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Chen J, Zhou C, Liu Y. Establishing a cancer driver gene signature-based risk model for predicting the prognoses of gastric cancer patients. Aging (Albany NY) 2022; 14:2383-2399. [PMID: 35288483 PMCID: PMC8954960 DOI: 10.18632/aging.203948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/24/2022] [Indexed: 12/09/2022]
Abstract
Despite the high prevalence of gastric cancer (GC), molecular biomarkers that can reliably detect GC are yet to be discovered. The present study aimed to establish a robust gene signature based on cancer driver genes (CDGs) that can predict GC prognosis. Transcriptional profiles and clinical data from GC patients were analyzed using univariate Cox regression analysis and the least absolute shrinkage and selection (LASSO)-penalized Cox regression analysis to select optimal prognosis-related genes for modeling. Time-dependent receiver operating characteristic (ROC) and Kaplan-Meier analyses were done to assess the predictive power of this gene signature. A nomogram model for prediction of survival of GC patients was established using the CDG signature and clinical information, and a seven-CDG signature was identified. Risk scores were calculated using this signature, and patients were subsequently divided into high- and low-risk groups; high-risk patients in the training and validation datasets had poorer prognoses than low-risk patients. Cox regression analysis revealed that the CDG signature is an independent prognostic factor for GC. The signature and other clinical features were used to construct a nomogram for predicting overall GC patient survival. Calibration and decision curve analysis showed that the nomogram accurately predicted survival, highlighting its clinical utility. Thus, we established a novel CDG signature and nomogram for predicting GC prognosis, which may facilitate personalized treatment of GC.
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Affiliation(s)
- Jun Chen
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, People's Republic of China
| | - Chao Zhou
- Department of Neurology, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang 330006, Jiangxi, People's Republic of China
| | - Ying Liu
- Department of Emergency, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, People's Republic of China
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MEKK1-dependent activation of the CRL4 complex is important for DNA damage-induced degradation of p21 and DDB2 and cell survival. Mol Cell Biol 2021; 41:e0008121. [PMID: 34251884 PMCID: PMC8462458 DOI: 10.1128/mcb.00081-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cullin-4 ubiquitin ligase (CRL4) complexes are differentially composed and highly dynamic protein assemblies that control many biological processes including the global genome nucleotide excision repair (GG-NER) pathway. Here we identified the kinase mitogen-activated protein kinase kinase kinase 1 (MEKK1) as a novel constitutive interactor of a cytosolic CRL4 complex that disassembles after DNA damage due to the Caspase-mediated cleavage of MEKK1. The kinase activity of MEKK1 was important to trigger auto-ubiquitination of the CRL4 complex by K48- and K63-linked ubiquitin chains. MEKK1 knockdown prohibited DNA damage-induced degradation of the CRL4 component DNA-damage binding protein 2 (DDB2) and the CRL4 substrate p21 and also cell recovery and survival. A ubiquitin replacement strategy revealed a contribution of K63-branched ubiquitin chains for DNA damage-induced DDB2/p21 decay, cell cycle regulation and cell survival. These data might have also implications for cancer, as frequently occurring mutations of MEKK1 might have an impact on genome stability and the therapeutic efficacy of CRL4-dependent immunomodulatory drugs such as thalidomide-derivatives.
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3
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Dobre M, Boscencu R, Neagoe IV, Surcel M, Milanesi E, Manda G. Insight into the Web of Stress Responses Triggered at Gene Expression Level by Porphyrin-PDT in HT29 Human Colon Carcinoma Cells. Pharmaceutics 2021; 13:pharmaceutics13071032. [PMID: 34371724 PMCID: PMC8309054 DOI: 10.3390/pharmaceutics13071032] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/03/2021] [Accepted: 07/04/2021] [Indexed: 01/21/2023] Open
Abstract
Photodynamic therapy (PDT), a highly targeted therapy with acceptable side effects, has emerged as a promising therapeutic option in oncologic pathology. One of the issues that needs to be addressed is related to the complex network of cellular responses developed by tumor cells in response to PDT. In this context, this study aims to characterize in vitro the stressors and the corresponding cellular responses triggered by PDT in the human colon carcinoma HT29 cell line, using a new asymmetric porphyrin derivative (P2.2) as a photosensitizer. Besides investigating the ability of P2.2-PDT to reduce the number of viable tumor cells at various P2.2 concentrations and fluences of the activating light, we assessed, using qRT-PCR, the expression levels of 84 genes critically involved in the stress response of PDT-treated cells. Results showed a fluence-dependent decrease of viable tumor cells at 24 h post-PDT, with few cells that seem to escape from PDT. We highlighted following P2.2-PDT the concomitant activation of particular cellular responses to oxidative stress, hypoxia, DNA damage and unfolded protein responses and inflammation. A web of inter-connected stressors was induced by P2.2-PDT, which underlies cell death but also elicits protective mechanisms that may delay tumor cell death or even defend these cells against the deleterious effects of PDT.
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Affiliation(s)
- Maria Dobre
- Radiobiology Department, Victor Babes National Institute of Pathology, 99-101 Splaiul Independentei, 050096 Bucharest, Romania
| | - Rica Boscencu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania
| | - Ionela Victoria Neagoe
- Radiobiology Department, Victor Babes National Institute of Pathology, 99-101 Splaiul Independentei, 050096 Bucharest, Romania
| | - Mihaela Surcel
- Radiobiology Department, Victor Babes National Institute of Pathology, 99-101 Splaiul Independentei, 050096 Bucharest, Romania
| | - Elena Milanesi
- Radiobiology Department, Victor Babes National Institute of Pathology, 99-101 Splaiul Independentei, 050096 Bucharest, Romania
| | - Gina Manda
- Radiobiology Department, Victor Babes National Institute of Pathology, 99-101 Splaiul Independentei, 050096 Bucharest, Romania
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Gilson P, Drouot G, Witz A, Merlin JL, Becuwe P, Harlé A. Emerging Roles of DDB2 in Cancer. Int J Mol Sci 2019; 20:ijms20205168. [PMID: 31635251 PMCID: PMC6834144 DOI: 10.3390/ijms20205168] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/12/2019] [Accepted: 10/15/2019] [Indexed: 01/10/2023] Open
Abstract
Damage-specific DNA-binding protein 2 (DDB2) was originally identified as a DNA damage recognition factor that facilitates global genomic nucleotide excision repair (GG-NER) in human cells. DDB2 also contributes to other essential biological processes such as chromatin remodeling, gene transcription, cell cycle regulation, and protein decay. Recently, the potential of DDB2 in the development and progression of various cancers has been described. DDB2 activity occurs at several stages of carcinogenesis including cancer cell proliferation, survival, epithelial to mesenchymal transition, migration and invasion, angiogenesis, and cancer stem cell formation. In this review, we focus on the current state of scientific knowledge regarding DDB2 biological effects in tumor development and the underlying molecular mechanisms. We also provide insights into the clinical consequences of DDB2 activity in cancers.
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Affiliation(s)
- Pauline Gilson
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Université de Lorraine, CNRS UMR 7039 CRAN, 54519 Vandœuvre-lès-Nancy CEDEX, France.
| | - Guillaume Drouot
- Faculté des Sciences et Technologies, Université de Lorraine, CNRS UMR 7039 CRAN, 54506 Vandœuvre-lès-Nancy CEDEX, France.
| | - Andréa Witz
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Université de Lorraine, CNRS UMR 7039 CRAN, 54519 Vandœuvre-lès-Nancy CEDEX, France.
| | - Jean-Louis Merlin
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Université de Lorraine, CNRS UMR 7039 CRAN, 54519 Vandœuvre-lès-Nancy CEDEX, France.
| | - Philippe Becuwe
- Faculté des Sciences et Technologies, Université de Lorraine, CNRS UMR 7039 CRAN, 54506 Vandœuvre-lès-Nancy CEDEX, France.
| | - Alexandre Harlé
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Université de Lorraine, CNRS UMR 7039 CRAN, 54519 Vandœuvre-lès-Nancy CEDEX, France.
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孙 灯, 刘 牧, 吴 华, 黄 福. [Bioinformatics analysis of expression and function of EXD3 gene in gastric cancer]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2019; 39:215-221. [PMID: 30890511 PMCID: PMC6765637 DOI: 10.12122/j.issn.1673-4254.2019.02.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To investigate the differentially expressed genes between gastric cancer and normal gastric mucosa by bioinformatics analysis, identify the important gene participating in the occurrence and progression of gastric cancer, and predict the functions of these genes. METHODS The gene expression microarray data GSE100935 (including 18 gastric cancer samples and normal gastric mucosal tissues) downloaded from the GEO expression profile database were analyzed using Morpheus to obtain the differentially expressed genes in gastric cancer, and a cluster analysis heat map was constructed. The online database UALCAN was used to obtain the expression levels of these differentially expressed genes in gastric cancer and normal gastric mucosa. The prognostic value of the differentially expressed genes in gastric cancer was evaluated with Kaplan-Meier survival analysis. GO functional enrichment analysis was performed using Fun-Rich software, and the STRING database was exploited to establish a PPI network for the differentially expressed genes. RESULTS A total of 45119 differentially expressed genes were identified from GSE100935 microarray data. Analysis with UALCAN showed an obvious high expression of EXD3 gene in gastric cancer, and survival analysis suggested that a high expression level of EXD3 was associated with a poorer prognosis of the patients with gastric cancer. GO functional enrichment analysis found that the differentially expressed genes in gastric cancer were involved mainly in the regulation of nucleotide metabolism and the activity of transcription factors in the cancer cells. CONCLUSIONS EXD3 may be a potential oncogene in gastric cancer possibly in relation to DNA damage repair. The up-regulation of EXD3 plays an important role in the development and prognosis of gastric cancer, and may serve as an important indicator for prognostic evaluation of the patients.
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Affiliation(s)
- 灯众 孙
- 蚌埠医学院 第一附属医院胃肠外科,安徽 蚌埠 233003Department of Gastrointestinal Surgery, Bengbu Medical College, Bengbu 233003, China
| | - 牧林 刘
- 蚌埠医学院 第一附属医院胃肠外科,安徽 蚌埠 233003Department of Gastrointestinal Surgery, Bengbu Medical College, Bengbu 233003, China
| | - 华彰 吴
- 蚌埠医学院 生物科学系,安徽 蚌埠 233003First Affiliated Hospital, Department of Biological Sciences, Bengbu Medical College, Bengbu 233003, China
| | - 福新 黄
- 蚌埠医学院 生物科学系,安徽 蚌埠 233003First Affiliated Hospital, Department of Biological Sciences, Bengbu Medical College, Bengbu 233003, China
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6
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Bommi PV, Ravindran S, Raychaudhuri P, Bagchi S. DDB2 regulates Epithelial-to-Mesenchymal Transition (EMT) in Oral/Head and Neck Squamous Cell Carcinoma. Oncotarget 2018; 9:34708-34718. [PMID: 30410671 PMCID: PMC6205178 DOI: 10.18632/oncotarget.26168] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/08/2018] [Indexed: 01/21/2023] Open
Abstract
DDB2 is a sensor of DNA damage and it plays an important role in Global Genomic Repair (GG-NER). Our previous studies show that DDB2 is involved in the regulation of metastasis in colon adenocarcinoma. Squamous Cell Carcinomas in the Oral/Head & Neck region (HNSCC) are particularly aggressive due to high incidence of recurrence and distant metastasis. In this study, we show that DDB2 expression is downregulated in advanced HNSCCs and loss of DDB2 expression coincides with reduced survival. Recent meta-analysis of gene expression data characterized the mesenchymal-type (EMT-type) as one most aggressive cancer cluster in HNSCC. Here, we report that DDB2 constitutively represses mRNA expression of the EMT- regulatory transcription factors SNAIL, ZEB1, and angiogenic factor VEGF in HNSCC cells. As a result, re-expression of DDB2 in metastatic cells reversed EMT with transcriptional upregulation of epithelial marker E-cadherin, and downregulation of mesenchymal markers N-cadherin, Vimentin, and Fibronectin. Interestingly, in a reverse assay, depletion of DDB2 in non-metastatic cells induced expression of the same EMT-regulatory transcription factors. TGFβs are major regulators of Snail and Zeb1, and we observed that DDB2 transcriptionally regulates expression of TGFB2 in HNSCC cells. Re-expression of DDB2 in mouse embryonic fibroblasts (MEFs) isolated from Ddb2 (-/-) knockout-mice resulted in repression of EMT-regulatory factors Zeb1, Snail and Tgfb2. Taken together, these results support the active role of DDB2 as a candidate suppressor of the EMT-process in HNSCC. Early detection leads to significantly higher survival in HNSCC and DDB2 expression in tumors can be a predictor of EMT progression.
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Affiliation(s)
- Prashant V Bommi
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, USA.,Current Address: Department of Clinical Cancer Prevention, Biological Sciences Research Building (BSRB), University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sriram Ravindran
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Pradip Raychaudhuri
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Srilata Bagchi
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, USA
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7
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Forestier A, Douki T, De Rosa V, Béal D, Rachidi W. Combination of Aβ Secretion and Oxidative Stress in an Alzheimer-Like Cell Line Leads to the Over-Expression of the Nucleotide Excision Repair Proteins DDB2 and XPC. Int J Mol Sci 2015; 16:17422-44. [PMID: 26263968 PMCID: PMC4581200 DOI: 10.3390/ijms160817422] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/19/2015] [Accepted: 06/29/2015] [Indexed: 12/21/2022] Open
Abstract
Repair of oxidative DNA damage, particularly Base Excision Repair (BER), impairment is often associated with Alzheimer’s disease pathology. Here, we aimed at investigating the complete Nucleotide Excision Repair (NER), a DNA repair pathway involved in the removal of bulky DNA adducts, status in an Alzheimer-like cell line. The level of DNA damage was quantified using mass spectrometry, NER gene expression was assessed by qPCR, and the NER protein activity was analysed through a modified version of the COMET assay. Interestingly, we found that in the presence of the Amyloid β peptide (Aβ), NER factors were upregulated at the mRNA level and that NER capacities were also specifically increased following oxidative stress. Surprisingly, NER capacities were not differentially improved following a typical NER-triggering of ultraviolet C (UVC) stress. Oxidative stress generates a differential and specific DNA damage response in the presence of Aβ. We hypothesized that the release of NER components such as DNA damage binding protein 2 (DDB2) and Xeroderma Pigmentosum complementation group C protein (XPC) following oxidative stress might putatively involve their apoptotic role rather than DNA repair function.
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Affiliation(s)
- Anne Forestier
- Laboratoire Lésions des Acides Nucléiques, Université Joseph Fourier-Grenoble 1/CEA/Institut Nanoscience et Cryogénie/SCIB, UMR-E3, Grenoble, France.
| | - Thierry Douki
- Laboratoire Lésions des Acides Nucléiques, Université Joseph Fourier-Grenoble 1/CEA/Institut Nanoscience et Cryogénie/SCIB, UMR-E3, Grenoble, France.
| | - Viviana De Rosa
- Laboratoire Lésions des Acides Nucléiques, Université Joseph Fourier-Grenoble 1/CEA/Institut Nanoscience et Cryogénie/SCIB, UMR-E3, Grenoble, France.
| | - David Béal
- Laboratoire Lésions des Acides Nucléiques, Université Joseph Fourier-Grenoble 1/CEA/Institut Nanoscience et Cryogénie/SCIB, UMR-E3, Grenoble, France.
| | - Walid Rachidi
- Laboratoire Lésions des Acides Nucléiques, Université Joseph Fourier-Grenoble 1/CEA/Institut Nanoscience et Cryogénie/SCIB, UMR-E3, Grenoble, France.
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8
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Dai W, Ma W, Li Q, Tao Y, Ding P, Zhu R, Jin J. The 5'-UTR of DDB2 harbors an IRES element and upregulates translation during stress conditions. Gene 2015; 573:57-63. [PMID: 26187069 DOI: 10.1016/j.gene.2015.07.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 07/08/2015] [Accepted: 07/09/2015] [Indexed: 11/15/2022]
Abstract
DDB2 is a tumor-inhibiting factor not only involved a major DNA repair mechanism in the Nucleotide Excision Repair (NER), but also correlated with cell apoptosis in the DNA damage response pathway. During serum-starvation, we noted that the translation levels of DDB2 were increased. To evaluate whether the 5'-UTR of DDB2 harbors an IRES element, we used a bicistronic luciferase plasmid with the 5'-UTR of DDB2 inserted between two cistron coding regions. We found that DDB2 5'-UTR could initiate the downstream reporter, demonstrating that the 5'-UTR of DDB2 contained an IRES. The 5'-UTR of DDB2 was predicted into a relatively stable secondary structure by the Mfold program. We deleted the stem-loops in turn to analyze the core part of IRES and found that full length of the 5'-UTR was significant for the IRES activity. Furthermore, our data demonstrated that the DDB2 IRES activity was promoted during stress conditions. These results reveal a novel mechanism contributing to DDB2 expression.
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Affiliation(s)
- Wenyan Dai
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu Province 214122, PR China
| | - Wennan Ma
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu Province 214122, PR China
| | - Qi Li
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu Province 214122, PR China
| | - Yifen Tao
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu Province 214122, PR China
| | - Pengpeng Ding
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu Province 214122, PR China
| | - Ruiyu Zhu
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu Province 214122, PR China.
| | - Jian Jin
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu Province 214122, PR China.
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9
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Matsumoto S, Fischer ES, Yasuda T, Dohmae N, Iwai S, Mori T, Nishi R, Yoshino KI, Sakai W, Hanaoka F, Thomä NH, Sugasawa K. Functional regulation of the DNA damage-recognition factor DDB2 by ubiquitination and interaction with xeroderma pigmentosum group C protein. Nucleic Acids Res 2015; 43:1700-13. [PMID: 25628365 PMCID: PMC4330392 DOI: 10.1093/nar/gkv038] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In mammalian nucleotide excision repair, the DDB1-DDB2 complex recognizes UV-induced DNA photolesions and facilitates recruitment of the XPC complex. Upon binding to damaged DNA, the Cullin 4 ubiquitin ligase associated with DDB1-DDB2 is activated and ubiquitinates DDB2 and XPC. The structurally disordered N-terminal tail of DDB2 contains seven lysines identified as major sites for ubiquitination that target the protein for proteasomal degradation; however, the precise biological functions of these modifications remained unknown. By exogenous expression of mutant DDB2 proteins in normal human fibroblasts, here we show that the N-terminal tail of DDB2 is involved in regulation of cellular responses to UV. By striking contrast with behaviors of exogenous DDB2, the endogenous DDB2 protein was stabilized even after UV irradiation as a function of the XPC expression level. Furthermore, XPC competitively suppressed ubiquitination of DDB2 in vitro, and this effect was significantly promoted by centrin-2, which augments the DNA damage-recognition activity of XPC. Based on these findings, we propose that in cells exposed to UV, DDB2 is protected by XPC from ubiquitination and degradation in a stochastic manner; thus XPC allows DDB2 to initiate multiple rounds of repair events, thereby contributing to the persistence of cellular DNA repair capacity.
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Affiliation(s)
- Syota Matsumoto
- Biosignal Research Center, Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Japan Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Eric S Fischer
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Takeshi Yasuda
- National Institute of Radiological Sciences, Chiba 263-8555, Japan
| | - Naoshi Dohmae
- Global Research Cluster, RIKEN, Wako 351-0198, Japan
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University, Toyonaka 560-8531, Japan
| | - Toshio Mori
- Advanced Medical Research Center, Nara Medical University, Kashihara 634-8521, Japan
| | - Ryotaro Nishi
- Biosignal Research Center, Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Japan
| | - Ken-ichi Yoshino
- Biosignal Research Center, Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Japan
| | - Wataru Sakai
- Biosignal Research Center, Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Japan Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Fumio Hanaoka
- Faculty of Science, Gakushuin University, Tokyo 171-8588, Japan
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Kaoru Sugasawa
- Biosignal Research Center, Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Japan Graduate School of Science, Kobe University, Kobe 657-8501, Japan
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Chen Z, Sui J, Zhang F, Zhang C. Cullin family proteins and tumorigenesis: genetic association and molecular mechanisms. J Cancer 2015; 6:233-42. [PMID: 25663940 PMCID: PMC4317758 DOI: 10.7150/jca.11076] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 12/08/2014] [Indexed: 12/13/2022] Open
Abstract
Cullin family proteins function as scaffolds to form numerous E3 ubiquitin ligases with RING proteins, adaptor proteins and substrate recognition receptors. These E3 ligases further recognize numerous substrates to participate in a variety of cellular processes, such as DNA damage and repair, cell death and cell cycle progression. Clinically, cullin-associated E3 ligases have been identified to involve numerous human diseases, especially with regard to multiple cancer types. Over the past few years, our understanding of cullin proteins and their functions in genome stability and tumorigenesis has expanded enormously. Herein, this review briefly provides current perspectives on cullin protein functions, and mainly summarizes and discusses molecular mechanisms of cullin proteins in tumorigenesis.
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Affiliation(s)
- Zhi Chen
- 1. Orthopedics Department, Changhai Hospital Affiliated to Second Military Medical University, Shanghai, China, 200433
| | - Jie Sui
- 2. Orthopedics Department, 102 Hospital of People's Liberation Army, Changzhou, Jiangsu, China, 213003
| | - Fan Zhang
- 1. Orthopedics Department, Changhai Hospital Affiliated to Second Military Medical University, Shanghai, China, 200433
| | - Caiguo Zhang
- 3. Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA, 80045
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11
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Melanson BD, Cabrita MA, Bose R, Hamill JD, Pan E, Brochu C, Marcellus KA, Zhao TT, Holcik M, McKay BC. A novel cis-acting element from the 3'UTR of DNA damage-binding protein 2 mRNA links transcriptional and post-transcriptional regulation of gene expression. Nucleic Acids Res 2013; 41:5692-703. [PMID: 23605047 PMCID: PMC3675493 DOI: 10.1093/nar/gkt279] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The DNA damage-binding protein 2 (DDB2) is an adapter protein that can direct a modular Cul4-DDB1-RING E3 Ligase complex to sites of ultraviolet light-induced DNA damage to ubiquitinate substrates during nucleotide excision repair. The DDB2 transcript is ultraviolet-inducible; therefore, its regulation is likely important for its function. Curiously, the DDB2 mRNA is reportedly short-lived, but the transcript does not contain any previously characterized cis-acting determinants of mRNA stability in its 3' untranslated region (3'UTR). Here, we used a tetracycline regulated d2EGFP reporter construct containing specific 3'UTR sequences from DDB2 to identify novel cis-acting elements that regulate mRNA stability. Synthetic 3'UTRs corresponding to sequences as short as 25 nucleotides from the central region of the 3'UTR of DDB2 were sufficient to accelerate decay of the heterologous reporter mRNA. Conversely, these same 3'UTRs led to more rapid induction of the reporter mRNA, export of the message to the cytoplasm and the subsequent accumulation of the encoded reporter protein, indicating that this newly identified cis-acting element affects transcriptional and post-transciptional processes. These results provide clear evidence that nuclear and cytoplasmic processing of the DDB2 mRNA is inextricably linked.
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Affiliation(s)
- Brian D Melanson
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada, K1H 8L6
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12
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Zhang L, Lubin A, Chen H, Sun Z, Gong F. The deubiquitinating protein USP24 interacts with DDB2 and regulates DDB2 stability. Cell Cycle 2012; 11:4378-84. [PMID: 23159851 PMCID: PMC3552920 DOI: 10.4161/cc.22688] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Damage-specific DNA-binding protein 2 (DDB2) was first isolated as a subunit of the UV-DDB heterodimeric complex that is involved in DNA damage recognition in the nucleotide excision repair pathway (NER). DDB2 is required for efficient repair of CPDs in chromatin and is a component of the CRL4DDB2 E3 ligase that targets XPC, histones and DDB2 itself for ubiquitination. In this study, a yeast two-hybrid screening of a human cDNA library was performed to identify potential DDB2 cellular partners. We identified a deubiquitinating enzyme, USP24, as a likely DDB2-interacting partner. Interaction between DDB2 and USP24 was confirmed by co-precipitation. Importantly, knockdown of USP24 in two human cell lines decreased the steady-state levels of DDB2, indicating that USP24-mediated DDB2 deubiquitination prevents DDB2 degradation. In addition, we demonstrated that USP24 can cleave an ubiquitinated form of DDB2 in vitro. Taken together, our results suggest that the ubiquitin-specific protease USP24 is a novel regulator of DDB2 stability.
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Affiliation(s)
- Ling Zhang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL USA
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Roy N, Elangovan I, Kopanja D, Bagchi S, Raychaudhuri P. Tumor regression by phenethyl isothiocyanate involves DDB2. Cancer Biol Ther 2012; 14:108-16. [PMID: 23114715 DOI: 10.4161/cbt.22631] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Phenethyl isothiocyanate (PEITC) is a promising cancer chemopreventive agent commonly found in edible cruciferous vegetables. It has been implicated also for therapy, and is in clinical trial for lung cancer. Here, we provide evidence that the tumor suppressive effect of PEITC is related to its ability to induce expression of damaged DNA binding protein 2 (DDB2), a DNA repair protein involved also in apoptosis and premature senescence. DDB2 expression is attenuated in a wide variety of cancers including the aggressive colon cancers. We show that, in colon cancer cells, reactive oxygen species, which are induced by PEITC, augment expression of DDB2 through the p38MAPK/JNK pathway, independently of p53. PEITC-induced expression of DDB2 is critical for inhibition of tumor progression by PEITC. Tumors derived from DDB2-deficient colon cancer cells are refractory to PEITC-treatments, resulting from deficiencies in apoptosis and senescence. The DDB2-proficient tumors, on the other hand, respond effectively to PEITC. The results show that PEITC can be used to induce expression of DDB2, and that expression of DDB2 is critical for effective response of tumors to PEITC.
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Affiliation(s)
- Nilotpal Roy
- Department of Biochemistry and Molecular Genetics, Cancer Center, University of Illinois at Chicago, Chicago, IL, USA
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14
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Damaged DNA binding protein 2 in reactive oxygen species (ROS) regulation and premature senescence. Int J Mol Sci 2012; 13:11012-11026. [PMID: 23109835 PMCID: PMC3472727 DOI: 10.3390/ijms130911012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 08/22/2012] [Accepted: 08/28/2012] [Indexed: 11/16/2022] Open
Abstract
Premature senescence induced by DNA damage or oncogene is a critical mechanism of tumor suppression. Reactive oxygen species (ROS) have been implicated in the induction of premature senescence response. Several pathological disorders such as cancer, aging and age related neurological abnormalities have been linked to ROS deregulation. Here, we discuss how Damaged DNA binding Protein-2 (DDB2), a nucleotide excision repair protein, plays an important role in ROS regulation by epigenetically repressing the antioxidant genes MnSOD and Catalase. We further revisit a model in which DDB2 plays an instrumental role in DNA damage induced ROS accumulation, ROS induced premature senescence and inhibition of skin tumorigenesis.
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Sajnani MR, Patel AK, Bhatt VD, Tripathi AK, Ahir VB, Shankar V, Shah S, Shah TM, Koringa PG, Jakhesara SJ, Joshi CG. Identification of novel transcripts deregulated in buccal cancer by RNA-seq. Gene 2012; 507:152-8. [PMID: 22846364 DOI: 10.1016/j.gene.2012.07.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 07/03/2012] [Accepted: 07/18/2012] [Indexed: 12/11/2022]
Abstract
The differential transcriptome analysis provides better understanding of molecular pathways leading to cancer, which in turn allows designing the effective strategies for diagnosis, therapeutic intervention and prediction of therapeutic outcome. This study describes the transcriptome analysis of buccal cancer and normal tissue by CLC Genomics Workbench from the data generated by Roche's 454 sequencing platform, which identified total of 1797 and 2655 genes uniquely expressed in normal and cancer tissues, respectively with 2466 genes expressed in both tissues. Among the genes expressed in both tissues, 1842 were up-regulated whereas 624 were down-regulated in cancer tissue. Besides transcripts known to be involved in cancer, this study led to the identification of novel transcripts, with significantly altered expression in buccal cancer tissue, providing potential targets for diagnosis and cancer therapeutics. The functional categorization by the KEGG pathway and gene ontology analysis revealed enrichment of differentially expressed transcripts to various pathways leading to cancer, including the p53 signaling pathway. Moreover, the gene ontology analysis unfolded suppression of transcripts involved in actin mediated cell contraction process. The down-regulation of four of these transcripts MYL1, ACTA1, TCAP and DESMIN in buccal cancer were further supported by quantitative PCR signifying its possible implication in the cancer progression.
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Affiliation(s)
- Manisha R Sajnani
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand-388 001, Gujarat, India
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16
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Stoyanova T, Roy N, Bhattacharjee S, Kopanja D, Valli T, Bagchi S, Raychaudhuri P. p21 cooperates with DDB2 protein in suppression of ultraviolet ray-induced skin malignancies. J Biol Chem 2011; 287:3019-28. [PMID: 22167187 DOI: 10.1074/jbc.m111.295816] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Exposure to ultraviolet rays (UV) in sunlight is the main cause of skin cancer. Here, we show that the p53-induced genes DDB2 and p21 are down-regulated in skin cancer, and in the mouse model they functionally cooperate to prevent UV-induced skin cancer. Our previous studies demonstrated an antagonistic role of DDB2 and p21 in nucleotide excision repair and apoptosis. Surprisingly, we find that the loss of p21 restores nucleotide excision repair and apoptosis in Ddb2(-/-) mice, but it does not protect from UV-mediated skin carcinogenesis. In contrast, Ddb2(-/-)p21(-/-) mice are significantly more susceptible to UV-induced skin cancer than the Ddb2(-/-) or the p21(-/-) mice. We provide evidence that p21 deletion in the Ddb2(-/-) background causes a strong increase in cell proliferation. The increased proliferation in the Ddb2(-/-)p21(-/-) background is related to a severe deficiency in UV-induced premature senescence. Also, the oncogenic pro-proliferation transcription factor FOXM1 is overexpressed in the p21(-/-) background. Our results show that the anti-proliferative and the pro-senescence pathways of DDB2 and p21 are critical protection mechanisms against skin malignancies.
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Affiliation(s)
- Tanya Stoyanova
- Department of Biochemistry and Molecular Genetics, Cancer Center, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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Jones KL, Zhang L, Seldeen KL, Gong F. Detection of bulky DNA lesions: DDB2 at the interface of chromatin and DNA repair in eukaryotes. IUBMB Life 2010; 62:803-11. [DOI: 10.1002/iub.391] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Tu CH, Liu WP, Dong M, Cai LP, Mo YQ, Yang DZ. Protection of CHO cells by transfer of survivin driven by ovarian-specific promoter OSP-2. Mol Biol Rep 2010; 38:2323-8. [PMID: 21080083 DOI: 10.1007/s11033-010-0365-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2009] [Accepted: 10/28/2010] [Indexed: 01/05/2023]
Abstract
Chemotherapy is the major therapy for cancer in clinic. However, chemotherapeutic agents can harm the other tissues/organs besides cancer. Thus, there are great interests in protecting the innocents by the transfer of protective genes. There are two problems to be solved, one is the selection of protective genes and the other is the orientation of the exotic genes. Recent researches demonstrated that the principal mechanism of chemotherapeutics was through apoptosis. Hereby, introduction of anti-apoptosis genes might interrupt the processes of apoptosis to avoid side effect from chemotherapeutics. On the other hand, tissue-specific promoters, which control gene expression in a tissue-specific manner, might be an alternative tool to guarantee the location of target genes. In this research, we applied gene therapy to chemoprotection using anti-apoptosis gene survivin and ovarian-specific promoter OSP-2. The results showed that OSP-2 could specifically drive the expression of survivin in ovarian cells and survivin could protect cells via inhibiting apoptosis. This might put a light on the future of chemoprotective gene therapy.
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Affiliation(s)
- Chun-Hua Tu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006, China.
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Rajabi M, Signorelli P, Gorincioi E, Ghidoni R, Santaniello E. Antiproliferative Activity of N6-Isopentenyladenosine on MCF-7 Breast Cancer Cells: Cell Cycle Analysis and DNA-Binding Study. DNA Cell Biol 2010; 29:687-91. [DOI: 10.1089/dna.2010.1073] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Mehdi Rajabi
- Laboratory of Biochemistry and Molecular Biology, Polo Universitario S. Paolo, Università degli Studi di Milano, Milano, Italy
- Laboratory of Medical Chemistry, Department of Medicine, Surgery and Dentistry, Faculty of Medicine, Polo Universitario S. Paolo, Università degli Studi di Milano, Milano, Italy
| | - Paola Signorelli
- Laboratory of Biochemistry and Molecular Biology, Polo Universitario S. Paolo, Università degli Studi di Milano, Milano, Italy
| | - Elena Gorincioi
- Laboratory of Medical Chemistry, Department of Medicine, Surgery and Dentistry, Faculty of Medicine, Polo Universitario S. Paolo, Università degli Studi di Milano, Milano, Italy
| | - Riccardo Ghidoni
- Laboratory of Biochemistry and Molecular Biology, Polo Universitario S. Paolo, Università degli Studi di Milano, Milano, Italy
| | - Enzo Santaniello
- Laboratory of Medical Chemistry, Department of Medicine, Surgery and Dentistry, Faculty of Medicine, Polo Universitario S. Paolo, Università degli Studi di Milano, Milano, Italy
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