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Proteomic Analysis of Decellularized Extracellular Matrix: Achieving a Competent Biomaterial for Osteogenesis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:6884370. [PMID: 36267842 PMCID: PMC9578822 DOI: 10.1155/2022/6884370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/29/2022] [Accepted: 09/09/2022] [Indexed: 11/25/2022]
Abstract
Decellularized ECMs have been used as biological scaffolds for tissue repair due to their tissue-specific biochemical and mechanical composition, poorly simulated by other materials. It is used as patches and powders, and it could be further processed via enzymatic digestion under acidic conditions using pepsin. However, part of the bioactivity is lost during the digestion process due to protein denaturation. Here, stepwise digestion was developed to prepare a competent biomaterial for osteogenesis from three different ECM sources. In addition, three different proteases were compared to evaluate the most effective digestion protocol for specific cellular processes. GAGs and peptide quantification showed that the stepwise method yielded a higher concentration of bioactive residues. Circular dichroism analysis also showed that the stepwise approach preserved the secondary structures better. The protein profiles of the digested ECMs were analyzed, and it was found to be highly diverse and tissue-specific. The digestion of ECM from pericardium produced peptides originated from 94 different proteins, followed by 48 proteins in ECM from tendon and 35 proteins in ECM from bone. In addition, digested products from pericardium ECM yielded increased proliferation and differentiation of bone marrow mesenchymal stem cells to mature osteoblasts.
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Jiang T, Wei F, Xie K. Clinical significance of pancreatic ductal metaplasia. J Pathol 2022; 257:125-139. [PMID: 35170758 DOI: 10.1002/path.5883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/06/2022] [Accepted: 02/14/2022] [Indexed: 11/08/2022]
Abstract
Pancreatic ductal metaplasia (PDM) is the stepwise replacement of differentiated somatic cells with ductal or ductal-like cells in the pancreas. PDM is usually triggered by cellular and environmental insults. PDM development may involve all cell lineages of the pancreas, and acinar cells with the highest plasticity are the major source of PDM. Pancreatic progenitor cells are also involved as cells of origin or transitional intermediates. PDM is heterogeneous at the histological, cellular, and molecular levels and only certain subsets of PDM develop further into pancreatic intraepithelial neoplasia (PanIN) and then pancreatic ductal adenocarcinoma (PDAC). The formation and evolution of PDM is regulated at the cellular and molecular levels through a complex network of signaling pathways. The key molecular mechanisms that drive PDM formation and its progression into PanIN/PDAC remain unclear, but represent key targets for reversing or inhibiting PDM. Alternatively, PDM could be a source of pancreas regeneration, including both exocrine and endocrine components. Cellular aging and apoptosis are obstacles to PDM-to-PanIN progression or pancreas regeneration. Functional identification of the cellular and molecular events driving senescence and apoptosis in PDM and its progression would help not only to restrict the development of PDM into PanIN/PDAC, but may also facilitate pancreatic regeneration. This review systematically assesses recent advances in the understanding of PDM physiology and pathology, with a focus on its implications for enhancing regeneration and prevention of cancer. © 2022 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Tingting Jiang
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, PR China
- Department of Pathology, The South China University of Technology School of Medicine, Guangzhou, PR China
| | - Fang Wei
- Institute of Digestive Diseases Research, The South China University of Technology School of Medicine, Guangzhou, PR China
| | - Keping Xie
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, PR China
- Department of Pathology, The South China University of Technology School of Medicine, Guangzhou, PR China
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Woods ML, Weiss A, Sokol AM, Graumann J, Boettger T, Richter AM, Schermuly RT, Dammann RH. Epigenetically silenced apoptosis-associated tyrosine kinase (AATK) facilitates a decreased expression of Cyclin D1 and WEE1, phosphorylates TP53 and reduces cell proliferation in a kinase-dependent manner. Cancer Gene Ther 2022; 29:1975-1987. [PMID: 35902728 PMCID: PMC9750878 DOI: 10.1038/s41417-022-00513-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 06/28/2022] [Accepted: 07/13/2022] [Indexed: 01/25/2023]
Abstract
Silencing of the Apoptosis associated Tyrosine Kinase gene (AATK) has been described in cancer. In our study, we specifically investigated the epigenetic inactivation of AATK in pancreatic adenocarcinoma, lower grade glioma, lung, breast, head, and neck cancer. The resulting loss of AATK correlates with impaired patient survival. Inhibition of DNA methyltransferases (DNMTs) reactivated AATK in glioblastoma and pancreatic cancer. In contrast, epigenetic targeting via the CRISPR/dCas9 system with either EZH2 or DNMT3A inhibited the expression of AATK. Via large-scale kinomic profiling and kinase assays, we demonstrate that AATK acts a Ser/Thr kinase that phosphorylates TP53 at Ser366. Furthermore, whole transcriptome analyses and mass spectrometry associate AATK expression with the GO term 'regulation of cell proliferation'. The kinase activity of AATK in comparison to the kinase-dead mutant mediates a decreased expression of the key cell cycle regulators Cyclin D1 and WEE1. Moreover, growth suppression through AATK relies on its kinase activity. In conclusion, the Ser/Thr kinase AATK represses growth and phosphorylates TP53. Furthermore, expression of AATK was correlated with a better patient survival for different cancer entities. This data suggests that AATK acts as an epigenetically inactivated tumor suppressor gene.
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Affiliation(s)
- Michelle L. Woods
- grid.8664.c0000 0001 2165 8627Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Astrid Weiss
- grid.8664.c0000 0001 2165 8627Department of Internal Medicine, Justus-Liebig-University Giessen, 35392 Giessen, Germany ,grid.452624.3German Center for Lung Research (DZL), Giessen, Germany
| | - Anna M. Sokol
- grid.418032.c0000 0004 0491 220XScientific Service Group Biomolecular Mass Spectrometry, Max-Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Johannes Graumann
- grid.418032.c0000 0004 0491 220XScientific Service Group Biomolecular Mass Spectrometry, Max-Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany ,grid.10253.350000 0004 1936 9756Present Address: Institute for Translational Proteomics, Department of Medicine, Philipps-University, 35037 Marburg, Germany
| | - Thomas Boettger
- grid.418032.c0000 0004 0491 220XMax-Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Antje M. Richter
- grid.8664.c0000 0001 2165 8627Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Ralph T. Schermuly
- grid.8664.c0000 0001 2165 8627Department of Internal Medicine, Justus-Liebig-University Giessen, 35392 Giessen, Germany ,grid.452624.3German Center for Lung Research (DZL), Giessen, Germany
| | - Reinhard H. Dammann
- grid.8664.c0000 0001 2165 8627Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany ,grid.440517.3German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center, 35392 Giessen, Germany
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Tandon N, Luxami V, Kant D, Tandon R, Paul K. Current progress, challenges and future prospects of indazoles as protein kinase inhibitors for the treatment of cancer. RSC Adv 2021; 11:25228-25257. [PMID: 35478899 PMCID: PMC9037120 DOI: 10.1039/d1ra03979b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/29/2021] [Indexed: 01/19/2023] Open
Abstract
The indazole core is an interesting pharmacophore due to its applications in medicinal chemistry. In the past few years, this moiety has been used for the synthesis of kinase inhibitors. Many researchers have demonstrated the use of indazole derivatives as specific kinase inhibitors, including tyrosine kinase and serine/threonine kinases. A number of anticancer drugs with an indazole core are commercially available, e.g. axitinib, linifanib, niraparib, and pazopanib. Indazole derivatives are applied for the targeted treatment of lung, breast, colon, and prostate cancers. In this review, we compile the current development of indazole derivatives as kinase inhibitors and their application as anticancer agents in the past five years.
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Affiliation(s)
- Nitin Tandon
- School of Chemical Engineering and Physical Sciences, Lovely Professional University Phagwara-144411 India
| | - Vijay Luxami
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology Patiala-147004 India
| | - Divya Kant
- School of Chemical Engineering and Physical Sciences, Lovely Professional University Phagwara-144411 India
| | - Runjhun Tandon
- School of Chemical Engineering and Physical Sciences, Lovely Professional University Phagwara-144411 India
| | - Kamaldeep Paul
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology Patiala-147004 India
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Ma J, Yan T, Bai Y, Ye M, Ma C, Ma X, Zhang L. TMEM100 negatively regulated by microRNA‑106b facilitates cellular apoptosis by suppressing survivin expression in NSCLC. Oncol Rep 2021; 46:185. [PMID: 34278505 DOI: 10.3892/or.2021.8136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/28/2021] [Indexed: 11/06/2022] Open
Abstract
Non‑small cell lung cancer (NSCLC) is a common malignant tumour. Nevertheless, the 5‑year survival rate of NSCLC patients remains poor. Thus, identifying critical factors involved in regulating the progression of NSCLC is important for providing potential treatment targets. In the present study, it was observed that transmembrane protein 100 (TMEM100) was significantly downregulated in NSCLC tissues compared with paired peritumoral tissues. Decreased TMEM100 expression was associated with poor clinical outcomes in NSCLC patients. Moreover, TMEM100 overexpression inhibited colony formation and facilitated apoptosis by suppressing survivin expression in NSCLC cells, whereas TMEM100 knockdown had the opposite effect. In addition, microRNA (miR)‑106b, a miR with controversial roles in different human cancers, was upregulated in NSCLC and directly downregulated TMEM100 expression. The roles of miR‑106b in cell survival were mitigated by the restoration of TMEM100. The aforementioned results indicated that TMEM100 induced cell apoptosis and inhibited cell survival by serving as a tumour suppressor and that miR‑106b‑mitigatedTMEM100 expression defined a potentially oncogenic pathway in NSCLC.
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Affiliation(s)
- Jun Ma
- Eye Institute, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai 200031, P.R. China
| | - Tingting Yan
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Yongrui Bai
- Department of Radiation Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Ming Ye
- Department of Radiation Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Chunhui Ma
- Department of Orthopedic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, P.R. China
| | - Xiumei Ma
- Department of Radiation Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Lei Zhang
- Department of Radiation Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
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Küster MM, Schneider MA, Richter AM, Richtmann S, Winter H, Kriegsmann M, Pullamsetti SS, Stiewe T, Savai R, Muley T, Dammann RH. Epigenetic Inactivation of the Tumor Suppressor IRX1 Occurs Frequently in Lung Adenocarcinoma and Its Silencing Is Associated with Impaired Prognosis. Cancers (Basel) 2020; 12:E3528. [PMID: 33256112 PMCID: PMC7760495 DOI: 10.3390/cancers12123528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022] Open
Abstract
Iroquois homeobox (IRX) encodes members of homeodomain containing genes which are involved in development and differentiation. Since it has been reported that the IRX1 gene is localized in a lung cancer susceptibility locus, the epigenetic regulation and function of IRX1 was investigated in lung carcinogenesis. We observed frequent hypermethylation of the IRX1 promoter in non-small cell lung cancer (NSCLC) compared to small cell lung cancer (SCLC). Aberrant IRX1 methylation was significantly correlated with reduced IRX1 expression. In normal lung samples, the IRX1 promoter showed lower median DNA methylation levels (<10%) compared to primary adenocarcinoma (ADC, 22%) and squamous cell carcinoma (SQCC, 14%). A significant hypermethylation and downregulation of IRX1 was detected in ADC and SQCC compared to matching normal lung samples (p < 0.0001). Low IRX1 expression was significantly correlated with impaired prognosis of ADC patients (p = 0.001). Reduced survival probability was also associated with higher IRX1 promoter methylation (p = 0.02). Inhibition of DNA methyltransferase (DNMT) activity reactivated IRX1 expression in human lung cancer cell lines. Induced DNMT3A and EZH2 expression was correlated with downregulation of IRX1. On the cellular level, IRX1 exhibits nuclear localization and expression of IRX1 induced fragmented nuclei in cancer cells. Localization of IRX1 and induction of aberrant nuclei were dependent on the presence of the homeobox of IRX1. By data mining, we showed that IRX1 is negatively correlated with oncogenic pathways and IRX1 expression induces the proapoptotic regulator BAX. In conclusion, we report that IRX1 expression is significantly associated with improved survival probability of ADC patients. IRX1 hypermethylation may serve as molecular biomarker for ADC diagnosis and prognosis. Our data suggest that IRX1 acts as an epigenetically regulated tumor suppressor in the pathogenesis of lung cancer.
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Affiliation(s)
- Miriam M. Küster
- Faculty of Biology, Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany; (M.M.K.); (A.M.R.)
| | - Marc A. Schneider
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany; (M.A.S.); (S.R.); (T.M.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
| | - Antje M. Richter
- Faculty of Biology, Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany; (M.M.K.); (A.M.R.)
| | - Sarah Richtmann
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany; (M.A.S.); (S.R.); (T.M.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
| | - Hauke Winter
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Surgery, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Mark Kriegsmann
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Pathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Soni S. Pullamsetti
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Thorsten Stiewe
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University, 35032 Marburg, Germany
| | - Rajkumar Savai
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany; (M.A.S.); (S.R.); (T.M.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
| | - Reinhard H. Dammann
- Faculty of Biology, Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany; (M.M.K.); (A.M.R.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
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Afrose SS, Junaid M, Akter Y, Tania M, Zheng M, Khan MA. Targeting kinases with thymoquinone: a molecular approach to cancer therapeutics. Drug Discov Today 2020; 25:2294-2306. [PMID: 32721537 DOI: 10.1016/j.drudis.2020.07.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/01/2020] [Accepted: 07/20/2020] [Indexed: 01/02/2023]
Abstract
Kinases are enzymes that are important for cellular functions, but their overexpression has strong connections with carcinogenesis, rendering them important targets for anticancer drugs. Thymoquinone (TQ) is a natural compound with proven anticancer activities, at least in preclinical studies. TQ can target several kinases, including phosphoinositide 3-kinase (PI3K), mitogen-activated protein kinase (MAPK), Janus kinase/signal transducers and activators of transcription (JAK/STAT), polo-like kinase 1 (PLK1), and tyrosine kinase in different cancer cells and animal models. Inhibiting the activity of kinases or suppressing their expression might be among the mechanisms of TQ anticancer activity. In this review, we discuss the role of TQ in kinase regulation in different cancer models.
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Affiliation(s)
| | - Md Junaid
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, Bangladesh Council of Scientific and Industrial Research, Chattogram, Bangladesh
| | - Yeasmin Akter
- Department of Biotechnology and Genetic Engineering, Noakhali Science & Technology University, Noakhali, Bangladesh
| | - Mousumi Tania
- Division of Molecular Cancer, Red Green Research Center, Dhaka, Bangladesh
| | - Meiling Zheng
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China
| | - Md Asaduzzaman Khan
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China.
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Ding LY, Hou YC, Kuo IY, Hsu TY, Tsai TC, Chang HW, Hsu WY, Tsao CC, Tian CC, Wang PS, Wang HC, Lee CT, Wang YC, Lin SH, Hughes MW, Chuang WJ, Lu PJ, Shan YS, Huang PH. Epigenetic silencing of AATK in acinar to ductal metaplasia in murine model of pancreatic cancer. Clin Epigenetics 2020; 12:87. [PMID: 32552862 PMCID: PMC7301993 DOI: 10.1186/s13148-020-00878-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/31/2020] [Indexed: 02/07/2023] Open
Abstract
Background Cancer subtype switching, which involves unclear cancer cell origin, cell fate decision, and transdifferentiation of cells within a confined tumor microenvironment, remains a major problem in pancreatic cancer (PDA). Results By analyzing PDA subtypes in The Cancer Genome Atlas, we identified that epigenetic silencing of apoptosis-associated tyrosine kinase (AATK) inversely was correlated with mRNA expression and was enriched in the quasi-mesenchymal cancer subtype. By comparing early mouse pancreatic lesions, the non-invasive regions showed AATK co-expression in cells with acinar-to-ductal metaplasia, nuclear VAV1 localization, and cell cycle suppression; but the invasive lesions conversely revealed diminished AATK expression in those with poorly differentiated histology, cytosolic VAV1 localization, and co-expression of p63 and HNF1α. Transiently activated AATK initiates acinar differentiation into a ductal cell fate to establish apical-basal polarization in acinar-to-ductal metaplasia. Silenced AATK and ectopically expressed p63 and HNF1α allow the proliferation of ductal PanINs in mice. Conclusion Epigenetic silencing of AATK regulates the cellular transdifferentiation, proliferation, and cell cycle progression in converting PDA-subtypes.
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Affiliation(s)
- Li-Yun Ding
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Chin Hou
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - I-Ying Kuo
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ting-Yi Hsu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tsung-Ching Tsai
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsiu-Wei Chang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Yu Hsu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Chieh Tsao
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chung-Chen Tian
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Shun Wang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hao-Chen Wang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chung-Ta Lee
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Ching Wang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sheng-Hsiang Lin
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Biostatistics Consulting Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Michael W Hughes
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,International Center for Wound Repair & Regeneration, National Cheng Kung University, Tainan, Taiwan
| | - Woei-Jer Chuang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Jung Lu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yan-Shen Shan
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan. .,Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Po-Hsien Huang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan. .,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Richter AM, Woods ML, Küster MM, Walesch SK, Braun T, Boettger T, Dammann RH. RASSF10 is frequently epigenetically inactivated in kidney cancer and its knockout promotes neoplasia in cancer prone mice. Oncogene 2020; 39:3114-3127. [PMID: 32047266 PMCID: PMC7142015 DOI: 10.1038/s41388-020-1195-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/21/2020] [Accepted: 01/27/2020] [Indexed: 12/22/2022]
Abstract
Kidney cancer incidences are rising globally, thereby fueling the demand for targeted therapies and precision medicine. In our previous work, we have identified and characterized the Ras-Association Domain Family encoding ten members that are often aberrantly expressed in human cancers. In this study, we created and analyzed the Rassf10 knockout mice. Here we show that Rassf10 haploinsufficiency promotes neoplasia formation in two established mouse cancer models (Rassf1A-/- and p53-/-). Haploinsufficient Rassf10 knockout mice were significantly prone to various diseases including lymphoma (Rassf1A-/- background) and thymoma (p53-/- background). Especially Rassf10-/- and p53-deficient mice exhibited threefold increased rates of kidney cysts compared with p53-/- controls. Moreover, we observed that in human kidney cancer, RASSF10 is frequently epigenetically inactivated by its CpG island promoter hypermethylation. Primary tumors of renal clear cell and papillary cell carcinoma confirmed that RASSF10 methylation is associated with decreased expression in comparison to normal kidney tissue. In independent data sets, we could validate that RASSF10 inactivation clinically correlated with decreased survival and with progressed disease state of kidney cancer patients and polycystic kidney size. Functionally, we revealed that the loss of Rassf10 was significantly associated with upregulation of KRAS signaling and MYC expression. In summary, we could show that Rassf10 functions as a haploinsufficient tumor suppressor. In combination with other markers, RASSF10 silencing can serve as diagnostic and prognostic cancer biomarker in kidney diseases.
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Affiliation(s)
- Antje M Richter
- Institute for Genetics, University of Giessen, 35392, Giessen, Germany. .,Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany.
| | - Michelle L Woods
- Institute for Genetics, University of Giessen, 35392, Giessen, Germany
| | - Miriam M Küster
- Institute for Genetics, University of Giessen, 35392, Giessen, Germany
| | - Sara K Walesch
- Institute for Genetics, University of Giessen, 35392, Giessen, Germany
| | - Thomas Braun
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany.,German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center, 35392, Giessen, Germany
| | - Thomas Boettger
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Reinhard H Dammann
- Institute for Genetics, University of Giessen, 35392, Giessen, Germany. .,German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center, 35392, Giessen, Germany.
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10
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Yu N, Yong S, Kim HK, Choi YL, Jung Y, Kim D, Seo J, Lee YE, Baek D, Lee J, Lee S, Lee JE, Kim J, Kim J, Lee S. Identification of tumor suppressor miRNAs by integrative miRNA and mRNA sequencing of matched tumor-normal samples in lung adenocarcinoma. Mol Oncol 2019; 13:1356-1368. [PMID: 30913346 PMCID: PMC6547618 DOI: 10.1002/1878-0261.12478] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/09/2019] [Accepted: 02/28/2019] [Indexed: 12/20/2022] Open
Abstract
The roles of miRNAs in lung cancer have not yet been explored systematically at the genome scale despite their important regulatory functions. Here, we report an integrative analysis of miRNA and mRNA sequencing data for matched tumor–normal samples from 109 Korean female patients with non‐small‐cell lung adenocarcinoma (LUAD). We produced miRNA sequencing (miRNA‐Seq) and RNA‐Seq data for 48 patients and RNA‐Seq data for 61 additional patients. Subsequent differential expression analysis with stringent criteria yielded 44 miRNAs and 2322 genes. Integrative gene set analysis of the differentially expressed miRNAs and genes using miRNA–target information revealed several regulatory processes related to the cell cycle that were targeted by tumor suppressor miRNAs (TSmiR). We performed colony formation assays in A549 and NCI‐H460 cell lines to test the tumor‐suppressive activity of downregulated miRNAs in cancer and identified 7 novel TSmiRs (miR‐144‐5p, miR‐218‐1‐3p, miR‐223‐3p, miR‐27a‐5p, miR‐30a‐3p, miR‐30c‐2‐3p, miR‐338‐5p). Two miRNAs, miR‐30a‐3p and miR‐30c‐2‐3p, showed differential survival characteristics in the Tumor Cancer Genome Atlas (TCGA) LUAD patient cohort indicating their prognostic value. Finally, we identified a network cluster of miRNAs and target genes that could be responsible for cell cycle regulation. Our study not only provides a dataset of miRNA as well as mRNA sequencing from the matched tumor–normal samples, but also reports several novel TSmiRs that could potentially be developed into prognostic biomarkers or therapeutic RNA drugs.
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Affiliation(s)
- Namhee Yu
- Department of Life Science, Ewha Womans University, Seoul, Korea.,Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul, Korea
| | - Seunghui Yong
- Department of Life Science, Ewha Womans University, Seoul, Korea
| | - Hong Kwan Kim
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoon-La Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yeonjoo Jung
- Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul, Korea
| | - Doyeon Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
| | - Jihae Seo
- Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul, Korea
| | - Ye Eun Lee
- Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul, Korea
| | - Daehyun Baek
- Center for RNA Research, Institute for Basic Science, Seoul, Korea.,School of Biological Sciences, Seoul National University, Korea
| | - Jinseon Lee
- Samsung Biomedical Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | | | - Jaesang Kim
- Department of Life Science, Ewha Womans University, Seoul, Korea.,Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul, Korea
| | - Jhingook Kim
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sanghyuk Lee
- Department of Life Science, Ewha Womans University, Seoul, Korea.,Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul, Korea
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11
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Cicenas J, Zalyte E, Bairoch A, Gaudet P. Kinases and Cancer. Cancers (Basel) 2018; 10:cancers10030063. [PMID: 29494549 PMCID: PMC5876638 DOI: 10.3390/cancers10030063] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 02/28/2018] [Accepted: 02/28/2018] [Indexed: 12/17/2022] Open
Abstract
Protein kinases are a large family of enzymes catalyzing protein phosphorylation. The human genome contains 518 protein kinase genes, 478 of which belong to the classical protein kinase family and 40 are atypical protein kinases [...].
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Affiliation(s)
- Jonas Cicenas
- Department of Microbiology, Immunology and Genetics, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria.
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Sauletekio al. 7, LT-10257 Vilnius, Lithuania.
- MAP Kinase Resource, Bioinformatics, Melchiorstrasse 9, 3027 Bern, Switzerland.
| | - Egle Zalyte
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Sauletekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Amos Bairoch
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
- Faculty of Medicine; University of Geneva; 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
| | - Pascale Gaudet
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
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12
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MECP2 promotes the growth of gastric cancer cells by suppressing miR-338-mediated antiproliferative effect. Oncotarget 2017; 7:34845-59. [PMID: 27166996 PMCID: PMC5085194 DOI: 10.18632/oncotarget.9197] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 03/31/2016] [Indexed: 12/30/2022] Open
Abstract
The methyl-CpG-binding protein 2 (MECP2), a transcriptional suppressor, is involved in gene regulation by binding to methylated promoters. We found that MECP2 is overexpressed in gastric cancer (GC), and that Mecp2 knockdown affects the growth of GC cells both in vitro and in vivo. MECP2 can directly bind to the methylated-CpG island of miR-338 promoter and suppress the expression of two mature microRNAs, namely, miR-338-3p and miR-338-5p. Furthermore, miR-338-5p can suppress GC cell growth by targeting BMI1 (B lymphoma Mo-MLV insertion region 1 homolog). We additionally found that decreased miR-338-5p expression in GC tissues, relative to normal tissues, was significantly negatively correlated with increased BMI1 expression. Silencing MECP2 can indirectly lead to reduced expression of P-REX2, which has been identified as the miR-338-3p target, as well as BMI1 and increasing expression of P16 or P21 both in vitro and in vivo. Altogether, our results indicate that MECP2 promote the proliferation of GC cells via miR-338 (miR-338-3p and miR-338-5p)-mediated antitumor and gene regulatory effect.
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13
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Kuang Y, Lu F, Guo J, Xu H, Wang Q, Xu C, Zeng L, Yi S. Histone demethylase KDM2B upregulates histone methyltransferase EZH2 expression and contributes to the progression of ovarian cancer in vitro and in vivo. Onco Targets Ther 2017; 10:3131-3144. [PMID: 28706445 PMCID: PMC5495092 DOI: 10.2147/ott.s134784] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aberrant histone methylation contributes to the progression and development of many tumors. Histone methylation is a dynamic process regulated by both histone demethylase and histone methyltransferase, which ultimately alters the levels of gene transcription. However, the relationship between histone demethylase and histone methyltransferase, as well as their regulatory mechanisms in ovarian cancer development, is still unclear. Lysine-specific demethylase 2B (KDM2B) is a key demethylase of H3K36me3 and H3K4me3 that regulates gene expression and plays a role in tumorigenesis via epigenetic mechanisms. To determine the expression pattern of KDM2B in ovarian neoplasms, we analyzed the mRNA and protein levels of KDM2B and the histone methyltransferase enhancer of zester homolog 2 (EZH2) in normal, benign, borderline, and malignant ovarian tissue samples. We found that KDM2B expression was gradually increased in ovarian tumors, with the highest expression found in the malignant ovarian tissues, and the differences in KDM2B expression among the different International Federation of Gynecology and Obstetrics stages and pathological grades/types were statistically significant. Moreover, KDM2B expression was positively correlated with EZH2 expression in ovarian tissues. To determine the role of KDM2B in tumorigenesis in vitro and in vivo, we silenced KDM2B expression in ovarian cancer cells using the KDM2B short hairpin RNA expression lentivirus and established a nude mouse xenograft model. Downregulation of endogenous KDM2B decreased the expression of EZH2 and reduced the proliferation and migration of ovarian cancer cells. Loss of KDM2B suppressed ovarian tumor formation in vivo. Our results suggest that KDM2B plays an important role in the tumorigenesis of ovarian cancer, with a possible mechanism of increasing the expression of the oncogene EZH2; this indicates that certain histone methyltransferase may be positively regulated by certain histone demethylase in the epigenetic regulation of ovarian tumors. KDM2B may be a novel therapeutic target for the clinical treatment of ovarian cancer.
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Affiliation(s)
- Yan Kuang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning
| | - Fangfang Lu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning
| | - Jianfeng Guo
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Hong Xu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning
| | - Qi Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning
| | - Chaohuan Xu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning
| | - Longjia Zeng
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning
| | - Suyi Yi
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning
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14
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Abstract
Epigenetic deregulation is of importance in tumorigenesis. In particular CpG islands (CGI), are frequently hypermethylated. Here, genome-wide DNA-methylation profiles of 480,000 CpGs in lung cancer cells were generated. It was observed that intra- and intergenic CGI exhibited higher methylation compared to normal cells. The functional annotation of hypermethylated CGI revealed that the hypermethylation was associated with homeobox domain genes and targets marked by repressive histone modifications. The strongest methylation variation was observed in transitional areas of CGI, termed shores. 5'-shores of promoter-associated CGI in lung cancer cell lines were higher methylated than 3'-shores. Within two tandem-oriented genes, a significant hypermethylation of the downstream-located CGI promoters was revealed. Hypermethylation correlates with the length of the intergenic region between such tandem genes. As the RASSF1A tumor suppressor gene represents such a downstream tandem gene, its silencing was analyzed using an inducible system. It was determined that the induction of an upstream gene led to a repression of RASSF1A through a process involving histone deacetylases and CPSF1. A tumor-specific increase in expression of histone deacetylases and CPSF1 was detected in lung cancer. Our results suggest that the downstream gene could be susceptible to epigenetic silencing when organized in a tandem orientation.
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15
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Zhang G, Zheng H, Zhang G, Cheng R, Lu C, Guo Y, Zhao G. MicroRNA-338-3p suppresses cell proliferation and induces apoptosis of non-small-cell lung cancer by targeting sphingosine kinase 2. Cancer Cell Int 2017; 17:46. [PMID: 28428733 PMCID: PMC5392967 DOI: 10.1186/s12935-017-0415-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/03/2017] [Indexed: 02/06/2023] Open
Abstract
Background Lung cancer is the major cause of cancer-related death worldwide, and 80% patients of lung cancer are non-small-cell lung cancer (NSCLC) cases. MicroRNAs are important gene regulators with critical roles in diverse biological processes, including tumorigenesis. Studies indicate that sphingosine kinase 2 (SphK2) promotes tumor progression in NSCLC, but how this occurs is unclear. Thus, we explored the effect of miR-338-3p targeting SphK2 on proliferation and apoptosis of NSCLC cells. Methods Expression of miR-338-3p and SphK2 in NSCLC A549 and H1299 cell lines was measured using qRT-PCR and Western blot. CCK-8 and colony formation assays were used to assess the effect of miR-338-3p on NSCLC cell line proliferation. Flow cytometry was used to study the effect of miR-338-3p on NSCLC apoptosis. Luciferase reporter assay and Western blot were used to confirm targeting of SphK2 by miR-338-3p. Finally, in vivo tumorigenesis studies were used to demonstrate subcutaneous tumor growth. Results miR-338-3p expression in 34 NSCLC clinical samples was downregulated and this was correlated with TNM stage. miR-338-3p significantly suppressed proliferation and induced apoptosis of NSCLC A549 and H1299 cells in vitro. SphK2 was a direct target of miR-338-3p. Overexpression of miR-338-3p significantly inhibited SphK2 expression and reduced luciferase reporter activity containing the SphK2 3′-untranslated region (3′-UTR) through the first binding site. SphK2 lacking 3′-UTR restored the effects of miR-338-3p on cell proliferation inhibition. miR-338-3p significantly inhibited tumorigenicity of NSCLC A549 and H1299 cells in a nude mouse xenograft model. Conclusions Collectively, miR-338-3p inhibited cell proliferation and induced apoptosis of NSCLC cells by targeting and down-regulating SphK2, and miR-338-3p could inhibit NSCLC cells A549 and H1299 growth in vivo, suggesting a potential mechanism of NSCLC progression. Therapeutically, miR-338-3p may serve as a potential target in the treatment of human lung cancer.
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Affiliation(s)
- Guowei Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan People's Republic of China.,Department of Respiratory Medicine, Henan Cancer Hospital, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008 Henan People's Republic of China
| | - Hao Zheng
- School of Basic Medical Sciences, Zhengzhou University, No.100 Kexue Road, Zhengzhou, 450001 Henan People's Republic of China
| | - Guojun Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan People's Republic of China
| | - Ruirui Cheng
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan People's Republic of China
| | - Chunya Lu
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan People's Republic of China
| | - Yijie Guo
- Zhengzhou Foreign Language School, High School (16) Class, Fengyang Road, Zhengzhou, 450001 Henan People's Republic of China
| | - Guoqiang Zhao
- School of Basic Medical Sciences, Zhengzhou University, No.100 Kexue Road, Zhengzhou, 450001 Henan People's Republic of China
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16
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Changes in 30K protein synthesis during delayed degeneration of the silk gland by a caspase-dependent pathway in a Bombyx (silkworm) mutant. J Comp Physiol B 2016; 186:689-700. [DOI: 10.1007/s00360-016-0990-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/29/2016] [Accepted: 04/03/2016] [Indexed: 12/19/2022]
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17
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Amacher DE. A 2015 survey of established or potential epigenetic biomarkers for the accurate detection of human cancers. Biomarkers 2016; 21:387-403. [PMID: 26983778 DOI: 10.3109/1354750x.2016.1153724] [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] [Indexed: 02/07/2023]
Abstract
Context The silencing or activation of cancer-associated genes by epigenetic mechanisms can ultimately lead to the clonal expansion of cancer cells. Objective The aim of this review is to summarize all relevant epigenetic biomarkers that have been proposed to date for the diagnosis of some prevalent human cancers. Methods A Medline search for the terms epigenetic biomarkers, human cancers, DNA methylation, histone modifications and microRNAs was performed. Results One hundred fifty-seven relevant publications were found and reviewed. Conclusion To date, a significant number of potential epigenetic cancer biomarkers of human cancer have been investigated, and some have advanced to clinical implementation.
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18
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Richter AM, Walesch SK, Dammann RH. Aberrant Promoter Methylation of the Tumour Suppressor RASSF10 and Its Growth Inhibitory Function in Breast Cancer. Cancers (Basel) 2016; 8:cancers8030026. [PMID: 26927176 PMCID: PMC4810110 DOI: 10.3390/cancers8030026] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/03/2016] [Accepted: 02/19/2016] [Indexed: 01/07/2023] Open
Abstract
Breast cancer is the most common cancer in women, with 1.7 million new cases each year. As early diagnosis and prognosis are crucial factors in cancer treatment, we investigated potential DNA methylation biomarkers of the tumour suppressor family Ras-association domain family (RASSF). Promoter hypermethylation of tumour suppressors leads to their inactivation and thereby promotes cancer development and progression. In this study we analysed the tumour suppressors RASSF1A and RASSF10. Our study shows that RASSF10 is expressed in normal breast but inactivated by methylation in breast cancer. We observed a significant inactivating promoter methylation of RASSF10 in primary breast tumours. RASSF10 is inactivated in 63% of primary breast cancer samples but only 4% of normal control breast tissue is methylated (p < 0.005). RASSF1A also shows high promoter methylation levels in breast cancer of 56% vs. 8% of normal tissue (p < 0.005). Interestingly more than 80% of breast cancer samples harboured a hypermethylation of RASSF10 and/or RASSF1A promoter. Matching samples exhibited a strong tumour specific promoter methylation of RASSF10 in comparison to the normal control breast tissue. Demethylation treatment of breast cancer cell lines MCF7 and T47D reversed RASSF10 promoter hypermethylation and re-established RASSF10 expression. In addition, we could show the growth inhibitory potential of RASSF10 in breast cancer cell lines MCF7 and T47D upon exogenous expression of RASSF10 by colony formation. We could further show, that RASSF10 induced apoptotic changes in MCF7 and T47D cells, which was verified by a significant increase in the apoptotic sub G1 fraction by 50% using flow cytometry for MCF7 cells. In summary, our study shows the breast tumour specific inactivation of RASSF10 and RASSF1A due to DNA methylation of their CpG island promoters. Furthermore RASSF10 was characterised by the ability to block growth of breast cancer cell lines by apoptosis induction.
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Affiliation(s)
- Antje M Richter
- Institute for Genetics, University of Giessen, Giessen 35392, Germany.
| | - Sara K Walesch
- Institute for Genetics, University of Giessen, Giessen 35392, Germany.
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19
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Haag T, Richter AM, Schneider MB, Jiménez AP, Dammann RH. The dual specificity phosphatase 2 gene is hypermethylated in human cancer and regulated by epigenetic mechanisms. BMC Cancer 2016; 16:49. [PMID: 26833217 PMCID: PMC4736155 DOI: 10.1186/s12885-016-2087-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/27/2016] [Indexed: 12/31/2022] Open
Abstract
Background Dual specificity phosphatases are a class of tumor-associated proteins involved in the negative regulation of the MAP kinase pathway. Downregulation of the dual specificity phosphatase 2 (DUSP2) has been reported in cancer. Epigenetic silencing of tumor suppressor genes by abnormal promoter methylation is a frequent mechanism in oncogenesis. It has been shown that the epigenetic factor CTCF is involved in the regulation of tumor suppressor genes. Methods We analyzed the promoter hypermethylation of DUSP2 in human cancer, including primary Merkel cell carcinoma by bisulfite restriction analysis and pyrosequencing. Moreover we analyzed the impact of a DNA methyltransferase inhibitor (5-Aza-dC) and CTCF on the epigenetic regulation of DUSP2 by qRT-PCR, promoter assay, chromatin immuno-precipitation and methylation analysis. Results Here we report a significant tumor-specific hypermethylation of DUSP2 in primary Merkel cell carcinoma (p = 0.05). An increase in methylation of DUSP2 was also found in 17 out of 24 (71 %) cancer cell lines, including skin and lung cancer. Treatment of cancer cells with 5-Aza-dC induced DUSP2 expression by its promoter demethylation, Additionally we observed that CTCF induces DUSP2 expression in cell lines that exhibit silencing of DUSP2. This reactivation was accompanied by increased CTCF binding and demethylation of the DUSP2 promoter. Conclusions Our data show that aberrant epigenetic inactivation of DUSP2 occurs in carcinogenesis and that CTCF is involved in the epigenetic regulation of DUSP2 expression. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2087-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tanja Haag
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58-62, D-35392, Giessen, Germany.
| | - Antje M Richter
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58-62, D-35392, Giessen, Germany.
| | - Martin B Schneider
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58-62, D-35392, Giessen, Germany.
| | - Adriana P Jiménez
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58-62, D-35392, Giessen, Germany.
| | - Reinhard H Dammann
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58-62, D-35392, Giessen, Germany. .,Universities of Giessen and Marburg Lung Center, 35392, Giessen, Germany.
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20
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Noguchi S, Mori T, Igase M, Mizuno T. A novel apoptosis-inducing mechanism of 5-aza-2′-deoxycitidine in melanoma cells: Demethylation of TNF-α and activation of FOXO1. Cancer Lett 2015; 369:344-53. [DOI: 10.1016/j.canlet.2015.08.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/19/2015] [Accepted: 08/24/2015] [Indexed: 10/23/2022]
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21
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Maragozidis P, Papanastasi E, Scutelnic D, Totomi A, Kokkori I, Zarogiannis SG, Kerenidi T, Gourgoulianis KI, Balatsos NAA. Poly(A)-specific ribonuclease and Nocturnin in squamous cell lung cancer: prognostic value and impact on gene expression. Mol Cancer 2015; 14:187. [PMID: 26541675 PMCID: PMC4635609 DOI: 10.1186/s12943-015-0457-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/19/2015] [Indexed: 11/17/2022] Open
Abstract
Background Lung cancer is the leading cause of cancer mortality worldwide, mainly due to late diagnosis, poor prognosis and tumor heterogeneity. Thus, the need for biomarkers that will aid classification, treatment and monitoring remains intense and challenging and depends on the better understanding of the tumor pathobiology and underlying mechanisms. The deregulation of gene expression is a hallmark of cancer and a critical parameter is the stability of mRNAs that may lead to increased oncogene and/or decreased tumor suppressor transcript and protein levels. The shortening of mRNA poly(A) tails determines mRNA stability, as it is usually the first step in mRNA degradation, and is catalyzed by deadenylases. Herein, we assess the clinical significance of deadenylases and we study their role on gene expression in squamous cell lung carcinoma (SCC). Methods Computational transcriptomic analysis from a publicly available microarray was performed in order to examine the expression of deadenylases in SCC patient samples. Subsequently we employed real-time PCR in clinical samples in order to validate the bioinformatics results regarding the gene expression of deadenylases. Selected deadenylases were silenced in NCI-H520 and Hep2 human cancer cell lines and the effect on gene expression was analyzed with cDNA microarrays. Results The in silico analysis revealed that the expression of several deadenylases is altered in SCC. Quantitative real-time PCR showed that four deadenylases, PARN, CNOT6, CNOT7 and NOC, are differentially expressed in our SCC clinical samples. PARN overexpression correlated with younger patient age and CNOT6 overexpression with non-metastatic tumors. Kaplan-Meier analysis suggests that increased levels of PARN and NOC correlate with significantly increased survival. Gene expression analysis upon PARN and NOC silencing in lung cancer cells revealed gene expression deregulation that was functionally enriched for gene ontologies related to cell adhesion, cell junction, muscle contraction and metabolism. Conclusions Our results highlight the clinical significance of PARN and NOC on the survival in SCC diagnosed patients. We demonstrate that the enzymes are implicated in important phenotypes pertinent to cancer biology and provide information on their role in the regulation of gene expression in SCC. Overall, our results support an emerging role for deadenylases in SCC and contribute to the understanding of their role in cancer biology. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0457-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Panagiotis Maragozidis
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26, Larissa, 412 21, Greece. .,Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 415 00, Greece.
| | - Eirini Papanastasi
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26, Larissa, 412 21, Greece.
| | - Diana Scutelnic
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26, Larissa, 412 21, Greece.
| | - Athina Totomi
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26, Larissa, 412 21, Greece.
| | - Ioanna Kokkori
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 415 00, Greece. .,Department of Pneumonology - Oncology, Theagenio Cancer Hospital, Al. Symeonidi 2, Thessaloniki, 540 07, Greece.
| | - Sotirios G Zarogiannis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 415 00, Greece. .,Department of Physiology, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 415 00, Greece.
| | - Theodora Kerenidi
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 415 00, Greece.
| | - Konstantinos I Gourgoulianis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 415 00, Greece.
| | - Nikolaos A A Balatsos
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26, Larissa, 412 21, Greece.
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Claudin11 Promoter Hypermethylation Is Frequent in Malignant Melanoma of the Skin, but Uncommon in Nevus Cell Nevi. Cancers (Basel) 2015. [PMID: 26198249 PMCID: PMC4586767 DOI: 10.3390/cancers7030834] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Epigenetic inactivation of tumor-related genes is an important characteristic in the pathology of human cancers, including melanomagenesis. We analyzed the epigenetic inactivation of Claudin 11 (CLDN11) in malignant melanoma (MM) of the skin, including six melanoma cell lines, 39 primary melanoma, 41 metastases of MM and 52 nevus cell nevi (NCN). CLDN11 promoter hypermethylation was found in 19 out of 39 (49%) of the primary MM and in 21 out of 41 (51%) of the MM metastases, but only in eight out of 52 (15%) of NCN (p = 0.001 and p = 0.0003, respectively). Moreover, a significant increase in the methylation level of CLDN11 from primary melanomas to MM metastases was revealed (p = 0.003). Methylation of CLDN11 was significantly more frequent in skin metastases (79%) compared to brain metastases (31%; p = 0.007). CLDN11 methylation was also found in five out of six MM cell lines (83%) and its promoter hypermethylation correlated with a reduced expression. Treatment of MM cell lines with a DNA methylation inhibitor reactivated CLDN11 transcription by its promoter demethylation. In summary, CLDN11 proved to be an epigenetically inactivated tumor related gene in melanomagenesis, and analysis of CLDN11 methylation level represents a potential tool for assisting in the discrimination between malignant melanoma and nevus cell nevi.
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Richter AM, Zimmermann T, Haag T, Walesch SK, Dammann RH. Promoter methylation status of Ras-association domain family members in pheochromocytoma. Front Endocrinol (Lausanne) 2015; 6:21. [PMID: 25750636 PMCID: PMC4333862 DOI: 10.3389/fendo.2015.00021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/05/2015] [Indexed: 01/05/2023] Open
Abstract
Pheochromocytomas (PCCs) are rare neuroendocrine tumors that arise from the medulla of the adrenal gland or the sympathetic ganglia and are characterized by the secretion of catecholamines. In 30-40% of patients, PCCs are genetically determined by susceptibility genes as various as RET, VHL, and NF1. We have analyzed the Ras-association domain family members (RASSFs) in PCCs regarding their inactivating promoter hypermethylation status. Previously, we reported a promoter methylation in PCC for the first family member RASSF1A. Promoter hypermethylation of CpG islands leads to the silencing of the according transcript and is a common mechanism for inactivation of tumor suppressors. In this study, we observed inactivating DNA modifications for the RASSF members RASSF2, RASSF5A, RASSF9, and RASSF10, but not for the members RASSF3, RASSF4, RASSF5C, RASSF6, RASSF7, and RASSF8. The degree of promoter methylation was 19% for RASSF2, 67% for RASSF5A, 18% for RASSF9, and 74% for RASSF10. Interestingly, the degree of hypermethylation for RASSF10 in hereditary PCCs was 89 vs. 60% in sporadic PCCs. A similar but less dramatic effect was observed in RASSF5A and RASSF9. Including all RASSF members, we found that of 25 PCCs, 92% show promoter methylation in at least in one RASSF member. In 75% of the hereditary PCC samples, we found two or more methylated RASSF promoters, whereas in sporadic PCCs only 46% were observed. In summary, we could show that in PCC several RASSF members are strongly hypermethylated in their promoter regions and methylation of more than one RASSF member occurs in the majority of PCCs. This adds the inactivation of genes of the RASSF tumor suppressor family to the already known deregulated genes of PCC.
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Affiliation(s)
- Antje M. Richter
- Institute for Genetics, University of Giessen, Giessen, Germany
- *Correspondence: Antje M. Richter, Heinrich-Buff Ring 58, Giessen, Hessen, Germany e-mail:
| | | | - Tanja Haag
- Institute for Genetics, University of Giessen, Giessen, Germany
| | - Sara K. Walesch
- Institute for Genetics, University of Giessen, Giessen, Germany
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