1
|
Hu L, Wu N, Wang J, Yao M, Han B. Network Pharmacology Combined with Bioinformatics Analysis to Texplore the Potential Mechanism of Phellodendri Chinensis Cortex Against Bladder Cancer. Cell Biochem Biophys 2024:10.1007/s12013-024-01414-6. [PMID: 39023680 DOI: 10.1007/s12013-024-01414-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2024] [Indexed: 07/20/2024]
Abstract
The pharmacological mechanism of Phellodendri Chinensis cortex (PCC) against diseases, especially bladder cancer (BC), has never been reported systematically. This study was designed to explore potential mechanism of PCC in treatment of BC. First, we used network pharmacology to discover the potential mechanism of Phellodendri Chinensis cortex and phellodendrine against bladder cancer. Then, we used bioinformatics analysis to verify the correlation between gene expression analysis, survival analysis and common targets. Finally, molecular docking was used to calculate the binding energies of phellodendrine and common targets.A total of 264 targets for PCC were predicted, and 391 BC-related targets were obtained from 4 databases. There were 54 potential targets, 315 biological processes, and 120 signaling pathways involved for PCC against BC. The CDKN2A expression increased and the ESR1, JUN, IL6, AR, and PTGS2 levels decreased in BC according to Gene Expression Profiling Interactive Analysis version 2. The high expression of JUN, MYC, EGFR, and EGF and low expression of VEGFA and PPARG were associated with short overall survival (OS). The high expression of AKT1, EGFR, and EGF and low expression of IL1β were associated with poor disease-free survival (DFS). The search of the intersection of phellodendrine and BC targets yielded 11 common targets, 50 biological processes, and 13 signaling pathways involved. High AURKA and FASN and low ESR1, JUN, ABCB1, and PTGS1 were expressed in BC. The high expression of FASN, ABCC1, PTGS1, JUN, and PIK3CA was associated with short OS, the high expression of PIK3CA and ABCC1 was associated with poor DFS prognosis. Phellodendrine showed a better binding affinity for PTGS2 protein with a docking score of -7.183 and a MM-GBSA result of -46.47 kcal/mol. This study revealed potential mechanism of PCC and phellodendrine against BC through network pharmacology and bioinformatics.
Collapse
Affiliation(s)
- Lili Hu
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, China.
- College of Basic Medicine, Shanxi University of Chinese Medicine, Jinzhong, 030619, China.
- Shanxi Di'an Medical Inspection Center Co., Ltd., Taiyuan, 030006, China.
| | - Na Wu
- College of Basic Medicine, Shanxi University of Chinese Medicine, Jinzhong, 030619, China
| | - Jue Wang
- College of Basic Medicine, Shanxi University of Chinese Medicine, Jinzhong, 030619, China
| | - Mingze Yao
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, China
| | - Bo Han
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, China.
- College of Basic Medicine, Shanxi University of Chinese Medicine, Jinzhong, 030619, China.
| |
Collapse
|
2
|
Song Z, Gui S, Xiao S, Rao X, Cong N, Deng H, Yu Z, Zeng T. A novel anoikis-related gene signature identifies LYPD1 as a novel therapy target for bladder cancer. Sci Rep 2024; 14:3198. [PMID: 38332160 PMCID: PMC10853254 DOI: 10.1038/s41598-024-53272-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
Bladder cancer (BLCA) is a malignant tumor associated with unfavorable outcomes. Studies suggest that anoikis plays a crucial role in tumor progression and cancer cell metastasis. However, its specific role in bladder cancer remains poorly understood. Our objective was to identify anoikis-related genes (ARGs) and subsequently construct a risk model to assess their potential for predicting the prognosis of bladder cancer.The transcriptome data and clinical data of BLCA patients were sourced from The Cancer Genome Atlas and GEO database. We then performed the differential expression analysis to screen differentially expressed ARGs. Subsequently, we conducted non-negative matrix factorization (NMF) clustering analysis to establish molecular subtypes based on the differentially expressed ARGs. The CIBERSORT algorithm was used to estimate the quantification of different cell infiltration in BLCA tumor microenviroment. A prognostic risk model containing 7 ARGs was established using Lasso-Cox regression analysis. The nomogram was built for predicting the survival probability of BLCA patients. To determine the drug sensitivity of each sample from the high- and low-risk groups, the R package "pRRophetic" was performed. Finally, the role of LYPD1 was explored in BLCA cell lines.We identified 90 differential expression ARGs and NMF clustering categorizated the BLCA patientss into two distinct groups (cluster A and B). Patients in cluster A had a better prognosis than those in cluster B. Then, we established a ARGs risk model including CALR, FASN, FOSL1, JUN, LYPD1, MST1R, and SATB1, which was validated in the train and test set. The results suggested overall survival rate was much higher in low risk group than high risk group. The cox regression analysis, ROC curve analysis, and nomogram collectively demonstrated that the risk model served as an independent prognostic factor. The high risk group had a higher level TME scores compared to the low risk group. Furthermore, LYPD1 was low expression in BLCA cells and overexpression of LYPD1 inhibits the prolifearation, migration and invasion.In the current study, we have identified differential expression ARGs and constructed a risk model with the promise for guiding prognostic predictions and provided a therapeutic target for patients with BLCA.
Collapse
Affiliation(s)
- Zhen Song
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, Jiangxi Province, China
- Nanchang University, Nanchang, 330000, Jiangxi Province, China
| | - Shikai Gui
- Nanchang University, Nanchang, 330000, Jiangxi Province, China
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, Jiangxi Province, China
| | - Shuaiyun Xiao
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, Jiangxi Province, China
- Nanchang University, Nanchang, 330000, Jiangxi Province, China
| | - Xuepeng Rao
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, Jiangxi Province, China
- Nanchang University, Nanchang, 330000, Jiangxi Province, China
| | - Na Cong
- Ganzhou Medical Emergency Center, Ganzhou, 341000, Jiangxi Province, China
| | - Huanhuan Deng
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, Jiangxi Province, China
| | - Zhaojun Yu
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, Jiangxi Province, China
- Nanchang University, Nanchang, 330000, Jiangxi Province, China
| | - Tao Zeng
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, Jiangxi Province, China.
- Nanchang University, Nanchang, 330000, Jiangxi Province, China.
| |
Collapse
|
3
|
Venkadakrishnan J, Lahane G, Dhar A, Xiao W, Bhat KM, Pandita TK, Bhat A. Implications of Translesion DNA Synthesis Polymerases on Genomic Stability and Human Health. Mol Cell Biol 2023; 43:401-425. [PMID: 37439479 PMCID: PMC10448981 DOI: 10.1080/10985549.2023.2224199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/03/2023] [Accepted: 06/01/2023] [Indexed: 07/14/2023] Open
Abstract
Replication fork arrest-induced DNA double strand breaks (DSBs) caused by lesions are effectively suppressed in cells due to the presence of a specialized mechanism, commonly referred to as DNA damage tolerance (DDT). In eukaryotic cells, DDT is facilitated through translesion DNA synthesis (TLS) carried out by a set of DNA polymerases known as TLS polymerases. Another parallel mechanism, referred to as homology-directed DDT, is error-free and involves either template switching or fork reversal. The significance of the DDT pathway is well established. Several diseases have been attributed to defects in the TLS pathway, caused either by mutations in the TLS polymerase genes or dysregulation. In the event of a replication fork encountering a DNA lesion, cells switch from high-fidelity replicative polymerases to low-fidelity TLS polymerases, which are associated with genomic instability linked with several human diseases including, cancer. The role of TLS polymerases in chemoresistance has been recognized in recent years. In addition to their roles in the DDT pathway, understanding noncanonical functions of TLS polymerases is also a key to unraveling their importance in maintaining genomic stability. Here we summarize the current understanding of TLS pathway in DDT and its implication for human health.
Collapse
Affiliation(s)
| | - Ganesh Lahane
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Hyderabad Campus, Hyderabad, India
| | - Arti Dhar
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Hyderabad Campus, Hyderabad, India
| | - Wei Xiao
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Krishna Moorthi Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, Florida, USA
| | - Tej K. Pandita
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, Texas, USA
| | - Audesh Bhat
- Center for Molecular Biology, Central University of Jammu, UT Jammu and Kashmir, India
| |
Collapse
|
4
|
Abstract
High-fidelity DNA replication is critical for the faithful transmission of genetic information to daughter cells. Following genotoxic stress, specialized DNA damage tolerance pathways are activated to ensure replication fork progression. These pathways include translesion DNA synthesis, template switching and repriming. In this Review, we describe how DNA damage tolerance pathways impact genome stability, their connection with tumorigenesis and their effects on cancer therapy response. We discuss recent findings that single-strand DNA gap accumulation impacts chemoresponse and explore a growing body of evidence that suggests that different DNA damage tolerance factors, including translesion synthesis polymerases, template switching proteins and enzymes affecting single-stranded DNA gaps, represent useful cancer targets. We further outline how the consequences of DNA damage tolerance mechanisms could inform the discovery of new biomarkers to refine cancer therapies.
Collapse
Affiliation(s)
- Emily Cybulla
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
| |
Collapse
|
5
|
Response of the Urothelial Carcinoma Cell Lines to Cisplatin. Int J Mol Sci 2022; 23:ijms232012488. [PMID: 36293346 PMCID: PMC9604399 DOI: 10.3390/ijms232012488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/15/2022] [Accepted: 10/16/2022] [Indexed: 12/09/2022] Open
Abstract
Cisplatin (CDDP)-based chemotherapy is the standard of care in patients with muscle-invasive bladder cancer. However, in a large number of cases, the disease becomes resistant or does not respond to CDDP, and thus progresses and disseminates. In such cases, prognosis of patients is very poor. CDDP manifests its cytotoxic effects mainly through DNA damage induction. Hence, response to CDDP is mainly dependent on DNA damage repair and tolerance mechanisms. Herein, we have examined CDDP response in a panel of the urothelial carcinoma cell (UCC) lines. We characterized these cell lines with regard to viability after CDDP treatment, as well as kinetics of induction and repair of CDDP-induced DNA damage. We demonstrate that repair of CDDP-induced DNA lesions correlates, at least to some extent, with CDDP sensitivity. Furthermore, we monitored expression of the key genes involved in selected DNA repair and tolerance mechanisms, nucleotide excision repair, homologous recombination and translesion DNA synthesis, and show that it differs in the UCC lines and positively correlates with CDDP resistance. Our data indicate that CDDP response in the UCC lines is dependent on DNA damage repair and tolerance factors, which may, therefore, represent valuable therapeutic targets in this malignancy.
Collapse
|
6
|
Predicting the Prognostic Value of POLI Expression in Different Cancers via a Machine Learning Approach. Int J Mol Sci 2022; 23:ijms23158571. [PMID: 35955705 PMCID: PMC9369001 DOI: 10.3390/ijms23158571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022] Open
Abstract
Translesion synthesis (TLS) is a cell signaling pathway that facilitates the tolerance of replication stress. Increased TLS activity, the particularly elevated expression of TLS polymerases, has been linked to resistance to cancer chemotherapeutics and significantly altered patient outcomes. Building upon current knowledge, we found that the expression of one of these TLS polymerases (POLI) is associated with significant differences in cervical and pancreatic cancer survival. These data led us to hypothesize that POLI expression is associated with cancer survival more broadly. However, when cancers were grouped cancer type, POLI expression did not have a significant prognostic value. We presented a binary cancer random forest classifier using 396 genes that influence the prognostic characteristics of POLI in cervical and pancreatic cancer selected via graphical least absolute shrinkage and selection operator. The classifier was then used to cluster patients with bladder, breast, colorectal, head and neck, liver, lung, ovary, melanoma, stomach, and uterus cancer when high POLI expression was associated with worsened survival (Group I) or with improved survival (Group II). This approach allowed us to identify cancers where POLI expression is a significant prognostic factor for survival (p = 0.028 in Group I and p = 0.0059 in Group II). Multiple independent validation approaches, including the gene ontology enrichment analysis and visualization tool and network visualization support the classification scheme. The functions of the selected genes involving mitochondrial translational elongation, Wnt signaling pathway, and tumor necrosis factor-mediated signaling pathway support their association with TLS and replication stress. Our multidisciplinary approach provides a novel way of identifying tumors where increased TLS polymerase expression is associated with significant differences in cancer survival.
Collapse
|
7
|
Ler AAL, Carty MP. DNA Damage Tolerance Pathways in Human Cells: A Potential Therapeutic Target. Front Oncol 2022; 11:822500. [PMID: 35198436 PMCID: PMC8859465 DOI: 10.3389/fonc.2021.822500] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/30/2021] [Indexed: 12/26/2022] Open
Abstract
DNA lesions arising from both exogenous and endogenous sources occur frequently in DNA. During DNA replication, the presence of unrepaired DNA damage in the template can arrest replication fork progression, leading to fork collapse, double-strand break formation, and to genome instability. To facilitate completion of replication and prevent the generation of strand breaks, DNA damage tolerance (DDT) pathways play a key role in allowing replication to proceed in the presence of lesions in the template. The two main DDT pathways are translesion synthesis (TLS), which involves the recruitment of specialized TLS polymerases to the site of replication arrest to bypass lesions, and homology-directed damage tolerance, which includes the template switching and fork reversal pathways. With some exceptions, lesion bypass by TLS polymerases is a source of mutagenesis, potentially contributing to the development of cancer. The capacity of TLS polymerases to bypass replication-blocking lesions induced by anti-cancer drugs such as cisplatin can also contribute to tumor chemoresistance. On the other hand, during homology-directed DDT the nascent sister strand is transiently utilised as a template for replication, allowing for error-free lesion bypass. Given the role of DNA damage tolerance pathways in replication, mutagenesis and chemoresistance, a more complete understanding of these pathways can provide avenues for therapeutic exploitation. A number of small molecule inhibitors of TLS polymerase activity have been identified that show synergy with conventional chemotherapeutic agents in killing cancer cells. In this review, we will summarize the major DDT pathways, explore the relationship between damage tolerance and carcinogenesis, and discuss the potential of targeting TLS polymerases as a therapeutic approach.
Collapse
Affiliation(s)
- Ashlynn Ai Li Ler
- Biochemistry, School of Biological and Chemical Sciences, The National University of Ireland (NUI) Galway, Galway, Ireland
| | - Michael P. Carty
- Biochemistry, School of Biological and Chemical Sciences, The National University of Ireland (NUI) Galway, Galway, Ireland
- DNA Damage Response Laboratory, Centre for Chromosome Biology, NUI Galway, Galway, Ireland
- *Correspondence: Michael P. Carty,
| |
Collapse
|
8
|
Probing altered enzyme activity in the biochemical characterization of cancer. Biosci Rep 2022; 42:230680. [PMID: 35048115 PMCID: PMC8819661 DOI: 10.1042/bsr20212002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/10/2022] [Accepted: 01/19/2022] [Indexed: 11/30/2022] Open
Abstract
Enzymes have evolved to catalyze their precise reactions at the necessary rates, locations, and time to facilitate our development, to respond to a variety of insults and challenges, and to maintain a healthy, balanced state. Enzymes achieve this extraordinary feat through their unique kinetic parameters, myriad regulatory strategies, and their sensitivity to their surroundings, including substrate concentration and pH. The Cancer Genome Atlas (TCGA) highlights the extraordinary number of ways in which the finely tuned activities of enzymes can be disrupted, contributing to cancer development and progression often due to somatic and/or inherited genetic alterations. Rather than being limited to the domain of enzymologists, kinetic constants such as kcat, Km, and kcat/Km are highly informative parameters that can impact a cancer patient in tangible ways—these parameters can be used to sort tumor driver mutations from passenger mutations, to establish the pathways that cancer cells rely on to drive patients’ tumors, to evaluate the selectivity and efficacy of anti-cancer drugs, to identify mechanisms of resistance to treatment, and more. In this review, we will discuss how changes in enzyme activity, primarily through somatic mutation, can lead to altered kinetic parameters, new activities, or changes in conformation and oligomerization. We will also address how changes in the tumor microenvironment can affect enzymatic activity, and briefly describe how enzymology, when combined with additional powerful tools, and can provide us with tremendous insight into the chemical and molecular mechanisms of cancer.
Collapse
|
9
|
López-Ginés C, Muñoz-Hidalgo L, San-Miguel T, Megías J, Triviño JC, Calabuig S, Roldán P, Cerdá-Nicolás M, Monleón D. Whole-exome sequencing, EGFR amplification and infiltration patterns in human glioblastoma. Am J Cancer Res 2021; 11:5543-5558. [PMID: 34873478 PMCID: PMC8640814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023] Open
Abstract
Glioblastoma (GBM) is the most common malignant primary brain tumor in adults. This cancer shows rapid, highly infiltrative growth, that invades individually or in small groups the surrounding tissue. The aggressive tumor biology of GBM has devastating consequences with a median survival of 15 months. GBM often has Epidermal Growth Factor Receptor (EGFR) abnormalities. Despite recent advances in the study of GBM tumor biology, it is unclear whether mutations in GBM are related to EGFR amplification and relevant phenotypes like tumor infiltration. This study aimed to perform whole-exome sequencing analysis in 30 human GBM samples for identifying mutational portraits associated with EGFR amplification and infiltrative patterns. Our results show that EGFR-amplified tumors have overall higher mutation rates than EGFR-no-amplified. Six genes out of 2029 candidate genes show mutations associated with EGFR amplification status. Mutations in these genes for GBM are novel, not previously reported in GBM, and with little presence in the TCGA database. GPR179, USP48, and BLK show mutation only in EGFR-amplified cases, and all the affected cases exhibit diffuse infiltrative patterns. On the other hand, mutations in ADGB, EHHADH, and PTPN13, were present only in the EGFR-no-amplified group with a more diverse infiltrative phenotype. Overall, our work identified different mutational portraits of GBM related to well-established features like EGFR amplification and tumor infiltration.
Collapse
Affiliation(s)
| | | | | | - Javier Megías
- Departament of Pathology, University of ValenciaValencia, Spain
| | | | - Silvia Calabuig
- Departament of Pathology, University of ValenciaValencia, Spain
| | - Pedro Roldán
- Department of Neurosurgery, University Clinical Hospital ValenciaValencia, Spain
| | | | - Daniel Monleón
- Departament of Pathology, University of ValenciaValencia, Spain
- Health Research Institute INCLIVAValencia, Spain
- CIBERFES_ISCIIIValencia, Spain
| |
Collapse
|
10
|
Su Z, Gao A, Li X, Zou S, He C, Wu J, Ding WQ, Zhou J. DNA Polymerase Iota Promotes Esophageal Squamous Cell Carcinoma Proliferation Through Erk-OGT-Induced G6PD Overactivation. Front Oncol 2021; 11:706337. [PMID: 34354953 PMCID: PMC8329663 DOI: 10.3389/fonc.2021.706337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most lethal cancers with rapid progression and a high mortality rate. Our previous study demonstrated that DNA polymerase iota (Pol ι) is overexpressed in ESCC tumors and correlates with poor prognosis. However, its role in ESCC proliferation remains obscure. We report here that Pol ι promotes ESCC proliferation and progression through Erk- O-GlcNAc transferase (OGT) regulated Glucose-6-phosphate dehydrogenase (G6PD) overactivation. Cell clonogenic ability was assessed by colony formation assay. Cell proliferation was assessed by EdU incorporation assay. Our transcriptome data was reanalyzed by GSEA and validated by analysis of cellular metabolism, G6PD activity, and cellular NADPH concentration. The level of Pol ι, OGT, G6PD and O-GlcNAcylation in ESCC cells and patient samples were analyzed. The MEK inhibitor PD98059 was applied to confirm OGT expression regulation by the Erk signaling. The G6PD inhibitor polydatin was used to examine the role of G6PD activation in Pol ι promoted proliferation. We found that Pol ι promotes ESCC proliferation. It shunted the glucose flux towards the pentose phosphate pathway (PPP) by activating G6PD through OGT-promoted O-GlcNAcylation. The expression of OGT was positively correlated with Pol ι expression and O-GlcNAcylation. Notably, elevated O-GlcNAcylation was correlated with poor prognosis in ESCC patients. Pol ι was shown to stimulate Erk signaling to enhance OGT expression, and the G6PD inhibitor polydatin attenuated Pol ι induced tumor growth in vitro and in vivo. In conclusion, Pol ι activates G6PD through Erk-OGT-induced O-GlcNAcylation to promote the proliferation and progression of ESCC, supporting the notion that Pol ι is a potential biomarker and therapeutic target of ESCC.
Collapse
Affiliation(s)
- Zhenzi Su
- Department of Radiation Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Aidi Gao
- Suzhou Cancer Center Core Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Xiaoqing Li
- Suzhou Cancer Center Core Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Shitao Zou
- Suzhou Cancer Center Core Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Chao He
- Suzhou Cancer Center Core Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Jinchang Wu
- Department of Radiation Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Wei-Qun Ding
- Department of Pathology, University of Oklahoma Health Science Center, Oklahoma City, OK, United States
| | - Jundong Zhou
- Department of Radiation Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Suzhou Cancer Center Core Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| |
Collapse
|
11
|
DNA Polymerase and dRP-lyase activities of polymorphic variants of human Pol ι. Biochem J 2021; 478:1399-1412. [PMID: 33600564 DOI: 10.1042/bcj20200491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 11/17/2022]
Abstract
Y-family DNA polymerase iota (Pol ι) is involved in DNA damage response and tolerance. Mutations and altered expression level of POLI gene are linked to a higher incidence of cancer. We biochemically characterized five active site polymorphic variants of human Pol ι: R71G (rs3218778), P118L (rs554252419), I236M (rs3218784), E251K (rs3218783) and P365R (rs200852409). We analyzed fidelity of nucleotide incorporation on undamaged DNA, efficiency and accuracy of DNA damage bypass, as well as 5'-deoxyribophosphate lyase (dRP-lyase) activity. The I236M and P118L variants were indistinguishable from the wild-type Pol ι in activity. The E251K and P365R substitutions altered the spectrum of nucleotide incorporation opposite several undamaged DNA bases. The P365R variant also reduced the dRP-lyase activity and possessed the decreased TLS activity opposite 8-oxo-G. The R71G mutation dramatically affected the catalytic activities of Pol ι. The reduced DNA polymerase activity of the R71G variant correlated with an enhanced fidelity of nucleotide incorporation on undamaged DNA, altered lesion-bypass activity and reduced dRP-lyase activity. Therefore, this amino acid substitution likely alters Pol ι functions in vivo.
Collapse
|
12
|
Shilkin ES, Boldinova EO, Stolyarenko AD, Goncharova RI, Chuprov-Netochin RN, Khairullin RF, Smal MP, Makarova AV. Translesion DNA Synthesis and Carcinogenesis. BIOCHEMISTRY (MOSCOW) 2021; 85:425-435. [PMID: 32569550 DOI: 10.1134/s0006297920040033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Tens of thousands of DNA lesions are formed in mammalian cells each day. DNA translesion synthesis is the main mechanism of cell defense against unrepaired DNA lesions. DNA polymerases iota (Pol ι), eta (Pol η), kappa (Pol κ), and zeta (Pol ζ) have active sites that are less stringent toward the DNA template structure and efficiently incorporate nucleotides opposite DNA lesions. However, these polymerases display low accuracy of DNA synthesis and can introduce mutations in genomic DNA. Impaired functioning of these enzymes can lead to an increased risk of cancer.
Collapse
Affiliation(s)
- E S Shilkin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - E O Boldinova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - A D Stolyarenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - R I Goncharova
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, 220072, Republic of Belarus
| | - R N Chuprov-Netochin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - R F Khairullin
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420012, Russia
| | - M P Smal
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, 220072, Republic of Belarus.
| | - A V Makarova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
| |
Collapse
|
13
|
Unravelling roles of error-prone DNA polymerases in shaping cancer genomes. Oncogene 2021; 40:6549-6565. [PMID: 34663880 PMCID: PMC8639439 DOI: 10.1038/s41388-021-02032-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/01/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
Mutagenesis is a key hallmark and enabling characteristic of cancer cells, yet the diverse underlying mutagenic mechanisms that shape cancer genomes are not understood. This review will consider the emerging challenge of determining how DNA damage response pathways-both tolerance and repair-act upon specific forms of DNA damage to generate mutations characteristic of tumors. DNA polymerases are typically the ultimate mutagenic effectors of DNA repair pathways. Therefore, understanding the contributions of DNA polymerases is critical to develop a more comprehensive picture of mutagenic mechanisms in tumors. Selection of an appropriate DNA polymerase-whether error-free or error-prone-for a particular DNA template is critical to the maintenance of genome stability. We review different modes of DNA polymerase dysregulation including mutation, polymorphism, and over-expression of the polymerases themselves or their associated activators. Based upon recent findings connecting DNA polymerases with specific mechanisms of mutagenesis, we propose that compensation for DNA repair defects by error-prone polymerases may be a general paradigm molding the mutational landscape of cancer cells. Notably, we demonstrate that correlation of error-prone polymerase expression with mutation burden in a subset of patient tumors from The Cancer Genome Atlas can identify mechanistic hypotheses for further testing. We contrast experimental approaches from broad, genome-wide strategies to approaches with a narrower focus on a few hundred base pairs of DNA. In addition, we consider recent developments in computational annotation of patient tumor data to identify patterns of mutagenesis. Finally, we discuss the innovations and future experiments that will develop a more comprehensive portrait of mutagenic mechanisms in human tumors.
Collapse
|
14
|
Wilkinson NA, Mnuskin KS, Ashton NW, Woodgate R. Ubiquitin and Ubiquitin-Like Proteins Are Essential Regulators of DNA Damage Bypass. Cancers (Basel) 2020; 12:cancers12102848. [PMID: 33023096 PMCID: PMC7600381 DOI: 10.3390/cancers12102848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Ubiquitin and ubiquitin-like proteins are conjugated to many other proteins within the cell, to regulate their stability, localization, and activity. These modifications are essential for normal cellular function and the disruption of these processes contributes to numerous cancer types. In this review, we discuss how ubiquitin and ubiquitin-like proteins regulate the specialized replication pathways of DNA damage bypass, as well as how the disruption of these processes can contribute to cancer development. We also discuss how cancer cell survival relies on DNA damage bypass, and how targeting the regulation of these pathways by ubiquitin and ubiquitin-like proteins might be an effective strategy in anti-cancer therapies. Abstract Many endogenous and exogenous factors can induce genomic instability in human cells, in the form of DNA damage and mutations, that predispose them to cancer development. Normal cells rely on DNA damage bypass pathways such as translesion synthesis (TLS) and template switching (TS) to replicate past lesions that might otherwise result in prolonged replication stress and lethal double-strand breaks (DSBs). However, due to the lower fidelity of the specialized polymerases involved in TLS, the activation and suppression of these pathways must be tightly regulated by post-translational modifications such as ubiquitination in order to limit the risk of mutagenesis. Many cancer cells rely on the deregulation of DNA damage bypass to promote carcinogenesis and tumor formation, often giving them heightened resistance to DNA damage from chemotherapeutic agents. In this review, we discuss the key functions of ubiquitin and ubiquitin-like proteins in regulating DNA damage bypass in human cells, and highlight ways in which these processes are both deregulated in cancer progression and might be targeted in cancer therapy.
Collapse
Affiliation(s)
| | | | - Nicholas W. Ashton
- Correspondence: (N.W.A.); (R.W.); Tel.: +1-301-435-1115 (N.W.A.); +1-301-435-0740 (R.W.)
| | - Roger Woodgate
- Correspondence: (N.W.A.); (R.W.); Tel.: +1-301-435-1115 (N.W.A.); +1-301-435-0740 (R.W.)
| |
Collapse
|
15
|
McIntyre J. Polymerase iota - an odd sibling among Y family polymerases. DNA Repair (Amst) 2019; 86:102753. [PMID: 31805501 DOI: 10.1016/j.dnarep.2019.102753] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 12/14/2022]
Abstract
It has been two decades since the discovery of the most mutagenic human DNA polymerase, polymerase iota (Polι). Since then, the biochemical activity of this translesion synthesis (TLS) enzyme has been extensively explored, mostly through in vitro experiments, with some insight into its cellular activity. Polι is one of four members of the Y-family of polymerases, which are the best characterized DNA damage-tolerant polymerases involved in TLS. Polι shares some common Y-family features, including low catalytic efficiency and processivity, high infidelity, the ability to bypass some DNA lesions, and a deficiency in 3'→5' exonucleolytic proofreading. However, Polι exhibits numerous properties unique among the Y-family enzymes. Polι has an unusual catalytic pocket structure and prefers Hoogsteen over Watson-Crick pairing, and its replication fidelity strongly depends on the template; further, it prefers Mn2+ ions rather than Mg2+ as catalytic activators. In addition to its polymerase activity, Polι possesses also 5'-deoxyribose phosphate (dRP) lyase activity, and its ability to participate in base excision repair has been shown. As a highly error-prone polymerase, its regulation is crucial and mostly involves posttranslational modifications and protein-protein interactions. The upregulation and downregulation of Polι are correlated with different types of cancer and suggestions regarding the possible function of this polymerase have emerged from studies of various cancer lines. Nonetheless, after twenty years of research, the biological function of Polι certainly remains unresolved.
Collapse
Affiliation(s)
- Justyna McIntyre
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106, Warsaw, Poland.
| |
Collapse
|
16
|
Xu Z, Wang C, Xiang X, Li J, Huang J. Characterization of mRNA Expression and Endogenous RNA Profiles in Bladder Cancer Based on The Cancer Genome Atlas (TCGA) Database. Med Sci Monit 2019; 25:3041-3060. [PMID: 31020952 PMCID: PMC6498884 DOI: 10.12659/msm.915487] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background Bladder cancer is a multifactorial disease with increasing incidence and mortality. Genetic alterations and altered expressions of mRNAs, long non-coding RNAs (lncRNAs), and miRNAs have been shown to play important roles in the tumorigenesis of bladder cancer. However, the functions of key RNAs and their regulatory network in bladder cancer are still to be elucidated. Material/Methods RNA profiles were downloaded from The Cancer Genome Atlas (TCGA) database. The differentially expressed mRNAs, lncRNAs, and miRNAs in bladder cancer were acquired through analyses of data from 414 bladder cancer tissues and 19 normal bladder tissues. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis was performed by using “DAVID6.8” and the R package “ClusterProfile”. Protein–protein interaction and competing endogenous RNA (ceRNA) networks were constructed by using “STRING” database and Cytoscape 3.6.2. Based on the clinical data and Cox regression, a prognosis model was established, and survival analysis was performed. Results A total of 1819 mRNAs, 659 lncRNAs, and 160 miRNAs were identified as significantly differentially expressed in bladder cancer of which 52 mRNAs, 58 lncRNAs, and 22 miRNAs were incorporated in the ceRNA network. CFL2 and TPM2 were found to be downregulated and showed significant correlation to each other in bladder cancer. HOXB5 and 6 lncRNAs (ADAMTS9-AS1, AC112721.1, LINC00460, AC110491.1, LINC00163, and HCG22) were strongly associated with high-grade, disease stages, and overall survival. Conclusions In this study, we have identified differentially expressed mRNAs, lncRNAs, and miRNAs in bladder cancer which were strongly associated with oncogenesis and prognosis. Further experimental studies are necessary to validate these results.
Collapse
Affiliation(s)
- Zhipeng Xu
- Department of Urology, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China (mainland)
| | - Chuang Wang
- Department of Urology, People' Hospital of Guilin, Guilin, Guangxi, China (mainland)
| | - Xuebao Xiang
- Department of Urology, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China (mainland)
| | - Junming Li
- Department of Urology, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China (mainland)
| | - Jiefu Huang
- Department of Urology, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China (mainland)
| |
Collapse
|
17
|
Zou S, Xu Y, Chen X, He C, Gao A, Zhou J, Chen Y. DNA polymerase iota (Pol ι) promotes the migration and invasion of breast cancer cell via EGFR-ERK-mediated epithelial to mesenchymal transition. Cancer Biomark 2019; 24:363-370. [PMID: 30829610 DOI: 10.3233/cbm-181516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Shitao Zou
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215001, China
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215001, China
| | - Yan Xu
- Health Management Center, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215123, China
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215001, China
| | - Xingxing Chen
- Department of Radio-Oncology, Fudan university Shanghai Cancer Center, Shanghai 200433, China
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215001, China
| | - Chao He
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215001, China
| | - Aidi Gao
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215001, China
| | - Jundong Zhou
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215001, China
| | - Yihong Chen
- Department of Radio-Oncology, The First Affiliated Hospital of Wannan Medical College, Wuhu, Anhui 241001, China
| |
Collapse
|
18
|
Mancuso N, Gayther S, Gusev A, Zheng W, Penney KL, Kote-Jarai Z, Eeles R, Freedman M, Haiman C, Pasaniuc B. Large-scale transcriptome-wide association study identifies new prostate cancer risk regions. Nat Commun 2018; 9:4079. [PMID: 30287866 PMCID: PMC6172280 DOI: 10.1038/s41467-018-06302-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/28/2018] [Indexed: 12/16/2022] Open
Abstract
Although genome-wide association studies (GWAS) for prostate cancer (PrCa) have identified more than 100 risk regions, most of the risk genes at these regions remain largely unknown. Here we integrate the largest PrCa GWAS (N = 142,392) with gene expression measured in 45 tissues (N = 4458), including normal and tumor prostate, to perform a multi-tissue transcriptome-wide association study (TWAS) for PrCa. We identify 217 genes at 84 independent 1 Mb regions associated with PrCa risk, 9 of which are regions with no genome-wide significant SNP within 2 Mb. 23 genes are significant in TWAS only for alternative splicing models in prostate tumor thus supporting the hypothesis of splicing driving risk for continued oncogenesis. Finally, we use a Bayesian probabilistic approach to estimate credible sets of genes containing the causal gene at a pre-defined level; this reduced the list of 217 associations to 109 genes in the 90% credible set. Overall, our findings highlight the power of integrating expression with PrCa GWAS to identify novel risk loci and prioritize putative causal genes at known risk loci.
Collapse
Affiliation(s)
- Nicholas Mancuso
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, 90095, CA, USA.
| | - Simon Gayther
- The Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, 90048, CA, USA
| | | | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, 37232, TN, USA
| | - Kathryn L Penney
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, 02115, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, 02115, MA, USA
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Matthew Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, 02215, MA, USA
| | - Christopher Haiman
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, 90015, CA, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, 90095, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, 90095, CA, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, 90095, CA, USA
| |
Collapse
|
19
|
Li L, Tian H, Cheng C, Li S, Ming L, Qi L. siRNA of DNA polymerase iota inhibits the migration and invasion in the lung cancer cell A549. Acta Biochim Biophys Sin (Shanghai) 2018; 50:929-933. [PMID: 30060029 DOI: 10.1093/abbs/gmy089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Indexed: 12/13/2022] Open
Abstract
DNA polymerase iota (polɩ) is a member of low-fidelity Y-family of DNA polymerases. Our previous studies have demonstrated that the overexpression of polι is associated with the poorer prognosis in lung cancer patients. Here, we designed the small interfering RNA (siRNA) targeting polɩ gene (POLI) to investigate the effect of polɩ on the proliferation, apoptosis, and invasion of the lung cancer cell line A549 in order to reveal the role of polι in lung cancer progression. Our results showed that siRNA of POLI had no significant effect on the proliferation and apoptosis of the lung cancer cell line A549. However, siRNA of POLI could inhibit the migration and invasion of the lung cancer cell line A549 by upregulating the E-cadherin expression and downregulating the expressions of N-cadherin, MMP2, and MMP9. Together, our findings indicate that polι plays a positive role in lung cancer progression via promoting the migration and invasion of lung cancer cells. Therefore, polι might be a potential target for the clinical treatment of lung cancer in the future.
Collapse
Affiliation(s)
- Lin Li
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Hui Tian
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Chuanle Cheng
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Shuhai Li
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Lu Ming
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Lei Qi
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, China
| |
Collapse
|
20
|
Yang Y, Gao Y, Zlatanou A, Tateishi S, Yurchenko V, Rogozin IB, Vaziri C. Diverse roles of RAD18 and Y-family DNA polymerases in tumorigenesis. Cell Cycle 2018; 17:833-843. [PMID: 29683380 PMCID: PMC6056224 DOI: 10.1080/15384101.2018.1456296] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Mutagenesis is a hallmark and enabling characteristic of cancer cells. The E3 ubiquitin ligase RAD18 and its downstream effectors, the ‘Y-family’ Trans-Lesion Synthesis (TLS) DNA polymerases, confer DNA damage tolerance at the expense of DNA replication fidelity. Thus, RAD18 and TLS polymerases are attractive candidate mediators of mutagenesis and carcinogenesis. The skin cancer-propensity disorder xeroderma pigmentosum-variant (XPV) is caused by defects in the Y-family DNA polymerase Pol eta (Polη). However it is unknown whether TLS dysfunction contributes more generally to other human cancers. Recent analyses of cancer genomes suggest that TLS polymerases generate many of the mutational signatures present in diverse cancers. Moreover biochemical studies suggest that the TLS pathway is often reprogrammed in cancer cells and that TLS facilitates tolerance of oncogene-induced DNA damage. Here we review recent evidence supporting widespread participation of RAD18 and the Y-family DNA polymerases in the different phases of multi-step carcinogenesis.
Collapse
Affiliation(s)
- Yang Yang
- a Department of Pathology and Laboratory Medicine , University of North Carolina at Chapel Hill Chapel Hill , NC , USA
| | - Yanzhe Gao
- a Department of Pathology and Laboratory Medicine , University of North Carolina at Chapel Hill Chapel Hill , NC , USA
| | - Anastasia Zlatanou
- a Department of Pathology and Laboratory Medicine , University of North Carolina at Chapel Hill Chapel Hill , NC , USA
| | - Satoshi Tateishi
- b Division of Cell Maintenance , Institute of Molecular Embryology and Genetics (IMEG) , Kumamoto University , Kumamoto , Japan
| | - Vyacheslav Yurchenko
- c Life Science Research Center , University of Ostrava , Ostrava , Czech Republic
| | - Igor B Rogozin
- d National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA
| | - Cyrus Vaziri
- a Department of Pathology and Laboratory Medicine , University of North Carolina at Chapel Hill Chapel Hill , NC , USA
| |
Collapse
|
21
|
Liu J, Zhai R, Zhao J, Kong F, Wang J, Jiang W, Xin Q, Xue X, Luan Y. Programmed cell death 4 overexpression enhances sensitivity to cisplatin via the JNK/c-Jun signaling pathway in bladder cancer. Int J Oncol 2018; 52:1633-1642. [PMID: 29512740 DOI: 10.3892/ijo.2018.4303] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 02/28/2018] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to evaluate the effects of programmed cell death 4 (PDCD4) on cell proliferation and apoptosis, and to elucidate the potential role of the Jun N-terminal kinase (JNK)/c-Jun pathway in human bladder cancer (BCa) cells. Mixed BCa cells were transfected with plasmids containing PDCD4 (PDCD4-pcDNA3). The sensitivity to cisplatin was analyzed using cell viability, invasion/migration, apoptosis, flow cytometry, wound healing and Transwell assays at different transfection times. Furthermore, epithelial-to-mesenchymal transition (EMT) markers were detected by immunofluorescence staining, and the protein expression of c-Jun, and phosphorylated Jun N-terminal kinase (p-JNK) and c-Jun (p-c-Jun, Ser-73) were also tested using western blotting. It was observed that BCa cell proliferation and invasion and tumor growth were significantly inhibited, whereas apoptosis was enhanced in PDCD4-transfected cells treated with cisplatin compared with controls. Moreover, the western blotting and immunofluorescence results demonstrated that PDCD4 upregulated the expression of epithelial cell markers, but downregulated the expression of mesenchymal cell markers. Furthermore, overexpression of PDCD4 reduced the protein levels of p-JNK and p-c-Jun. Taken together, the findings of the present study indicate that PDCD4 enhances the sensitivity of BCa cells to cisplatin, partially via regulation of the JNK/c-Jun pathway, and reverses EMT. In conclusion, the results of the present study suggested that PDCD4, a nuclear/cytoplasmic shuttling protein with multiple functions, plays an important role in the development and progression of human BCa.
Collapse
Affiliation(s)
- Junli Liu
- Laboratory of Clinical Molecular Biology, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Ruirui Zhai
- Department of Pediatrics, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Jingjie Zhao
- Laboratory of Clinical Molecular Biology, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Feng Kong
- Central Research Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Jue Wang
- Central Research Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Wen Jiang
- Central Research Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Qian Xin
- Central Research Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Xia Xue
- Department of Pharmacy, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Yun Luan
- Central Research Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| |
Collapse
|
22
|
Huang M, Zhong Z, Lv M, Shu J, Tian Q, Chen J. Comprehensive analysis of differentially expressed profiles of lncRNAs and circRNAs with associated co-expression and ceRNA networks in bladder carcinoma. Oncotarget 2018; 7:47186-47200. [PMID: 27363013 PMCID: PMC5216934 DOI: 10.18632/oncotarget.9706] [Citation(s) in RCA: 199] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/16/2016] [Indexed: 12/23/2022] Open
Abstract
Accumulating evidences indicate that long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) play important roles in tumorigenesis. However, the mechanisms remain largely unknown. To explore lncRNAs and circRNAs expression profiling and their biological functions in bladder cancer, we surveyed the lncRNA/circRNA and mRNA expression profiles of bladder cancer and para-cancer tissues using microarray for four patients. Thousands of significantly changed lncRNAs and mRNAs as well as hundreds of circRNAs were identified. Five dysregulated lncRNAs and four mRNAs were confirmed by quantitative real-time PCR in 30 pairs of samples. GO and KEGG pathway enrichment analyses were executed to determine the principal functions of the significantly deregulated genes. Further more, we constructed correlated expression networks including coding-noncoding co-expression (CNC), competing endogenous RNAs (ceRNA), cis regulation, lncRNAs-transcription factor (TF)-mRNA with bioinformatics methods. Co-expression analysis showed lncRNA APLP2 expression is correlated with apoptosis-related genes, including PTEN and TP53INP1. CeRNA network inferred that lncRNA H19 and circRNA MYLK could bind competitively with miRNA-29a-3p increasing target gene DNMT3B, VEGFA and ITGB1 expressions. Moreover, the nearby genes pattern displayed that overexpressing ADAM2 and C8orf4 are cis-regulated by lncRNA RP11-359E19.2, involving in progression of bladder cancer. In addition, lncRNAs-TF-mRNA diagram indicated that lncRNA BC041488 could trans-regulate CDK1 mRNA expression through SRF transcription factor. Taken together, these results suggested lncRNAs and circRNAs could implicate in the pathogenesis and development of bladder cancer. Our findings provide a novel perspective on lncRNAs and circRNAs and lay the foundation for future research of potential roles of lncRNAs and circRNAs in bladder carcinoma.
Collapse
Affiliation(s)
- Mengge Huang
- College of Clinical Medicine, Southwest Medical University, Luzhou 646000, China
| | - Zhenyu Zhong
- The First Clinical College, Chongqing Medical University, Chongqing 400016, China
| | - Mengxin Lv
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Jing Shu
- Department of Clinical Laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Qiang Tian
- Department of Cell Biology and Genetics, Southwest Medical University, Luzhou 646000, China
| | - Junxia Chen
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, China
| |
Collapse
|
23
|
He C, Wu S, Gao A, Su Y, Min H, Shang ZF, Wu J, Yang L, Ding WQ, Zhou J. Phosphorylation of ETS-1 is a critical event in DNA polymerase iota-induced invasion and metastasis of esophageal squamous cell carcinoma. Cancer Sci 2017; 108:2503-2510. [PMID: 28905458 PMCID: PMC5715348 DOI: 10.1111/cas.13399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/30/2017] [Accepted: 09/09/2017] [Indexed: 01/02/2023] Open
Abstract
An aberrantly elevated expression of DNA polymerase ι (Pol ι) is significantly associated with poor prognosis of patients with esophageal squamous cell carcinoma (ESCC), yet the mechanisms behind this phenomenon remain obscure. Based on the RNA-Seq transcriptome and real-time PCR analysis, we identified ETS-1 as a candidate gene involved in Pol ι-mediated progression of ESCC. Wound-healing and transwell assay indicated that downregulation of ETS-1 attenuates Pol ι-mediated invasiveness of ESCC. Signaling pathway analysis showed that Pol ι enhances ETS-1 phosphorylation at threonine-38 through the Erk signaling pathway in ESCC cells. Kaplan-Meier analysis, based on 93 clinical tissue samples, revealed that ETS-1 phosphorylation at threonine-38 is associated with poor prognosis of ESCC patients. The present study thus demonstrates that phosphorylation of ETS-1 is a critical event in the Pol ι-induced invasion and metastasis of ESCC.
Collapse
Affiliation(s)
- Chao He
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China
| | - Shuhua Wu
- Department of Geriatrics, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Aidi Gao
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China
| | - Ye Su
- Jerry M. Wallace School of Osteopathic Medicine, Leon Levine Hall of Medical Science, Campbell University, Lillington, North Carolina, USA
| | - Han Min
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China
| | - Zeng-Fu Shang
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Jinchang Wu
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China
| | - Li Yang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wei-Qun Ding
- Department of Pathology, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA
| | - Jundong Zhou
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China
| |
Collapse
|
24
|
|
25
|
Bournique E, Dall'Osto M, Hoffmann JS, Bergoglio V. Role of specialized DNA polymerases in the limitation of replicative stress and DNA damage transmission. Mutat Res 2017; 808:62-73. [PMID: 28843435 DOI: 10.1016/j.mrfmmm.2017.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 01/31/2023]
Abstract
Replication stress is a strong and early driving force for genomic instability and tumor development. Beside replicative DNA polymerases, an emerging group of specialized DNA polymerases is involved in the technical assistance of the replication machinery in order to prevent replicative stress and its deleterious consequences. During S-phase, altered progression of the replication fork by endogenous or exogenous impediments induces replicative stress, causing cells to reach mitosis with genomic regions not fully duplicated. Recently, specific mechanisms to resolve replication intermediates during mitosis with the aim of limiting DNA damage transmission to daughter cells have been identified. In this review, we detail the two major actions of specialized DNA polymerases that limit DNA damage transmission: the prevention of replicative stress by non-B DNA replication and the recovery of stalled replication forks.
Collapse
Affiliation(s)
- Elodie Bournique
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France
| | - Marina Dall'Osto
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France
| | - Jean-Sébastien Hoffmann
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France
| | - Valérie Bergoglio
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France.
| |
Collapse
|
26
|
Li Y, Guo G, Song J, Cai Z, Yang J, Chen Z, Wang Y, Huang Y, Gao Q. B7-H3 Promotes the Migration and Invasion of Human Bladder Cancer Cells via the PI3K/Akt/STAT3 Signaling Pathway. J Cancer 2017; 8:816-824. [PMID: 28382144 PMCID: PMC5381170 DOI: 10.7150/jca.17759] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/16/2016] [Indexed: 12/30/2022] Open
Abstract
Bladder cancer is one of most common malignant cancer. Although previous studies have found abnormal expression of B7-H3 in human bladder cancer tissues, the exact role and molecular mechanism of B7-H3 in bladder cancer remain unknown. In this study, we first detected the expression of B7-H3 in human bladder cancer samples and cell lines, and analyzed its correlations with clinicopathological pathological parameters. Next, siRNAs or overexpression plasmids of B7-H3 were transfected into T24 or 5637 cells, and cell proliferation, apoptosis, migration and invasion were analyzed via CCK-8, colony formation, flow cytometry and transwell assays, protein expression levels were determined by western blotting. The results presented here showed B7-H3 was upregulated in bladder cancer samples compared with normal tissues, and the expression level was correlated with local invasion status. B7-H3 did not affect cell proliferation and apoptosis, but cell migration and invasion were changed through the regulation of matrix metalloproteinase (MMP) 2/9. Knockdown of B7-H3 resulted in decreased activity of the STAT3 and PI3K/Akt pathways, and the Akt served as an upstream regulator of the STAT3. Our results suggest that the overexpression of B7-H3 promotes the migration and invasion of human bladder cancer cells through the PI3K/Akt/STAT3 signaling pathway.
Collapse
Affiliation(s)
- Yuchao Li
- Department of Cell Biology, Third Military Medical University, Chongqing 400038, China;; Trainee Brigade, Third Military Medical University, Chongqing 400038, China
| | - Guoning Guo
- Department of Emergency, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Jie Song
- Trainee Brigade, Third Military Medical University, Chongqing 400038, China
| | - Zhiping Cai
- Trainee Brigade, Third Military Medical University, Chongqing 400038, China
| | - Jin Yang
- Department of Cell Biology, Third Military Medical University, Chongqing 400038, China
| | - Zhiwen Chen
- Urology Center, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Yun Wang
- Department of Cell Biology, Third Military Medical University, Chongqing 400038, China
| | - Yaqin Huang
- Department of Cell Biology, Third Military Medical University, Chongqing 400038, China
| | - Qiangguo Gao
- Department of Cell Biology, Third Military Medical University, Chongqing 400038, China
| |
Collapse
|
27
|
Barnes R, Eckert K. Maintenance of Genome Integrity: How Mammalian Cells Orchestrate Genome Duplication by Coordinating Replicative and Specialized DNA Polymerases. Genes (Basel) 2017; 8:genes8010019. [PMID: 28067843 PMCID: PMC5295014 DOI: 10.3390/genes8010019] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/19/2016] [Accepted: 12/27/2016] [Indexed: 12/30/2022] Open
Abstract
Precise duplication of the human genome is challenging due to both its size and sequence complexity. DNA polymerase errors made during replication, repair or recombination are central to creating mutations that drive cancer and aging. Here, we address the regulation of human DNA polymerases, specifically how human cells orchestrate DNA polymerases in the face of stress to complete replication and maintain genome stability. DNA polymerases of the B-family are uniquely adept at accurate genome replication, but there are numerous situations in which one or more additional DNA polymerases are required to complete genome replication. Polymerases of the Y-family have been extensively studied in the bypass of DNA lesions; however, recent research has revealed that these polymerases play important roles in normal human physiology. Replication stress is widely cited as contributing to genome instability, and is caused by conditions leading to slowed or stalled DNA replication. Common Fragile Sites epitomize “difficult to replicate” genome regions that are particularly vulnerable to replication stress, and are associated with DNA breakage and structural variation. In this review, we summarize the roles of both the replicative and Y-family polymerases in human cells, and focus on how these activities are regulated during normal and perturbed genome replication.
Collapse
Affiliation(s)
- Ryan Barnes
- Biomedical Sciences Graduate Program, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| | - Kristin Eckert
- Departments of Pathology and Biochemistry & Molecular Biology, The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| |
Collapse
|
28
|
Choi JY, Patra A, Yeom M, Lee YS, Zhang Q, Egli M, Guengerich FP. Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase ι. J Biol Chem 2016; 291:21063-21073. [PMID: 27555320 DOI: 10.1074/jbc.m116.748285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Indexed: 12/13/2022] Open
Abstract
DNA polymerase (pol) ι is a Y-family polymerase involved in translesion synthesis, exhibiting higher catalytic activity with Mn2+ than Mg2+ The human germline R96G variant impairs both Mn2+-dependent and Mg2+-dependent activities of pol ι, whereas the Δ1-25 variant selectively enhances its Mg2+-dependent activity. We analyzed pre-steady-state kinetic and structural effects of these two metal ions and genetic variations on pol ι using pol ι core (residues 1-445) proteins. The presence of Mn2+ (0.15 mm) instead of Mg2+ (2 mm) caused a 770-fold increase in efficiency (kpol/Kd,dCTP) of pol ι for dCTP insertion opposite G, mainly due to a 450-fold decrease in Kd,dCTP The R96G and Δ1-25 variants displayed a 53-fold decrease and a 3-fold increase, respectively, in kpol/Kd,dCTP for dCTP insertion opposite G with Mg2+ when compared with wild type, substantially attenuated by substitution with Mn2+ Crystal structures of pol ι ternary complexes, including the primer terminus 3'-OH and a non-hydrolyzable dCTP analogue opposite G with the active-site Mg2+ or Mn2+, revealed that Mn2+ achieves more optimal octahedral coordination geometry than Mg2+, with lower values in average coordination distance geometry in the catalytic metal A-site. Crystal structures of R96G revealed the loss of three H-bonds of residues Gly-96 and Tyr-93 with an incoming dNTP, due to the lack of an arginine, as well as a destabilized Tyr-93 side chain secondary to the loss of a cation-π interaction between both side chains. These results provide a mechanistic basis for alteration in pol ι catalytic function with coordinating metals and genetic variation.
Collapse
Affiliation(s)
- Jeong-Yun Choi
- From the Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Gyeonggi-do 16419, Republic of Korea
| | - Amritaj Patra
- the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, and
| | - Mina Yeom
- From the Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Gyeonggi-do 16419, Republic of Korea
| | - Young-Sam Lee
- the Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea
| | - Qianqian Zhang
- the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, and
| | - Martin Egli
- the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, and
| | - F Peter Guengerich
- the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, and
| |
Collapse
|
29
|
Engström W, Darbre P, Eriksson S, Gulliver L, Hultman T, Karamouzis MV, Klaunig JE, Mehta R, Moorwood K, Sanderson T, Sone H, Vadgama P, Wagemaker G, Ward A, Singh N, Al-Mulla F, Al-Temaimi R, Amedei A, Colacci AM, Vaccari M, Mondello C, Scovassi AI, Raju J, Hamid RA, Memeo L, Forte S, Roy R, Woodrick J, Salem HK, Ryan EP, Brown DG, Bisson WH. The potential for chemical mixtures from the environment to enable the cancer hallmark of sustained proliferative signalling. Carcinogenesis 2015; 36 Suppl 1:S38-60. [PMID: 26106143 DOI: 10.1093/carcin/bgv030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The aim of this work is to review current knowledge relating the established cancer hallmark, sustained cell proliferation to the existence of chemicals present as low dose mixtures in the environment. Normal cell proliferation is under tight control, i.e. cells respond to a signal to proliferate, and although most cells continue to proliferate into adult life, the multiplication ceases once the stimulatory signal disappears or if the cells are exposed to growth inhibitory signals. Under such circumstances, normal cells remain quiescent until they are stimulated to resume further proliferation. In contrast, tumour cells are unable to halt proliferation, either when subjected to growth inhibitory signals or in the absence of growth stimulatory signals. Environmental chemicals with carcinogenic potential may cause sustained cell proliferation by interfering with some cell proliferation control mechanisms committing cells to an indefinite proliferative span.
Collapse
Affiliation(s)
- Wilhelm Engström
- Department of Biosciences and Veterinary Public Health, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, PO Box 7028, 75007 Uppsala, Sweden,
| | - Philippa Darbre
- School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Staffan Eriksson
- Department of Biochemistry, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Box 575, 75123 Uppsala, Sweden
| | - Linda Gulliver
- Faculty of Medicine, University of Otago, PO Box 913, Dunedin 9050, New Zealand
| | - Tove Hultman
- Department of Biosciences and Veterinary Public Health, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, PO Box 7028, 75007 Uppsala, Sweden, School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Michalis V Karamouzis
- Department of Biological Chemistry Medical School, Institute of Molecular Medicine and Biomedical Research, University of Athens, Marasli 3, Kolonaki, Athens 10676, Greece
| | - James E Klaunig
- Department of Environmental Health, School of Public Health, Indiana University Bloomington , 1025 E. 7th Street, Suite 111, Bloomington, IN 47405, USA
| | - Rekha Mehta
- Regulatory Toxicology Research Division, Bureau of Chemical Safety, Food Directorate, HPFB, Health Canada, 251 Sir F.G. Banting Driveway, AL # 2202C, Tunney's Pasture, Ottawa, Ontario K1A 0K9, Canada
| | - Kim Moorwood
- Department of Biochemistry and Biology, University of Bath , Claverton Down, Bath BA2 7AY, UK
| | - Thomas Sanderson
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Quebec H7V 1B7, Canada
| | - Hideko Sone
- Environmental Exposure Research Section, Center for Environmental Risk Research, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibraki 3058506, Japan
| | - Pankaj Vadgama
- IRC in Biomedical Materials, School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Gerard Wagemaker
- Center for Stem Cell Research and Development, Hacettepe University, Ankara 06100, Turkey
| | - Andrew Ward
- Department of Biochemistry and Biology, University of Bath , Claverton Down, Bath BA2 7AY, UK
| | - Neetu Singh
- Centre for Advanced Research, King George's Medical University, Chowk, Lucknow, Uttar Pradesh 226003, India
| | - Fahd Al-Mulla
- Department of Pathology, Kuwait University, Safat 13110, Kuwait
| | | | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Anna Maria Colacci
- Center for Environmental Carcinogenesis and Risk Assessment, Environmental Protection and Health Prevention Agency, Bologna 40126, Italy
| | - Monica Vaccari
- Center for Environmental Carcinogenesis and Risk Assessment, Environmental Protection and Health Prevention Agency, Bologna 40126, Italy
| | - Chiara Mondello
- Institute of Molecular Genetics, National Research Council, Pavia 27100, Italy
| | - A Ivana Scovassi
- Institute of Molecular Genetics, National Research Council, Pavia 27100, Italy
| | - Jayadev Raju
- Regulatoty Toxicology Research Division, Bureau of Chemical Safety, Food Directorate, HPFB, Health Canada, Ottawa, Ontario K1A0K9, Canada
| | - Roslida A Hamid
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Lorenzo Memeo
- Mediterranean Institute of Oncology, Viagrande 95029, Italy
| | - Stefano Forte
- Mediterranean Institute of Oncology, Viagrande 95029, Italy
| | - Rabindra Roy
- Molecular Oncology Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Jordan Woodrick
- Molecular Oncology Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Hosni K Salem
- Urology Dept. kasr Al-Ainy School of Medicine, Cairo University, El Manial, Cairo 12515, Egypt
| | - Elizabeth P Ryan
- Department of Environmental and Radiological Sciences, Colorado State University//Colorado School of Public Health, Fort Collins CO 80523-1680, USA and
| | - Dustin G Brown
- Department of Environmental and Radiological Sciences, Colorado State University//Colorado School of Public Health, Fort Collins CO 80523-1680, USA and
| | - William H Bisson
- Environmental and Molecular Toxicology, Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331, USA
| |
Collapse
|
30
|
Yang XH, Wang B, Cunningham JM. Identification of epigenetic modifications that contribute to pathogenesis in therapy-related AML: Effective integration of genome-wide histone modification with transcriptional profiles. BMC Med Genomics 2015; 8 Suppl 2:S6. [PMID: 26043758 PMCID: PMC4460748 DOI: 10.1186/1755-8794-8-s2-s6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Background Therapy-related, secondary acute myeloid leukemia (t-AML) is an increasingly frequent complication of intensive chemotherapy. This malignancy is often characterized by abnormalities of chromosome 7, including large deletions or chromosomal loss. A variety of studies suggest that decreased expression of the EZH2 gene located at 7q36.1 is critical in disease pathogenesis. This histone methyltransferase has been implicated in transcriptional repression through modifying histone H3 on lysine 27 (H3k27). However, the critical target genes of EZH2 and their regulatory roles remain unclear. Method To characterize the subset of EZH2 target genes that might contribute to t-AML pathogenesis, we developed a novel computational analysis to integrate tissue-specific histone modifications and genome-wide transcriptional regulation. Initial integrative analysis utilized a novel "seq2gene" strategy to explore largely the target genes of chromatin immuneprecipitation sequencing (ChIP-seq) enriched regions. By combining seq2gene with our Phenotype-Genotype-Network (PGNet) algorithm, we enriched genes with similar expression profiles and genomic or functional characteristics into "biomodules". Results Initial studies identified SEMA3A (semaphoring 3A) as a novel oncogenic candidate that is regulated by EZH2-silencing, using data derived from both normal and leukemic cell lines as well as murine cells deficient in EZH2. A microsatellite marker at the SEMA3A promoter has been associated with chemosensitivity and radiosensitivity. Notably, our subsequent studies in primary t-AML demonstrate an expected up-regulation of SEMA3A that is EZH2-modulated. Furthermore, we have identified three biomodules that are co-expressed with SEMA3A and up-regulated in t-AML, one of which consists of previously characterized EZH2-repressed gene targets. The other two biomodules include MAPK8 and TATA box targets. Together, our studies suggest an important role for EZH2 targets in t-AML pathogenesis that warrants further study. Conclusion These developed computational algorithms and systems biology strategies will enhance the knowledge discovery and hypothesis-driven analysis of multiple next generation sequencing data, for t-AML and other complex diseases.
Collapse
|
31
|
Sun H, Zou S, Zhang S, Liu B, Meng X, Li X, Yu J, Wu J, Zhou J. Elevated DNA polymerase iota (Poli) is involved in the acquisition of aggressive phenotypes of human esophageal squamous cell cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:3591-3601. [PMID: 26097541 PMCID: PMC4466928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 03/17/2015] [Indexed: 06/04/2023]
Abstract
DNA polymerase iota (Polι) can repair several types of DNA damage but has extremely low fidelity. Previous studies have shown an aberrantly elevated Polι expression in human esophageal squamous cell cancer tissues. However, there were few reports describing the role of Polι in esophageal cancer progression. Based on Real-time PCR assay, we found Polι expression was up-regulated in esophageal cancer tissues compared to adjacent normal tissues and overexpression of Polι was correlated to lymph node metastasis. Clonogenic assay and transwell chamber assay showed that overexpression of Polι had higher clongenic capability and invasive tendency in human esophageal squamous cell cancer cells. Expression of cyclin D1, an important cell cycle regulator, was found to be associated with that of Polι in tissue samples and cancer cells as analyzed by real-time PCR, immunohistochemistry, Western blotting and immunofluorescence assay. Flow cytometry analysis further showed that cell cycle distribution was altered in Polι overexpressing cells. These results indicated that expression of Polι correlates significantly with tumor proliferation and invasion. We conclude that Polι is involved in the degree of aggressiveness of human esophageal squamous cell cancer.
Collapse
Affiliation(s)
- Haoyao Sun
- Department of Radio-Oncology, Nanjing Medical University Affiliated Suzhou HospitalSuzhou 215001, Jiangsu, P. R. China
| | - Shitao Zou
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou HospitalSuzhou 215001, Jiangsu, P.R. China
| | - Shuyu Zhang
- School of Radiation Medicine and Protection, Medical College of Soochow UniversitySuzhou 215123, Jiangsu, P. R. China
| | - Biao Liu
- Department of Pathology, Nanjing Medical University Affiliated Suzhou HospitalSuzhou 215001, Jiangsu, P. R. China
| | - Xingjun Meng
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou HospitalSuzhou 215001, Jiangsu, P.R. China
| | - Xiaoqing Li
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou HospitalSuzhou 215001, Jiangsu, P.R. China
| | - Jian Yu
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou HospitalSuzhou 215001, Jiangsu, P.R. China
| | - Jinchang Wu
- Department of Radio-Oncology, Nanjing Medical University Affiliated Suzhou HospitalSuzhou 215001, Jiangsu, P. R. China
| | - Jundong Zhou
- Department of Radio-Oncology, Nanjing Medical University Affiliated Suzhou HospitalSuzhou 215001, Jiangsu, P. R. China
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou HospitalSuzhou 215001, Jiangsu, P.R. China
| |
Collapse
|
32
|
Luo G, Zhou Y, Yi W, Yi H. Lactotransferrin expression is downregulated and affects the mitogen-activated protein kinase pathway in gastric cancer. Oncol Lett 2015; 9:2409-2413. [PMID: 26137081 DOI: 10.3892/ol.2015.3011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 02/17/2015] [Indexed: 11/06/2022] Open
Abstract
Gastric cancer (GC) is the second leading cause of cancer-associated mortality worldwide. In advanced and metastatic GC, conventional chemotherapy results in limited efficacy and the average survival rate is currently approximately 10 months. Dysregulated activation of numerous genes, including zinc finger, DHHC-type containing 14; caspase-associated recruitment domain-containing protein; and Ras association domain family member 10, have been implicated in GC. The tumor suppressor function of lactotransferrin (LTF) has been reported in a variety of tumors, including GC, nasopharyngeal carcinoma (NPC) and prostate cancer. However, the mechanism of the tumor suppressor function of LTF in GC remains unclear. In the present study, the expression levels of LTF in patient GC tissue samples were investigated using reverse transcription-quantitative polymerase chain reaction, and it was demonstrated that the LTF mRNA expression level in GC tissue samples was reduced by ~20-fold compared with the adjacent non-cancerous tissues (t=4.56, P<0.01). A similar trend in LTF protein expression was observed by western blot analysis. Furthermore, the present study demonstrated that the mitogen-activated protein kinase (MAPK) signaling pathway intermediates p38, c-Jun N-terminal kinase (JNK) and c-Jun were highly expressed in GC tissue samples, and indicated that LTF downregulation may be associated with the dysregulation of the MAPK signaling pathway in GC tissues. In addition, the present study indicated that LTF overexpression reduced the expression of p38, JNK2 and c-Jun in the GC cell line, SGC7901. The present study demonstrates that LTF expression is downregulated in GC tissues and that LTF may serve an important role in the dysregulation of the MAPK signaling pathway.
Collapse
Affiliation(s)
- Gengqiu Luo
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yanhong Zhou
- Molecular Genetics Laboratory, Cancer Research Institute, Central South University, Changsha, Hunan 410078, P.R. China
| | - Wei Yi
- Molecular Genetics Laboratory, Cancer Research Institute, Central South University, Changsha, Hunan 410078, P.R. China
| | - Hong Yi
- Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| |
Collapse
|
33
|
Kim J, Song I, Jo A, Shin JH, Cho H, Eoff RL, Guengerich FP, Choi JY. Biochemical analysis of six genetic variants of error-prone human DNA polymerase ι involved in translesion DNA synthesis. Chem Res Toxicol 2014; 27:1837-52. [PMID: 25162224 PMCID: PMC4203391 DOI: 10.1021/tx5002755] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
DNA
polymerase (pol) ι is the most error-prone among the
Y-family polymerases that participate in translesion synthesis (TLS).
Pol ι can bypass various DNA lesions, e.g., N2-ethyl(Et)G, O6-methyl(Me)G,
8-oxo-7,8-dihydroguanine (8-oxoG), and an abasic site, though frequently
with low fidelity. We assessed the biochemical effects of six reported
genetic variations of human pol ι on its TLS properties, using
the recombinant pol ι (residues 1–445) proteins and DNA
templates containing a G, N2-EtG, O6-MeG, 8-oxoG, or abasic site. The Δ1–25
variant, which is the N-terminal truncation of 25
residues resulting from an initiation codon variant (c.3G > A)
and
also is the formerly misassigned wild-type, exhibited considerably
higher polymerase activity than wild-type with Mg2+ (but
not with Mn2+), coinciding with its steady-state kinetic
data showing a ∼10-fold increase in kcat/Km for nucleotide incorporation
opposite templates (only with Mg2+). The R96G variant,
which lacks a R96 residue known to interact with the incoming nucleotide,
lost much of its polymerase activity, consistent with the kinetic
data displaying 5- to 72-fold decreases in kcat/Km for nucleotide incorporation
opposite templates either with Mg2+ or Mn2+,
except for that opposite N2-EtG with Mn2+ (showing a 9-fold increase for dCTP incorporation). The
Δ1–25 variant bound DNA 20- to 29-fold more tightly than
wild-type (with Mg2+), but the R96G variant bound DNA 2-fold
less tightly than wild-type. The DNA-binding affinity of wild-type,
but not of the Δ1–25 variant, was ∼7-fold stronger
with 0.15 mM Mn2+ than with Mg2+. The results
indicate that the R96G variation severely impairs most of the Mg2+- and Mn2+-dependent TLS abilities of pol ι,
whereas the Δ1–25 variation selectively and substantially
enhances the Mg2+-dependent TLS capability of pol ι,
emphasizing the potential translational importance of these pol ι
genetic variations, e.g., individual differences in TLS, mutation,
and cancer susceptibility to genotoxic carcinogens.
Collapse
Affiliation(s)
- Jinsook Kim
- Division of Pharmacology, Department of Molecular Cell Biology, and ‡Department of Physiology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 440-746, Republic of Korea
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Makarova AV, Ignatov A, Miropolskaya N, Kulbachinskiy A. Roles of the active site residues and metal cofactors in noncanonical base-pairing during catalysis by human DNA polymerase iota. DNA Repair (Amst) 2014; 22:67-76. [PMID: 25108837 DOI: 10.1016/j.dnarep.2014.07.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/12/2014] [Accepted: 07/14/2014] [Indexed: 12/15/2022]
Abstract
Human DNA polymerase iota (Pol ι) is a Y-family polymerase that can bypass various DNA lesions but possesses very low fidelity of DNA synthesis in vitro. Structural analysis of Pol ι revealed a narrow active site that promotes noncanonical base-pairing during catalysis. To better understand the structure-function relationships in the active site of Pol ι we investigated substitutions of individual amino acid residues in its fingers domain that contact either the templating or the incoming nucleotide. Two of the substitutions, Y39A and Q59A, significantly decreased the catalytic activity but improved the fidelity of Pol ι. Surprisingly, in the presence of Mn(2+) ions, the wild-type and mutant Pol ι variants efficiently incorporated nucleotides opposite template purines containing modifications that disrupted either Hoogsteen or Watson-Crick base-pairing, suggesting that Pol ι may use various types of interactions during nucleotide addition. In contrast, in Mg(2+) reactions, wild-type Pol ι was dependent on Hoogsteen base-pairing, the Y39A mutant was essentially inactive, and the Q59A mutant promoted Watson-Crick interactions with template purines. The results suggest that Pol ι utilizes distinct mechanisms of nucleotide incorporation depending on the metal cofactor and reveal important roles of specific residues from the fingers domain in base-pairing and catalysis.
Collapse
Affiliation(s)
- Alena V Makarova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
| | - Artem Ignatov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | | | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
| |
Collapse
|