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Xie J, Zhang Z. Recent Advances and Therapeutic Implications of 2-Oxoglutarate-Dependent Dioxygenases in Ischemic Stroke. Mol Neurobiol 2024; 61:3949-3975. [PMID: 38041714 DOI: 10.1007/s12035-023-03790-1] [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: 08/04/2023] [Accepted: 11/08/2023] [Indexed: 12/03/2023]
Abstract
Ischemic stroke is a common disease with a high disability rate and mortality, which brings heavy pressure on families and medical insurance. Nowadays, the golden treatments for ischemic stroke in the acute phase mainly include endovascular therapy and intravenous thrombolysis. Some drugs are used to alleviate brain injury in patients with ischemic stroke, such as edaravone and 3-n-butylphthalide. However, no effective neuroprotective drug for ischemic stroke has been acknowledged. 2-Oxoglutarate-dependent dioxygenases (2OGDDs) are conserved and common dioxygenases whose activities depend on O2, Fe2+, and 2OG. Most 2OGDDs are expressed in the brain and are essential for the development and functions of the brain. Therefore, 2OGDDs likely play essential roles in ischemic brain injury. In this review, we briefly elucidate the functions of most 2OGDDs, particularly the effects of regulations of 2OGDDs on various cells in different phases after ischemic stroke. It would also provide promising potential therapeutic targets and directions of drug development for protecting the brain against ischemic injury and improving outcomes of ischemic stroke.
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Affiliation(s)
- Jian Xie
- Department of Neurology, Affiliated Zhongda Hospital, Research Institution of Neuropsychiatry, School of Medicine, Southeast University, Nanjing, 210009, Jiangsu, China
| | - Zhijun Zhang
- Department of Neurology, Affiliated Zhongda Hospital, Research Institution of Neuropsychiatry, School of Medicine, Southeast University, Nanjing, 210009, Jiangsu, China.
- Shenzhen Key Laboratory of Precision Diagnosis and Treatment of Depression, Department of Mental Health and Public Health, Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China.
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2
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Luo Q, Zhu H, Wang C, Li Y, Zou X, Hu Z. A U-Box Type E3 Ubiquitin Ligase Prp19-Like Protein Negatively Regulates Lipid Accumulation and Cell Size in Chlamydomonas reinhardtii. Front Microbiol 2022; 13:860024. [PMID: 35464935 PMCID: PMC9019728 DOI: 10.3389/fmicb.2022.860024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Microalgae lipid triacylglycerol is considered as a promising feedstock for national production of biofuels. A hotspot issue in the biodiesel study is to increase TAG content and productivity of microalgae. Precursor RNA processing protein (Prp19), which is the core component of eukaryotic RNA splice NTC (nineteen associated complex), plays important roles in the mRNA maturation process in eukaryotic cells, has a variety of functions in cell development, and is even directly involved in the biosynthesis of oil bodies in mouse. Nevertheless, its function in Chlamydomonas reinhardtii remains unknown. Here, transcriptional level of CrPrp19 under nutrition deprivation was analyzed, and both its RNA interference and overexpressed transformants were constructed. The expression level of CrPrp19 was suppressed by nitrogen or sulfur deficiency. Cell densities of CrPrp19 RNAi lines decreased, and their neutral lipid contents increased 1.33 and 1.34 times over those of controls. The cells of CrPrp19 RNAi lines were larger and more resistant to sodium acetate than control. Considerably none of the alterations in growth or neutral lipid contents was found in the CrPrp19 overexpression transformants than wild type. Fatty acids were also significantly increased in CrPrp19 RNAi transformants. Subcellular localization and yeast two-hybrid analysis showed that CrPrp19 was a nuclear protein, which might be involved in cell cycle regulation. In conclusion, CrPrp19 protein was necessary for negatively regulating lipid enrichment and cell size, but not stimulatory for lipid storage.
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Affiliation(s)
- Qiulan Luo
- School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou, China
| | - Hui Zhu
- School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou, China
| | - Chaogang Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, China
| | - Yajun Li
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-Resources, Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xianghui Zou
- School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou, China
| | - Zhangli Hu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, China
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3
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Yu XN, Zhang GC, Liu HN, Zhu JM, Liu TT, Song GQ, Dong L, Yin J, Shen XZ. Pre-mRNA processing factor 19 functions in DNA damage repair and radioresistance by modulating cyclin D1 in hepatocellular carcinoma. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:390-403. [PMID: 35036052 PMCID: PMC8728313 DOI: 10.1016/j.omtn.2021.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 12/07/2021] [Indexed: 01/10/2023]
Abstract
Pre-mRNA processing factor 19 (PRP19) is elevated in hepatocellular carcinoma (HCC); however, little is known about its function in DNA damage repair in HCC. In this study, analysis of The Cancer Genome Atlas data and our tumor models after ionizing radiation (IR) treatment indicated that increased expression of PRP19 was positively correlated with DNA damage repair. Gain of PRP19 expression induced by plasmids resulted in decreases in apoptosis and double-strand breaks (DSBs), and an increase in cell survival after IR. Loss of PRP19 expression induced by small interfering RNAs resulted in the accumulation of apoptosis and DSBs, and a decrease in cell survival. Mechanistically, the effect of PRP19 on DNA damage repair was mediated by the modulation of cyclin D1 expression in HCC. PRP19 controlled the translation of cyclin D1 by modulating eukaryotic initiation factor 4E. PRP19 affected the DNA damage repair ability of cyclin D1 by interacting with the WD40 domain. The combination of PRP19 and cyclin D1 was more valuable than each single marker for predicting the prognosis of patients. Taken together, the present results demonstrate that PRP19 promotes DNA damage repair by modulating cyclin D1 expression and function, thereby contributing to the radioresistance in HCC.
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Affiliation(s)
- Xiang-Nan Yu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China.,Shanghai Institute of Liver disease, Shanghai 200032, China
| | - Guang-Cong Zhang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China.,Shanghai Institute of Liver disease, Shanghai 200032, China
| | - Hai-Ning Liu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China.,Shanghai Institute of Liver disease, Shanghai 200032, China
| | - Jin-Min Zhu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China.,Shanghai Institute of Liver disease, Shanghai 200032, China
| | - Tao-Tao Liu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China.,Shanghai Institute of Liver disease, Shanghai 200032, China
| | - Guang-Qi Song
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China.,Shanghai Institute of Liver disease, Shanghai 200032, China
| | - Ling Dong
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China.,Shanghai Institute of Liver disease, Shanghai 200032, China
| | - Jie Yin
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China.,Shanghai Institute of Liver disease, Shanghai 200032, China
| | - Xi-Zhong Shen
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China.,Shanghai Institute of Liver disease, Shanghai 200032, China.,Key Laboratory of Medical Molecular Virology, Shanghai Medical College of Fudan University, Shanghai 200032, China
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4
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Egners A, Rezaei M, Kuzmanov A, Poitz DM, Streichert D, Müller-Reichert T, Wielockx B, Breier G. PHD3 Acts as Tumor Suppressor in Mouse Osteosarcoma and Influences Tumor Vascularization via PDGF-C Signaling. Cancers (Basel) 2018; 10:cancers10120496. [PMID: 30563292 PMCID: PMC6316346 DOI: 10.3390/cancers10120496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 02/06/2023] Open
Abstract
Cancer cell proliferation and insufficient blood supply can lead to the development of hypoxic areas in the tumor tissue. The adaptation to the hypoxic environment is mediated by a transcriptional complex called hypoxia-inducible factor (HIF). HIF protein levels are tightly controlled by oxygen-dependent prolyl hydroxylase domain proteins (PHDs). However, the precise roles of these enzymes in tumor progression and their downstream signaling pathways are not fully characterized. Here, we study PHD3 function in murine experimental osteosarcoma. Unexpectedly, PHD3 silencing in LM8 cells affects neither HIF-1α protein levels, nor the expression of various HIF-1 target genes. Subcutaneous injection of PHD3-silenced tumor cells accelerated tumor progression and was accompanied by dramatic phenotypic changes in the tumor vasculature. Blood vessels in advanced PHD3-silenced tumors were enlarged whereas their density was greatly reduced. Examination of the molecular pathways underlying these alterations revealed that platelet-derived growth factor (PDGF)-C signaling is activated in the vasculature of PHD3-deficient tumors. Silencing of PDGF-C depleted tumor growth, increased vessel density and reduced vessel size. Our data show that PHD3 controls tumor growth and vessel architecture in LM8 osteosarcoma by regulating the PDGF-C pathway, and support the hypothesis that different members of the PHD family exert unique functions in tumors.
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Affiliation(s)
- Antje Egners
- Department of General, Visceral and Transplantation Surgery, RWTH University Hospital, 52074 Aachen, Germany.
- Department of Pathology, TU Dresden, 01307 Dresden, Germany.
| | - Maryam Rezaei
- Department of Biochemistry, University of Münster, 48149 Münster, Germany.
| | - Aleksandar Kuzmanov
- Department of Dermatology, University Hospital Zurich, CH-8952 Schlieren, Switzerland.
| | - David M Poitz
- Institute for Clinical Chemistry and Laboratory Medicine, TU Dresden, 01307 Dresden, Germany.
| | - Doreen Streichert
- Core Facility Cellular Imaging, Experimental Center, Faculty of Medicine, TU Dresden, 01307 Dresden, Germany.
| | - Thomas Müller-Reichert
- Core Facility Cellular Imaging, Experimental Center, Faculty of Medicine, TU Dresden, 01307 Dresden, Germany.
| | - Ben Wielockx
- Institute for Clinical Chemistry and Laboratory Medicine, TU Dresden, 01307 Dresden, Germany.
| | - Georg Breier
- Division of Medical Biology, Department of Psychiatry and Psychotherapy, TU Dresden, 01307 Dresden, Germany.
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Zhang Y, Li Y, Liang X, Zhu Z, Sun H, He H, Min J, Liao S, Liu Y. Crystal structure of the WD40 domain of human PRPF19. Biochem Biophys Res Commun 2017; 493:1250-1253. [PMID: 28962858 DOI: 10.1016/j.bbrc.2017.09.145] [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: 09/21/2017] [Accepted: 09/26/2017] [Indexed: 12/31/2022]
Abstract
Human Pre-mRNA Processing factor 19 (hPRPF19) is an important component in human spliceosome machinery. hPRPF19 contains a WD40 repeats domain at its C-terminus, which is also conserved in yeast. Here we determined the crystal structure of the C-terminal WD40 repeat domain of hPRPF19 by X-ray crystallography. Our structural analysis revealed some significantly different structure features between the human and yeast Prp19 WD40 repeat domain. However, there are also conserved clusters of residues at the bottom surface of the fourth and the fifth WD40 repeats, which provides the important implication for the conserved Prp19 proteins in both human and yeast.
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Affiliation(s)
- Yuzhe Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada; Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali 671000, PR China
| | - Yue Li
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, PR China
| | - Xiao Liang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Zhongliang Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, PR China
| | - Hongbin Sun
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Academy of Sciences of China, Hefei 230031, PR China
| | - Hao He
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Shanhui Liao
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, PR China.
| | - Yanli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
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Catalytic-independent inhibition of cIAP1-mediated RIP1 ubiquitination by EGLN3. Cell Signal 2015; 28:72-80. [PMID: 26612615 DOI: 10.1016/j.cellsig.2015.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 11/11/2015] [Accepted: 11/19/2015] [Indexed: 12/30/2022]
Abstract
EGLN3 belongs to the EGLN family of prolyl hydroxylases that are able to catalyze the hydroxylation of proteins such as the α subunits of hypoxia-inducible factor. We and others have shown that EGLN3 negatively regulates the canonical NFκB pathway. Mechanistically, we demonstrated that EGLN3 inhibits ubiquitination of IKKγ (the regulatory subunit of IκB kinase complex) which is vitally important for NFκB activation. Polyubiquitination of the RIP1 (receptor-interacting protein 1) kinase is important for NFκB activation triggered by tumor necrosis factor α. It remains to be determined whether EGLN3 is able to modulate RIP1 ubiquitination catalyzed by cIAP1 (cellular inhibitor of apoptosis protein 1). This study shows that EGLN3 interacts with cIAP1 and suppresses cIAP1-mediated RIP1 ubiquitination via the C-terminal region. The hydroxylase activity is not required for the ability of EGLN3 to restrain RIP1 ubiquitination. Furthermore, EGLN3 is a novel binding protein of RIP1. The C-terminal region of EGLN3 is responsible for its interaction with RIP1. EGLN3 hydroxylase activity is not essential for the EGLN3-RIP1 interaction. EGLN3 interferes with the association between RIP1 and cIAP1, and attenuates RIP1-induced NFκB activation. This study provides novel insight into the mechanism underlying EGLN3 inhibition of NFκB signaling and sheds light on the regulation of RIP1 ubiquitination.
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7
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Kikuchi D, Minamishima YA, Nakayama K. Prolyl-hydroxylase PHD3 interacts with pyruvate dehydrogenase (PDH)-E1β and regulates the cellular PDH activity. Biochem Biophys Res Commun 2014; 451:288-94. [PMID: 25088999 DOI: 10.1016/j.bbrc.2014.07.114] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 07/24/2014] [Indexed: 01/25/2023]
Abstract
Cells are frequently exposed to hypoxia in physiological and pathophysiological conditions in organisms. Control of energy metabolism is one of the critical functions of the hypoxic response. Hypoxia-Inducible Factor (HIF) is a central transcription factor that regulates the hypoxic response. HIF prolyl-hydroxylase PHDs are the enzymes that hydroxylate the α subunit of HIF and negatively regulate its expression. To further understand the physiological role of PHD3, proteomics were used to identify PHD3-interacting proteins, and pyruvate dehydrogenase (PDH)-E1β was identified as such a protein. PDH catalyzes the conversion of pyruvate to acetyl-coA, thus playing a key role in cellular energy metabolism. PDH activity was significantly decreased in PHD3-depleted MCF7 breast cancer cells and PHD3(-/-) MEFs. PHD3 depletion did not affect the expression of the PDH-E1α, E1β, and E2 subunits, or the phosphorylation status of E1α, but destabilized the PDH complex (PDC), resulting in less functional PDC. Finally, PHD3(-/-) cells were resistant to cell death in prolonged hypoxia with decreased production of ROS. Taken together, the study reveals that PHD3 regulates PDH activity in cells by physically interacting with PDC.
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Affiliation(s)
- Daisuke Kikuchi
- Oxygen Biology Laboratory, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yoji Andrew Minamishima
- Department of Biochemistry, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Japan; Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Suematsu Gas Biology Project, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Koh Nakayama
- Oxygen Biology Laboratory, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan.
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Lu S, Wang R, Cai C, Liang J, Xu L, Miao S, Wang L, Song W. Small kinetochore associated protein (SKAP) promotes UV-induced cell apoptosis through negatively regulating pre-mRNA processing factor 19 (Prp19). PLoS One 2014; 9:e92712. [PMID: 24718257 PMCID: PMC3981699 DOI: 10.1371/journal.pone.0092712] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 02/25/2014] [Indexed: 01/14/2023] Open
Abstract
Apoptosis is a regulated cellular suicide program that is critical for the development and maintenance of healthy tissues. Previous studies have shown that small kinetochore associated protein (SKAP) cooperates with kinetochore and mitotic spindle proteins to regulate mitosis. However, the role of SKAP in apoptosis has not been investigated. We have identified a new interaction involving SKAP, and we propose a mechanism through which SKAP regulates cell apoptosis. Our experiments demonstrate that both overexpression and knockdown of SKAP sensitize cells to UV-induced apoptosis. Further study has revealed that SKAP interacts with Pre-mRNA processing Factor 19 (Prp19). We find that UV-induced apoptosis can be inhibited by ectopic expression of Prp19, whereas silencing Prp19 has the opposite effect. Additionally, SKAP negatively regulates the protein levels of Prp19, whereas Prp19 does not alter SKAP expression. Finally, rescue experiments demonstrate that the pro-apoptotic role of SKAP is executed through Prp19. Taken together, these findings suggest that SKAP promotes UV-induced cell apoptosis by negatively regulating the anti-apoptotic protein Prp19.
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Affiliation(s)
- Shan Lu
- State Key Laboratory of Medical Molecular Biology, Dept. of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Renxian Wang
- State Key Laboratory of Medical Molecular Biology, Dept. of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Congli Cai
- State Key Laboratory of Medical Molecular Biology, Dept. of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Junbo Liang
- State Key Laboratory of Medical Molecular Biology, Dept. of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Longchang Xu
- State Key Laboratory of Medical Molecular Biology, Dept. of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Shiying Miao
- State Key Laboratory of Medical Molecular Biology, Dept. of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Linfang Wang
- State Key Laboratory of Medical Molecular Biology, Dept. of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Wei Song
- State Key Laboratory of Medical Molecular Biology, Dept. of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- * E-mail:
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9
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Yin J, Zhang YA, Liu TT, Zhu JM, Shen XZ. DNA damage induces down-regulation of Prp19 via impairing Prp19 stability in hepatocellular carcinoma cells. PLoS One 2014; 9:e89976. [PMID: 24587161 PMCID: PMC3938560 DOI: 10.1371/journal.pone.0089976] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/24/2014] [Indexed: 11/18/2022] Open
Abstract
Pre-mRNA processing factor 19 (Prp19) activates pre-mRNA spliceosome and also mediates DNA damage response. Prp19 overexpression in cells with functional p53 leads to decreased apoptosis and increases cell survival after DNA damage. Here we showed that in hepatocellular carcinoma (HCC) cells with inactive p53 or functional p53, Prp19 was down-regulated due to the impaired stability under chemotherapeutic drug treatment. Silencing Prp19 expression enhanced apoptosis of HCC cells with or without chemotherapeutic drug treatment. Furthermore high level of Prp19 may inhibit chemotherapeutic drugs induced apoptosis in hepatocellular carcinoma cells through modulating myeloid leukemia cell differentiation 1 expression. These results indicated that targeting Prp19 may potentiate pro-apoptotic effect of chemotherapeutic agents on HCC.
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Affiliation(s)
- Jie Yin
- Department of Gastroenterology, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Yi-An Zhang
- Department of Gastroenterology, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Tao-Tao Liu
- Department of Gastroenterology, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Ji-Min Zhu
- Department of Gastroenterology, Zhongshan Hospital of Fudan University, Shanghai, China
- * E-mail: (XZS); (JMZ)
| | - Xi-Zhong Shen
- Department of Gastroenterology, Zhongshan Hospital of Fudan University, Shanghai, China
- * E-mail: (XZS); (JMZ)
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Cremaschi P, Rovida S, Sacchi L, Lisa A, Calvi F, Montecucco A, Biamonti G, Bione S, Sacchi G. CorrelaGenes: a new tool for the interpretation of the human transcriptome. BMC Bioinformatics 2014; 15 Suppl 1:S6. [PMID: 24564370 PMCID: PMC4016313 DOI: 10.1186/1471-2105-15-s1-s6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background The amount of gene expression data available in public repositories has grown exponentially in the last years, now requiring new data mining tools to transform them in information easily accessible to biologists. Results By exploiting expression data publicly available in the Gene Expression Omnibus (GEO) database, we developed a new bioinformatics tool aimed at the identification of genes whose expression appeared simultaneously altered in different experimental conditions, thus suggesting co-regulation or coordinated action in the same biological process. To accomplish this task, we used the 978 human GEO Curated DataSets and we manually performed the selection of 2,109 pair-wise comparisons based on their biological rationale. The lists of differentially expressed genes, obtained from the selected comparisons, were stored in a PostgreSQL database and used as data source for the CorrelaGenes tool. Our application uses a customized Association Rule Mining (ARM) algorithm to identify sets of genes showing expression profiles correlated with a gene of interest. The significance of the correlation is measured coupling the Lift, a well-known standard ARM index, and the χ2 p value. The manually curated selection of the comparisons and the developed algorithm constitute a new approach in the field of gene expression profiling studies. Simulation performed on 100 randomly selected target genes allowed us to evaluate the efficiency of the procedure and to obtain preliminary data demonstrating the consistency of the results. Conclusions The preliminary results of the simulation showed how CorrelaGenes could contribute to the characterization of molecular pathways and biological processes integrating data obtained from other applications and available in public repositories.
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11
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Place TL, Nauseef JT, Peterson MK, Henry MD, Mezhir JJ, Domann FE. Prolyl-4-hydroxylase 3 (PHD3) expression is downregulated during epithelial-to-mesenchymal transition. PLoS One 2013; 8:e83021. [PMID: 24367580 PMCID: PMC3867438 DOI: 10.1371/journal.pone.0083021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/06/2013] [Indexed: 01/28/2023] Open
Abstract
Prolyl-4-hydroxylation by the intracellular prolyl-4-hydroxylase enzymes (PHD1-3) serves as a master regulator of environmental oxygen sensing. The activity of these enzymes is tightly tied to tumorigenesis, as they regulate cell metabolism and angiogenesis through their control of hypoxia-inducible factor (HIF) stability. PHD3 specifically, is gaining attention for its broad function and rapidly accumulating array of non-HIF target proteins. Data from several recent studies suggest a role for PHD3 in the regulation of cell morphology and cell migration. In this study, we aimed to investigate this role by closely examining the relationship between PHD3 expression and epithelial-to-mesenchymal transition (EMT); a transcriptional program that plays a major role in controlling cell morphology and migratory capacity. Using human pancreatic ductal adenocarcinoma (PDA) cell lines and Madin-Darby Canine Kidney (MDCK) cells, we examined the correlation between several markers of EMT and PHD3 expression. We demonstrated that loss of PHD3 expression in PDA cell lines is highly correlated with a mesenchymal-like morphology and an increase in cell migratory capacity. We also found that induction of EMT in MDCK cells resulted in the specific downregulation of PHD3, whereas the expression of the other HIF-PHD enzymes was not affected. The results of this study clearly support a model by which the basal expression and hypoxic induction of PHD3 is suppressed by the EMT transcriptional program. This may be a novel mechanism by which migratory or metastasizing cells alter signaling through specific pathways that are sensitive to regulation by O2. The identification of downstream pathways that are affected by the suppression of PHD3 expression during EMT may provide important insight into the crosstalk between O2 and the migratory and metastatic potential of tumor cells.
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Affiliation(s)
- Trenton L. Place
- Molecular and Cellular Biology Program, The University of Iowa, Iowa City, Iowa, United States of America
- Department of Radiation Oncology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Jones T. Nauseef
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, Iowa, United States of America
| | - Maina K. Peterson
- Department of Anatomy and Cell Biology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Michael D. Henry
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, Iowa, United States of America
| | - James J. Mezhir
- Department of Surgery, The University of Iowa, Iowa City, Iowa, United States of America
| | - Frederick E. Domann
- Molecular and Cellular Biology Program, The University of Iowa, Iowa City, Iowa, United States of America
- Department of Radiation Oncology, The University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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12
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Place TL, Domann FE. Prolyl-hydroxylase 3: Evolving Roles for an Ancient Signaling Protein. HYPOXIA 2013; 2013:13-17. [PMID: 24672806 PMCID: PMC3963164 DOI: 10.2147/hp.s50091] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The ability of cells to sense oxygen is a highly evolved process that facilitates adaptations to the local oxygen environment and is critical to energy homeostasis. In vertebrates, this process is largely controlled by three intracellular prolyl-4-hydroxylases (PHD) 1–3. These related enzymes share the ability to hydroxylate the hypoxia-inducible transcription factor (HIF), and therefore control the transcription of genes involved in metabolism and vascular recruitment. However, it is becoming increasingly apparent that PHD controls much more than HIF signaling, with PHD3 emerging as an exceptionally unique and functionally diverse PHD isoform. In fact, PHD3-mediated hydroxylation has recently been purported to function in such diverse roles as sympathetic neuronal and muscle development, sepsis, glycolytic metabolism, and cell fate. PHD3 expression is also highly distinct from that of the other PHD enzymes, and varies considerably between different cell types and oxygen concentrations. This review will examine the evolution of oxygen sensing by the HIF family of PHD enzymes, with a specific focus on the complex nature of PHD3 expression and function in mammalian cells.
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Affiliation(s)
- Trenton L Place
- Molecular and Cellular Biology Program, The University of Iowa, Iowa City, Iowa, USA
| | - Frederick E Domann
- Molecular and Cellular Biology Program, The University of Iowa, Iowa City, Iowa, USA ; Department of Radiation Oncology, The University of Iowa, Iowa City, Iowa, USA
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Overexpression of the HIF hydroxylase PHD3 is a favorable prognosticator for gastric cancer. Med Oncol 2013; 29:2710-5. [PMID: 22290580 DOI: 10.1007/s12032-012-0171-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Accepted: 01/17/2012] [Indexed: 10/14/2022]
Abstract
Hypoxia-induced factors (HIFs) play a central role in the adaptive mechanisms of cancer cells to survive under conditions of hypoxia. HIFs are regulated by prolyl hydroxylases (PHDs) among which PHD3 is implicated as a tumor suppressor. We aimed to correlate PHD3 expression with clinicopathologic parameters and to evaluate its prognostic significance in gastric cancer. The 101 tissue samples were collected from 83 resected stages I–IV gastric cancer patients, which were grouped as non-cancerous mucosa (n=18) and primary carcinoma (n=83). PHD3 expression was evaluated by immunohistochemistry. We adopted Pearson chi-square test, univariate analysis, multivariate analysis and Kaplan–Meier method. The positive frequency of PHD3 in cancer cells was 42.2%, whereas non-cancerous mucosa had no detectable PHD3. The expression of PHD3 increased significantly from non-cancerous mucosa to cancer. A significant difference was observed between PHD3 expression and tumor differentiation (P=0.007). The overexpression of PHD3 was associated with well differentiation. In univariate analyses, American Joint Committee on Cancer (AJCC) stage (P<0.0001), pT classification (P<0.0001), pN classification (P<0.0001), differentiation (P=0.0121), peritoneal metastasis (P=0.0006) and gross features (P=0.0104) were significantly associated with survival except PHD3 (P=0.2228) (Table 3). In multivariate analysis, AJCC stage was prognostically independent [hazard ratio (HR), 3.078; 95% confidence interval (CI), 2.228–4.252; P<0.0001]. Overexpression of PHD3 is a favorable prognosticator for gastric cancer. AJCC stage is an independent prognostic factor of gastric cancer.
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Nakayama K. cAMP-response element-binding protein (CREB) and NF-κB transcription factors are activated during prolonged hypoxia and cooperatively regulate the induction of matrix metalloproteinase MMP1. J Biol Chem 2013; 288:22584-95. [PMID: 23775082 DOI: 10.1074/jbc.m112.421636] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Responses to low levels of oxygen (hypoxia) are essential to maintain homeostasis. During the hypoxic response, gene expression is altered by various transcription factors. The transcription factor, hypoxia-inducible factor (HIF), plays a central role in the hypoxic response. The α subunit of HIF, which is actively degraded during normoxia, becomes stabilized during hypoxia, which leads to HIF activation. A microarray analysis of HeLa cells showed that expression of matrix metalloproteinase 1 (MMP1) was markedly induced during prolonged hypoxia. CREB and NF-κB binding sites were identified in the MMP1 promoter region between 1945 and 1896 nucleotides upstream of the transcription start site. Assays with luciferase reporters demonstrated that HIF activity was induced during the early phase of hypoxia, whereas CREB and NF-κB were activated during the later (prolonged) phase. Depletion of CREB and/or NF-κB reduced MMP1 induction during prolonged hypoxia both at the mRNA and protein levels. A chromatin immunoprecipitation assay demonstrated binding of CREB and NF-κB to the MMP1 promoter. Finally, cell migration and invasion on a collagen matrix and pulmonary metastasis in nude mice were inhibited after depletion of CREB and NF-κB in MDA-MB-231 cells. Taken together, these results suggest that the cooperative action of CREB and NF-κB plays an important role to induce MMP1 expression during prolonged hypoxia and regulates cell migration and invasion in cancer cells.
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Affiliation(s)
- Koh Nakayama
- Oxygen Biology Laboratory, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan.
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EGLN3 inhibition of NF-κB is mediated by prolyl hydroxylase-independent inhibition of IκB kinase γ ubiquitination. Mol Cell Biol 2013; 33:3050-61. [PMID: 23732909 DOI: 10.1128/mcb.00273-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
NF-κB transcription factors are crucial regulators of inflammation, immunity, stress responses, and cell differentiation. Many studies have demonstrated that ubiquitination of IκB kinase γ (IKKγ), a regulatory subunit of IKK, is instrumental in the activation of IKK and NF-κB. We and others previously identified EGLN3, a member of a family of prolyl hydroxylases, as a negative regulator of the NF-κB pathway. Here we report that EGLN3, but not EGLN1 or -2, interacts with and inhibits K63-linked ubiquitination of IKKγ. The effect appears to be related to inhibition of IKKγ ubiquitination mediated by cIAP1 rather than to stimulation of IKKγ deubiquitination by the deubiquitinases A20 and CYLD (cylindromatosis). EGLN3 does not affect the protein levels of cIAP1 or its E2 ubiquitin-conjugating enzymes UbcH5 and Ubc13. EGLN3 hydroxylase activity is not responsible for its effect on IKKγ ubiquitination and NF-κB signaling. Instead, interaction with IKKγ is required for the ability of EGLN3 to inhibit IKKγ ubiquitination and IKK-NF-κB signaling. EGLN3 competes with cIAP1 for IKKγ binding, leading to inhibition of cIAP1-IKKγ interaction, IKKγ ubiquitination, and IKK-NF-κB signaling. This study provides novel insights into EGLN3 function and sheds new light on the regulation of IKKγ ubiquitination and NF-κB.
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Abstract
Oxygen-sensing prolyl hydroxylase domain enzymes (PHDs) target hypoxia-inducible factor (HIF)-α subunits for proteasomal degradation in normoxia through hydroxylation. Recently, novel mechanisms of PHD activation and function have been unveiled. Interestingly, PHD3 can unexpectedly amplify HIF signaling through hydroxylation of the glycolytic enzyme pyruvate kinase (PK) muscle isoform 2 (PKM2). Recent studies have also yielded insight into HIF-independent PHD functions, including the control of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor trafficking in synaptic transmission and the activation of transient receptor potential cation channel member A1 (TRPA1) ion channels by oxygen levels in sensory nerves. Finally, PHD activation has been shown to involve the iron chaperoning function of poly(rC) binding protein (PCBP)1 and the (R)-enantiomer of 2-hydroxyglutarate (2-HG). The intersection of these regulatory pathways and interactions highlight the complexity of PHD regulation and function.
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Yin J, Zhu JM, Shen XZ. New insights into pre-mRNA processing factor 19: A multi-faceted protein in humans. Biol Cell 2012; 104:695-705. [DOI: 10.1111/boc.201200011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Accepted: 09/06/2012] [Indexed: 11/27/2022]
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Dellago H, Khan A, Nussbacher M, Gstraunthaler A, Lämmermann I, Schosserer M, Mück C, Anrather D, Scheffold A, Ammerer G, Jansen-Dürr P, Rudolph KL, Voglauer-Grillari R, Grillari J. ATM-dependent phosphorylation of SNEVhPrp19/hPso4 is involved in extending cellular life span and suppression of apoptosis. Aging (Albany NY) 2012; 4:290-304. [PMID: 22529335 PMCID: PMC3371764 DOI: 10.18632/aging.100452] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Defective DNA repair is widely acknowledged to negatively impact on healthy aging, since mutations in DNA repair factors lead to accelerated and premature aging. However, the opposite, namely if improved DNA repair will also increase the life or health span is less clear, and only few studies have tested if overexpression of DNA repair factors modulates life and health span in cells or organisms. Recently, we identified and characterized SNEVhPrp19/hPso4, a protein that plays a role in DNA repair and pre-mRNA splicing, and observed a doubling of the replicative life span upon ectopic overexpression, accompanied by lower basal DNA damage and apoptosis levels as well as an increased resistance to oxidative stress. Here we find that SNEVhPrp19/hPso4 is phosphorylated at S149 in an ataxia telangiectasia mutated protein (ATM)-dependent manner in response to oxidative stress and DNA double strand break inducing agents. By overexpressing wild-type SNEVhPrp19/hPso4 and a phosphorylation-deficient point-mutant, we found that S149 phosphorylation is necessary for mediating the resistance to apoptosis upon oxidative stress and is partially necessary for elongating the cellular life span. Therefore, ATM dependent phosphorylation of SNEVhPrp19/hPso4 upon DNA damage or oxidative stress might represent a novel axis capable of modulating cellular life span.
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Affiliation(s)
- Hanna Dellago
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
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Prolyl hydroxylase PHD3 enhances the hypoxic survival and G1 to S transition of carcinoma cells. PLoS One 2011; 6:e27112. [PMID: 22087251 PMCID: PMC3210766 DOI: 10.1371/journal.pone.0027112] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 10/10/2011] [Indexed: 11/19/2022] Open
Abstract
Hypoxia restricts cell proliferation and cell cycle progression at the G1/S interface but at least a subpopulation of carcinoma cells can escape the restriction. In carcinoma hypoxia may in fact select for cells with enhanced hypoxic survival and increased aggressiveness. The cellular oxygen sensors HIF proline hydroxylases (PHDs) adapt the cellular functions to lowered environmental oxygen tension. PHD3 isoform has shown the strongest hypoxic upregulation among the family members. We detected a strong PHD3 mRNA expression in tumors of head and neck squamous cell carcinoma (HNSCC). The PHD3 expression associated with expression of hypoxic marker gene. Using siRNA in cell lines derived from HNSCC we show that specific inhibition of PHD3 expression in carcinoma cells caused reduced cell survival in hypoxia. The loss of PHD3, but not that of PHD2, led to marked cell number reduction. Although caspase-3 was activated at early hypoxia no induction of apoptosis was detected. However, hypoxic PHD3 inhibition caused a block in cell cycle progression. Cell population in G1 phase was increased and the population in S phase reduced demonstrating a block in G1 to S transition under PHD3 inhibition. In line with this, the level of hyperphosphorylated retinoblastoma protein Rb was reduced by PHD3 knock-down in hypoxia. PHD3 loss led to increase in cyclin-dependent kinase inhibitor p27 expression but not that of p21 or p16. The data demonstrated that increased PHD3 expression under hypoxia enhances cell cycle progression and survival of carcinoma cells.
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Su Y, Loos M, Giese N, Hines OJ, Diebold I, Görlach A, Metzen E, Pastorekova S, Friess H, Büchler P. PHD3 regulates differentiation, tumour growth and angiogenesis in pancreatic cancer. Br J Cancer 2010; 103:1571-9. [PMID: 20978507 PMCID: PMC2990580 DOI: 10.1038/sj.bjc.6605936] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Purpose: Tumour hypoxia activates hypoxia-inducible factor-1 (HIF-1) and indluences angiogenesis, cell survival and invasion. Prolyl hydroxylase-3 (PHD3) regulates degradation of HIF-1α. The effects of PHD3 in tumour growth are largely unknown. Experimental design: PHD3 expression was analysed in human pancreatic cancer tissues and cancer cell lines by real-time quantitative PCR and immunohistochemistry. PHD3 overexpression was established by stable transfection and downregulation by short interfering RNA technology. VEGF was quantified by enzyme-linked immunosorbent assay. Matrigel invasion assays were performed to examine tumour cell invasion. Apoptosis was measured by annexin-V staining and caspase-3 assays. The effect of PHD3 on tumour growth in vivo was evaluated in an established orthotopic murine model. Results: PHD3 was upregulated in well-differentiated human tumours and cell lines, and regulated hypoxic VEGF secretion. PHD3 overexpression mediated tumour cell growth and invasion by induction of apoptosis in a nerve growth factor-dependent manner by the activation of caspase-3 and phosphorylation of focal adhesion kinase HIF-1 independently. In vivo, PHD3 inhibited tumour growth by abrogation of tumour angiogenesis. Conclusion: Our results indicate essential functions of PHD3 in tumour growth, apoptosis and angiogenesis and through HIF-1-dependent and HIF-1-independent pathways.
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Affiliation(s)
- Y Su
- Department of General Surgery, University of Heidelberg, Im Neuenheimer Feld 110, Heidelberg 69120, Germany
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