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Wei J, Wang J, Chen X, Zhang L, Peng M. Novel application of the ferroptosis-related genes risk model associated with disulfidptosis in hepatocellular carcinoma prognosis and immune infiltration. PeerJ 2024; 12:e16819. [PMID: 38317842 PMCID: PMC10840499 DOI: 10.7717/peerj.16819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/31/2023] [Indexed: 02/07/2024] Open
Abstract
Hepatocellular carcinoma (HCC) stands as the prevailing manifestation of primary liver cancer and continues to pose a formidable challenge to human well-being and longevity, owing to its elevated incidence and mortality rates. Nevertheless, the quest for reliable predictive biomarkers for HCC remains ongoing. Recent research has demonstrated a close correlation between ferroptosis and disulfidptosis, two cellular processes, and cancer prognosis, suggesting their potential as predictive factors for HCC. In this study, we employed a combination of bioinformatics algorithms and machine learning techniques, leveraging RNA sequencing data, mutation profiles, and clinical data from HCC samples in The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and the International Cancer Genome Consortium (ICGC) databases, to develop a risk prognosis model based on genes associated with ferroptosis and disulfidptosis. We conducted an unsupervised clustering analysis, calculating a risk score (RS) to predict the prognosis of HCC using these genes. Clustering analysis revealed two distinct HCC clusters, each characterized by significantly different prognostic and immune features. The median RS stratified HCC samples in the TCGA, GEO, and ICGC cohorts into high-and low-risk groups. Importantly, RS emerged as an independent prognostic factor in all three cohorts, with the high-risk group demonstrating poorer prognosis and a more active immunosuppressive microenvironment. Additionally, the high-risk group exhibited higher expression levels of tumor mutation burden (TMB), immune checkpoints (ICs), and human leukocyte antigen (HLA), suggesting a heightened responsiveness to immunotherapy. A cancer stem cell infiltration analysis revealed a higher similarity between tumor cells and stem cells in the high-risk group. Furthermore, drug sensitivity analysis highlighted significant differences in response to antitumor drugs between the two risk groups. In summary, our risk prognostic model, constructed based on ferroptosis-related genes associated with disulfidptosis, effectively predicts HCC prognosis. These findings hold potential implications for patient stratification and clinical decision-making, offering valuable theoretical insights in this field.
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Affiliation(s)
- Jiayan Wei
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jinsong Wang
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xinyi Chen
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Li Zhang
- Basic Medical Sciences, Wuhan University School of Basic Medical Sciences, Wuhan, Hubei, China
| | - Min Peng
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
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2
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Mahnashi M, Alshahrani MM, Al Ali A, Asiri A, Abou-Salim MA. Novel Glu-based pyrazolo[3,4-d]pyrimidine analogues: design, synthesis and biological evaluation as DHFR and TS dual inhibitors. J Enzyme Inhib Med Chem 2023; 38:2203879. [PMID: 37080777 PMCID: PMC10120551 DOI: 10.1080/14756366.2023.2203879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
A novel series of multifunctional pyrazolo[3,4-d]pyrimidine-based glutamate analogs (6a-l and 7a,b) have been designed and synthesized as antifolate anticancer agents. Among the tested compounds, 6i exhibited the most potent anti-proliferative activity towards NSCLC, CNS, Ovarian, Prostate, Colon, Melanoma, Breast, and Renal cancers with good to weak cytostatic activity and non-lethal actions. 6i demonstrated higher selectivity for cancer than normal cells. 6i could significantly increase the accumulation of S-phase cells during the cell cycle distribution of cancer cells with high potency in the induction of apoptosis. The results unveiled that 6i probably acts through dual inhibition of DHFR and TS enzymes (IC50 = 2.41 and 8.88 µM, correspondingly). Docking studies of 6i displayed that N1-p-bromophenyl and C3-Methyl groups participate in substantial hydrophobic interactions. The drug-likeness features inferred that 6i met the acceptance criteria of Pfizer. Taking together, 6i could be a promising prototype for further optimization as an effective anticancer drug.
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Affiliation(s)
- Mater Mahnashi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Najran University, Najran, Saudi Arabia
| | - Mohammed Merae Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Amer Al Ali
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, University of Bisha, Bisha, Saudi Arabia
| | - Abdulaziz Asiri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, University of Bisha, Bisha, Saudi Arabia
| | - Mahrous A Abou-Salim
- Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
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Pierzynska-Mach A, Czada C, Vogel C, Gwosch E, Osswald X, Bartoschek D, Diaspro A, Kappes F, Ferrando-May E. DEK oncoprotein participates in heterochromatin replication via SUMO-dependent nuclear bodies. J Cell Sci 2023; 136:jcs261329. [PMID: 37997922 PMCID: PMC10753498 DOI: 10.1242/jcs.261329] [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: 05/12/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023] Open
Abstract
The correct inheritance of chromatin structure is key for maintaining genome function and cell identity and preventing cellular transformation. DEK, a conserved non-histone chromatin protein, has recognized tumor-promoting properties, its overexpression being associated with poor prognosis in various cancer types. At the cellular level, DEK displays pleiotropic functions, influencing differentiation, apoptosis and stemness, but a characteristic oncogenic mechanism has remained elusive. Here, we report the identification of DEK bodies, focal assemblies of DEK that regularly occur at specific, yet unidentified, sites of heterochromatin replication exclusively in late S-phase. In these bodies, DEK localizes in direct proximity to active replisomes in agreement with a function in the early maturation of heterochromatin. A high-throughput siRNA screen, supported by mutational and biochemical analyses, identifies SUMO as one regulator of DEK body formation, linking DEK to the complex SUMO protein network that controls chromatin states and cell fate. This work combines and refines our previous data on DEK as a factor essential for heterochromatin integrity and facilitating replication under stress, and delineates an avenue of further study for unraveling the contribution of DEK to cancer development.
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Affiliation(s)
| | - Christina Czada
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
| | - Christopher Vogel
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
| | - Eva Gwosch
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
| | - Xenia Osswald
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
| | - Denis Bartoschek
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
| | - Alberto Diaspro
- Nanoscopy & NIC@IIT, Istituto Italiano di Tecnologia, Genoa 16152, Italy
- DIFILAB, Department of Physics, University of Genoa, Genoa 16146, Italy
| | - Ferdinand Kappes
- Duke Kunshan University, Division of Natural and Applied Sciences, Kunshan 215316, People's Republic of China
| | - Elisa Ferrando-May
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
- German Cancer Research Center, Heidelberg 69120, Germany
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Yin ZN, Lai FL, Gao F. Unveiling human origins of replication using deep learning: accurate prediction and comprehensive analysis. Brief Bioinform 2023; 25:bbad432. [PMID: 38008420 PMCID: PMC10676776 DOI: 10.1093/bib/bbad432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/11/2023] [Accepted: 11/06/2023] [Indexed: 11/28/2023] Open
Abstract
Accurate identification of replication origins (ORIs) is crucial for a comprehensive investigation into the progression of human cell growth and cancer therapy. Here, we proposed a computational approach Ori-FinderH, which can efficiently and precisely predict the human ORIs of various lengths by combining the Z-curve method with deep learning approach. Compared with existing methods, Ori-FinderH exhibits superior performance, achieving an area under the receiver operating characteristic curve (AUC) of 0.9616 for K562 cell line in 10-fold cross-validation. In addition, we also established a cross-cell-line predictive model, which yielded a further improved AUC of 0.9706. The model was subsequently employed as a fitness function to support genetic algorithm for generating artificial ORIs. Sequence analysis through iORI-Euk revealed that a vast majority of the created sequences, specifically 98% or more, incorporate at least one ORI for three cell lines (Hela, MCF7 and K562). This innovative approach could provide more efficient, accurate and comprehensive information for experimental investigation, thereby further advancing the development of this field.
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Affiliation(s)
- Zhen-Ning Yin
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Fei-Liao Lai
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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Tan Y, Ding L, Li G. MCM4 acts as a biomarker for LUAD prognosis. J Cell Mol Med 2023; 27:3354-3362. [PMID: 37817427 PMCID: PMC10623528 DOI: 10.1111/jcmm.17819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 04/16/2023] [Accepted: 06/14/2023] [Indexed: 10/12/2023] Open
Abstract
MCM4 forms the pre-replication complex (MCM2-7) with five other minichromosome maintenance (MCM) proteins. This complex binds to replication origins at G1 stage in cell cycle process, playing a critical role in DNA replication initiation. Recently, MCM4 is reported to have a complex interaction with multiple cancer progression, including gastric, ovarian and cervical cancer. Here, this study mainly focused on the expression of MCM4 and its values in lung adenocarcinoma (LUAD). MCM4 was highly expressed in LUAD tumours and cells, and had an important effect on the overall survival. Overexpression of MCM4 promoted the proliferation, and suppressed the apoptosis in LUAD cells. However, MCM4 silence led to the opposite results. In vivo, knockdown of MCM4 inhibited tumour volume and weight in xenograft mouse model. As a member of DNA helicase, knockdown of MCM4 caused cell cycle arrest at G1 stage through inducing the expression of P21, a CDK inhibitor. These findings indicate that MCM4 may be a possible new therapeutic target for LUAD in the future.
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Affiliation(s)
- Yue Tan
- Branch of Minhang, Department of Medical OncologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Lei Ding
- Department of Ultrasonic DiagnosisSecond Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Guiyuan Li
- Department of Oncology, School of Medicine, Tongji HospitalTongji UniversityShanghaiChina
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Shen M, Zhang Y, Tang L, Fu Q, Zhang J, Xu Y, Zeng H, Li Y. CDC6, a key replication licensing factor, is overexpressed and confers poor prognosis in diffuse large B-cell lymphoma. BMC Cancer 2023; 23:978. [PMID: 37833632 PMCID: PMC10571299 DOI: 10.1186/s12885-023-11186-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 07/17/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Cell division cycle 6 (CDC6) is a key licensing factor in the assembly of pre-replicative complexes at origins of replication. The role of CDC6 in the pathogenesis of in diffuse larger B-cell lymphoma (DLBCL) remains unknown. We aim to investigate the effects of CDC6 on the proliferation, apoptosis and cell cycle regulation in DLBCL cells, delineate its underlying mechanism, and to correlate CDC6 expression with clinical characteristics and prognosis of patients with DLBCL. METHODS Initial bioinformatic analysis was performed to screen the potential role of CDC6 in DLBCL. Lentiviral constructs harboring CDC6 or shCDC6 was transfected to overexpress or knockdown CDC6 in SUDHL4 and OCI-LY7 cells. The cell proliferation was evaluated by CCK-8 assay, cell apoptosis was detected by Annexin-V APC/7-AAD double staining, and cell cycle was measured by flow cytometry. Real time quantitative PCR and western blot was used to characterize CDC6 expression and its downstream signaling pathways. The clinical data of DLBCL patients were retrospectively reviewed, the CDC6 expression in DLBCL or lymph node reactive hyperplasia tissues was evaluated by immunohistochemistry. RESULTS In silico data suggest that CDC6 overexpression is associated with inferior prognosis of DLBCL. We found that CDC6 overexpression increased SUDHL4 or OCI-LY7 cell proliferation, while knockdown of CDC6 inhibited cell proliferation in a time-dependent manner. Upon overexpression, CDC6 reduced cells in G1 phase and did not affect cell apoptosis; CDC6 knockdown led to significant cell cycle arrest in G1 phase and increase in cell apoptosis. Western blot showed that CDC6 inhibited the expression of INK4, E-Cadherin and ATR, accompanied by increased Bcl-2 and deceased Bax expression. The CDC6 protein was overexpressed DLBCL compared with lymph node reactive hyperplasia, and CDC6 overexpression was associated with non-GCB subtype, and conferred poor PFS and OS in patients with DLBCL. CONCLUSION CDC6 promotes cell proliferation and survival of DLBCL cells through regulation of G1/S cell cycle checkpoint and apoptosis. CDC6 is overexpressed and serves as a novel prognostic marker in DLBCL.
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Affiliation(s)
- Mingfang Shen
- Department of Hematology, the First Hospital of Jiaxing, 314001, Zhejiang, China
| | - Yunfeng Zhang
- Department of Hematology, the First Hospital of Jiaxing, 314001, Zhejiang, China
| | - Lun Tang
- Department of Hematology, the First Hospital of Jiaxing, 314001, Zhejiang, China
| | - Qinyan Fu
- Department of Hematology, the First Hospital of Jiaxing, 314001, Zhejiang, China
| | - Jiawei Zhang
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Zhejiang, China
| | - Yang Xu
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Zhejiang, China
| | - Hui Zeng
- Department of Hematology, the First Hospital of Jiaxing, 314001, Zhejiang, China.
| | - Yuan Li
- Department of Hematology, the First Hospital of Jiaxing, 314001, Zhejiang, China.
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7
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Identification of mutational signature for lung adenocarcinoma prognosis and immunotherapy prediction. J Mol Med (Berl) 2022; 100:1755-1769. [PMID: 36367565 DOI: 10.1007/s00109-022-02266-4] [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: 05/31/2022] [Revised: 10/04/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022]
Abstract
There is no robust genomic signature to predict the prognosis of patients with early-stage lung adenocarcinoma (LUAD). It was known that clonal heterogeneity was closely associated to tumour progression and prognosis prediction. Herein, using stage I patients from The Cancer Genome Atlas, we identified the clonal/subclonal events of each gene and preselected a set of genes with prognosis-specific mutation patterns based on a robust published transcriptomic prognostic signature. Subsequently, we constructed a mutational prognostic signature (MPS), whose prognostic performance was independently validated in two datasets of stage I samples. The predicted high-risk patients had significantly higher immune cell infiltration, along with higher expression of cytotoxic and immune checkpoint genes, and an integrated dataset with 88 samples confirmed that high-risk patients could benefit from immunotherapy. The developed MPS can identify the high-risk patients with stage I LUAD and improve individualised treatment planning of high-risk patients who might benefit from immunotherapy. KEY MESSAGES: We creatively developed a prognostic signature (57-MPS) based on clonal diversity. The high-risk samples displayed an underlying immunosuppressive mechanism. 57-MPS improved the predictive performance of PD-L1 for immunotherapy.
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8
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MUTYH is a potential prognostic biomarker and correlates with immune infiltrates in hepatocellular carcinoma. LIVER RESEARCH 2022. [DOI: 10.1016/j.livres.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Feu S, Unzueta F, Ercilla A, Pérez-Venteo A, Jaumot M, Agell N. RAD51 is a druggable target that sustains replication fork progression upon DNA replication stress. PLoS One 2022; 17:e0266645. [PMID: 35969531 PMCID: PMC9377619 DOI: 10.1371/journal.pone.0266645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/19/2022] [Indexed: 11/18/2022] Open
Abstract
Solving the problems that replication forks encounter when synthesizing DNA is essential to prevent genomic instability. Besides their role in DNA repair in the G2 phase, several homologous recombination proteins, specifically RAD51, have prominent roles in the S phase. Using different cellular models, RAD51 has been shown not only to be present at ongoing and arrested replication forks but also to be involved in nascent DNA protection and replication fork restart. Through pharmacological inhibition, here we study the specific role of RAD51 in the S phase. RAD51 inhibition in non-transformed cell lines did not have a significant effect on replication fork progression under non-perturbed conditions, but when the same cells were subjected to replication stress, RAD51 became necessary to maintain replication fork progression. Notably, the inhibition or depletion of RAD51 did not compromise fork integrity when subjected to hydroxyurea treatment. RAD51 inhibition also did not decrease the ability to restart, but rather compromised fork progression during reinitiation. In agreement with the presence of basal replication stress in human colorectal cancer cells, RAD51 inhibition reduced replication fork speed in these cells and increased γH2Ax foci under control conditions. These alterations could have resulted from the reduced association of DNA polymerase α to chromatin, as observed when inhibiting RAD51. It may be possible to exploit the differential dependence of non-transformed cells versus colorectal cancer cells on RAD51 activity under basal conditions to design new therapies that specifically target cancer cells.
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Affiliation(s)
- Sonia Feu
- Dept. Biomedicina, Universitat de Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Fernando Unzueta
- Dept. Biomedicina, Universitat de Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Amaia Ercilla
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | | | - Montserrat Jaumot
- Dept. Biomedicina, Universitat de Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Neus Agell
- Dept. Biomedicina, Universitat de Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- * E-mail:
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10
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Alfaro Alfaro ÁE, Murillo Castillo B, Cordero García E, Tascón J, Morales AI. Colon Cancer Pharmacogenetics: A Narrative Review. PHARMACY 2022; 10:95. [PMID: 36005935 PMCID: PMC9413567 DOI: 10.3390/pharmacy10040095] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 12/16/2022] Open
Abstract
Currently, metastatic colon cancer is treated with monotherapeutic regimens such as folinic acid, fluorouracil, and oxaliplatin (FOLFOX), capecitabine and oxaliplatin (CapeOX), and leucovorin, fluorouracil, and irinotecan hydrochloride (FOLFIRI). Other treatments include biological therapies and immunotherapy with drugs such as bevacizumab, panitumumab, cetuximab, and pembrolizumab. After the research, it was found that some mutations make those treatments not as effective in all patients. In this bibliographic review, we investigated the pharmacogenetic explanations for how mutations in the genes coding for rat sarcoma virus (RAS) and rapidly accelerated fibrosarcoma (RAF) reduce the effectiveness of these treatments and allow the continued proliferation of tumors. Furthermore, we note that patients with mutations in the dihydropyrimidine dehydrogenase (DPDY) gene usually require lower doses of therapies such as 5-fluorouracyl (5-FU) and capecitabine to avoid severe adverse effects. Some other mutations in the thymidylate synthase gene (TSYM), methylenetetrahydrofolate reductase gene (MTHFR), and ATP binding cassette transporter B (ABCB1 and ABCB2) affect efficacy and security of the treatments. It is important to address the clinical implication of the oncologist in the study of gene mutations than can influence in the antitumoral response and safety of colon cancer treatments.
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Affiliation(s)
| | | | | | - Javier Tascón
- Toxicology Unit, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Ana I. Morales
- Toxicology Unit, Universidad de Salamanca, 37007 Salamanca, Spain
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Bialic M, Al Ahmad Nachar B, Koźlak M, Coulon V, Schwob E. Measuring S-Phase Duration from Asynchronous Cells Using Dual EdU-BrdU Pulse-Chase Labeling Flow Cytometry. Genes (Basel) 2022; 13:genes13030408. [PMID: 35327961 PMCID: PMC8951228 DOI: 10.3390/genes13030408] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/17/2022] [Accepted: 02/20/2022] [Indexed: 02/07/2023] Open
Abstract
Eukaryotes duplicate their chromosomes during the cell cycle S phase using thousands of initiation sites, tunable fork speed and megabase-long spatio-temporal replication programs. The duration of S phase is fairly constant within a given cell type, but remarkably plastic during development, cell differentiation or various stresses. Characterizing the dynamics of S phase is important as replication defects are associated with genome instability, cancer and ageing. Methods to measure S-phase duration are so far indirect, and rely on mathematical modelling or require cell synchronization. We describe here a simple and robust method to measure S-phase duration in cell cultures using a dual EdU-BrdU pulse-labeling regimen with incremental thymidine chases, and quantification by flow cytometry of cells entering and exiting S phase. Importantly, the method requires neither cell synchronization nor genome engineering, thus avoiding possible artifacts. It measures the duration of unperturbed S phases, but also the effect of drugs or mutations on it. We show that this method can be used for both adherent and suspension cells, cell lines and primary cells of different types from human, mouse and Drosophila. Interestingly, the method revealed that several commonly-used cancer cell lines have a longer S phase compared to untransformed cells.
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Affiliation(s)
- Marta Bialic
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, 34293 Montpellier, France; (M.B.); (B.A.A.N.); (M.K.); (E.S.)
- Institut de Médecine Régénératrice et Biothérapie, INSERM, CHU, 34295 Montpellier, France
| | - Baraah Al Ahmad Nachar
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, 34293 Montpellier, France; (M.B.); (B.A.A.N.); (M.K.); (E.S.)
| | - Maria Koźlak
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, 34293 Montpellier, France; (M.B.); (B.A.A.N.); (M.K.); (E.S.)
| | - Vincent Coulon
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, 34293 Montpellier, France; (M.B.); (B.A.A.N.); (M.K.); (E.S.)
- Correspondence: ; Tel.: +33-43435-9679
| | - Etienne Schwob
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, 34293 Montpellier, France; (M.B.); (B.A.A.N.); (M.K.); (E.S.)
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12
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Ma X, Zhuang H, Wang Q, Yang L, Xie Z, Zhang Z, Tan W, Tang C, Chen Y, Shang C. SLC39A1 Overexpression is Associated with Immune Infiltration in Hepatocellular Carcinoma and Promotes Its Malignant Progression. J Hepatocell Carcinoma 2022; 9:83-98. [PMID: 35211427 PMCID: PMC8858589 DOI: 10.2147/jhc.s349966] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/25/2022] [Indexed: 12/19/2022] Open
Abstract
Background Solute carrier family 39 member 1 (SLC39A1) has been identified as a zinc ion transport protein that possesses oncogenic properties in various types of cancers. However, its potential function in hepatocellular carcinoma (HCC) remains unknown. This study aimed to investigate the expression profile and potential mechanisms of SLC39A1 in HCC. Methods SLC39A1 expression was analyzed using multiple databases. The clinical significance and associated biological pathways of SLC39A1 were investigated using bioinformatics analysis. Potential correlations between SLC39A1 expression and tumor immunity in HCC were also evaluated using single-sample gene set enrichment analysis (GSEA). Sixty paired HCC samples were used to verify the expression pattern of SLC39A1. In vitro studies were performed to investigate the oncogenic effects of SLC39A1 in HCC. Western blot analysis was conducted to further investigate the possible involved signaling pathways. Results The overexpression of SLC39A1 in HCC was determined by bioinformatics analysis and was confirmed in tissues from our center. SLC39A1 overexpression was also significantly correlated with worse prognosis, advanced TNM stage, and histological grade. GSEA analysis demonstrated that SLC39A1 overexpression was involved in various tumor-related pathways, such as the cell cycle and Wnt signaling pathway. SLC39A1 knockdown repressed the proliferation, invasion, and migration abilities of HCC cells. Furthermore, SLC39A1 knockdown decreased the expression of the tumor progression-related proteins (eg, cyclin D1 and MMP2) and Wnt signaling pathway-related proteins (eg, Wnt3A and β-catenin). In addition, SLC39A1 overexpression may be associated with impaired tumor immunity in HCC, as evidenced by the increased infiltration of Th2 cells and reduced infiltration of cytotoxic cells. Conclusion These findings preliminarily suggested the crucial effect of SLC39A1 overexpression on HCC tumor progression and immunosuppression, suggesting its potential as a novel prognostic and therapeutic target in HCC.
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Affiliation(s)
- Xiaowu Ma
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, People’s Republic of China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Hongkai Zhuang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, People’s Republic of China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Qingbin Wang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, People’s Republic of China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Lei Yang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, People’s Republic of China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Zhiqin Xie
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, People’s Republic of China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Ziyu Zhang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, People’s Republic of China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Wenliang Tan
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, People’s Republic of China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Chenwei Tang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, People’s Republic of China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Yajin Chen
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, People’s Republic of China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
- Correspondence: Yajin Chen; Changzhen Shang, Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, People’s Republic of China, Tel +86-2034070701, Email ;
| | - Changzhen Shang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, People’s Republic of China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
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13
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High-throughput, Label-free Proteomics Identifies Salient Proteins and Genes in MDA-MB-231 Cells Treated with Natural Neem-based Electrochemotherapy. Appl Biochem Biotechnol 2022; 194:148-166. [DOI: 10.1007/s12010-021-03787-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2021] [Indexed: 11/02/2022]
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14
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Qu H, Fan C, Chen M, Zhang X, Yan Q, Wang Y, Zhang S, Gong Z, Shi L, Li X, Liao Q, Xiang B, Zhou M, Guo C, Li G, Zeng Z, Wu X, Xiong W. Recent advances of fluorescent biosensors based on cyclic signal amplification technology in biomedical detection. J Nanobiotechnology 2021; 19:403. [PMID: 34863202 PMCID: PMC8645109 DOI: 10.1186/s12951-021-01149-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/17/2021] [Indexed: 12/18/2022] Open
Abstract
The cyclic signal amplification technology has been widely applied for the ultrasensitive detection of many important biomolecules, such as nucleic acids, proteins, enzymes, adenosine triphosphate (ATP), metal ions, exosome, etc. Due to their low content in the complex biological samples, traditional detection methods are insufficient to satisfy the requirements for monitoring those biomolecules. Therefore, effective and sensitive biosensors based on cyclic signal amplification technology are of great significance for the quick and simple diagnosis and treatment of diseases. Fluorescent biosensor based on cyclic signal amplification technology has become a research hotspot due to its simple operation, low cost, short time, high sensitivity and high specificity. This paper introduces several cyclic amplification methods, such as rolling circle amplification (RCA), strand displacement reactions (SDR) and enzyme-assisted amplification (EAA), and summarizes the research progress of using this technology in the detection of different biomolecules in recent years, in order to provide help for the research of more efficient and sensitive detection methods.
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Affiliation(s)
- Hongke Qu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chunmei Fan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Mingjian Chen
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Xiangyan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Qijia Yan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.,Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yumin Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.,Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shanshan Zhang
- Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lei Shi
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiayu Li
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Bo Xiang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Xu Wu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.
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15
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Kobalamina – właściwości biomedyczne i niedobór w ujęciu biochemicznym. POSTEP HIG MED DOSW 2021. [DOI: 10.2478/ahem-2021-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstrakt
Kobalamina (witamina B12) jest rozpuszczalnym w wodzie związkiem organicznym, zaliczanym do witamin grupy B. Złożona budowa i polarność cząsteczki witaminy B12 sprawiają, że do jej prawidłowego wykorzystania i przemian w organizmie człowieka niezbędny jest udział wyspecjalizowanych białek. Głównym źródłem kobalaminy człowieka jest pokarm pochodzenia zwierzęcego. Ze względu na rezerwy tkankowe tej witaminy, jej niedobór ujawnia się dopiero po kilku latach niewystarczającej podaży z pożywieniem. Badania przesiewowe pod kątem deficytu kobalaminy są jednak uzasadnione u osób z czynnikami ryzyka hipokobalaminemii, takimi jak: stan po resekcji żołądka lub jelita cienkiego, dieta wegańska, długotrwałe stosowanie metforminy, antagonistów receptora histaminowego H2 oraz leków z grupy inhibitorów pompy protonowej, a także podeszły wiek.
Witamina B12 jako kofaktor enzymatyczny uczestniczy w licznych przemianach wewnątrzmitochondrialnych oraz w syntezie metioniny, niezbędnej do powstania S-adenozylometioniny istotnej w procesie metylacji cząsteczek biologicznie czynnych. Przez powiązania metaboliczne z kwasem foliowym kobalamina wpływa na proces syntezy DNA i podział komórki. Obecnie coraz częściej zwraca się uwagę na potencjalny udział niedoboru witaminy B12 w patogenezie chorób neurodegeneracyjnych, a także nowotworowych. Niedobór kobalaminy na poziomie molekularnym destabilizuje genom komórek, zwiększając ryzyko ich złośliwej transformacji. Jednak u osób z chorobą nowotworową lub obciążonych ryzykiem jej rozwoju witamina B12 może nasilać ekspansję komórek neoplastycznych.
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16
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Feng H, Zeng J, Gao L, Zhou Z, Wang L. GINS Complex Subunit 2 Facilitates Gastric Adenocarcinoma Proliferation and Indicates Poor Prognosis. TOHOKU J EXP MED 2021; 255:111-121. [PMID: 34629365 DOI: 10.1620/tjem.255.111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Gastric cancer is the one of the most lethal malignancies of digestive system. Identifying molecular biomarkers is invaluable in help predicting clinical outcomes and developing targeted chemotherapies. GINS complex subunit 2 (GINS2) plays an essential role in the initiation and elongation of DNA replication. Although there have been studies revealing the prognostic significance of GINS2 in breast cancer and lung cancer, its involvement and function in gastric cancer need to be elucidated. We retrospectively enrolled a cohort of gastric adenocarcinoma patients after surgical resection (n = 123). By analyzing the mRNA and protein levels of GINS2 in tissue samples, we found that GINS2 presented a higher expression in tumor tissues than in adjacent normal stomach tissues. Besides, GINS2 level was positively correlated with tumor size and gastric adenocarcinoma tumor stage, implying its potential role as a tumor promoter. Univariate and multivariate analyses identified that patients with lower GINS2 showed a better overall survival compared to those with higher GINS2 expression. In addition, cellular and xenograft experiments confirmed the role of GINS2 in facilitating tumor proliferation both in vitro and in vivo. To our knowledge, this is the initial finding on GINS2 in promoting gastric adenocarcinoma progression. In conclusion, our study revealed a pro-oncogenic role of GINS2 in gastric cancer.
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Affiliation(s)
- Hongjun Feng
- Department of Gastroenterology, Sanya Central Hospital (Hainan Third People's Hospital)
| | - Juntao Zeng
- Department of Gastroenterology, Sanya Central Hospital (Hainan Third People's Hospital)
| | - Lei Gao
- Department of Gastroenterology, Sanya Central Hospital (Hainan Third People's Hospital)
| | - Zhenzhen Zhou
- Department of Gastroenterology, Sanya Central Hospital (Hainan Third People's Hospital)
| | - Liya Wang
- Department of Gastroenterology, Sanya Central Hospital (Hainan Third People's Hospital)
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17
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Wei J, Wang B, Gao X, Sun D. Prognostic Value of a Novel Signature With Nine Hepatitis C Virus-Induced Genes in Hepatic Cancer by Mining GEO and TCGA Databases. Front Cell Dev Biol 2021; 9:648279. [PMID: 34336819 PMCID: PMC8322788 DOI: 10.3389/fcell.2021.648279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/25/2021] [Indexed: 01/29/2023] Open
Abstract
Background Hepatitis C virus-induced genes (HCVIGs) play a critical role in regulating tumor development in hepatic cancer. The role of HCVIGs in hepatic cancer remains unknown. This study aimed to construct a prognostic signature and assess the value of the risk model for predicting the prognosis of hepatic cancer. Methods Differentially expressed HCVIGs were identified in hepatic cancer data from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases using the library (“limma”) package of R software. The protein–protein interaction (PPI) network was constructed using the Cytoscape software. Functional enrichment analysis was performed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Univariate and multivariate Cox proportional hazard regression analyses were applied to screen for prognostic HCVIGs. The signature of HCVIGs was constructed. Gene Set Enrichment Analysis (GSEA) compared the low-risk and high-risk groups. Finally, the International Cancer Genome Consortium (ICGC) database was used to validate this prognostic signature. Polymerase chain reaction (PCR) was performed to validate the expression of nine HCVIGs in the hepatic cancer cell lines. Results A total of 143 differentially expressed HCVIGs were identified in TCGA hepatic cancer dataset. Functional enrichment analysis showed that DNA replication was associated with the development of hepatic cancer. The risk score signature was constructed based on the expression of ZIC2, SLC7A11, PSRC1, TMEM106C, TRAIP, DTYMK, FAM72D, TRIP13, and CENPM. In this study, the risk score was an independent prognostic factor in the multivariate Cox regression analysis [hazard ratio (HR) = 1.433, 95% CI = 1.280–1.605, P < 0.001]. The overall survival curve revealed that the high-risk group had a poor prognosis. The Kaplan–Meier Plotter online database showed that the survival time of hepatic cancer patients with overexpression of HCVIGs in this signature was significantly shorter. The prognostic signature-associated GO and KEGG pathways were significantly enriched in the risk group. This prognostic signature was validated using external data from the ICGC databases. The expression of nine prognostic genes was validated in HepG2 and LO-2. Conclusion This study evaluates a potential prognostic signature and provides a way to explore the mechanism of HCVIGs in hepatic cancer.
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Affiliation(s)
- Jianming Wei
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Bo Wang
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Xibo Gao
- Department of Dermatology, Tianjin Children's Hospital, Tianjin, China
| | - Daqing Sun
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, China
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18
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TSCCA: A tensor sparse CCA method for detecting microRNA-gene patterns from multiple cancers. PLoS Comput Biol 2021; 17:e1009044. [PMID: 34061840 PMCID: PMC8195367 DOI: 10.1371/journal.pcbi.1009044] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 06/11/2021] [Accepted: 05/05/2021] [Indexed: 12/22/2022] Open
Abstract
Existing studies have demonstrated that dysregulation of microRNAs (miRNAs or miRs) is involved in the initiation and progression of cancer. Many efforts have been devoted to identify microRNAs as potential biomarkers for cancer diagnosis, prognosis and therapeutic targets. With the rapid development of miRNA sequencing technology, a vast amount of miRNA expression data for multiple cancers has been collected. These invaluable data repositories provide new paradigms to explore the relationship between miRNAs and cancer. Thus, there is an urgent need to explore the complex cancer-related miRNA-gene patterns by integrating multi-omics data in a pan-cancer paradigm. In this study, we present a tensor sparse canonical correlation analysis (TSCCA) method for identifying cancer-related miRNA-gene modules across multiple cancers. TSCCA is able to overcome the drawbacks of existing solutions and capture both the cancer-shared and specific miRNA-gene co-expressed modules with better biological interpretations. We comprehensively evaluate the performance of TSCCA using a set of simulated data and matched miRNA/gene expression data across 33 cancer types from the TCGA database. We uncover several dysfunctional miRNA-gene modules with important biological functions and statistical significance. These modules can advance our understanding of miRNA regulatory mechanisms of cancer and provide insights into miRNA-based treatments for cancer. MicroRNAs (miRNAs) are a class of small non-coding RNAs. Previous studies have revealed that miRNA-gene regulatory modules play key roles in the occurrence and development of cancer. However, little has been done to discover miRNA-gene regulatory modules from a pan-cancer view. Thus, it is urgently needed to develop new methods to explore the complex cancer-related miRNA-gene patterns by integrating multi-omics data of multi-cancers. To build the connections between miRNA-gene regulatory modules across different cancer types, we propose a tensor sparse canonical correlation analysis (TSCCA) method. Our specific contributions are two-fold: (1) We propose a sparse statistical learning model TSCCA and an efficient block-coordinate descent algorithm to solve it. (2) We apply TSCCA to a multi-omics data set of 33 cancer types from TCGA and identify some cancer-related miRNA-gene modules with important biological functions and statistical significance.
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19
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Elevated expression of minichromosome maintenance 3 indicates poor outcomes and promotes G1/S cell cycle progression, proliferation, migration and invasion in colorectal cancer. Biosci Rep 2021; 40:225547. [PMID: 32597491 PMCID: PMC7350890 DOI: 10.1042/bsr20201503] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
Background: The minichromosome maintenance (MCM) family, a core component of DNA replication, is involved in cell cycle process. Abnormal proliferation has been identified as a crucial process in the evolution of colorectal cancer (CRC). However, the roles of the MCM family in CRC remain largely unknown. Methods: Here, the expression, prognostic significance and functions of the MCM family in CRC were systematically analyzed through a series of online databases including CCLE, Oncomine, HPA, cBioPortal and cancerSEA. Results: We found all MCM family members were highly expressed in CRC, but only elevation of MCM3 expression was associated with poor prognosis of patients with CRC. Further in vitro and in vivo experiments were performed to examine the role of MCM3 in CRC. Analysis of CCLE database and qRT-PCR assay confirmed that MCM3 was overexpressed in CRC cell lines. Moreover, knockdown of MCM3 significantly suppressed transition of G1 to S phase in CRC cells. Furthermore, down-regulation of MCM3 inhibited CRC cell proliferation, migration, invasion and promoted apoptosis. Conclusion: These findings reveal that MCM3 may function as an oncogene and a potential prognosis biomarker. Thus, the association between abnormal expression of MCM3 and the initiation of CRC deserves further exploration.
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20
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Samad A, Haque F, Nain Z, Alam R, Al Noman MA, Rahman Molla MH, Hossen MS, Islam MR, Khan MI, Ahammad F. Computational assessment of MCM2 transcriptional expression and identification of the prognostic biomarker for human breast cancer. Heliyon 2020; 6:e05087. [PMID: 33024849 PMCID: PMC7530310 DOI: 10.1016/j.heliyon.2020.e05087] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/09/2020] [Accepted: 09/24/2020] [Indexed: 12/24/2022] Open
Abstract
Minichromosome maintenance protein 2 (MCM2) is a highly conserved protein from the MCM protein family that plays an important role in eukaryotic DNA replication as well as in cell cycle progression. In addition, it maintains the ploidy level consistency in eukaryotic cells, hence, mutations or alteration of this protein could result in the disintegration of the fine-tuned molecular machinery that can lead to uncontrolled cell proliferation. Moreover, MCM2 has been found to be an important marker for progression and prognosis in different cancers. Therefore, we aimed to analyze the MCM2 expression and the associated outcome in breast cancer (BC) patients based on the publicly available online databases. In this study, server-based gene expression analyses indicate the upregulation of MCM2 (p < 10-6; fold change>2.0) in various BC subtypes as compared to the respective normal tissues. Besides, the evaluation of histological sections from healthy and cancer tissues showed strong staining signals indicating higher expression of MCM2 protein. The overexpression of MCM2 was significantly correlated to promoter methylation and was related to patients' clinical features. Further, mutation analysis suggested missense as the predominant type of mutation (71.4%) with 18 copy-number alterations and 0.2% mutation frequency in the MCM2 gene. This study revealed a significant correlation (Cox p ≤ 0.05) between the higher MCM2 expression and lower patient survival. Finally, we identified the co-expressed genes with gene ontological features and signaling pathways associated in BC development. We believe that this study will provide a basis for MCM2 to be a significant biomarker for human BC prognosis.
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Affiliation(s)
- Abdus Samad
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Farhana Haque
- Department of Biotechnology and Genetic Engineering, Khulna University, Khulna, 9208, Bangladesh
| | - Zulkar Nain
- Department of Genetic Engineering and Biotechnology, Faculty of Sciences and Engineering, East West University, Dhaka, 1212, Bangladesh.,Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003, Bangladesh
| | - Rahat Alam
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.,Molecular and Cellular Biology Laboratory, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Abdullah Al Noman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.,Molecular and Cellular Biology Laboratory, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Mohammad Habibur Rahman Molla
- Institute of Marine Sciences and Fisheries, University of Chittagong, Chittagong, 4331, Bangladesh.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Md Saddam Hossen
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Raquibul Islam
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Iqbal Khan
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.,Department of Biotechnology and Genetic Engineering, Khulna University, Khulna, 9208, Bangladesh
| | - Foysal Ahammad
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.,Molecular and Cellular Biology Laboratory, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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21
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Zhang J, Si J, Gan L, Zhou R, Guo M, Zhang H. Harnessing the targeting potential of differential radiobiological effects of photon versus particle radiation for cancer treatment. J Cell Physiol 2020; 236:1695-1711. [PMID: 32691425 DOI: 10.1002/jcp.29960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/09/2020] [Indexed: 01/04/2023]
Abstract
Radiotherapy is one of the major modalities for malignancy treatment. High linear energy transfer (LET) charged-particle beams, like proton and carbon ions, exhibit favourable depth-dose distributions and radiobiological enhancement over conventional low-LET photon irradiation, thereby marking a new era in high precision medicine. Tumour cells have developed multicomponent signal transduction networks known as DNA damage responses (DDRs), which initiate cell-cycle checkpoints and induce double-strand break (DSB) repairs in the nucleus by nonhomologous end joining or homologous recombination pathways, to manage ionising radiation (IR)-induced DNA lesions. DNA damage induction and DSB repair pathways are reportedly dependent on the quality of radiation delivered. In this review, we summarise various types of DNA lesion and DSB repair mechanisms, upon irradiation with low and high-LET radiation, respectively. We also analyse factors influencing DNA repair efficiency. Inhibition of DNA damage repair pathways and dysfunctional cell-cycle checkpoint sensitises tumour cells to IR. Radio-sensitising agents, including DNA-PK inhibitors, Rad51 inhibitors, PARP inhibitors, ATM/ATR inhibitors, chk1 inhibitors, wee1 kinase inhibitors, Hsp90 inhibitors, and PI3K/AKT/mTOR inhibitors have been found to enhance cell killing by IR through interference with DDRs, cell-cycle arrest, or other cellular processes. The cotreatment of these inhibitors with IR may represent a promising therapeutic strategy for cancer.
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Affiliation(s)
- Jinhua Zhang
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Si
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lu Gan
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rong Zhou
- Research Center for Ecological Impacts and Environmental Health Effects of Toxic and Hazardous Chemicals, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Nanjing, China
| | - Menghuan Guo
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Hong Zhang
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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22
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Pennycook BR, Vesela E, Peripolli S, Singh T, Barr AR, Bertoli C, de Bruin RAM. E2F-dependent transcription determines replication capacity and S phase length. Nat Commun 2020; 11:3503. [PMID: 32665547 PMCID: PMC7360579 DOI: 10.1038/s41467-020-17146-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/04/2020] [Indexed: 01/06/2023] Open
Abstract
DNA replication timing is tightly regulated during S-phase. S-phase length is determined by DNA synthesis rate, which depends on the number of active replication forks and their velocity. Here, we show that E2F-dependent transcription, through E2F6, determines the replication capacity of a cell, defined as the maximal amount of DNA a cell can synthesise per unit time during S-phase. Increasing or decreasing E2F-dependent transcription during S-phase increases or decreases replication capacity, and thereby replication rates, thus shortening or lengthening S-phase, respectively. The changes in replication rate occur mainly through changes in fork speed without affecting the number of active forks. An increase in fork speed does not induce replication stress directly, but increases DNA damage over time causing cell cycle arrest. Thus, E2F-dependent transcription determines the DNA replication capacity of a cell, which affects the replication rate, controlling the time it takes to duplicate the genome and complete S-phase.
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Affiliation(s)
- Betheney R Pennycook
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK
- MRC London Institute of Medical Science Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Eva Vesela
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK
| | - Silvia Peripolli
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK
| | - Tanya Singh
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK
| | - Alexis R Barr
- MRC London Institute of Medical Science Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Imperial College London, London, W12 0NN, UK
| | - Cosetta Bertoli
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK.
| | - Robertus A M de Bruin
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK.
- UCL Cancer Institute, University College London, London, WC1E 6BT, UK.
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23
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Chen S, Gong Z, Letcher RJ, Liu C. Promotion effect of liver tumor progression in male kras transgenic zebrafish induced by tris (1, 3-dichloro-2-propyl) phosphate. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 191:110220. [PMID: 31991394 DOI: 10.1016/j.ecoenv.2020.110220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
A previous study reported that exposure to tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) could promote the progression of hepatocellular carcinoma (HCC) in female HCC model zebrafish. Due to the existence of gender disparity in the development of HCC between females and males, whether the promotion effect of TDCIPP still exists in male HCC model zebrafish remains unclear. In this study, Tg(fabp10:rtTA2s-M2; TRE2:EGFP-krasG12V), referred as kras transgenic zebrafish which was shown to be an inducible liver tumor model, was applied as experimental model to assess the promotion potential of TDCIPP for HCC in males. In brief, kras males were exposed to 20 mg/L doxycycline (DOX), 0.3 mg/L TDCIPP and a binary mixture of 20 mg/L DOX with 0.3 mg/L TDCIPP, and after exposure liver size, histopathology and transcriptional profiles of liver from these treatments were examined. With the involvement of TDCIPP, the liver size was significantly increased and the lesion of hepatocyte became more aggressive. Furthermore, expressions of genes involved in DNA replication and inflammatory response were simultaneously up-regulated in the treatment of TDCIPP compared with the solvent control and in the treatment of the binary mixture of the two chemicals compared to the single DOX treatment. Overall, our results suggested that TDCIPP had promotion effect on the progression of liver tumor in kras males.
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Affiliation(s)
- Sheng Chen
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhiyuan Gong
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Robert J Letcher
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, National Wildlife Research Centre, Carleton University, Ottawa, Ontario, K1A 0H3, Canada
| | - Chunsheng Liu
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
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Physiological and Pathological Roles of RAD52 at DNA Replication Forks. Cancers (Basel) 2020; 12:cancers12020402. [PMID: 32050645 PMCID: PMC7072239 DOI: 10.3390/cancers12020402] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 02/07/2023] Open
Abstract
Understanding basic molecular mechanisms underlying the biology of cancer cells is of outmost importance for identification of novel therapeutic targets and biomarkers for patient stratification and better therapy selection. One of these mechanisms, the response to replication stress, fuels cancer genomic instability. It is also an Achille’s heel of cancer. Thus, identification of pathways used by the cancer cells to respond to replication-stress may assist in the identification of new biomarkers and discovery of new therapeutic targets. Alternative mechanisms that act at perturbed DNA replication forks and involve fork degradation by nucleases emerged as crucial for sensitivity of cancer cells to chemotherapeutics agents inducing replication stress. Despite its important role in homologous recombination and recombinational repair of DNA double strand breaks in lower eukaryotes, RAD52 protein has been considered dispensable in human cells and the full range of its cellular functions remained unclear. Very recently, however, human RAD52 emerged as an important player in multiple aspects of replication fork metabolism under physiological and pathological conditions. In this review, we describe recent advances on RAD52’s key functions at stalled or collapsed DNA replication forks, in particular, the unexpected role of RAD52 as a gatekeeper, which prevents unscheduled processing of DNA. Last, we will discuss how these functions can be exploited using specific inhibitors in targeted therapy or for an informed therapy selection.
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25
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Jing Z, Guo S, Zhang P, Liang Z. LncRNA-Associated ceRNA Network Reveals Novel Potential Biomarkers of Laryngeal Squamous Cell Carcinoma. Technol Cancer Res Treat 2020; 19:1533033820985787. [PMID: 33371795 PMCID: PMC7780331 DOI: 10.1177/1533033820985787] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/30/2020] [Accepted: 12/10/2020] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE This study aims to construct a systematic mRNA-miRNA-lncRNA network to identify novel lncRNAs and miRNAs biomarkers for laryngeal squamous cell carcinoma (LSCC). METHODS The mRNA, miRNA and lncRNA expression profiles of LSCC were obtained from Gene Expression Omnibus (GEO) database. The differentially expressed mRNAs, miRNAs and lncRNAs (DEmRNAs, DEmiRNAs and DElncRNAs) were screened between LSCC tissues and controls. Functional analysis of DEmRNAs, DEmRNAs targeted by DEmiRNAs and DEmRNAs targeted by DElncRNAs were respectively performed. The miRWalk, starbase and DIANA-LncBase were respectively used to predict DEmiRNAs-DEmRNAs, DElncRNAs-DEmRNAs and DElncRNAs-DEmiRNAs pairs. ceRNA network was built by DEmiRNAs-DEmRNAs and DElncRNAs-DEmiRNAs pairs. LncRNA subcellular localization was predicted using lncLocator. Using published The Cancer Genome Atlas (TCGA) and external datasets (GSE127165 and GSE133632), we also validated the expression of key DElncRNAs and DEmiRNAs in ceRNA network. The diagnostic and prognostic value of candidate genes was evaluated by ROC curve analysis and survival analysis, respectively. RESULTS There were 5 mRNA datasets, 3 miRNA datasets and 2 lncRNA datasets in this study. Totally, 2957 DEmRNAs, 61 DElncRNAs and 23 DEmiRNAs were identified. Functional analysis of DEmRNAs shows that they were significantly enriched in cancer-related pathways, such as DNA replication and extracellular matrix organization. There were 11 DEmiRNAs, 17 DElncRNAs and 967 DEmRNAs in the ceRNA network. Notably, up-regulated lncRNA DGCR5-down-regulated has-miR-338-3p/has-miR-139-5p pairs in this network were experimentally validated. Moreover, down-regulated AL121839.2, down-regulated LINC02147, up-regulated AC079328.2, up-regulated AC004943.2 and up-regulated HMGA2-AS1 were located in the cytoplasm. AL121839.2 and LINC02147 interacted with has-miR-1246. AC004943.2, AC079328.2 and HMGA2-AS1 targeted has-miR-3185, has-miR-3137 and has-miR-582-5p, respectively. Based on the TCGA and external datasets (GSE127165 and GSE133632), DGCR5 and AC004943.2 were significantly up-regulated while AL121839.2 and LINC02147, has-miR-338-3p, has-miR-139-5p and has-miR-582-5p were significantly down-regulated, which were consistent with our integration analysis. DGCR5, AL121839.2, LINC02147, AC004943.2, has-miR-338-3p, has-miR-139-5p and has-miR-582-5p could predict the occurrence of LSCC. Survival analysis suggested that only, AL121839.2 has potential prognostic value for LSCC. CONCLUSION This study provided novel insights into the ceRNA network and uncovered novel lncRNAs and miRNAs with diagnostic value in LSCC.
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Affiliation(s)
- Zhibin Jing
- Department of Otorhinolaryngology, Tianjin Medical University General Hospital, Tianjin, China
| | - Sitong Guo
- Department of Otorhinolaryngology, Tianjin Medical University General Hospital, Tianjin, China
| | - Peng Zhang
- Department of Otorhinolaryngology, Tianjin Medical University General Hospital, Tianjin, China
| | - Zheng Liang
- Department of Otorhinolaryngology, Tianjin Medical University General Hospital, Tianjin, China
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26
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Azenha D, Lopes MC, Martins TC. Claspin: From replication stress and DNA damage responses to cancer therapy. DNA Repair (Amst) 2019; 115:203-246. [DOI: 10.1016/bs.apcsb.2018.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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27
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Tian S, Meng G, Zhang W. A six-mRNA prognostic model to predict survival in head and neck squamous cell carcinoma. Cancer Manag Res 2018; 11:131-142. [PMID: 30588115 PMCID: PMC6305138 DOI: 10.2147/cmar.s185875] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Transcriptional dysregulation is one of the most important features of cancer genesis and progression. Applying gene expression dysregulation information to predict the development of cancers is useful for cancer diagnosis. However, previous studies mainly focused on the relationship between a single gene and cancer. Prognostic prediction using combined gene models remains limited. MATERIALS AND METHODS Gene expression profiles were downloaded from The Cancer Genome Atlas and the data sets were randomly divided into training data sets and test data sets. A six-gene signature associated with head and neck squamous cell carcinoma (HNSCC) and overall survival (OS) was identified according to a training cohort by using weighted gene correlation network analysis and least absolute shrinkage and selection operator Cox regression. The test data set and gene expression omnibus (GEO) data set were used to validate this signature. RESULTS We identified six candidate genes, namely, FOXL2NB, PCOLCE2, SPINK6, ULBP2, KCNJ18, and RFPL1, and, using a six-gene model, predicted the risk of death of head and neck squamous cell carcinoma in The Cancer Genome Atlas. At a selected cutoff, patients were clustered into low- and high-risk groups. The OS curves of the two groups of patients had significant differences, and the time-dependent receiver operating characteristics of OS, disease-specific survival (DSS), and progression-free survival (PFS) were as high as 0.766, 0.731, and 0.623, respectively. Then, the test data set and the GEO data set were used to evaluate our model, and we found that the OS time in the high-risk group was significantly shorter than in the low-risk group in both data sets, and the receiver operating characteristics of test data set were 0.669, 0.675, and 0.614, respectively. Furthermore, univariate and multivariate Cox regression analyses showed that the risk score was independent of clinicopathological features. CONCLUSION The six-gene model could predict the OS of HNSCC patients and improve therapeutic decision-making.
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Affiliation(s)
- Saisai Tian
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, Shanghai 200433, People's Republic of China,
| | - Guofeng Meng
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China,
| | - Weidong Zhang
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, Shanghai 200433, People's Republic of China,
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China,
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28
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Liu Z, Dong X, Li Y. A Genome-Wide Study of Allele-Specific Expression in Colorectal Cancer. Front Genet 2018; 9:570. [PMID: 30538721 PMCID: PMC6277598 DOI: 10.3389/fgene.2018.00570] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/06/2018] [Indexed: 12/30/2022] Open
Abstract
Accumulating evidence from small-scale studies has suggested that allele-specific expression (ASE) plays an important role in tumor initiation and progression. However, little is known about genome-wide ASE in tumors. In this study, we conducted a comprehensive analysis of ASE in individuals with colorectal cancer (CRC) on a genome-wide scale. We identified 5.4 thousand genome-wide ASEs of single nucleotide variations (SNVs) from tumor and normal tissues of 59 individuals with CRC. We observed an increased ASE level in tumor samples and the ASEs enriched as hotspots on the genome. Around 63% of the genes located there were previously reported to contain complex regulatory elements, e.g., human leukocyte antigen (HLA), or were implicated in tumor progression. Focussing on the allelic expression of somatic mutations, we found that 37.5% of them exhibited ASE, and genes harboring such somatic mutations, were enriched in important pathways implicated in cancers. In addition, by comparing the expected and observed ASE events in tumor samples, we identified 50 tumor specific ASEs which possibly contributed to the somatic events in the regulatory regions of the genes and significantly enriched known cancer driver genes. By analyzing CRC ASEs from several perspectives, we provided a systematic understanding of how ASE is implicated in both tumor and normal tissues and will be of critical value in guiding ASE studies in cancer.
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Affiliation(s)
- Zhi Liu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Yixue Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, China.,Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
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29
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Yamamoto K, Makino N, Nagai M, Honma Y, Araki H, Ushimaru T. TORC1 signaling regulates DNA replication via DNA replication protein levels. Biochem Biophys Res Commun 2018; 505:1128-1133. [DOI: 10.1016/j.bbrc.2018.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/04/2018] [Indexed: 02/07/2023]
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30
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GINS2 promotes cell proliferation and inhibits cell apoptosis in thyroid cancer by regulating CITED2 and LOXL2. Cancer Gene Ther 2018; 26:103-113. [PMID: 30177819 DOI: 10.1038/s41417-018-0045-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/14/2018] [Accepted: 07/01/2018] [Indexed: 12/27/2022]
Abstract
To explore the mechanisms of GINS2 on cell proliferation and apoptosis in thyroid cancer (TC) cells. Expressions of GINS2 were inhibited in K1 and SW579 cells using gene interference technology. The abilities of proliferation and apoptosis, and cell cycle were determined by MTT assay and flow cytometric assay. The downstream molecules of GINS2 were searched by microarray and bioinformatics and validated by qRT-PCR and western blotting. In the in vivo study, the tumor growth was compared and the whole-body fluorescent imaging was analyzed. After GINS2 was interfered, cell proliferation was significantly inhibited (P < 0.01) and apoptosis rate increased (P < 0.01) in both K1 and SW579 cells. Cell cycle changed significantly in K1 cells, but not in SW579 cells. With bioinformatics upstream analysis, TGF-β1 was found as the most significantly upstream regulator. Expressions of TGF-β1 and its downstream target molecules CITED2 and LOXL2 were validated and found downregulated significantly in mRNA and protein levels (P < 0.05). The results of the nude mouse xenograft assay suggested that the volume and weight of tumor in ones infected with shGINS2 were statistically smaller than controls (P < 0.05). GINS2 plays an important role in cell proliferation and apoptosis of thyroid cancer by regulating the expressions of CITED2 and LOXL2, which may be a potential biomarker for diagnosis or prognosis and a drug target for therapy.
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31
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Chen J, Peng H, Han G, Cai H, Cai J. HOGMMNC: a higher order graph matching with multiple network constraints model for gene–drug regulatory modules identification. Bioinformatics 2018; 35:602-610. [DOI: 10.1093/bioinformatics/bty662] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/18/2018] [Accepted: 07/23/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jiazhou Chen
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Lab of Computational Intelligence and Cyberspace Information, South China University of Technology, Guangzhou, China
| | - Hong Peng
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
| | - Guoqiang Han
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
| | - Hongmin Cai
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Lab of Computational Intelligence and Cyberspace Information, South China University of Technology, Guangzhou, China
| | - Jiulun Cai
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
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32
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Kurashima K, Sekimoto T, Oda T, Kawabata T, Hanaoka F, Yamashita T. Polη, a Y-family translesion synthesis polymerase, promotes cellular tolerance of Myc-induced replication stress. J Cell Sci 2018; 131:jcs.212183. [PMID: 29777036 DOI: 10.1242/jcs.212183] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 05/10/2018] [Indexed: 12/30/2022] Open
Abstract
Growth of precancerous and cancer cells relies on their tolerance of oncogene-induced replication stress (RS). Translesion synthesis (TLS) plays an essential role in the cellular tolerance of various types of RS and bypasses replication barriers by employing specialized polymerases. However, limited information is available about the role of TLS polymerases in oncogene-induced RS. Here, we report that Polη, a Y-family TLS polymerase, promotes cellular tolerance of Myc-induced RS. Polη was recruited to Myc-induced RS sites, and Polη depletion enhanced the Myc-induced slowing and stalling of replication forks and the subsequent generation of double-strand breaks (DSBs). Overexpression of a catalytically dead Polη also promoted Myc-induced DSB formation. In the absence of Polη, Myc-induced DSB formation depended on MUS81-EME2 (the S-phase-specific endonuclease complex), and concomitant depletion of MUS81-EME2 and Polη enhanced RS and cell death in a synergistic manner. Collectively, these results indicate that Polη facilitates fork progression during Myc-induced RS, thereby helping cells tolerate the resultant deleterious effects. Additionally, the present study highlights the possibility of a synthetic sickness or lethality between Polη and MUS81-EME2 in cells experiencing Myc-induced RS.
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Affiliation(s)
- Kiminori Kurashima
- Laboratory of Molecular Genetics, Institute for Molecular and Cellular Regulation, Gunma University, 371-8512 Gunma, Japan
| | - Takayuki Sekimoto
- Laboratory of Molecular Genetics, Institute for Molecular and Cellular Regulation, Gunma University, 371-8512 Gunma, Japan
| | - Tsukasa Oda
- Laboratory of Molecular Genetics, Institute for Molecular and Cellular Regulation, Gunma University, 371-8512 Gunma, Japan
| | - Tsuyoshi Kawabata
- Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University, 852-8523 Nagasaki, Japan
| | - Fumio Hanaoka
- Department of Life Science, Faculty of Science, Gakushuin University, 171-8588 Tokyo, Japan
| | - Takayuki Yamashita
- Laboratory of Molecular Genetics, Institute for Molecular and Cellular Regulation, Gunma University, 371-8512 Gunma, Japan
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33
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Petrovic V, Nepal A, Olaisen C, Bachke S, Hira J, Søgaard CK, Røst LM, Misund K, Andreassen T, Melø TM, Bartsova Z, Bruheim P, Otterlei M. Anti-Cancer Potential of Homemade Fresh Garlic Extract Is Related to Increased Endoplasmic Reticulum Stress. Nutrients 2018; 10:nu10040450. [PMID: 29621132 PMCID: PMC5946235 DOI: 10.3390/nu10040450] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/14/2022] Open
Abstract
The use of garlic and garlic-based extracts has been linked to decreased incidence of cancer in epidemiological studies. Here we examine the molecular and cellular activities of a simple homemade ethanol-based garlic extract (GE). We show that GE inhibits growth of several different cancer cells in vitro, as well as cancer growth in vivo in a syngeneic orthotopic breast cancer model. Multiple myeloma cells were found to be especially sensitive to GE. The GE was fractionated using solid-phase extractions, and we identified allicin in one GE fraction; however, growth inhibitory activities were found in several additional fractions. These activities were lost during freeze or vacuum drying, suggesting that the main anti-cancer compounds in GE are volatile. The anti-cancer activity was stable for more than six months in −20 °C. We found that GE enhanced the activities of chemotherapeutics, as well as MAPK and PI3K inhibitors. Furthermore, GE affected hundreds of proteins involved in cellular signalling, including changes in vital cell signalling cascades regulating proliferation, apoptosis, and the cellular redox balance. Our data indicate that the reduced proliferation of the cancer cells treated by GE is at least partly mediated by increased endoplasmic reticulum (ER) stress.
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Affiliation(s)
- Voin Petrovic
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Anala Nepal
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Camilla Olaisen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Siri Bachke
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Jonathan Hira
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Caroline K Søgaard
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Lisa M Røst
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Kristine Misund
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Trygve Andreassen
- MR core facility, Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Torun M Melø
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Zdenka Bartsova
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Per Bruheim
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
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34
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Ji L, Yang S, Li S, Liu S, Tang S, Liu Z, Meng X, Yu S. A novel triazolonaphthalimide induces apoptosis and inhibits tumor growth by targeting DNA and DNA-associated processes. Oncotarget 2018; 8:37394-37408. [PMID: 28445124 PMCID: PMC5514917 DOI: 10.18632/oncotarget.16962] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 03/27/2017] [Indexed: 12/28/2022] Open
Abstract
DNA and DNA-associated processes have been classes of the most important targets of chemotherapeutic drugs. As classic DNA intercalators and topoisomerase inhibitors, naphthalimides have been extensively investigated as potential anti-cancer drugs. We recently synthesized a novel series of triazolonaphthalimides with excellent anti-cancer activities. In the present study, one of the most potent triazolonaphthalimides, LSS-11, was investigated. LSS-11 bound to DNA in vitro and in cell mainly by minor groove binding and significantly increased the stability of DNA, which could be fundamental for the biological activities of LSS-11. In addition to inhibiting DNA topoisomerase II-catalyzed decatenation of knotted circulated DNA, LSS-11 dramatically inhibited DNA replication mediated by polymerase chain reaction and isothermal helicase-dependent amplification, as well as the expression of luciferase driven by a minimal TA promoter in cell. Furthermore, LSS-11 exhibited strong cytotoxicity in selected human colon cancer cell lines by inducing cell cycle arrest and apoptosis, which was accompanied by DNA damage response. Finally, LSS-11 potently inhibited the growth of S180 murine sarcoma and SW480 human colorectal cancer xenografts in vivo without significant major toxicities. These results suggest that LSS-11 deserves further research and development as a novel anti-cancer agent, and provided new understandings of mechanisms by which LSS-11 inhibited multiple DNA-associated processes and tumor growth.
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Affiliation(s)
- Liyan Ji
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China.,International Institute for Translational Chinese Medicine, Guangzhou Traditional Chinese Medicine University, Guangzhou 510006, China
| | - Simin Yang
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| | - Shasha Li
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| | - Shan Liu
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| | - Shunan Tang
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou Traditional Chinese Medicine University, Guangzhou 510006, China
| | - Xiangbao Meng
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| | - Siwang Yu
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
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35
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Wang Y, Wang Y, Duan X, Wang Y, Zhang Z. Interleukin-1 receptor-associated kinase 1 correlates with metastasis and invasion in endometrial carcinoma. J Cell Biochem 2017; 119:2545-2555. [PMID: 28980703 DOI: 10.1002/jcb.26416] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/03/2017] [Indexed: 12/11/2022]
Abstract
Endometrial carcinoma (EC) is one of the most common malignancies in the world. Previous studies have investigated the altered expression of interleukin-1 receptor-associated kinase 1 (IRAK1) in various cancers. We aimed at exploring the biological function and the underlying molecular mechanism of IRAK1 in EC. In this study, IRAK1 was found elevated in EC compared with normal tissues. Further, high IRAK1 expression level was correlated with higher tumor stage, lymph node metastasis, myometrial invasion, and lower survival rate. Knockdown of IRAK1 in two EC cell lines, HEC-1-B and JEC, significantly inhibited cell proliferation in vitro and in vivo. We also found that down-regulation of IRAK1 in EC cells notably induced cell cycle arrest and apoptois, and also inhibited cell migration and invasion. Gene set enrichment analysis on The Cancer Genome Atlas dataset showed that Kyoto Encyclopedia of Genes and Genomes (KEGG) mitotic cell cycle and cell division pathways were correlative with the IRAK1 expression, which was further confirmed in EC cells by Western blot. The expression of mitotic cell cycle (CDK1 and Cdc45) and cell division pathway (Cdc7 and MCM2) related factors was significantly suppressed by IRAK1 knockdown. These collective data indicated that IRAK1 overexpression promotes EC tumorigenesis by activating mitotic cell cycle and cell division pathways, and IRAK1 may serve as a promising therapeutic strategy for EC.
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Affiliation(s)
- Yilin Wang
- Department of Gynecology and Obstetrics, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, China.,Department of Gynecology and Obstetrics, People's Hospital of the Inner Mongolia Autonomous Region, Hohhot, China
| | - Yanyan Wang
- Department of Gynecology and Obstetrics, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, China
| | - Xianzhi Duan
- Department of Gynecology and Obstetrics, Beijing Tongren Hospital Affiliated to Capital Medical University, Beijing, China
| | - Yinuo Wang
- Department of Gynecology and Obstetrics, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, China
| | - Zhenyu Zhang
- Department of Gynecology and Obstetrics, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, China
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36
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Qiu Z, Oleinick NL, Zhang J. ATR/CHK1 inhibitors and cancer therapy. Radiother Oncol 2017; 126:450-464. [PMID: 29054375 DOI: 10.1016/j.radonc.2017.09.043] [Citation(s) in RCA: 210] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 08/01/2017] [Accepted: 09/30/2017] [Indexed: 02/06/2023]
Abstract
The cell cycle checkpoint proteins ataxia-telangiectasia-mutated-and-Rad3-related kinase (ATR) and its major downstream effector checkpoint kinase 1 (CHK1) prevent the entry of cells with damaged or incompletely replicated DNA into mitosis when the cells are challenged by DNA damaging agents, such as radiation therapy (RT) or chemotherapeutic drugs, that are the major modalities to treat cancer. This regulation is particularly evident in cells with a defective G1 checkpoint, a common feature of cancer cells, due to p53 mutations. In addition, ATR and/or CHK1 suppress replication stress (RS) by inhibiting excess origin firing, particularly in cells with activated oncogenes. Those functions of ATR/CHK1 make them ideal therapeutic targets. ATR/CHK1 inhibitors have been developed and are currently used either as single agents or paired with radiotherapy or a variety of genotoxic chemotherapies in preclinical and clinical studies. Here, we review the status of the development of ATR and CHK1 inhibitors. We also discuss the potential mechanisms by which ATR and CHK1 inhibition induces cell killing in the presence or absence of exogenous DNA damaging agents, such as RT and chemotherapeutic agents. Lastly, we discuss synthetic lethality interactions between the inhibition of ATR/CHK1 and defects in other DNA damage response (DDR) pathways/genes.
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Affiliation(s)
- Zhaojun Qiu
- Department of Radiation Oncology, School of Medicine, Case Western Reserve University, Cleveland, USA
| | - Nancy L Oleinick
- Department of Radiation Oncology, School of Medicine, Case Western Reserve University, Cleveland, USA; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, USA
| | - Junran Zhang
- Department of Radiation Oncology, School of Medicine, Case Western Reserve University, Cleveland, USA; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, USA.
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37
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Wu S, Wu F, Jiang Z. Identification of hub genes, key miRNAs and potential molecular mechanisms of colorectal cancer. Oncol Rep 2017; 38:2043-2050. [PMID: 28902367 PMCID: PMC5652954 DOI: 10.3892/or.2017.5930] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/17/2017] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is the most common cancer of the digestive system. The aim of the present study was to identify the potential biomarkers and uncover the underlying mechanisms. The gene and miRNA expression profiles were obtained from GEO database. The differentially expressed genes (DEGs) and miRNAs (DE miRNAs) were identified by GEO2R. The Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed by KOBAS 3.0. The protein-protein interaction (PPI) network and miRNA-gene network were constructed by Cytoscape software. Then, the identified genes were verified by quantitative real-time PCR in both CRC tissue samples and cell lines. A total of 600 upregulated DEGs, 283 downregulated DEGs, 13 upregulated DE miRNAs and 7 downregulated DE miRNAs were identified. GO analysis results showed that upregulated DEGs were significantly enriched in binding, organelle and cellular process. Downregulated DEGs were enriched in binding, extracellular region and chemical homeostasis. KEGG analysis showed that the DEGs were mostly enriched in cell cycle and pathways in cancer. A total of eight genes were identified as biomarkers, including CAD, ITGA2, E2F3, BCL2, PRKACB, IGF1, SGK1 and NR3C1. Experimental validation showed that seven of the eight identified genes had the same expression trend as predicted, except for ITGA2. Besides, hsa-miR-552 and hsa-miR-30a were identified as key miRNAs. The present study provides a series of biomarkers and mechanisms for the diagnosis and therapy of CRC. We also prove that although bioinformatics analysis is a wonderful approach, experiment validation is necessary.
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Affiliation(s)
- Shasha Wu
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Feixiang Wu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Zheng Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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38
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Crefcoeur RP, Zgheib O, Halazonetis TD. A Model to Investigate Single-Strand DNA Responses in G1 Human Cells via a Telomere-Targeted, Nuclease-Deficient CRISPR-Cas9 System. PLoS One 2017; 12:e0169126. [PMID: 28046023 PMCID: PMC5207518 DOI: 10.1371/journal.pone.0169126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/11/2016] [Indexed: 12/22/2022] Open
Abstract
DNA replication stress has the potential to compromise genomic stability and, therefore, cells have developed elaborate mechanisms to detect and resolve problems that may arise during DNA replication. The presence of single-stranded DNA (ssDNA) is often associated with DNA replication stress and serves as a signal for both checkpoint and repair responses. In this study, we exploited a CRISPR-Cas9 system to induce regions of ssDNA in the genome. Specifically, single-guide RNAs bearing sequence complementarity to human telomeric repeats, were used to target nuclease-deficient Cas9 (dCas9) to telomeres. Such targeting was associated with the formation of DNA-RNA hybrids, leaving one telomeric DNA strand single-stranded. This ssDNA then recruited DNA repair and checkpoint proteins, such as RPA, ATRIP, BLM and Rad51, at the telomeres. Interestingly, targeting of all these proteins to telomeric ssDNA was observed even in cells that were in the G1 phase of the cell cycle. Therefore, this system has the potential to serve as a platform for further investigation of DNA replication stress responses at specific loci in the human genome and in all phases of the cell cycle.
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Affiliation(s)
- Remco P. Crefcoeur
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Omar Zgheib
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
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39
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Williams DT, Staples CJ. Approaches for Identifying Novel Targets in Precision Medicine: Lessons from DNA Repair. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1007:1-16. [PMID: 28840549 DOI: 10.1007/978-3-319-60733-7_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome stability is maintained by a number of elegant mechanisms, which sense and repair damaged DNA. Germline defects that compromise genomic integrity result in cancer predisposition, exemplified by rare syndromes caused by mutations in certain DNA repair genes. These individuals often exhibit other symptoms including progeria and neurodegeneration. Paradoxically, some of these deleterious genetic alterations provide novel therapeutic opportunities to target cancer cells; an excellent example of such an approach being the recent development of poly (ADP-ribose) polymerase inhibitors as the first 'synthetic lethal' medicine for patients with BRCA-mutant cancers. The therapeutic exploitation of synthetic lethal interactions has enabled a novel approach to personalised medicine based on continued molecular profiling of patient and tumour material. This profiling may also aid clinicians in the identification of specific drug resistance mechanisms following relapse, and enable appropriate modification of the therapeutic regimen. This chapter focuses on therapeutic strategies designed to target aspects of the DNA damage response, and examines emerging themes demonstrating mechanistic overlap between DNA repair and neurodegeneration.
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Affiliation(s)
- Dean T Williams
- School of Medical Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK.,Department of Vascular Surgery, Ysbyty Gwynedd, Bangor, LL57 2PW, UK
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40
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Distinct functions of human RecQ helicases during DNA replication. Biophys Chem 2016; 225:20-26. [PMID: 27876204 DOI: 10.1016/j.bpc.2016.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/13/2016] [Accepted: 11/13/2016] [Indexed: 12/31/2022]
Abstract
DNA replication is the most vulnerable process of DNA metabolism in proliferating cells and therefore it is tightly controlled and coordinated with processes that maintain genomic stability. Human RecQ helicases are among the most important factors involved in the maintenance of replication fork integrity, especially under conditions of replication stress. RecQ helicases promote recovery of replication forks being stalled due to different replication roadblocks of either exogenous or endogenous source. They prevent generation of aberrant replication fork structures and replication fork collapse, and are involved in proper checkpoint signaling. The essential role of human RecQ helicases in the genome maintenance during DNA replication is underlined by association of defects in their function with cancer predisposition.
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41
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Kushwaha PP, Rapalli KC, Kumar S. Geminin a multi task protein involved in cancer pathophysiology and developmental process: A review. Biochimie 2016; 131:115-127. [PMID: 27702582 DOI: 10.1016/j.biochi.2016.09.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/29/2016] [Indexed: 02/05/2023]
Abstract
DNA replicates in a timely manner with each cell division. Multiple proteins and factors are involved in the initiation of DNA replication including a dynamic interaction between Cdc10-dependent transcript (Cdt1) and Geminin (GMNN). A conformational change between GMNN-Cdt1 heterotrimer and heterohexamer complex is responsible for licensing or inhibition of the DNA replication. This molecular switch ensures a faithful DNA replication during each S phase of cell cycle. GMNN inhibits Cdt1-mediated minichromosome maintenance helicases (MCM) loading onto the chromatin-bound origin recognition complex (ORC) which results in the inhibition of pre-replication complex assembly. GMNN modulates DNA replication by direct binding to Cdt1, and thereby alters its stability and activity. GMNN is involved in various stages of development such as pre-implantation, germ layer formation, cell commitment and specification, maintenance of genome integrity at mid blastula transition, epithelial to mesenchymal transition during gastrulation, neural development, organogenesis and axis patterning. GMNN interacts with different proteins resulting in enhanced hematopoietic stem cell activity thereby activating the development-associated genes' transcription. GMNN expression is also associated with cancer pathophysiology and development. In this review we discussed the structure and function of GMNN in detail. Inhibitors of GMNN and their role in DNA replication, repair, cell cycle and apoptosis are reviewed. Further, we also discussed the role of GMNN in virus infected host cells.
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Affiliation(s)
- Prem Prakash Kushwaha
- School of Basic and Applied Sciences, Centre for Biochemistry and Microbial Sciences, Central University of Punjab, Bathinda, 151001, India
| | - Krishna Chaitanya Rapalli
- School of Basic and Applied Sciences, Centre for Animal Sciences, Central University of Punjab, Bathinda, 151001, India
| | - Shashank Kumar
- School of Basic and Applied Sciences, Centre for Biochemistry and Microbial Sciences, Central University of Punjab, Bathinda, 151001, India.
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42
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Long NP, Lee WJ, Huy NT, Lee SJ, Park JH, Kwon SW. Novel Biomarker Candidates for Colorectal Cancer Metastasis: A Meta-analysis of In Vitro Studies. Cancer Inform 2016; 15:11-7. [PMID: 27688707 PMCID: PMC5034882 DOI: 10.4137/cin.s40301] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common and lethal cancers. Although numerous studies have evaluated potential biomarkers for early diagnosis, current biomarkers have failed to reach an acceptable level of accuracy for distant metastasis. In this paper, we performed a gene set meta-analysis of in vitro microarray studies and combined the results from this study with previously published proteomic data to validate and suggest prognostic candidates for CRC metastasis. Two microarray data sets included found 21 significant genes. Of these significant genes, ALDOA, IL8 (CXCL8), and PARP4 had strong potential as prognostic candidates. LAMB2, MCM7, CXCL23A, SERPINA3, ABCA3, ALDH3A2, and POLR2I also have potential. Other candidates were more controversial, possibly because of the biologic heterogeneity of tumor cells, which is a major obstacle to predicting metastasis. In conclusion, we demonstrated a meta-analysis approach and successfully suggested ten biomarker candidates for future investigation.
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Affiliation(s)
| | | | - Nguyen Truong Huy
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea
| | - Seul Ji Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea
| | - Jeong Hill Park
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea
| | - Sung Won Kwon
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea
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Nicolas E, Golemis EA, Arora S. POLD1: Central mediator of DNA replication and repair, and implication in cancer and other pathologies. Gene 2016; 590:128-41. [PMID: 27320729 PMCID: PMC4969162 DOI: 10.1016/j.gene.2016.06.031] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/10/2016] [Accepted: 06/14/2016] [Indexed: 02/06/2023]
Abstract
The evolutionarily conserved human polymerase delta (POLD1) gene encodes the large p125 subunit which provides the essential catalytic activities of polymerase δ (Polδ), mediated by 5′–3′ DNA polymerase and 3′–5′ exonuclease moieties. POLD1 associates with three smaller subunits (POLD2, POLD3, POLD4), which together with Replication Factor C and Proliferating Nuclear Cell Antigen constitute the polymerase holoenzyme. Polδ function is essential for replication, with a primary role as the replicase for the lagging strand. Polδ also has an important proofreading ability conferred by the exonuclease activity, which is critical for ensuring replicative fidelity, but also serves to repair DNA lesions arising as a result of exposure to mutagens. Polδ has been shown to be important for multiple forms of DNA repair, including nucleotide excision repair, double strand break repair, base excision repair, and mismatch repair. A growing number of studies in the past decade have linked germline and sporadic mutations in POLD1 and the other subunits of Polδ with human pathologies. Mutations in Polδ in mice and humans lead to genomic instability, mutator phenotype and tumorigenesis. The advent of genome sequencing techniques has identified damaging mutations in the proofreading domain of POLD1 as the underlying cause of some inherited cancers, and suggested that mutations in POLD1 may influence therapeutic management. In addition, mutations in POLD1 have been identified in the developmental disorders of mandibular hypoplasia, deafness, progeroid features and lipodystrophy and atypical Werner syndrome, while changes in expression or activity of POLD1 have been linked to senescence and aging. Intriguingly, some recent evidence suggests that POLD1 function may also be altered in diabetes. We provide an overview of critical Polδ activities in the context of these pathologic conditions.
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Affiliation(s)
- Emmanuelle Nicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Erica A Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Sanjeevani Arora
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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44
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Georgakilas AG, Gorgoulis VG. Systemic dna damage: Mechanisms, effects and mitigation strategies. Semin Cancer Biol 2016; 37-38:1-2. [PMID: 27113557 DOI: 10.1016/j.semcancer.2016.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Alexandros G Georgakilas
- DNA Damage Laboratory, Department of Physics, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Zografou 15780, Athens, Greece.
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece; Biomedical Research Foundation, Academy of Athens, Athens, Greece; Faculty Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
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