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Lin Y, Yang B, Huang Y, Zhang Y, Jiang Y, Ma L, Shen YQ. Mitochondrial DNA-targeted therapy: A novel approach to combat cancer. CELL INSIGHT 2023; 2:100113. [PMID: 37554301 PMCID: PMC10404627 DOI: 10.1016/j.cellin.2023.100113] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 08/10/2023]
Abstract
Mitochondrial DNA (mtDNA) encodes proteins and RNAs that are essential for mitochondrial function and cellular homeostasis, and participates in important processes of cellular bioenergetics and metabolism. Alterations in mtDNA are associated with various diseases, especially cancers, and are considered as biomarkers for some types of tumors. Moreover, mtDNA alterations have been found to affect the proliferation, progression and metastasis of cancer cells, as well as their interactions with the immune system and the tumor microenvironment (TME). The important role of mtDNA in cancer development makes it a significant target for cancer treatment. In recent years, many novel therapeutic methods targeting mtDNA have emerged. In this study, we first discussed how cancerogenesis is triggered by mtDNA mutations, including alterations in gene copy number, aberrant gene expression and epigenetic modifications. Then, we described in detail the mechanisms underlying the interactions between mtDNA and the extramitochondrial environment, which are crucial for understanding the efficacy and safety of mtDNA-targeted therapy. Next, we provided a comprehensive overview of the recent progress in cancer therapy strategies that target mtDNA. We classified them into two categories based on their mechanisms of action: indirect and direct targeting strategies. Indirect targeting strategies aimed to induce mtDNA damage and dysfunction by modulating pathways that are involved in mtDNA stability and integrity, while direct targeting strategies utilized molecules that can selectively bind to or cleave mtDNA to achieve the therapeutic efficacy. This study highlights the importance of mtDNA-targeted therapy in cancer treatment, and will provide insights for future research and development of targeted drugs and therapeutic strategies.
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Affiliation(s)
- Yumeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Bowen Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Yibo Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - You Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Yu Jiang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Longyun Ma
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Ying-Qiang Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
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Zhang Y, Zhang Q, Li L, Mu D, Hua K, Ci S, Shen L, Zheng L, Shen B, Guo Z. Arginine methylation of APE1 promotes its mitochondrial translocation to protect cells from oxidative damage. Free Radic Biol Med 2020; 158:60-73. [PMID: 32679368 PMCID: PMC8195256 DOI: 10.1016/j.freeradbiomed.2020.06.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 06/09/2020] [Accepted: 06/17/2020] [Indexed: 02/07/2023]
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) is an essential multifunctional protein in mammals that plays critical roles in DNA repair and redox signaling within the cell. Impaired APE1 function or dysregulation is associated with disease susceptibility and poor cancer prognosis. Orchestrated regulatory mechanisms are crucial to ensure its function in a specific subcellular location at specific time. Here, we report arginine methylation as a post-translational modification (PTM) that regulates APE1 translocation to mitochondria in HeLa and HEK-293 cells. Protein arginine methyl-transferase 1 (PRMT1) was shown to methylate APE1 in vitro. Site-directed mutagenesis identified R301 as the major methylation site. We confirmed that APE1 is methylated in cells and that the R301K mutation significantly reduces its methylation. Baseline mitochondrial APE1 levels were low under standard culture conditions, but they could be induced by oxidative agents. Methylation-deficient APE1 showed reduced mitochondrial translocation. Methylation affected the interaction of APE1 with Tom20, translocase of the outer mitochondrial membrane. Methylation-deficient APE1 resulted in increased mitochondrial DNA damage and increased cytochrome c release after stimuli. These data suggest that methylation of APE1 promotes its mitochondrial translocation and protects cells from oxidative damage. This work describes a novel PTM regulation model of APE1 subcellular distribution through arginine methylation.
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Affiliation(s)
- Yilan Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Qi Zhang
- Department of Infectious Disease, Nanjing Liuhe District People's Hospital, Yangzhou University, Nanjing, 211500, China
| | - LuLu Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Dan Mu
- Department of Radiology, Affiliated Drum Tower Hospital, Nanjing University School of Medicine, Nanjing, 210008, China
| | - Ke Hua
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Shusheng Ci
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Lei Shen
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, 91010, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, 91010, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, 91010, USA.
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China.
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Chidambaram SB, Bhat A, Ray B, Sugumar M, Muthukumar SP, Manivasagam T, Justin Thenmozhi A, Essa MM, Guillemin GJ, Sakharkar MK. Cocoa beans improve mitochondrial biogenesis via PPARγ/PGC1α dependent signalling pathway in MPP + intoxicated human neuroblastoma cells (SH-SY5Y). Nutr Neurosci 2018; 23:471-480. [PMID: 30207204 DOI: 10.1080/1028415x.2018.1521088] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Polyphenols are shown to protect from or delay the progression of chronic neurodegenerative diseases. Mitochondrial dysfunction plays a key role in the pathogenesis of Parkinson's disease (PD). This study was aims to gain insight into the role of ahydroalcoholic extract of cocoa (standardised for epicatechin content) on mitochondrial biogenesis in MPP+ intoxicated human neuroblastoma cells (SHSY5Y). The effects of cocoa on PPARγ, PGC1α, Nrf2 and TFAM protein expression and mitochondrial membrane potential were evaluated. A pre-exposure to cocoa extract decreased reactive oxygen species formation and restored mitochondrial membrane potential. The cocoa extract was found to up-regulate the expression of PPARγ and the downstream signalling proteins PGC1α, Nrf2 and TFAM. It increased the expression of the anti-apoptotic protein BCl2 and increased superoxide dismutase activity. Further, the cocoa extract down-regulated the expression of mitochondria fission 1 (Fis1) and up-regulated the expression of mitochondria fusion 2 (Mfn2) proteins, suggesting an improvement in mitochondrial functions in MPP+ intoxicated cells upon treatment with cocoa. Interestingly, cocoa up-regulates the expression of tyrosine hydroxylase, the rate limiting enzyme in dopamine synthesis. No change in the expression of PPARγ on treatment with cocoa extract was observed when the cells were pre-treated with PPARγ antagonist GW9662. This data suggests that cocoa mediates mitochondrial biogenesis via a PPARγ/PGC1α dependent signalling pathway and also has the ability to improve dopaminergic functions by increasing tyrosine hydroxylase expression. Based on our data, we propose that a cocoa bean extract and products thereof could be used as potential nutritional supplements for neuroprotection in PD.
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Affiliation(s)
- Saravana Babu Chidambaram
- Dept of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, SS Nagar, Mysore 57 00 15, KA, India
| | - Abid Bhat
- Dept of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, SS Nagar, Mysore 57 00 15, KA, India
| | - Bipul Ray
- Dept of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, SS Nagar, Mysore 57 00 15, KA, India
| | - Mani Sugumar
- Research and Development Centre, Bharathiar University, Coimbatore 641046, TN, India
| | - Serva Peddha Muthukumar
- Department of Biochemistry, CSIR - Central Food Technological Research Institute, Mysore 570020, KA, India
| | - Thamilarasan Manivasagam
- Department of Biochemistry and Biotechnology, Faculty of Science, Annamalai University, Annamalai nagar, Tamilnadu, India
| | - Arokiasamy Justin Thenmozhi
- Department of Biochemistry and Biotechnology, Faculty of Science, Annamalai University, Annamalai nagar, Tamilnadu, India
| | | | - Gilles J Guillemin
- Neuropharmacology group, Faculty of Medicine and Health Sciences, Deb Bailey MND Research Laboratory, Macquarie University, NSW 2109, Australia
| | - Meena Kishore Sakharkar
- College of Pharmacy and Nutrition, University of Saskatchewan, 107, Wiggins Road, Saskatoon, SK, Canada S7N 5C9
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Yu H, Zhang X, Liu R, Li H, Xiao X, Zhou Y, Wei C, Yang M, Liao M, Zhao J, Xia Z, Liao Q. Mcl-1 suppresses abasic site repair following bile acid-induced hepatic cellular DNA damage. Tumour Biol 2017; 39:1010428317712102. [PMID: 28681695 DOI: 10.1177/1010428317712102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In cholestasis, increases in bile acid levels result in the generation of reactive oxygen species and the induction of DNA damage and mutation. It is believed that bile acid accumulation is associated with liver tumorigenesis. However, the mechanism that underpins this phenomenon remains to be elucidated. Mcl-1, which is overexpressed in hepatic cells, is a pro-survival member of the Bcl-2 family. In this study, we observed that Mcl-1 potently suppresses the repair of bile acid-induced abasic (apurinic/apyrimidinic) sites in DNA lesions. Upon exposure of hepatic cells to glycochenodeoxycholate, one of the major conjugated human bile acids, we observed an increase in AP site accumulation along with induction of poly(ADP-ribose) polymerase and XRCC1 ( X-Ray Repair Cross Complementing 1). In addition, accumulation of Mcl-1 was observed in the nuclei of QGY-7703 cells in response to glycochenodeoxycholate stimulation. Knockdown of endogenous Mcl-1 by RNA interference significantly accelerated the repair of DNA lesions in glycochenodeoxycholate-treated cells. However, unlike XRCC1, poly(ADP-ribose) polymerase was induced following Mcl-1 knockdown. Conversely, poly(ADP-ribose) polymerase suppression was observed following glycochenodeoxycholate treatment of cells overexpressing Mcl-1. Moreover, AP-site counting analyses revealed that DNA repair activity was enhanced in cells overexpressing poly(ADP-ribose) polymerase under glycochenodeoxycholate stress conditions. It is well known that poly(ADP-ribose) polymerase plays a crucial role in the base excision repair pathway. Thus, our findings suggest that Mcl-1 suppresses base excision repair by inhibiting poly(ADP-ribose) polymerase induction following glycochenodeoxycholate-induced DNA damage. These results potentially explain how bile acid accumulation results in genetic instability and carcinogenesis.
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Affiliation(s)
- Haiyang Yu
- 1 Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Xiaoqing Zhang
- 2 The Fifth Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Ren Liu
- 3 Merck Research Laboratory, Kenilworth, NJ, USA
| | - Hui Li
- 4 State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, P.R. China
| | - Xiaolong Xiao
- 4 State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, P.R. China
| | - Yuzheng Zhou
- 4 State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, P.R. China
| | - Chaoying Wei
- 4 State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, P.R. China
| | - Manyi Yang
- 1 Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Mingmei Liao
- 1 Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Jinfeng Zhao
- 1 Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Zanxian Xia
- 4 State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, P.R. China
| | - Qiande Liao
- 1 Xiangya Hospital, Central South University, Changsha, P.R. China
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Yu D, Yang X, Lu X, Shi L, Feng B. Ethyl acetate extract of Peperomia tetraphylla induces cytotoxicity, cell cycle arrest, and apoptosis in lymphoma U937 cells. Biomed Pharmacother 2016; 84:1802-1809. [PMID: 27847202 DOI: 10.1016/j.biopha.2016.10.092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 10/24/2016] [Accepted: 10/30/2016] [Indexed: 01/10/2023] Open
Abstract
The current study evaluated the cytotoxicity and the mechanism of apoptotic induction by Peperomia tetraphylla in U937 lymphoma cells. The results showed that P. tetraphylla ethyl acetate extract (EAEPT) inhibited the cell growth in U937 cells by MTT assay. After the U937 cells were treated with EAEPT, the cells exhibited marked morphological features of apoptosis (Hoechst 33342 staining) and the number of apoptotic cell (Annexin V-FITC/PI staining) increased. The treatment of EAEPT could induce loss of mitochondrial membrane potential (MMP) and increase the ROS level. Moreover, EAEPT treatment resulted in the accumulation of cells at S phase. We found that EAEPT could induce the cleavage of the caspase 3, caspase 8, caspase 9 and Bid. And the treatment of EAEPT could increase expression of Bax and down-regulate the expression of CCNB1, CCND1 and CDK1. The sub-fraction of EAEPT, namely EASub1 demonstrated the highest cytotoxicity activity on U937 cells. It was confirmed that EAEPT could inhibit the growth of U937 cells by blocking the cell cycle and prompted apoptosis via the ROS-medicated mitochondria pathway in vitro.
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Affiliation(s)
- Dayong Yu
- The School of Life Science and Biotechnology, Dalian University, Dalian 116622, PR China.
| | - Xiuxiu Yang
- The School of Life Science and Biotechnology, Dalian University, Dalian 116622, PR China
| | - Xuan Lu
- The School of Life Science and Biotechnology, Dalian University, Dalian 116622, PR China
| | - Liying Shi
- The School of Life Science and Biotechnology, Dalian University, Dalian 116622, PR China
| | - Baomin Feng
- The School of Life Science and Biotechnology, Dalian University, Dalian 116622, PR China.
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Wang X, Guda C. Integrative exploration of genomic profiles for triple negative breast cancer identifies potential drug targets. Medicine (Baltimore) 2016; 95:e4321. [PMID: 27472710 PMCID: PMC5265847 DOI: 10.1097/md.0000000000004321] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Triple negative breast cancer (TNBC) is high-risk due to its rapid drug resistance and recurrence, metastasis, and lack of targeted therapy. So far, no molecularly targeted therapeutic agents have been clinically approved for TNBC. It is imperative that we discover new targets for TNBC therapy. OBJECTIVES A large volume of cancer genomics data are emerging and advancing breast cancer research. We may integrate different types of TNBC genomic data to discover molecular targets for TNBC therapy. DATA SOURCES We used publicly available TNBC tumor tissue genomic data in the Cancer Genome Atlas database in this study. METHODS We integratively explored genomic profiles (gene expression, copy number, methylation, microRNA [miRNA], and gene mutation) in TNBC and identified hyperactivated genes that have higher expression, more copy numbers, lower methylation level, or are targets of miRNAs with lower expression in TNBC than in normal samples. We ranked the hyperactivated genes into different levels based on all the genomic evidence and performed functional analyses of the sets of genes identified. More importantly, we proposed potential molecular targets for TNBC therapy based on the hyperactivated genes. RESULTS Some of the genes we identified such as FGFR2, MAPK13, TP53, SRC family, MUC family, and BCL2 family have been suggested to be potential targets for TNBC treatment. Others such as CSF1R, EPHB3, TRIB1, and LAD1 could be promising new targets for TNBC treatment. By utilizing this integrative analysis of genomic profiles for TNBC, we hypothesized that some of the targeted treatment strategies for TNBC currently in development are more likely to be promising, such as poly (ADP-ribose) polymerase inhibitors, while the others are more likely to be discouraging, such as angiogenesis inhibitors. LIMITATIONS The findings in this study need to be experimentally validated in the future. CONCLUSION This is a systematic study that combined 5 different types of genomic data to molecularly characterize TNBC and identify potential targets for TNBC therapy. The integrative analysis of genomic profiles for TNBC could assist in identifying potential new therapeutic targets and predicting the effectiveness of a targeted treatment strategy for TNBC therapy.
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Affiliation(s)
- Xiaosheng Wang
- School of Basic Medicine and Clinic Pharmacy, China Pharmaceutical University, Nanjing, China
- Correspondence: Xiaosheng Wang, China Pharmaceutical University, Nanjing, Jiangsu, China (e-mail: )
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy
- Bioinformatics and Systems Biology Core
- Department of Biochemistry and Molecular Biology
- Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
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Zhang HF, Wang KH. Relationship between mutations of mitochondrial DNA control region and tumors. Shijie Huaren Xiaohua Zazhi 2016; 24:2676-2681. [DOI: 10.11569/wcjd.v24.i17.2676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The mitochondrion is the main place of cell respiration and participates in the process of cell apoptosis and proliferation, nucleic acid synthesis, and the production of free radicals. Mitochondrial DNA (mtDNA) is susceptible to the attack by oxygen free radicals and their products, and tends to develop somatic mutations, because of the lack of protection by histones and complete repair system. Somatic mutations in mtDNA will finally promote tumorigenesis. The control region of mtDNA is a region with a high mutation frequency. The association between control region mutations and tumorigenesis has attracted wide attention. Therefore, it is of great significance to elucidate the relationship between mtDNA control region mutations and tumorigenesis.
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Molecular and Cellular Effects of Hydrogen Peroxide on Human Lung Cancer Cells: Potential Therapeutic Implications. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2016; 2016:1908164. [PMID: 27375834 PMCID: PMC4916325 DOI: 10.1155/2016/1908164] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/10/2016] [Indexed: 02/05/2023]
Abstract
Lung cancer has a very high mortality-to-incidence ratio, representing one of the main causes of cancer mortality worldwide. Therefore, new treatment strategies are urgently needed. Several diseases including lung cancer have been associated with the action of reactive oxygen species (ROS) from which hydrogen peroxide (H2O2) is one of the most studied. Despite the fact that H2O2 may have opposite effects on cell proliferation depending on the concentration and cell type, it triggers several antiproliferative responses. H2O2 produces both nuclear and mitochondrial DNA lesions, increases the expression of cell adhesion molecules, and increases p53 activity and other transcription factors orchestrating cancer cell death. In addition, H2O2 facilitates the endocytosis of oligonucleotides, affects membrane proteins, induces calcium release, and decreases cancer cell migration and invasion. Furthermore, the MAPK pathway and the expression of genes related to inflammation including interleukins, TNF-α, and NF-κB are also affected by H2O2. Herein, we will summarize the main effects of hydrogen peroxide on human lung cancer leading to suggesting it as a potential therapeutic tool to fight this disease. Because of the multimechanistic nature of this molecule, novel therapeutic approaches for lung cancer based on the use of H2O2 may help to decrease the mortality from this malignancy.
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Wang X, Zhang Y, Han ZG, He KY. Malignancy of Cancers and Synthetic Lethal Interactions Associated With Mutations of Cancer Driver Genes. Medicine (Baltimore) 2016; 95:e2697. [PMID: 26937901 PMCID: PMC4778998 DOI: 10.1097/md.0000000000002697] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The mutation status of cancer driver genes may correlate with different degrees of malignancy of cancers. The doubling time and multidrug resistance are 2 phenotypes that reflect the degree of malignancy of cancer cells. Because most of cancer driver genes are hard to target, identification of their synthetic lethal partners might be a viable approach to treatment of the cancers with the relevant mutations.The genome-wide screening for synthetic lethal partners is costly and labor intensive. Thus, a computational approach facilitating identification of candidate genes for a focus synthetic lethal RNAi screening will accelerate novel anticancer drug discovery.We used several publicly available cancer cell lines and tumor tissue genomic data in this study.We compared the doubling time and multidrug resistance between the NCI-60 cell lines with mutations in some cancer driver genes and those without the mutations. We identified some candidate synthetic lethal genes to the cancer driver genes APC, KRAS, BRAF, PIK3CA, and TP53 by comparison of their gene phenotype values in cancer cell lines with the relevant mutations and wild-type background. Further, we experimentally validated some of the synthetic lethal relationships we predicted.We reported that mutations in some cancer driver genes mutations in some cancer driver genes such as APC, KRAS, or PIK3CA might correlate with cancer proliferation or drug resistance. We identified 40, 21, 5, 43, and 18 potential synthetic lethal genes to APC, KRAS, BRAF, PIK3CA, and TP53, respectively. We found that some of the potential synthetic lethal genes show significantly higher expression in the cancers with mutations of their synthetic lethal partners and the wild-type counterparts. Further, our experiments confirmed several synthetic lethal relationships that are novel findings by our methods.We experimentally validated a part of the synthetic lethal relationships we predicted. We plan to perform further experiments to validate the other synthetic lethal relationships predicted by this study.Our computational methods achieve to identify candidate synthetic lethal partners to cancer driver genes for further experimental screening with multiple lines of evidences, and therefore contribute to development of anticancer drugs.
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Affiliation(s)
- Xiaosheng Wang
- From the School of Basic Medicine and Clinic Pharmacy (XW), China Pharmaceutical University, Nanjing; The First Clinical College of Harbin Medical University (YZ), Harbin, China; Division of Genetics and Development (YZ), The Toronto Western Research Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada; and Key Laboratory of Systems Biomedicine (Ministry of Education) (Z-GH, K-YH), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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