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Yamada K, St Croix C, Stolz DB, Tyurina YY, Tyurin VA, Bradley LR, Kapralov AA, Deng Y, Zhou X, Wei Q, Liao B, Fukuda N, Sullivan M, Trudeau J, Ray A, Kagan VE, Zhao J, Wenzel SE. Compartmentalized mitochondrial ferroptosis converges with optineurin-mediated mitophagy to impact airway epithelial cell phenotypes and asthma outcomes. Nat Commun 2024; 15:5818. [PMID: 38987265 PMCID: PMC11237105 DOI: 10.1038/s41467-024-50222-2] [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: 07/11/2023] [Accepted: 07/03/2024] [Indexed: 07/12/2024] Open
Abstract
A stable mitochondrial pool is crucial for healthy cell function and survival. Altered redox biology can adversely affect mitochondria through induction of a variety of cell death and survival pathways, yet the understanding of mitochondria and their dysfunction in primary human cells and in specific disease states, including asthma, is modest. Ferroptosis is traditionally considered an iron dependent, hydroperoxy-phospholipid executed process, which induces cytosolic and mitochondrial damage to drive programmed cell death. However, in this report we identify a lipoxygenase orchestrated, compartmentally-targeted ferroptosis-associated peroxidation process which occurs in a subpopulation of dysfunctional mitochondria, without promoting cell death. Rather, this mitochondrial peroxidation process tightly couples with PTEN-induced kinase (PINK)-1(PINK1)-Parkin-Optineurin mediated mitophagy in an effort to preserve the pool of functional mitochondria and prevent cell death. These combined peroxidation processes lead to altered epithelial cell phenotypes and loss of ciliated cells which associate with worsened asthma severity. Ferroptosis-targeted interventions of this process could preserve healthy mitochondria, reverse cell phenotypic changes and improve disease outcomes.
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Affiliation(s)
- Kazuhiro Yamada
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Respiratory Medicine, Graduate School of Medicine, Osaka Metropolitan University, Osaka, 545-8585, Japan
| | - Claudette St Croix
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Donna B Stolz
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Yulia Y Tyurina
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Vladimir A Tyurin
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Laura R Bradley
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Alexander A Kapralov
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Yanhan Deng
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Rheumatology and Immunology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiuxia Zhou
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Qi Wei
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Bo Liao
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Otolaryngology-Head & Neck Surgery, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Nobuhiko Fukuda
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Mara Sullivan
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - John Trudeau
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Anuradha Ray
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Jinming Zhao
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Sally E Wenzel
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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2
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Eguchi N, Vaziri ND, Dafoe DC, Ichii H. The Role of Oxidative Stress in Pancreatic β Cell Dysfunction in Diabetes. Int J Mol Sci 2021; 22:ijms22041509. [PMID: 33546200 PMCID: PMC7913369 DOI: 10.3390/ijms22041509] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 02/07/2023] Open
Abstract
Diabetes is a chronic metabolic disorder characterized by inappropriately elevated glucose levels as a result of impaired pancreatic β cell function and insulin resistance. Extensive studies have been conducted to elucidate the mechanism involved in the development of β cell failure and death under diabetic conditions such as hyperglycemia, hyperlipidemia, and inflammation. Of the plethora of proposed mechanisms, endoplasmic reticulum (ER) stress, mitochondrial dysfunction, and oxidative stress have been shown to play a central role in promoting β cell dysfunction. It has become more evident in recent years that these 3 factors are closely interrelated and importantly aggravate each other. Oxidative stress in particular is of great interest to β cell health and survival as it has been shown that β cells exhibit lower antioxidative capacity. Therefore, this review will focus on discussing factors that contribute to the development of oxidative stress in pancreatic β cells and explore the downstream effects of oxidative stress on β cell function and health. Furthermore, antioxidative capacity of β cells to counteract these effects will be discussed along with new approaches focused on preserving β cells under oxidative conditions.
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Affiliation(s)
- Natsuki Eguchi
- Department of Surgery, University of California, Irvine, CA 92697, USA; (N.E.); (D.C.D.)
| | | | - Donald C. Dafoe
- Department of Surgery, University of California, Irvine, CA 92697, USA; (N.E.); (D.C.D.)
| | - Hirohito Ichii
- Department of Surgery, University of California, Irvine, CA 92697, USA; (N.E.); (D.C.D.)
- Correspondence: ; Tel.: +1-714-456-8590
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3
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Bons J, Macron C, Aude-Garcia C, Vaca-Jacome SA, Rompais M, Cianférani S, Carapito C, Rabilloud T. A Combined N-terminomics and Shotgun Proteomics Approach to Investigate the Responses of Human Cells to Rapamycin and Zinc at the Mitochondrial Level. Mol Cell Proteomics 2019; 18:1085-1095. [PMID: 31154437 PMCID: PMC6553941 DOI: 10.1074/mcp.ra118.001269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/14/2019] [Indexed: 12/19/2022] Open
Abstract
All but thirteen mammalian mitochondrial proteins are encoded by the nuclear genome, translated in the cytosol and then imported into the mitochondria. For a significant proportion of the mitochondrial proteins, import is coupled with the cleavage of a presequence called the transit peptide, and the formation of a new N-terminus. Determination of the neo N-termini has been investigated by proteomic approaches in several systems, but generally in a static way to compile as many N-termini as possible. In the present study, we have investigated how the mitochondrial proteome and N-terminome react to chemical stimuli that alter mitochondrial metabolism, namely zinc ions and rapamycin. To this end, we have used a strategy that analyzes both internal and N-terminal peptides in a single run, the dN-TOP approach. We used these two very different stressors to sort out what could be a generic response to stress and what is specific to each of these stressors. Rapamycin and zinc induced different changes in the mitochondrial proteome. However, convergent changes to key mitochondrial enzymatic activities such as pyruvate dehydrogenase, succinate dehydrogenase and citrate synthase were observed for both treatments. Other convergent changes were seen in components of the N-terminal processing system and mitochondrial proteases. Investigations into the generation of neo-N-termini in mitochondria showed that the processing system is robust, as indicated by the lack of change in neo N-termini under the conditions tested. Detailed analysis of the data revealed that zinc caused a slight reduction in the efficiency of the N-terminal trimming system and that both treatments increased the degradation of mitochondrial proteins. In conclusion, the use of this combined strategy allowed a detailed analysis of the dynamics of the mitochondrial N-terminome in response to treatments which impact the mitochondria.
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Affiliation(s)
- Joanna Bons
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Charlotte Macron
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Catherine Aude-Garcia
- §Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS UMR5249, CEA, BIG-LCBM, 38000 Grenoble, France
| | - Sebastian Alvaro Vaca-Jacome
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Magali Rompais
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Sarah Cianférani
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Christine Carapito
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France;
| | - Thierry Rabilloud
- §Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS UMR5249, CEA, BIG-LCBM, 38000 Grenoble, France
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4
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Guo W, Dong W, Li M, Shen Y. Mitochondria P-glycoprotein confers paclitaxel resistance on ovarian cancer cells. Onco Targets Ther 2019; 12:3881-3891. [PMID: 31190887 PMCID: PMC6529025 DOI: 10.2147/ott.s193433] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 02/27/2019] [Indexed: 01/01/2023] Open
Abstract
Background: Subcellular expression of P-glycoprotein (P-gp) may play an essential role in multidrug resistance (MDR) in many cancers. However, the mitochondria expression and functional activity of P-gp in ovarian cancer are still unclear. In this study, we isolated mitochondria from A2780 cell line and its paclitaxel-resistant subline A2780T and investigated the expression and function of mitochondria P-gp. Methods: Immunocytochemistry was used to evaluate P-gp expression and subcellular localization in cancer cells. Immunofluorescence and laser confocal microscopy were used to detect the co-localization of P-gp and mitochondria both in ovarian cancer tissues and in cell lines. Western blotting (WB), transmission electron microscopy and JC-1 kit were used to evaluate the purity, integrity and activity of the isolated mitochondria. P-gp expression in the whole cell and the isolated mitochondria was evaluated by WB. Flow cytometry was used to evaluate the efflux function of mitochondria P-gp. Results: P-gp expression was detected at the membrane, cytoplasm and nuclei of the A2780T cells, but not in the A2780 cells. Co-localization of P-gp and mitochondria was observed in the A2780T cell line and ovarian cancer tissues, but not in A2780 cells. The purity, integration and activity of the isolated mitochondria are high. P-gp was highly expressed in the A2780T cells and the isolated mitochondria, but was not found in A2780 cells. Rho123 efflux rate was significantly increased in isolated A2780T mitochondria compared to those in A2780 (43.2% vs 9.6%), but it was partly reversed by cyclosporin A (CsA, a P-gp inhibitor). Conclusion: P-gp is highly expressed in mitochondria of taxol-resistant ovarian cancer cells and ovarian cancer tissues and mediates the drug efflux, which probably protect cancer cells from chemotherapy.
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Affiliation(s)
- Weina Guo
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Weihong Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Min Li
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yi Shen
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
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5
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An Y, Zhou L, Huang Z, Nice EC, Zhang H, Huang C. Molecular insights into cancer drug resistance from a proteomics perspective. Expert Rev Proteomics 2019; 16:413-429. [PMID: 30925852 DOI: 10.1080/14789450.2019.1601561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Resistance to chemotherapy and development of specific and effective molecular targeted therapies are major obstacles facing current cancer treatment. Comparative proteomic approaches have been employed for the discovery of putative biomarkers associated with cancer drug resistance and have yielded a number of candidate proteins, showing great promise for both novel drug target identification and personalized medicine for the treatment of drug-resistant cancer. Areas covered: Herein, we review the recent advances and challenges in proteomics studies on cancer drug resistance with an emphasis on biomarker discovery, as well as understanding the interconnectivity of proteins in disease-related signaling pathways. In addition, we highlight the critical role that post-translational modifications (PTMs) play in the mechanisms of cancer drug resistance. Expert opinion: Revealing changes in proteome profiles and the role of PTMs in drug-resistant cancer is key to deciphering the mechanisms of treatment resistance. With the development of sensitive and specific mass spectrometry (MS)-based proteomics and related technologies, it is now possible to investigate in depth potential biomarkers and the molecular mechanisms of cancer drug resistance, assisting the development of individualized therapeutic strategies for cancer patients.
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Affiliation(s)
- Yao An
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China.,b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
| | - Li Zhou
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China
| | - Zhao Huang
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China
| | - Edouard C Nice
- c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
| | - Canhua Huang
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China.,b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
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6
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Li Z, Liu H, Niu Z, Zhong W, Xue M, Wang J, Yang F, Zhou Y, Zhou Y, Xu T, Hou J. Temporal Proteomic Analysis of Pancreatic β-Cells in Response to Lipotoxicity and Glucolipotoxicity. Mol Cell Proteomics 2018; 17:2119-2131. [PMID: 30082485 DOI: 10.1074/mcp.ra118.000698] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 08/03/2018] [Indexed: 12/12/2022] Open
Abstract
Chronic hyperlipidemia causes the dysfunction of pancreatic β-cells, such as apoptosis and impaired insulin secretion, which are aggravated in the presence of hyperglycemia. The underlying mechanisms, such as endoplasmic reticulum (ER) stress, oxidative stress and metabolic disorders, have been reported before; however, the time sequence of these molecular events is not fully understood. Here, using isobaric labeling-based mass spectrometry, we investigated the dynamic proteomes of INS-1 cells exposed to high palmitate in the absence and presence of high glucose. Using bioinformatics analysis of differentially expressed proteins, including the time-course expression pattern, protein-protein interaction, gene set enrichment and KEGG pathway analysis, we analyzed the dynamic features of previously reported and newly identified lipotoxicity- and glucolipotoxicity-related molecular events in more detail. Our temporal data highlight cholesterol metabolism occurring at 4 h, earlier than fatty acid metabolism that started at 8 h and likely acting as an early toxic event highly associated with ER stress induced by palmitate. Interestingly, we found that the proliferation of INS-1 cells was significantly increased at 48 h by combined treatment of palmitate and glucose. Moreover, benefit from the time-course quantitative data, we identified and validated two new molecular targets: Setd8 for cell replication and Rhob for apoptosis, demonstrating that our temporal dataset serves as a valuable resource to identify potential candidates for mechanistic studies of lipotoxicity and glucolipotoxicity in pancreatic β-cells.
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Affiliation(s)
- Zonghong Li
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,§Jilin Province Key Laboratory on Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, 130024, China
| | - Hongyang Liu
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,‖Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhangjing Niu
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,‖Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen Zhong
- ***College of Life Science and Technology, HuaZhong University of Science and Technology, Wuhan 430074, China
| | - Miaomiao Xue
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,¶College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jifeng Wang
- ‡‡Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fuquan Yang
- ‡‡Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,¶College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Zhou
- §§ThermoFisher Scientific, Building 6, No. 27, Xin Jinqiao Rd, Pudong, Shanghai, 201206, China
| | - Yifa Zhou
- §Jilin Province Key Laboratory on Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, 130024, China;
| | - Tao Xu
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; .,¶College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junjie Hou
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
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7
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Zhong Y, Yang J, Xu WW, Wang Y, Zheng CC, Li B, He QY. KCTD12 promotes tumorigenesis by facilitating CDC25B/CDK1/Aurora A-dependent G2/M transition. Oncogene 2017; 36:6177-6189. [PMID: 28869606 PMCID: PMC5671937 DOI: 10.1038/onc.2017.287] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 06/19/2017] [Accepted: 07/14/2017] [Indexed: 02/06/2023]
Abstract
Cell cycle dysregulation leads to uncontrolled cell proliferation and tumorigenesis. Understanding the molecular mechanisms underlying cell cycle progression can provide clues leading to the identification of key proteins involved in cancer development. In this study, we performed proteomics analysis to identify novel regulators of the cell cycle. We found that potassium channel tetramerization domain containing 12 (KCTD12) was significantly upregulated in M phase compared with S phase. We also found that KCTD12 overexpression not only facilitated the G2/M transition and induced cancer cell proliferation, but also promoted the growth of subcutaneous tumors and Ki-67 proliferation index in mice. Regarding the mechanism underlying these phenomena, cyclin-dependent kinase 1 (CDK1) was identified as an interacting partner of KCTD12 by immunoprecipitation and mass spectrometry analysis, which showed that KCTD12 activated CDK1 and Aurora kinase A (Aurora A) and that the effects of KCTD12 on CDK1 phosphorylation and cell proliferation were abrogated by cell division cycle 25B (CDC25B) silencing. In addition, Aurora A phosphorylated KCTD12 at serine 243, thereby initiating a positive feedback loop necessary for KCTD12 to exert its cancer-promoting effects. Furthermore, we analyzed the expression levels of various genes and the correlations between the expression of these genes and survival using tumor tissue microarray and Gene Expression Omnibus (GEO) data sets. The data showed that KCTD12 expression was significantly upregulated in cervical and lung cancers. More importantly, high KCTD12 expression was associated with larger tumor sizes, higher pathological stages and poor patient survival. Collectively, our study demonstrate that KCTD12 binds to CDC25B and activates CDK1 and Aurora A to facilitate the G2/M transition and promote tumorigenesis and that Aurora A phosphorylates KCTD12 at serine 243 to trigger a positive feedback loop, thereby potentiating the effects of KCTD12. Thus, the KCTD12-CDC25B-CDK1-Aurora A axis has important implications for cancer diagnoses and prognoses.
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Affiliation(s)
- Y Zhong
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China.,Department of Pathology, Medical College, Jinan University, Guangzhou, China
| | - J Yang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - W W Xu
- Institute of Biomedicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, China
| | - Y Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - C-C Zheng
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - B Li
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Q-Y He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
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8
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Gbahou F, Cecon E, Viault G, Gerbier R, Jean-Alphonse F, Karamitri A, Guillaumet G, Delagrange P, Friedlander RM, Vilardaga JP, Suzenet F, Jockers R. Design and validation of the first cell-impermeant melatonin receptor agonist. Br J Pharmacol 2017; 174:2409-2421. [PMID: 28493341 DOI: 10.1111/bph.13856] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/27/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND AND PURPOSE The paradigm that GPCRs are able to prolong or initiate cellular signalling through intracellular receptors recently emerged. Melatonin binds to G protein-coupled MT1 and MT2 receptors. In contrast to most other hormones targeting GPCRs, melatonin and its synthetic analogues are amphiphilic molecules easily penetrating into cells, but the existence of intracellular receptors is still unclear mainly due to a lack of appropriate tools. EXPERIMENTAL APPROACH We therefore designed and synthesized a series of hydrophilic melatonin receptor ligands coupled to the Cy3 cyanin fluorophore to reliably monitor its inability to penetrate cells. Two compounds, one lipophilic and one hydrophilic, were then functionally characterized in terms of their affinity for human and murine melatonin receptors expressed in HEK293 cells and their signalling efficacy. KEY RESULTS Among the different ligands, ICOA-13 showed the desired properties as it was cell-impermeant and bound to human and mouse MT1 and MT2 receptors. ICOA-13 showed differential activities on melatonin receptors ranging from partial to full agonistic properties for the Gi /cAMP and ERK pathway and β-arrestin 2 recruitment. Notably, ICOA-13 enabled us to discriminate between Gi /cAMP signalling of the MT1 receptor initiated at the cell surface and neuronal mitochondria. CONCLUSIONS AND IMPLICATIONS We report here the first cell-impermeant melatonin receptor agonist, ICOA-13, which allows us to discriminate between signalling events initiated at the cell surface and intracellular compartments. Detection of mitochondrial MT1 receptors may have an important impact on the development of novel melatonin receptor ligands relevant for neurodegenerative diseases, such as Huntington disease.
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Affiliation(s)
- Florence Gbahou
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,Université Paris Descartes, Paris, France
| | - Erika Cecon
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,Université Paris Descartes, Paris, France
| | - Guillaume Viault
- Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans, UMR CNRS 7311, B.P. 6759, Orléans Cedex 2, France
| | - Romain Gerbier
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,Université Paris Descartes, Paris, France
| | - Frederic Jean-Alphonse
- Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Angeliki Karamitri
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,Université Paris Descartes, Paris, France
| | - Gérald Guillaumet
- Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans, UMR CNRS 7311, B.P. 6759, Orléans Cedex 2, France
| | - Philippe Delagrange
- Pôle d'Innovation Thérapeutique Neuropsychiatrie, Institut de Recherches Servier, Croissy, France
| | - Robert M Friedlander
- Neuroapoptosis Laboratory, Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jean-Pierre Vilardaga
- Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Franck Suzenet
- Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans, UMR CNRS 7311, B.P. 6759, Orléans Cedex 2, France
| | - Ralf Jockers
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,Université Paris Descartes, Paris, France
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9
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Smith AC, Robinson AJ. MitoMiner v3.1, an update on the mitochondrial proteomics database. Nucleic Acids Res 2015; 44:D1258-61. [PMID: 26432830 PMCID: PMC4702766 DOI: 10.1093/nar/gkv1001] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 09/22/2015] [Indexed: 01/05/2023] Open
Abstract
Mitochondrial proteins remain the subject of intense research interest due to their implication in an increasing number of different conditions including mitochondrial and metabolic disease, cancer, and neuromuscular degenerative and age-related disorders. However, the mitochondrial proteome has yet to be accurately and comprehensively defined, despite many studies. To support mitochondrial research, we developed MitoMiner (http://mitominer.mrc-mbu.cam.ac.uk), a freely accessible mitochondrial proteomics database. MitoMiner integrates different types of subcellular localisation evidence with protein information from public resources, and so provides a comprehensive central resource for data on mitochondrial protein localisation. Here we report important updates to the database including the addition of subcellular immunofluorescent staining results from the Human Protein Atlas, computational predictions of mitochondrial targeting sequences, and additional large-scale mass-spectrometry and GFP tagging data sets. This evidence is shared across the 12 species in MitoMiner (now including Schizosaccharomyces pombe) by homology mapping. MitoMiner provides multiple ways of querying the data including simple text searches, predefined queries and custom queries created using the interactive QueryBuilder. For remote programmatic access, API's are available for several programming languages. This combination of data and flexible querying makes MitoMiner a unique platform to investigate mitochondrial proteins, with application in mitochondrial research and prioritising candidate mitochondrial disease genes.
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Affiliation(s)
- Anthony C Smith
- MRC Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Alan J Robinson
- MRC Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
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10
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El Ouaamari A, Zhou JY, Liew CW, Shirakawa J, Dirice E, Gedeon N, Kahraman S, De Jesus DF, Bhatt S, Kim JS, Clauss TR, Camp DG, Smith RD, Qian WJ, Kulkarni RN. Compensatory Islet Response to Insulin Resistance Revealed by Quantitative Proteomics. J Proteome Res 2015; 14:3111-3122. [PMID: 26151086 DOI: 10.1021/acs.jproteome.5b00587] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Compensatory islet response is a distinct feature of the prediabetic insulin-resistant state in humans and rodents. To identify alterations in the islet proteome that characterize the adaptive response, we analyzed islets from 5 month old male control, high-fat diet fed (HFD), or obese ob/ob mice by LC-MS/MS and quantified ~1100 islet proteins (at least two peptides) with a false discovery rate < 1%. Significant alterations in abundance were observed for ~350 proteins among groups. The majority of alterations were common to both models, and the changes of a subset of ~40 proteins and 12 proteins were verified by targeted quantification using selected reaction monitoring and western blots, respectively. The insulin-resistant islets in both groups exhibited reduced expression of proteins controlling energy metabolism, oxidative phosphorylation, hormone processing, and secretory pathways. Conversely, an increased expression of molecules involved in protein synthesis and folding suggested effects in endoplasmic reticulum stress response, cell survival, and proliferation in both insulin-resistant models. In summary, we report a unique comparison of the islet proteome that is focused on the compensatory response in two insulin-resistant rodent models that are not overtly diabetic. These data provide a valuable resource of candidate proteins to the scientific community to undertake further studies aimed at enhancing β-cell mass in patients with diabetes. The data are available via the MassIVE repository, under accession no. MSV000079093.
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Affiliation(s)
- Abdelfattah El Ouaamari
- Islet Cell & Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215
| | - Jian-Ying Zhou
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Chong Wee Liew
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Jun Shirakawa
- Islet Cell & Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215
| | - Ercument Dirice
- Islet Cell & Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215
| | - Nicholas Gedeon
- Islet Cell & Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215
| | - Sevim Kahraman
- Islet Cell & Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215
| | - Dario F De Jesus
- Islet Cell & Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215
| | - Shweta Bhatt
- Islet Cell & Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215
| | - Jong-Seo Kim
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Therese Rw Clauss
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - David G Camp
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Rohit N Kulkarni
- Islet Cell & Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215
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11
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Chen X, Wei S, Ji Y, Guo X, Yang F. Quantitative proteomics using SILAC: Principles, applications, and developments. Proteomics 2015; 15:3175-92. [DOI: 10.1002/pmic.201500108] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/24/2015] [Accepted: 06/08/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Shasha Wei
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Yanlong Ji
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
| | - Xiaojing Guo
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
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12
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Du Y, Cai T, Li T, Xue P, Zhou B, He X, Wei P, Liu P, Yang F, Wei T. Lysine malonylation is elevated in type 2 diabetic mouse models and enriched in metabolic associated proteins. Mol Cell Proteomics 2014; 14:227-36. [PMID: 25418362 DOI: 10.1074/mcp.m114.041947] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Protein lysine malonylation, a newly identified protein post-translational modification (PTM), has been proved to be evolutionarily conserved and is present in both eukaryotic and prokaryotic cells. However, its potential roles associated with human diseases remain largely unknown. In the present study, we observed an elevated lysine malonylation in a screening of seven lysine acylations in liver tissues of db/db mice, which is a typical model of type 2 diabetes. We also detected an elevated lysine malonylation in ob/ob mice, which is another model of type 2 diabetes. We then performed affinity enrichment coupled with proteomic analysis on liver tissues of both wild-type (wt) and db/db mice and identified a total of 573 malonylated lysine sites from 268 proteins. There were more malonylated lysine sites and proteins in db/db than in wt mice. Five proteins with elevated malonylation were verified by immunoprecipitation coupled with Western blot analysis. Bioinformatic analysis of the proteomic results revealed the enrichment of malonylated proteins in metabolic pathways, especially those involved in glucose and fatty acid metabolism. In addition, the biological role of lysine malonylation was validated in an enzyme of the glycolysis pathway. Together, our findings support a potential role of protein lysine malonylation in type 2 diabetes with possible implications for its therapy in the future.
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Affiliation(s)
- Yipeng Du
- From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tanxi Cai
- §Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; ‖University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Li
- ¶Department of Biomedical Informatics, Peking University Health Science Center, Beijing 100191, China
| | - Peng Xue
- §Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Zhou
- From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; ‖University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolong He
- From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; ‖University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Wei
- From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; ‖University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pingsheng Liu
- From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fuquan Yang
- §Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
| | - Taotao Wei
- From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
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13
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Wang J, Yang J, Mao S, Chai X, Hu Y, Hou X, Tang Y, Bi C, Li X. MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria. PLoS One 2014; 9:e111187. [PMID: 25347823 PMCID: PMC4210245 DOI: 10.1371/journal.pone.0111187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 09/26/2014] [Indexed: 12/18/2022] Open
Abstract
Mitochondrion plays a central role in diverse biological processes in most eukaryotes, and its dysfunctions are critically involved in a large number of diseases and the aging process. A systematic identification of mitochondrial proteomes and characterization of functional linkages among mitochondrial proteins are fundamental in understanding the mechanisms underlying biological functions and human diseases associated with mitochondria. Here we present a database MitProNet which provides a comprehensive knowledgebase for mitochondrial proteome, interactome and human diseases. First an inventory of mammalian mitochondrial proteins was compiled by widely collecting proteomic datasets, and the proteins were classified by machine learning to achieve a high-confidence list of mitochondrial proteins. The current version of MitProNet covers 1124 high-confidence proteins, and the remainders were further classified as middle- or low-confidence. An organelle-specific network of functional linkages among mitochondrial proteins was then generated by integrating genomic features encoded by a wide range of datasets including genomic context, gene expression profiles, protein-protein interactions, functional similarity and metabolic pathways. The functional-linkage network should be a valuable resource for the study of biological functions of mitochondrial proteins and human mitochondrial diseases. Furthermore, we utilized the network to predict candidate genes for mitochondrial diseases using prioritization algorithms. All proteins, functional linkages and disease candidate genes in MitProNet were annotated according to the information collected from their original sources including GO, GEO, OMIM, KEGG, MIPS, HPRD and so on. MitProNet features a user-friendly graphic visualization interface to present functional analysis of linkage networks. As an up-to-date database and analysis platform, MitProNet should be particularly helpful in comprehensive studies of complicated biological mechanisms underlying mitochondrial functions and human mitochondrial diseases. MitProNet is freely accessible at http://bio.scu.edu.cn:8085/MitProNet.
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Affiliation(s)
- Jiabin Wang
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Jian Yang
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Song Mao
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Xiaoqiang Chai
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Yuling Hu
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Xugang Hou
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Yiheng Tang
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Cheng Bi
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Xiao Li
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
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14
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Chen X, Wei S, Ma Y, Lu J, Niu G, Xue Y, Chen X, Yang F. Quantitative proteomics analysis identifies mitochondria as therapeutic targets of multidrug-resistance in ovarian cancer. Am J Cancer Res 2014; 4:1164-75. [PMID: 25285166 PMCID: PMC4183995 DOI: 10.7150/thno.8502] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/14/2014] [Indexed: 12/31/2022] Open
Abstract
Doxorubicin is a widely used chemotherapeutic agent for the treatment of a variety of solid tumors. However, resistance to this anticancer drug is a major obstacle to the effective treatment of tumors. As mitochondria play important roles in cell life and death, we anticipate that mitochondria may be related to drug resistance. Here, stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomic strategy was applied to compare mitochondrial protein expression in doxorubicin sensitive OVCAR8 cells and its doxorubicin-resistant variant NCI_ADR/RES cells. A total of 2085 proteins were quantified, of which 122 proteins displayed significant changes in the NCI_ADR/RES cells. These proteins participated in a variety of cell processes including cell apoptosis, substance metabolism, transport, detoxification and drug metabolism. Then qRT-PCR and western blot were applied to validate the differentially expressed proteins quantified by SILAC. Further functional studies with RNAi demonstrated TOP1MT, a mitochondrial protein participated in DNA repair, was involved in doxorubicin resistance in NCI_ADR/RES cells. Besides the proteomic study, electron microscopy and fluorescence analysis also observed that mitochondrial morphology and localization were greatly altered in NCI_ADR/RES cells. Mitochondrial membrane potential was also decreased in NCI_ADR/RES cells. All these results indicate that mitochondrial function is impaired in doxorubicin-resistant cells and mitochondria play an important role in doxorubicin resistance. This research provides some new information about doxorubicin resistance, indicating that mitochondria could be therapeutic targets of doxorubicin resistance in ovarian cancer cells.
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