE expression following neoadjuvant-ACT was found (P=0.000001), and progression-free survival was worse in those patients who had HAGE+residual disease (P=0.0003). Conclusions: This is the first report to show HAGE to be a potential prognostic marker and a predictor of response to ACT in patients with BC.
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Bastani M, Vos L, Asgarian N, Deschenes J, Graham K, Mackey J, Greiner R. A machine learned classifier that uses gene expression data to accurately predict estrogen receptor status. PLoS One 2013; 8:e82144. [PMID: 24312637 PMCID: PMC3846850 DOI: 10.1371/journal.pone.0082144] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 10/30/2013] [Indexed: 01/13/2023] Open
Abstract
Background Selecting the appropriate treatment for breast cancer requires accurately determining the estrogen receptor (ER) status of the tumor. However, the standard for determining this status, immunohistochemical analysis of formalin-fixed paraffin embedded samples, suffers from numerous technical and reproducibility issues. Assessment of ER-status based on RNA expression can provide more objective, quantitative and reproducible test results. Methods To learn a parsimonious RNA-based classifier of hormone receptor status, we applied a machine learning tool to a training dataset of gene expression microarray data obtained from 176 frozen breast tumors, whose ER-status was determined by applying ASCO-CAP guidelines to standardized immunohistochemical testing of formalin fixed tumor. Results This produced a three-gene classifier that can predict the ER-status of a novel tumor, with a cross-validation accuracy of 93.17±2.44%. When applied to an independent validation set and to four other public databases, some on different platforms, this classifier obtained over 90% accuracy in each. In addition, we found that this prediction rule separated the patients' recurrence-free survival curves with a hazard ratio lower than the one based on the IHC analysis of ER-status. Conclusions Our efficient and parsimonious classifier lends itself to high throughput, highly accurate and low-cost RNA-based assessments of ER-status, suitable for routine high-throughput clinical use. This analytic method provides a proof-of-principle that may be applicable to developing effective RNA-based tests for other biomarkers and conditions.
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Affiliation(s)
- Meysam Bastani
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
| | - Larissa Vos
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Nasimeh Asgarian
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
- Alberta Innovates Centre for Machine Learning, Edmonton, Alberta, Canada
| | - Jean Deschenes
- Department of Pathology and Laboratory Medicine, University of Alberta, Edmonton, Alberta, Canada
- Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Kathryn Graham
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
- Cross Cancer Institute, Edmonton, Alberta, Canada
| | - John Mackey
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
- Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Russell Greiner
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
- Alberta Innovates Centre for Machine Learning, Edmonton, Alberta, Canada
- * E-mail:
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Tang Y, Mackey J, Lai R, Ghosh S, Santos C, Graham K, Damaraju S, Pasdar M, Li L. Quantitative proteomic analysis of HER2 normal and overexpressing MCF-7 breast cancer cells revealed proteomic changes accompanied with HER2 gene amplification. J Proteomics 2013; 91:200-9. [DOI: 10.1016/j.jprot.2013.06.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 06/29/2013] [Indexed: 12/18/2022]
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Robert F, Pelletier J. Perturbations of RNA helicases in cancer. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:333-49. [PMID: 23658027 DOI: 10.1002/wrna.1163] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Helicases are implicated in most stages of the gene expression pathway, ranging from DNA replication, RNA transcription, splicing, RNA transport, ribosome biogenesis, mRNA translation, RNA storage and decay. These enzymes utilize energy derived from nucleotide triphosphate hydrolysis to remodel ribonucleoprotein complexes, RNA, or DNA and in this manner affect the information content or output of RNA. Several RNA helicases have been implicated in the oncogenic process--either through altered expression levels, mutations, or due to their role in pathways required for tumor initiation, progression, maintenance, or chemosensitivity. The purpose of this review is to highlight those RNA helicases for which there is significant evidence implicating them in cancer biology.
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Affiliation(s)
- Francis Robert
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
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Abstract
Members of the DEAD box family of RNA helicases are known to be involved in most cellular processes that require manipulation of RNA structure and, in many cases, exhibit other functions in addition to their established ATP-dependent RNA helicase activities. They thus play critical roles in cellular metabolism and in many cases have been implicated in cellular proliferation and/or neoplastic transformation. These proteins generally act as components of multi-protein complexes; therefore their precise role is likely to be influenced by their interacting partners and to be highly context-dependent. This may also provide an explanation for the sometimes conflicting reports suggesting that DEAD box proteins have both pro- and anti-proliferative roles in cancer.
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Affiliation(s)
- Frances V Fuller-Pace
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland.
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Datta K, Hyduke DR, Suman S, Moon BH, Johnson MD, Fornace AJ. Exposure to ionizing radiation induced persistent gene expression changes in mouse mammary gland. Radiat Oncol 2012; 7:205. [PMID: 23216862 PMCID: PMC3551737 DOI: 10.1186/1748-717x-7-205] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 11/16/2012] [Indexed: 12/02/2022] Open
Abstract
Background Breast tissue is among the most sensitive tissues to the carcinogenic actions of ionizing radiation and epidemiological studies have linked radiation exposure to breast cancer. Currently, molecular understanding of radiation carcinogenesis in mammary gland is hindered due to the scarcity of in vivo long-term follow up data. We undertook this study to delineate radiation-induced persistent alterations in gene expression in mouse mammary glands 2-month after radiation exposure. Methods Six to eight week old female C57BL/6J mice were exposed to 2 Gy of whole body γ radiation and mammary glands were surgically removed 2-month after radiation. RNA was isolated and microarray hybridization performed for gene expression analysis. Ingenuity Pathway Analysis (IPA) was used for biological interpretation of microarray data. Real time quantitative PCR was performed on selected genes to confirm the microarray data. Results Compared to untreated controls, the mRNA levels of a total of 737 genes were significantly (p<0.05) perturbed above 2-fold of control. More genes (493 genes; 67%) were upregulated than the number of downregulated genes (244 genes; 33%). Functional analysis of the upregulated genes mapped to cell proliferation and cancer related canonical pathways such as ‘ERK/MAPK signaling’, ‘CDK5 signaling’, and ‘14-3-3-mediated signaling’. We also observed upregulation of breast cancer related canonical pathways such as ‘breast cancer regulation by Stathmin1’, and ‘HER-2 signaling in breast cancer’ in IPA. Interestingly, the downregulated genes mapped to fewer canonical pathways involved in cell proliferation. We also observed that a number of genes with tumor suppressor function (GPRC5A, ELF1, NAB2, Sema4D, ACPP, MAP2, RUNX1) persistently remained downregulated in response to radiation exposure. Results from qRT-PCR on five selected differentially expressed genes confirmed microarray data. The PCR data on PPP4c, ELF1, MAPK12, PLCG1, and E2F6 showed similar trend in up and downregulation as has been observed with the microarray. Conclusions Exposure to a clinically relevant radiation dose led to long-term activation of mammary gland genes involved in proliferative and metabolic pathways, which are known to have roles in carcinogenesis. When considered along with downregulation of a number of tumor suppressor genes, our study has implications for breast cancer initiation and progression after therapeutic radiation exposure.
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Affiliation(s)
- Kamal Datta
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, 3970 Reservoir Rd, Washington, DC, NW 20057-1468, USA.
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