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Li C, Chen H, Chen X, Wang P, Shi Y, Xie X, Chen Y, Cai X. Identification of inflammatory response-related molecular mechanisms based on the ATM/ATR/p53 pathway in tumor cells. Comput Biol Med 2024; 180:108776. [PMID: 39089116 DOI: 10.1016/j.compbiomed.2024.108776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/07/2024] [Accepted: 06/15/2024] [Indexed: 08/03/2024]
Abstract
Inflammatory response is a crucial factor that affects prognosis and therapeutic effect in tumor cells. Although some studies have shown that inflammation could make DNA more vulnerable to external attacks, resulting in serious DNA damage, the underlying mechanism remains unknown. Then, using tumor necrosis factor α (TNF-α) and lipopolysaccharide (LPS), this research elevated the level of inflammation in cancer cells, and hydrogen peroxide (H2O2) and ultraviolet (UV) were utilized as common reactive oxygen species (ROS)-induced DNA damage agents. We show that either H2O2 or UV achieved a more substantial antiproliferative effect in the inflammation environment compared with H2O2 or UV treatment alone. The inflammation environment enhanced H2O2- or UV-induced cell apoptosis and ROS production. Although the phenomenon that inflammation itself could trigger ROS-dependent DNA damage was well known, the underlying mechanism for the sensitization of inflammation to trigger intense DNA damage via ROS in cancer cells remains unclear. In this study, the inflammation-related genes and the corresponding expression information were obtained from the TCGA and fetched genes associated with inflammatory factors. Screening of thirteen inflammatory-related, including ATM, and prognostic genes. In addition, KEGG analysis of prognostic genes shows that biological processes such as DNA replication. ATM and ATR, which belong to the PI3/PI4-kinase family, can activate p53. Inflammation promotes the vulnerability of DNA by activating the ATM/ATR/p53 pathway, while not affecting the DNA damage repair pathway. In brief, this research suggested that inflammation made DNA vulnerable due to the amplifying H2O2- or UV-induced ROS production and the motoring ATM/ATR/p53 pathway. In addition, our findings revealed that inflammation's motoring of the ATM/ATR/p53 pathway plays a crucial role in DNA damage. Therefore, exploring the mechanism between inflammation and ROS-dependent DNA damage would be extremely valuable and innovative. This study would somewhat establish a better understanding of inflammation, DNA damage, and cancer.
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Affiliation(s)
- Chengye Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Hanbin Chen
- Department of Medical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Xiaojian Chen
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Peizhen Wang
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Yunjiao Shi
- Department of Medical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Xiaona Xie
- Department of Medical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Yanfan Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Xueding Cai
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China.
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Huang P, Wu L, Zhu N, Zhao H, Du J. The polymerase δ-interacting protein family and their emerging roles in diseases. Front Med (Lausanne) 2022; 9:1026931. [PMID: 36425112 PMCID: PMC9679015 DOI: 10.3389/fmed.2022.1026931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/24/2022] [Indexed: 10/08/2023] Open
Abstract
The polymerase δ-interacting protein (POLDIP) family is a new family that can interact with DNA polymerase δ (delta). The members of the POLDIP family include POLDIP1, POLDIP2, and POLDIP3. Screened by the two-hybrid method, POLDIP1, POLDIP2, and POLDIP3 were initially discovered and named for their ability to bind to the p50 subunit of DNA polymerase δ. Recent studies have confirmed that POLDIPs are involved in the regulation of signal transduction pathways in neurodevelopment, neuropsychiatric diseases, cardiovascular diseases, tumors, and other diseases. However, each protein participates in different signaling pathways. In this review, we elucidate upon the family in terms of their genes and protein structures, their biological functions, in addition to the pathways that they are involved in during the development of diverse diseases. Finally, to provide new insights to the scientific community, we used the TCGA database to analyze and summarize the gene expressions of POLDIP family members in various tumors, as well as the correlations between their expressions and the overall survival times of tumor patients. Our data summary will give researchers working on cancer new concepts.
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Affiliation(s)
- Peiluo Huang
- Department of Immunology, College of Basic Medicine, Guilin Medical University, Guilin, China
- College of Pharmacy, Guilin Medical University, Guilin, China
| | - Lei Wu
- College of Continuing Education, Guilin Medical University, Guilin, China
| | - Ningxia Zhu
- Department of Pathophysiology, College of Basic Medicine, Guilin Medical University, Guilin, China
| | - Hongtao Zhao
- Department of Immunology, College of Basic Medicine, Guilin Medical University, Guilin, China
| | - Juan Du
- Department of Immunology, College of Basic Medicine, Guilin Medical University, Guilin, China
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Zhu X, Yan F, Liu L, Huang Q. ZEB1 regulates bone metabolism in osteoporotic rats through inducing POLDIP2 transcription. J Orthop Surg Res 2022; 17:423. [PMID: 36123704 PMCID: PMC9484217 DOI: 10.1186/s13018-022-03312-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Background Osteoporosis (OP) is a common metabolic bone disease mainly involving bone remodeling and blood vessels. The current study aimed to explore the role of zinc finger E-box binding homeobox 1 (ZEB1) in OP. Methods First, gene expression microarrays for OP were downloaded from the Gene Expression Omnibus database and analyzed to screen for potential targets. Subsequently, a rat OP model was constructed using ovariectomy (OVX), and osteoblastic and osteoclastic differentiation and alterations in osteoporotic symptoms were observed upon intraperitoneal injection of oe-ZEB1 lentiviral vectors. DNA polymerase delta interacting protein 2 (POLDIP2) was predicted to be a downstream target of ZEB1, which was validated by ChIP-qPCR and dual-luciferase experiments. RAW264.7 cells were subjected to lentiviral vector infection of oe-ZEB1 and/or sh-POLDIP2, followed by RANKL treatment to induce osteoclast differentiation. Results ZEB1 was poorly expressed in blood samples of postmenopausal patients with OP and in bone tissues of OVX-treated rats. Overexpression of ZEB1 or POLDIP2 in OVX rats promoted osteoblastogenesis and inhibited osteoclast differentiation. In RANKL-treated RAW264.7 cells, the transcription factor ZEB1 enhanced the expression of POLDIP2, and silencing of POLDIP2 attenuated the inhibitory effect of oe-ZEB1 on the differentiation of macrophages RAW264.7 to osteoclasts. Conclusions ZEB1 promotes osteoblastogenesis and represses osteoclast differentiation, ultimately reducing the occurrence of postmenopausal OP by elevating the expression of POLDIP2.
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Affiliation(s)
- Xianwei Zhu
- Department of Orthopaedics, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, 215600, Jiangsu, People's Republic of China
| | - Fei Yan
- Department of Orthopaedics, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, 215600, Jiangsu, People's Republic of China
| | - Lipeng Liu
- Department of Obstetrics and Gynecology, The Affiliated Zhangjiagang Hospital of Soochow University, No. 68, Jiyangxi Road, Zhangjiagang District, Suzhou, 215600, Jiangsu, People's Republic of China.
| | - Qun Huang
- Department of Orthopaedics, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, 215600, Jiangsu, People's Republic of China
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Raina K, Rao BJ. Mammalian nuclear speckles exhibit stable association with chromatin: a biochemical study. Nucleus 2022; 13:58-73. [PMID: 35220893 PMCID: PMC8890396 DOI: 10.1080/19491034.2021.2024948] [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] [Indexed: 11/05/2022] Open
Abstract
Nuclear Speckles (NS) are phase-separated condensates of protein and RNA whose components dynamically coordinate RNA transcription, splicing, transport and DNA repair. NS, probed largely by imaging studies, remained historically well known as Interchromatin Granule Clusters, and biochemical properties, especially their association with Chromatin have been largely unexplored. In this study, we tested whether NS exhibit any stable association with chromatin and show that limited DNAse-1 nicking of chromatin leads to the collapse of NS into isotropic distribution or aggregates of constituent proteins without affecting other nuclear structures. Further biochemical probing revealed that NS proteins were tightly associated with chromatin, extractable only by high-salt treatment just like histone proteins. NS were also co-released with solubilised mono-dinucleosomal chromatin fraction following the MNase digestion of chromatin. We propose a model that NS-chromatin constitutes a “putative stable association” whose coupling might be subject to the combined regulation from both chromatin and NS changes. Abbreviations: NS: Nuclear speckles; DSB: double strand breaks; PTM: posttranslational modifications; DDR: DNA damage repair; RBP-RNA binding proteins; TAD: topologically associated domains; LCR: low complexity regions; IDR: intrinsically disordered regions.
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Affiliation(s)
- Komal Raina
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- Department of Biology, Indian Institute of Science Education and Research (Iiser) Tirupati, Transit Campus: Sree Rama Engineering College, Tirupati, India
| | - Basuthkar J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- Department of Biology, Indian Institute of Science Education and Research (Iiser) Tirupati, Transit Campus: Sree Rama Engineering College, Tirupati, India
- Department of Animal Biology, University of Hyderabad, Hyderabad, India
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Díaz-Talavera A, Montero-Conde C, Leandro-García LJ, Robledo M. PrimPol: A Breakthrough among DNA Replication Enzymes and a Potential New Target for Cancer Therapy. Biomolecules 2022; 12:248. [PMID: 35204749 PMCID: PMC8961649 DOI: 10.3390/biom12020248] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 02/01/2023] Open
Abstract
DNA replication can encounter blocking obstacles, leading to replication stress and genome instability. There are several mechanisms for evading this blockade. One mechanism consists of repriming ahead of the obstacles, creating a new starting point; in humans, PrimPol is responsible for carrying out this task. PrimPol is a primase that operates in both the nucleus and mitochondria. In contrast with conventional primases, PrimPol is a DNA primase able to initiate DNA synthesis de novo using deoxynucleotides, discriminating against ribonucleotides. In vitro, PrimPol can act as a DNA primase, elongating primers that PrimPol itself sythesizes, or as translesion synthesis (TLS) DNA polymerase, elongating pre-existing primers across lesions. However, the lack of evidence for PrimPol polymerase activity in vivo suggests that PrimPol only acts as a DNA primase. Here, we provide a comprehensive review of human PrimPol covering its biochemical properties and structure, in vivo function and regulation, and the processes that take place to fill the gap-containing lesion that PrimPol leaves behind. Finally, we explore the available data on human PrimPol expression in different tissues in physiological conditions and its role in cancer.
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Affiliation(s)
- Alberto Díaz-Talavera
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (C.M.-C.); (L.J.L.-G.); (M.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Cristina Montero-Conde
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (C.M.-C.); (L.J.L.-G.); (M.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Luis Javier Leandro-García
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (C.M.-C.); (L.J.L.-G.); (M.R.)
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (C.M.-C.); (L.J.L.-G.); (M.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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Poldip2/Nox4 Mediates Lipopolysaccharide-Induced Oxidative Stress and Inflammation in Human Lung Epithelial Cells. Mediators Inflamm 2022; 2022:6666022. [PMID: 35140544 PMCID: PMC8818432 DOI: 10.1155/2022/6666022] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 11/10/2021] [Accepted: 12/30/2021] [Indexed: 12/05/2022] Open
Abstract
NADPH oxidase 4 (Nox4) is an important source of reactive oxygen species (ROS) production, and its expression is increased in lipopolysaccharide- (LPS-) stimulated lung epithelial cells. Polymerase δ-interacting protein 2 (Poldip2) has been proved to bind Nox4 and participates in oxidative stress and inflammation. However, the role of Poldip2/Nox4 in LPS-induced oxidative stress and inflammation in lung epithelial cells remains unclear. Cell viability was measured via MTT assays. The expression of Poldip2, Nox4, heme oxygenase-1 (HO-1), cyclooxygenase-2 (COX-2), AKT, and p-AKT was detected by Western blotting and/or immunofluorescence. Poldip2 and Nox4 interaction was analyzed via coimmunoprecipitation (Co-IP) assay. NADPH enzymatic activity and production of ROS, prostaglandin E2 (PGE2), tumor necrosis factor-α (TNF-α), and interleukin-1β (IL-1β) were assessed simultaneously. The small interfering RNA (siRNA) or plasmid targeting Nox4 was used to downregulate or upregulate Nox4, and the lentiviral vector encoding Poldip2 was used to downregulate or upregulate Poldip2. The present study demonstrated that LPS stimulation significantly increased the protein levels of Poldip2 and Nox4 and proved that Poldip2 interacted with Nox4 proved by Co-IP. Importantly, Poldip2 acted as an upstream regulator of Nox4. The increased expression of Nox4 and COX-2; NADPH enzymatic activity; production of ROS, PGE2, TNF-α, and IL-1β; and decreased HO-1 expression were significantly suppressed by lentiviral Poldip2 shRNA downregulation but were increased by lentiviral upregulation of Poldip2. Furthermore, inhibiting of PI3K-AKT signaling notably attenuated LPS-induced Poldip2/Nox4 activation. Our study demonstrated that Poldip2 mediates LPS-induced oxidative stress and inflammation via interaction with Nox4 and was regulated by the PI3K-AKT signaling. Targeting Poldip2 could be a beneficial therapeutic strategy for the treatment of ALI.
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Lassègue B, Kumar S, Mandavilli R, Wang K, Tsai M, Kang DW, Demos C, Hernandes MS, San Martín A, Taylor WR, Jo H, Griendling KK. Characterization of Poldip2 knockout mice: Avoiding incorrect gene targeting. PLoS One 2021; 16:e0247261. [PMID: 34928942 PMCID: PMC8687530 DOI: 10.1371/journal.pone.0247261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 11/17/2021] [Indexed: 01/11/2023] Open
Abstract
POLDIP2 is a multifunctional protein whose roles are only partially understood. Our laboratory previously reported physiological studies performed using a mouse gene trap model, which suffered from three limitations: perinatal lethality in homozygotes, constitutive Poldip2 inactivation and inadvertent downregulation of the adjacent Tmem199 gene. To overcome these limitations, we developed a new conditional floxed Poldip2 model. The first part of the present study shows that our initial floxed mice were affected by an unexpected mutation, which was not readily detected by Southern blotting and traditional PCR. It consisted of a 305 kb duplication around Poldip2 with retention of the wild type allele and could be traced back to the original targeted ES cell clone. We offer simple suggestions to rapidly detect similar accidents, which may affect genome editing using both traditional and CRISPR-based methods. In the second part of the present study, correctly targeted floxed Poldip2 mice were generated and used to produce a new constitutive knockout line by crossing with a Cre deleter. In contrast to the gene trap model, many homozygous knockout mice were viable, in spite of having no POLDIP2 expression. To further characterize the effects of Poldip2 ablation in the vasculature, RNA-seq and RT-qPCR experiments were performed in constitutive knockout arteries. Results show that POLDIP2 inactivation affects multiple cellular processes and provide new opportunities for future in-depth study of its functions.
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Affiliation(s)
- Bernard Lassègue
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
| | - Sandeep Kumar
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Rohan Mandavilli
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
| | - Keke Wang
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
| | - Michelle Tsai
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
| | - Dong-Won Kang
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Catherine Demos
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Marina S. Hernandes
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
| | - Alejandra San Martín
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
| | - W. Robert Taylor
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, United States of America
- Division of Cardiology, Atlanta VA Medical Center, Decatur, GA, United States of America
| | - Hanjoong Jo
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Kathy K. Griendling
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
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Polymerase delta-interacting protein 38 (PDIP38) modulates the stability and activity of the mitochondrial AAA+ protease CLPXP. Commun Biol 2020; 3:646. [PMID: 33159171 PMCID: PMC7647994 DOI: 10.1038/s42003-020-01358-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/09/2020] [Indexed: 02/06/2023] Open
Abstract
Over a decade ago Polymerase δ interacting protein of 38 kDa (PDIP38) was proposed to play a role in DNA repair. Since this time, both the physiological function and subcellular location of PDIP38 has remained ambiguous and our present understanding of PDIP38 function has been hampered by a lack of detailed biochemical and structural studies. Here we show, that human PDIP38 is directed to the mitochondrion in a membrane potential dependent manner, where it resides in the matrix compartment, together with its partner protein CLPX. Our structural analysis revealed that PDIP38 is composed of two conserved domains separated by an α/β linker region. The N-terminal (YccV-like) domain of PDIP38 forms an SH3-like β-barrel, which interacts specifically with CLPX, via the adaptor docking loop within the N-terminal Zinc binding domain of CLPX. In contrast, the C-terminal (DUF525) domain forms an immunoglobin-like β-sandwich fold, which contains a highly conserved putative substrate binding pocket. Importantly, PDIP38 modulates the substrate specificity of CLPX and protects CLPX from LONM-mediated degradation, which stabilises the cellular levels of CLPX. Collectively, our findings shed new light on the mechanism and function of mitochondrial PDIP38, demonstrating that PDIP38 is a bona fide adaptor protein for the mitochondrial protease, CLPXP. Strack et al find that Polymerase δ interacting protein 38 (PDIP38) is targeted to the mitochondrial matrix where it colocalises with the mitochondrial AAA + protein CLPXP. PDIP38 modulates the specificity of CLPXP in vitro and alters the stability of CLPX in vitro and in cells. The PDIP38 structure leads the authors to speculate that PDIP38 is a CLPXP adaptor.
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A Multifunctional Protein PolDIP2 in DNA Translesion Synthesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1241:35-45. [PMID: 32383114 DOI: 10.1007/978-3-030-41283-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Polymerase δ-interacting protein 2 (PolDIP2) is involved in the multiple protein-protein interactions and plays roles in many cellular processes including regulation of the nuclear redox environment, organization of the mitotic spindle and chromosome segregation, pre-mRNA processing, mitochondrial morphology and functions, cell migration and cellular adhesion. PolDIP2 is also a binding partner of high-fidelity DNA polymerase delta, PCNA and a number of translesion and repair DNA polymerases. The growing evidence suggests that PolDIP2 is a general regulatory protein in DNA damage response. However PolDIP2 functions in DNA translesion synthesis and repair are not fully understood. In this review, we address the functional interaction of PolDIP2 with human DNA polymerases and discuss the possible functions in DNA damage response.
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Tang ZJ, Cao ZM, Guo XW, Chen HJ, Lian Y, Zheng WJ, Chen YJ, Lian HZ, Hu X. Cytotoxicity and toxicoproteomic analyses of human lung epithelial cells exposed to extracts of atmospheric particulate matters on PTFE filters using acetone and water. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 191:110223. [PMID: 31991395 DOI: 10.1016/j.ecoenv.2020.110223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/06/2020] [Accepted: 01/15/2020] [Indexed: 06/10/2023]
Abstract
Differences of cytotoxicity associated with exposure to different extracts of atmospheric particulate matters (PMs) are still not well characterized by in vitro toxicoproteomics. In this study, in vitro cytotoxicity assays and toxicoproteomic analyses were carried out to investigate toxic effects of PM collected using polytetrafluoroethylene (PTFE) filters extracted with acetone for PM2.1 and water for PM2.1 and PM10 on A549 human lung epithelial cells. The cytotoxicity assays based on cell viability, cell apoptosis and reactive oxygen species generation indicated that PM2.1 extracted with acetone had the highest toxicity. iTRAQ labeling and LC-MS/MS analyses indicated that the number of differentially expressed proteins in A549 cells affected by PM2.1 extracted with acetone was noticeably higher than that of the other two groups. Hierarchical cluster analyses showed that the influences of the extracts of PM2.1 and PM10 using water on the proteome of A549 cells were similar, whereas significantly different from the effect of PM2.1 extracted with acetone. Pathways analyses indicated that PM2.1 extracted with acetone influenced the expression of proteins involved in 14 pathways including glycolysis/gluconeogenesis, pentose phosphate pathway, proteasome, etc. PM2.1 extracted with water affected the expression of proteins involved in 3 pathways including non-homologous end-joining, ribosome and endocytosis. However, PM10 extracted with water affected the expression of proteins involved in only spliceosome pathway. The extracts of PM using different extractants to detach PM from PTFE filters influenced the cytotoxic effects of PM and the proteome of A549 cells. Therefore, extractants should be assessed carefully before the investigations on cytotoxicity to improve the compatibility of experimental results among research teams.
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Affiliation(s)
- Zhi-Jie Tang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, 210023, China
| | - Zhao-Ming Cao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, 210023, China
| | - Xue-Wen Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, 210023, China
| | - Hong-Juan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yi Lian
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, QC, H3A 1A2, Canada
| | - Wei-Juan Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yi-Jun Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, 210023, China
| | - Hong-Zhen Lian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, 210023, China.
| | - Xin Hu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, 210023, China.
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Nimeth BA, Riegler S, Kalyna M. Alternative Splicing and DNA Damage Response in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:91. [PMID: 32140165 PMCID: PMC7042379 DOI: 10.3389/fpls.2020.00091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/21/2020] [Indexed: 05/06/2023]
Abstract
Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants.
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Lv B, Liu C, Chen Y, Qi L, Wang L, Ji Y, Xue Z. Light-induced injury in mouse embryos revealed by single-cell RNA sequencing. Biol Res 2019; 52:48. [PMID: 31466525 PMCID: PMC6716870 DOI: 10.1186/s40659-019-0256-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/21/2019] [Indexed: 11/18/2022] Open
Abstract
Background Light exposure is a common stress factor in in vitro manipulation of embryos in the reproductive center. Many studies have shown the deleterious effects of high-intensity light exposure in different animal embryos. However, no transcriptomic studies have explored the light-induced injury and response in preimplantation embryos. Results Here, we adopt different time-courses and illumination intensities to treat mouse embryos at the 2-cell stage and evaluate their effects on blastulation. Meanwhile, single-cell transcriptomes from the 2-cell to blastocyst stage were analyzed after high-intensity light exposure. These data show that cells at each embryonic stage can be categorized into different light conditions. Further analyses of differentially expressed genes and GO terms revealed the light-induced injury as well as the potential repair response after high-intensity lighting. Maternal-to-zygote transition is also affected by the failure to remove maternal RNAs and deactivate zygotic genome expression. Conclusion Our work revealed an integrated response to high-intensity lighting, involving morphological changes, long-lasting injury effects, and intracellular damage repair mechanisms.
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Affiliation(s)
- Bo Lv
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Chaojie Liu
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yu Chen
- School of Life Sciences and Environment, Avans University of Applied Sciences, Breda, 4818 AJ, The Netherlands
| | - Lingbin Qi
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Lu Wang
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yazhong Ji
- Reproductive Medicine Center, Tongji Hospital, Tongji University, Shanghai, 200065, China.
| | - Zhigang Xue
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, 200092, China. .,Reproductive Medicine Center, Tongji Hospital, Tongji University, Shanghai, 200065, China.
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13
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Peddu C, Zhang S, Zhao H, Wong A, Lee EYC, Lee MYWT, Zhang Z. Phosphorylation Alters the Properties of Pol η: Implications for Translesion Synthesis. iScience 2018; 6:52-67. [PMID: 30240625 PMCID: PMC6137289 DOI: 10.1016/j.isci.2018.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/26/2018] [Accepted: 07/13/2018] [Indexed: 12/28/2022] Open
Abstract
There are significant ambiguities regarding how DNA polymerase η is recruited to DNA lesion sites in stressed cells while avoiding normal replication forks in non-stressed cells. Even less is known about the mechanisms responsible for Pol η-induced mutations in cancer genomes. We show that there are two safeguards to prevent Pol η from adventitious participation in normal DNA replication. These include sequestration by a partner protein and low basal activity. Upon cellular UV irradiation, phosphorylation enables Pol η to be released from sequestration by PDIP38 and activates its polymerase function through increased affinity toward monoubiquitinated proliferating cell nuclear antigen (Ub-PCNA). Moreover, the high-affinity binding of phosphorylated Pol η to Ub-PCNA limits its subsequent displacement by Pol δ. Consequently, activated Pol η replicates DNA beyond the lesion site and potentially introduces clusters of mutations due to its low fidelity. This mechanism could account for the prevalence of Pol η signatures in cancer genome. Pol η activation requires both ATR and PKC phosphorylation Phosphorylation directly enhances the affinity of Pol η toward Ub-PCNA PDIP38 sequesters Pol η away from normal replication fork Pol δ is not able to displace phosphorylated Pol η from Ub-PCNA complex
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Affiliation(s)
- Chandana Peddu
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Sufang Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Hong Zhao
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA
| | - Agnes Wong
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Ernest Y C Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Marietta Y W T Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Zhongtao Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
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14
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Mikolaskova B, Jurcik M, Cipakova I, Kretova M, Chovanec M, Cipak L. Maintenance of genome stability: the unifying role of interconnections between the DNA damage response and RNA-processing pathways. Curr Genet 2018; 64:971-983. [PMID: 29497809 DOI: 10.1007/s00294-018-0819-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 01/14/2023]
Abstract
Endogenous and exogenous factors can severely affect the integrity of genetic information by inducing DNA damage and impairing genome stability. The protection of genome integrity is ensured by the so-called "DNA damage response" (DDR), a set of evolutionary-conserved events that, triggered upon DNA damage detection, arrests the cell cycle, and attempts DNA repair. Here, we review the role of the DDR proteins as post-transcriptional regulators of gene expression, in addition to their roles in DNA damage recognition, signaling, and repair. At the same time, we discuss recent insights into how pre-mRNA splicing factors go beyond their splicing activities and play direct functions in detecting, signaling, and repairing DNA damage. The importance of extensive two-way crosstalk and interaction between the RNA processing and the DDR stems from growing evidence that the defects of their communication lead to genomic instability.
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Affiliation(s)
- B Mikolaskova
- Department of Genetics, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - M Jurcik
- Department of Genetics, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - I Cipakova
- Department of Genetics, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - M Kretova
- Department of Genetics, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - M Chovanec
- Department of Genetics, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - L Cipak
- Department of Genetics, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia.
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15
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Abstract
Polymerase δ-interacting protein 2 (Poldip2) is a multifunctional protein originally described as a binding partner of the p50 subunit of DNA polymerase δ and proliferating cell nuclear antigen. In addition to its role in DNA replication and damage repair, Poldip2 has been implicated in mitochondrial function, extracellular matrix regulation, cell cycle progression, focal adhesion turnover, and cell migration. However, Poldip2 functions are incompletely understood. In this review, we discuss recent literature on Poldip2 tissue distribution, subcellular localization, and function. We also address the putative function of Poldip2 in cardiovascular disease, neurodegenerative conditions and in renal pathophysiology.
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16
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Lee MYWT, Wang X, Zhang S, Zhang Z, Lee EYC. Regulation and Modulation of Human DNA Polymerase δ Activity and Function. Genes (Basel) 2017; 8:genes8070190. [PMID: 28737709 PMCID: PMC5541323 DOI: 10.3390/genes8070190] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/07/2017] [Accepted: 07/11/2017] [Indexed: 12/28/2022] Open
Abstract
This review focuses on the regulation and modulation of human DNA polymerase δ (Pol δ). The emphasis is on the mechanisms that regulate the activity and properties of Pol δ in DNA repair and replication. The areas covered are the degradation of the p12 subunit of Pol δ, which converts it from a heterotetramer (Pol δ4) to a heterotrimer (Pol δ3), in response to DNA damage and also during the cell cycle. The biochemical mechanisms that lead to degradation of p12 are reviewed, as well as the properties of Pol δ4 and Pol δ3 that provide insights into their functions in DNA replication and repair. The second focus of the review involves the functions of two Pol δ binding proteins, polymerase delta interaction protein 46 (PDIP46) and polymerase delta interaction protein 38 (PDIP38), both of which are multi-functional proteins. PDIP46 is a novel activator of Pol δ4, and the impact of this function is discussed in relation to its potential roles in DNA replication. Several new models for the roles of Pol δ3 and Pol δ4 in leading and lagging strand DNA synthesis that integrate a role for PDIP46 are presented. PDIP38 has multiple cellular localizations including the mitochondria, the spliceosomes and the nucleus. It has been implicated in a number of cellular functions, including the regulation of specialized DNA polymerases, mitosis, the DNA damage response, mouse double minute 2 homolog (Mdm2) alternative splicing and the regulation of the NADPH oxidase 4 (Nox4).
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Affiliation(s)
- Marietta Y W T Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Xiaoxiao Wang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Sufang Zhang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Zhongtao Zhang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Ernest Y C Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
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17
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Saez F, Hong NJ, Garvin JL. Luminal flow induces NADPH oxidase 4 translocation to the nuclei of thick ascending limbs. Physiol Rep 2016; 4:4/6/e12724. [PMID: 27033446 PMCID: PMC4814881 DOI: 10.14814/phy2.12724] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 02/05/2016] [Indexed: 01/11/2023] Open
Abstract
Superoxide (O2−) exerts its physiological actions in part by causing changes in gene transcription. In thick ascending limbs flow‐induced O2− production is mediated by NADPH oxidase 4 (Nox4) and is dependent on protein kinase C (PKC). Polymerase delta interacting protein 2 (Poldip2) increases Nox4 activity, but it is not known whether Nox4 translocates to the nucleus and whether Poldip2 participates in this process. We hypothesized that luminal flow causes Nox4 translocation to the nuclei of thick ascending limbs in a PKC‐dependent process facilitated by Poldip2. To test our hypothesis, we studied the subcellular localization of Nox4 and Poldip2 using confocal microscopy and O2− production in the absence and presence of luminal flow. Luminal flow increased the ratio of nuclear to cytoplasmic intensity of Nox4 (N/C) from 0.3 ± 0.1 to 0.7 ± 0.1 (P < 0.01) and O2− production from 89 ± 15 to 231 ± 16 AU/s (P < 0.001). In the presence of flow PKC inhibition reduced N/C from 0.5 ± 0.1 to 0.2 ± 0.1 (P < 0.01). Flow‐induced O2− production was also blocked (flow: 142 ± 20 AU/s; flow plus PKC inhibition 26 ± 12 AU/s; P < 0.01). The cytoskeleton disruptor cytochalasin D (1 μmol/L) decreased flow‐induced Nox4 translocation by 0.3 ± 0.01 (P < 0.01); however, it did not reduce flow‐induced O2−. Flow did not alter Poldip2 localization. We conclude that: (1) luminal flow elicits Nox4 translocation to the nucleus in a PKC‐ and cytoskeleton‐dependent process; (2) Nox4 activation occurs before translocation; and (3) Poldip2 is not involved in Nox4 nuclear translocation. Flow‐induced Nox4 translocation to the nucleus may play a role in O2−‐dependent changes in thick ascending limbs.
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Affiliation(s)
- Fara Saez
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Nancy J Hong
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Jeffrey L Garvin
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
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18
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Guilliam TA, Bailey LJ, Brissett NC, Doherty AJ. PolDIP2 interacts with human PrimPol and enhances its DNA polymerase activities. Nucleic Acids Res 2016; 44:3317-29. [PMID: 26984527 PMCID: PMC4838387 DOI: 10.1093/nar/gkw175] [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: 10/14/2015] [Accepted: 03/04/2016] [Indexed: 12/03/2022] Open
Abstract
Translesion synthesis (TLS) employs specialized DNA polymerases to bypass replication fork stalling lesions. PrimPol was recently identified as a TLS primase and polymerase involved in DNA damage tolerance. Here, we identify a novel PrimPol binding partner, PolDIP2, and describe how it regulates PrimPol's enzymatic activities. PolDIP2 stimulates the polymerase activity of PrimPol, enhancing both its capacity to bind DNA and the processivity of the catalytic domain. In addition, PolDIP2 stimulates both the efficiency and error-free bypass of 8-oxo-7,8-dihydrodeoxyguanosine (8-oxoG) lesions by PrimPol. We show that PolDIP2 binds to PrimPol's catalytic domain and identify potential binding sites. Finally, we demonstrate that depletion of PolDIP2 in human cells causes a decrease in replication fork rates, similar to that observed in PrimPol−/− cells. However, depletion of PolDIP2 in PrimPol−/− cells does not produce a further decrease in replication fork rates. Together, these findings establish that PolDIP2 can regulate the TLS polymerase and primer extension activities of PrimPol, further enhancing our understanding of the roles of PolDIP2 and PrimPol in eukaryotic DNA damage tolerance.
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Affiliation(s)
- Thomas A Guilliam
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Laura J Bailey
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Nigel C Brissett
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
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19
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Feng J, Li L, Tong L, Tang L, Wu S. The Involvement of Splicing Factor hnRNP A1 in UVB-induced Alternative Splicing of hdm2. Photochem Photobiol 2016; 92:318-324. [PMID: 26757361 DOI: 10.1111/php.12564] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/24/2015] [Indexed: 11/27/2022]
Abstract
Human homolog double minute 2 (hdm2), an oncoprotein, which binds to tumor suppressor p53 to facilitate its degradation, has been known to contribute to tumorigenesis. Its splicing variants are reported to be highly expressed in many cancers and can be induced by ultraviolet B light (UVB). However, the mechanisms of how UVB radiation induces hdm2 alternative splicing still remain unclear. In this study, we investigated the roles of two common splicing factors, heterogeneous nuclear ribonucleoproteins (hnRNP) A1 and serine/arginine-rich splicing factor 1 (SRSF1), in regulating UVB-induced hdm2 splicing. Our study indicated that while the expression of both hnRNP A1 and SRSF1 are induced, only hnRNP A1 is involved in hdm2 alternative splicing upon UVB irradiation. Overexpression of hnRNP A1 resulted in decrease of full-length hdm2 (hdm2-FL) and increase of hdm2B, one of hdm2 alternate-splicing forms; while down-regulated hnRNP A1 expression led to the decrease of the hdm2-FL and hdm2B in HaCaT cells. Protein-mRNA binding assay confirmed that UVB irradiation could increase the binding of hnRNP A1 to hdm2 pre-mRNA. In conclusion, we elucidated that UVB induces alternative splicing of hdm2 by increasing the expression and the binding of hnRNP A1 to hdm2 full-length mRNA.
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Affiliation(s)
- Jianguo Feng
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China.,Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH
| | - Li Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Lingying Tong
- Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Shiyong Wu
- Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH
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20
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Shkreta L, Chabot B. The RNA Splicing Response to DNA Damage. Biomolecules 2015; 5:2935-77. [PMID: 26529031 PMCID: PMC4693264 DOI: 10.3390/biom5042935] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/20/2015] [Accepted: 10/16/2015] [Indexed: 12/29/2022] Open
Abstract
The number of factors known to participate in the DNA damage response (DDR) has expanded considerably in recent years to include splicing and alternative splicing factors. While the binding of splicing proteins and ribonucleoprotein complexes to nascent transcripts prevents genomic instability by deterring the formation of RNA/DNA duplexes, splicing factors are also recruited to, or removed from, sites of DNA damage. The first steps of the DDR promote the post-translational modification of splicing factors to affect their localization and activity, while more downstream DDR events alter their expression. Although descriptions of molecular mechanisms remain limited, an emerging trend is that DNA damage disrupts the coupling of constitutive and alternative splicing with the transcription of genes involved in DNA repair, cell-cycle control and apoptosis. A better understanding of how changes in splice site selection are integrated into the DDR may provide new avenues to combat cancer and delay aging.
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Affiliation(s)
- Lulzim Shkreta
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
| | - Benoit Chabot
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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21
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Naro C, Bielli P, Pagliarini V, Sette C. The interplay between DNA damage response and RNA processing: the unexpected role of splicing factors as gatekeepers of genome stability. Front Genet 2015; 6:142. [PMID: 25926848 PMCID: PMC4397863 DOI: 10.3389/fgene.2015.00142] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/25/2015] [Indexed: 12/22/2022] Open
Abstract
Genome integrity is constantly threatened by endogenous and exogenous factors. However, its preservation is ensured by a network of pathways that prevent and/or repair the lesion, which constitute the DNA damage response (DDR). Expression of the key proteins involved in the DDR is controlled by numerous post-transcriptional mechanisms, among which pre-mRNA splicing stands out. Intriguingly, several splicing factors (SFs) have been recently shown to play direct functions in DNA damage prevention and repair, which go beyond their expected splicing activity. At the same time, evidence is emerging that DNA repair proteins (DRPs) can actively sustain the DDR by acting as post-transcriptional regulator of gene expression, in addition to their well-known role in the mechanisms of signaling and repair of the lesion. Herein, we will review these non-canonical functions of both SFs and DRPs, which suggest the existence of a tight interplay between splicing regulation and canonical DNA safeguard mechanisms ensuring genome stability.
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Affiliation(s)
- Chiara Naro
- Department of Biomedicine and Prevention, University of Rome Tor Vergata , Rome, Italy ; Laboratory of Neuroembryology, Fondazione Santa Lucia , Rome, Italy
| | - Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata , Rome, Italy ; Laboratory of Neuroembryology, Fondazione Santa Lucia , Rome, Italy
| | - Vittoria Pagliarini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata , Rome, Italy ; Laboratory of Neuroembryology, Fondazione Santa Lucia , Rome, Italy
| | - Claudio Sette
- Department of Biomedicine and Prevention, University of Rome Tor Vergata , Rome, Italy ; Laboratory of Neuroembryology, Fondazione Santa Lucia , Rome, Italy
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22
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Baqader NO, Radulovic M, Crawford M, Stoeber K, Godovac-Zimmermann J. Nuclear cytoplasmic trafficking of proteins is a major response of human fibroblasts to oxidative stress. J Proteome Res 2014; 13:4398-423. [PMID: 25133973 PMCID: PMC4259009 DOI: 10.1021/pr500638h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have used a subcellular spatial razor approach based on LC-MS/MS-based proteomics with SILAC isotope labeling to determine changes in protein abundances in the nuclear and cytoplasmic compartments of human IMR90 fibroblasts subjected to mild oxidative stress. We show that response to mild tert-butyl hydrogen peroxide treatment includes redistribution between the nucleus and cytoplasm of numerous proteins not previously associated with oxidative stress. The 121 proteins with the most significant changes encompass proteins with known functions in a wide variety of subcellular locations and of cellular functional processes (transcription, signal transduction, autophagy, iron metabolism, TCA cycle, ATP synthesis) and are consistent with functional networks that are spatially dispersed across the cell. Both nuclear respiratory factor 2 and the proline regulatory axis appear to contribute to the cellular metabolic response. Proteins involved in iron metabolism or with iron/heme as a cofactor as well as mitochondrial proteins are prominent in the response. Evidence suggesting that nuclear import/export and vesicle-mediated protein transport contribute to the cellular response was obtained. We suggest that measurements of global changes in total cellular protein abundances need to be complemented with measurements of the dynamic subcellular spatial redistribution of proteins to obtain comprehensive pictures of cellular function.
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Affiliation(s)
- Noor O. Baqader
- Division of Medicine, Center for Nephrology, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Marko Radulovic
- Division of Medicine, Center for Nephrology, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
- Insitute of Oncology and Radiology, Pasterova 14, 11000 Belgrade, Serbia
| | - Mark Crawford
- Division of Medicine, Center for Nephrology, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Kai Stoeber
- Research Department of Pathology and UCL Cancer Institute, Rockefeller Building, University College London, University Street, London WC1E 6JJ, United Kingdom
| | - Jasminka Godovac-Zimmermann
- Division of Medicine, Center for Nephrology, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
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23
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Amanso AM, Lassègue B, Joseph G, Landázuri N, Long JS, Weiss D, Taylor WR, Griendling KK. Polymerase δ-interacting protein 2 promotes postischemic neovascularization of the mouse hindlimb. Arterioscler Thromb Vasc Biol 2014; 34:1548-55. [PMID: 24855063 DOI: 10.1161/atvbaha.114.303873] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Collateral vessel formation can functionally compensate for obstructive vascular lesions in patients with atherosclerosis. Neovascularization processes are triggered by fluid shear stress, hypoxia, growth factors, chemokines, proteases, and inflammation, as well as reactive oxygen species, in response to ischemia. Polymerase δ-interacting protein 2 (Poldip2) is a multifunctional protein that regulates focal adhesion turnover and vascular smooth muscle cell migration and modifies extracellular matrix composition. We, therefore, tested the hypothesis that loss of Poldip2 impairs collateral formation. APPROACH AND RESULTS The mouse hindlimb ischemia model has been used to understand mechanisms involved in postnatal blood vessel formation. Poldip2(+/-) mice were subjected to femoral artery excision, and functional and morphological analysis of blood vessel formation was performed after injury. Heterozygous deletion of Poldip2 decreased the blood flow recovery and spontaneous running activity at 21 days after injury. H2O2 production, as well as the activity of matrix metalloproteinases-2 and -9, was reduced in these animals compared with Poldip2(+/+) mice. Infiltration of macrophages in the peri-injury muscle was also decreased; however, macrophage phenotype was similar between genotypes. In addition, the formation of capillaries and arterioles was impaired, as was angiogenesis, in agreement with a decrease in proliferation observed in endothelial cells treated with small interfering RNA against Poldip2. Finally, regression of newly formed vessels and apoptosis was more pronounced in Poldip2(+/-) mice. CONCLUSIONS Together, these results suggest that Poldip2 promotes ischemia-induced collateral vessel formation via multiple mechanisms that likely involve reactive oxygen species-dependent activation of matrix metalloproteinase activity, as well as enhanced vascular cell growth and survival.
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Affiliation(s)
- Angélica M Amanso
- From the Department of Medicine, Division of Cardiology (A.M.A., B.L., G.J., J.S.L., D.W., W.R.T., K.K.G.) and The Wallace H. Coulter Department of Biomedical Engineering (W.R.T.), Emory University, Atlanta, GA; and Department of Medicine, Division of Cardiology, Atlanta VA Medical Center, GA (W.R.T.)
| | - Bernard Lassègue
- From the Department of Medicine, Division of Cardiology (A.M.A., B.L., G.J., J.S.L., D.W., W.R.T., K.K.G.) and The Wallace H. Coulter Department of Biomedical Engineering (W.R.T.), Emory University, Atlanta, GA; and Department of Medicine, Division of Cardiology, Atlanta VA Medical Center, GA (W.R.T.)
| | - Giji Joseph
- From the Department of Medicine, Division of Cardiology (A.M.A., B.L., G.J., J.S.L., D.W., W.R.T., K.K.G.) and The Wallace H. Coulter Department of Biomedical Engineering (W.R.T.), Emory University, Atlanta, GA; and Department of Medicine, Division of Cardiology, Atlanta VA Medical Center, GA (W.R.T.)
| | - Natalia Landázuri
- From the Department of Medicine, Division of Cardiology (A.M.A., B.L., G.J., J.S.L., D.W., W.R.T., K.K.G.) and The Wallace H. Coulter Department of Biomedical Engineering (W.R.T.), Emory University, Atlanta, GA; and Department of Medicine, Division of Cardiology, Atlanta VA Medical Center, GA (W.R.T.)
| | - James S Long
- From the Department of Medicine, Division of Cardiology (A.M.A., B.L., G.J., J.S.L., D.W., W.R.T., K.K.G.) and The Wallace H. Coulter Department of Biomedical Engineering (W.R.T.), Emory University, Atlanta, GA; and Department of Medicine, Division of Cardiology, Atlanta VA Medical Center, GA (W.R.T.)
| | - Daiana Weiss
- From the Department of Medicine, Division of Cardiology (A.M.A., B.L., G.J., J.S.L., D.W., W.R.T., K.K.G.) and The Wallace H. Coulter Department of Biomedical Engineering (W.R.T.), Emory University, Atlanta, GA; and Department of Medicine, Division of Cardiology, Atlanta VA Medical Center, GA (W.R.T.)
| | - W Robert Taylor
- From the Department of Medicine, Division of Cardiology (A.M.A., B.L., G.J., J.S.L., D.W., W.R.T., K.K.G.) and The Wallace H. Coulter Department of Biomedical Engineering (W.R.T.), Emory University, Atlanta, GA; and Department of Medicine, Division of Cardiology, Atlanta VA Medical Center, GA (W.R.T.)
| | - Kathy K Griendling
- From the Department of Medicine, Division of Cardiology (A.M.A., B.L., G.J., J.S.L., D.W., W.R.T., K.K.G.) and The Wallace H. Coulter Department of Biomedical Engineering (W.R.T.), Emory University, Atlanta, GA; and Department of Medicine, Division of Cardiology, Atlanta VA Medical Center, GA (W.R.T.).
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Brown DI, Lassègue B, Lee M, Zafari R, Long JS, Saavedra HI, Griendling KK. Poldip2 knockout results in perinatal lethality, reduced cellular growth and increased autophagy of mouse embryonic fibroblasts. PLoS One 2014; 9:e96657. [PMID: 24797518 PMCID: PMC4010529 DOI: 10.1371/journal.pone.0096657] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 04/09/2014] [Indexed: 11/18/2022] Open
Abstract
Polymerase-δ interacting protein 2 (Poldip2) is an understudied protein, originally described as a binding partner of polymerase delta and proliferating cell nuclear antigen (PCNA). Numerous roles for Poldip2 have been proposed, including mitochondrial elongation, DNA replication/repair and ROS production via Nox4. In this study, we have identified a novel role for Poldip2 in regulating the cell cycle. We used a Poldip2 gene-trap mouse and found that homozygous animals die around the time of birth. Poldip2-/- embryos are significantly smaller than wild type or heterozygous embryos. We found that Poldip2-/- mouse embryonic fibroblasts (MEFs) exhibit reduced growth as measured by population doubling and growth curves. This effect is not due to apoptosis or senescence; however, Poldip2-/- MEFs have higher levels of the autophagy marker LC3b. Measurement of DNA content by flow cytometry revealed an increase in the percentage of Poldip2-/- cells in the G1 and G2/M phases of the cell cycle, accompanied by a decrease in the percentage of S-phase cells. Increases in p53 S20 and Sirt1 were observed in passage 2 Poldip2-/- MEFs. In passage 4/5 MEFs, Cdk1 and CyclinA2 are downregulated in Poldip2-/- cells, and these changes are reversed by transfection with SV40 large T-antigen, suggesting that Poldip2 may target the E2F pathway. In contrast, p21CIP1 is increased in passage 4/5 Poldip2-/- MEFs and its expression is unaffected by SV40 transfection. Overall, these results reveal that Poldip2 is an essential protein in development, and underline its importance in cell viability and proliferation. Because it affects the cell cycle, Poldip2 is a potential novel target for treating proliferative conditions such as cancer, atherosclerosis and restenosis.
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Affiliation(s)
- David I. Brown
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Bernard Lassègue
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Minyoung Lee
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Rostam Zafari
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - James S. Long
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Harold I. Saavedra
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Kathy K. Griendling
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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