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Huang W, Mei J, Liu YJ, Li JP, Zou X, Qian XP, Zhang Y. An Analysis Regarding the Association Between Proteasome (PSM) and Hepatocellular Carcinoma (HCC). J Hepatocell Carcinoma 2023; 10:497-515. [PMID: 37020465 PMCID: PMC10069642 DOI: 10.2147/jhc.s404396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Background The Proteasome (PSM) is a large multi-catalytic protease complex consisting of a 20S core particle and a 19S regulatory particle whose main function is to accept and degrade ubiquitinated substrates, are now considered as one of the potential regulators of tumor proliferation, and stemness maintenance. However, to date, studies on the relationship between PSM and hepatocellular carcinoma (HCC) are limited. Methods This study used a bioinformatics approach combining validation experiments to investigate the biological mechanisms that may be related with PSM. A series of experiments in vivo and in vitro were performed to explore the function of the 26S proteasome non-ATPase regulatory subunit 13 (PSMD13) in HCC. Results HCC patients can be divided into two clusters. Cluster 1 (C1) patients having a significantly worse prognosis than Cluster (C2). Two subtypes had significant differences in proliferation-related signaling. In particular, the frequency of TP53 mutation was significantly higher in C1 than in C2. In addition, PSM-associated genes were highly consistent with the expression of DNA repair-related signatures, suggesting a potential link between PSM and genomic instability. We also found that downregulation of PSMD13 expression significantly inhibited stemness of tumor cells and impaired the Epithelial mesenchymal transition (EMT) process. Finally, the correlation between the PSMD13 and Ki67 was found to be strong. Conclusion PSM is a valid predictor of prognosis and therapeutic response in patients with HCC disease. Furthermore, PSMD13 may be a potential therapeutic target.
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Affiliation(s)
- Wei Huang
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- Comprehensive Cancer Center, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210008, People’s Republic of China
| | - Jia Mei
- Department of Pathology, Nanjing Jinling Hospital, Nanjing, Jiangsu, 210001, People’s Republic of China
| | - Yuan-Jie Liu
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
| | - Jie-Pin Li
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
- Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, 215600, People’s Republic of China
| | - Xi Zou
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing, 210023, People’s Republic of China
| | - Xiao-Ping Qian
- Comprehensive Cancer Center, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210008, People’s Republic of China
- The Comprehensive Cancer Center of Nanjing Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, Jiangsu, 210008, People’s Republic of China
| | - Yu Zhang
- Department of Oncology, Nanjing Jinling Hospital, Nanjing, Jiangsu, 210001, People’s Republic of China
- Correspondence: Yu Zhang; Xiao-ping Qian, Email ;
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2
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Uhlmann C, Nickel AC, Picard D, Rossi A, Li G, Hildebrandt B, Brockerhoff G, Bendt F, Hübenthal U, Hewera M, Steiger HJ, Wieczorek D, Perrakis A, Zhang W, Remke M, Koch K, Tigges J, Croner RS, Fritsche E, Kahlert UD. Progenitor cells derived from gene-engineered human induced pluripotent stem cells as synthetic cancer cell alternatives for in vitro pharmacology. Biotechnol J 2022; 17:e2100693. [PMID: 35334498 DOI: 10.1002/biot.202100693] [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: 12/23/2021] [Revised: 02/25/2022] [Accepted: 03/08/2022] [Indexed: 11/08/2022]
Abstract
Limitations in genetic stability and recapitulating accurate physiological disease properties challenge the utility of patient-derived (PD) cancer models for reproducible and translational research. We have genetically engineered a portfolio of isogenic human induced pluripotent stem cells (hiPSCs) with different pan-cancer relevant oncoprotein signatures followed by differentiation into lineage-committed progenitor cells. Characterization on molecular and biological level validated successful stable genetic alterations in pluripotency state as well as upon differentiation to prove the functionality of our approach Meanwhile proposing core molecular networks possibly involved in early dysregulation of stem cell homeostasis, the application of our cell systems in comparative substance testing indicates the potential for cancer research such as identification of augmented therapy resistance of stem cells in response to activation of distinct oncogenic signatures. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Constanze Uhlmann
- Department for Neurosurgery, Medical Faculty and University Medical Center Düsseldorf, Heinrich-Heine-University, Düsseldorf, Germany
| | - Ann-Christin Nickel
- Department for Neurosurgery, Medical Faculty and University Medical Center Düsseldorf, Heinrich-Heine-University, Düsseldorf, Germany
| | - Daniel Picard
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany.,Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany.,Department of Neuropathology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Andrea Rossi
- Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Guanzhang Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, P. R. China
| | - Barbara Hildebrandt
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Germany
| | | | - Farina Bendt
- Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Ulrike Hübenthal
- Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Michael Hewera
- Department for Neurosurgery, Medical Faculty and University Medical Center Düsseldorf, Heinrich-Heine-University, Düsseldorf, Germany
| | - Hans-Jakob Steiger
- Department for Neurosurgery, Medical Faculty and University Medical Center Düsseldorf, Heinrich-Heine-University, Düsseldorf, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Germany
| | - Aristoteles Perrakis
- Molecular and Experimental Surgery, University Clinic for General, Visceral and Vascular Surgery, University Medical Center Magdeburg and Faculty of Medicine, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Wei Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, P. R. China
| | - Marc Remke
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany.,Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany.,Department of Neuropathology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Katharina Koch
- Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Julia Tigges
- Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Roland S Croner
- Molecular and Experimental Surgery, University Clinic for General, Visceral and Vascular Surgery, University Medical Center Magdeburg and Faculty of Medicine, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Ellen Fritsche
- Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany.,Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Ulf D Kahlert
- Molecular and Experimental Surgery, University Clinic for General, Visceral and Vascular Surgery, University Medical Center Magdeburg and Faculty of Medicine, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
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3
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Zhu X, Ye S, Yu D, Zhang Y, Li J, Zhang M, Leng Y, Yang T, Luo J, Chen X, Zhang H, Kong L. Physalin B attenuates liver fibrosis via suppressing LAP2α-HDAC1-mediated deacetylation of the transcription factor GLI1 and hepatic stellate cell activation. Br J Pharmacol 2021; 178:3428-3447. [PMID: 33864382 DOI: 10.1111/bph.15490] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/20/2021] [Accepted: 04/06/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND AND PURPOSE Liver fibrosis is one of the leading causes of morbidity and mortality worldwide but lacks any acceptable therapy. The transcription factor glioma-associated oncogene homologue 1 (GLI1) is a potentially important therapeutic target in liver fibrosis. This study investigates the anti-fibrotic activities and potential mechanisms of the phytochemical, physalin B. EXPERIMENTAL APPROACH Two mouse models (CCl4 challenge and bile duct ligation) were used to assess antifibrotic effects of physalin B in vivo. Mouse primary hepatic stellate cells (pHSCs) and human HSC line LX-2 also served as in vitro liver fibrosis models. Liver fibrogenic genes, GLI1 and GLI1 downstream genes were examined using Western blot and quantitative real-time PCR (qRT-PCR). GLI1 acetylation and LAP2α-HDAC1 interaction were analysed by co-immunoprecipitation. KEY RESULTS In vivo, physalin B administration attenuated hepatic histopathological injury and collagen accumulation and decreased expression of fibrogenic genes. Physalin B dose-dependently suppressed fibrotic marker expression in LX-2 cells and mouse pHSCs. Mechanistic studies showed that physalin B inhibited GLI activity by non-canonical Hedgehog signalling. Physalin B blocked formation of lamina-associated polypeptide 2α (LAP2α)/histone deacetylase 1 (HDAC1) complexes, thus inhibiting HDAC1-mediated GLI1 deacetylation. Physalin B up-regulated acetylation of GLI1, down-regulated expression of GLI1 and subsequently inhibited HSC activation. CONCLUSION AND IMPLICATIONS Physalin B exerted potent antifibrotic effects in vitro and in vivo by disrupting LAP2α/HDAC1 complexes, increasing GLI1 acetylation and inactivating GLI1. This indicates that the phytochemical physalin B may be a potential therapeutic candidate for the treatment of liver fibrosis.
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Affiliation(s)
- Xiaoyun Zhu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Shengtao Ye
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Dongke Yu
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yanqiu Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jie Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Meihui Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yingrong Leng
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Ting Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jianguang Luo
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xinlin Chen
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Hao Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Lingyi Kong
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
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4
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Dancik GM, Williams K, Zhang M, Romanenko N. Cancer Publication Portal: an online tool for summarizing and searching human cancer-genomic publications. F1000Res 2019. [DOI: 10.12688/f1000research.21463.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A search of PubMed lists >582,000 citations with the keywords “cancer” and “gene”. The large volume of cancer genomic publications necessitates the development of text-mining tools to help cancer researchers navigate and summarize articles efficiently. We developed a Cancer Publication Portal (CPP) to help researchers efficiently search and summarize cancer genomic publications, based on one or more genes of interest. CPP integrates data from several sources, including PubTator, the Medical Subject Headings (MeSH) database; the HUGO Gene Nomenclature Committee human gene name database; PubMed, a database of biomedical literature citations; and the National Cancer Institute (NCI) Thesaurus. Following each query, results are summarized and include the publication frequency for each cancer type, as well as publication frequencies for cancer terms, pharmacological agents, genomic mutations, and additional genes stratified by cancer type. Cancer terms were identified by comparing titles and abstracts from cancer-related (N=851,868) and non-cancer related articles (N=2,607,020). CPP allows a user to quickly obtain publication statistics, such as the frequency of articles mentioning EGFR across cancer types, and to explore associations, such as the association between pharmacological agent and cancer type. Result summaries are interactive, so additional filters can be easily added as the literature is explored. After a search is completed, a PubTator collection can be quickly created, in order to view article titles and abstracts in PubTator. CPP currently includes information for ~1.1 million cancer-related publications associated with >23,000 human genes. Database URL: https://gdancik.github.io/bioinformatics/CPP/.
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5
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Sahu AD, S Lee J, Wang Z, Zhang G, Iglesias-Bartolome R, Tian T, Wei Z, Miao B, Nair NU, Ponomarova O, Friedman AA, Amzallag A, Moll T, Kasumova G, Greninger P, Egan RK, Damon LJ, Frederick DT, Jerby-Arnon L, Wagner A, Cheng K, Park SG, Robinson W, Gardner K, Boland G, Hannenhalli S, Herlyn M, Benes C, Flaherty K, Luo J, Gutkind JS, Ruppin E. Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy. Mol Syst Biol 2019; 15:e8323. [PMID: 30858180 PMCID: PMC6413886 DOI: 10.15252/msb.20188323] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 12/31/2018] [Accepted: 01/21/2019] [Indexed: 01/09/2023] Open
Abstract
Most patients with advanced cancer eventually acquire resistance to targeted therapies, spurring extensive efforts to identify molecular events mediating therapy resistance. Many of these events involve synthetic rescue (SR) interactions, where the reduction in cancer cell viability caused by targeted gene inactivation is rescued by an adaptive alteration of another gene (the rescuer). Here, we perform a genome-wide in silico prediction of SR rescuer genes by analyzing tumor transcriptomics and survival data of 10,000 TCGA cancer patients. Predicted SR interactions are validated in new experimental screens. We show that SR interactions can successfully predict cancer patients' response and emerging resistance. Inhibiting predicted rescuer genes sensitizes resistant cancer cells to therapies synergistically, providing initial leads for developing combinatorial approaches to overcome resistance proactively. Finally, we show that the SR analysis of melanoma patients successfully identifies known mediators of resistance to immunotherapy and predicts novel rescuers.
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Affiliation(s)
- Avinash Das Sahu
- Department of Biostatistics and Computational Biology, Harvard School of Public Health, Boston, MA, USA
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Joo S Lee
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhiyong Wang
- Department of Pharmacology & Moores Cancer Center, University of California, San Diego La Jolla, CA, USA
| | - Gao Zhang
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
- Department of Neurosurgery and The Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC, USA
| | | | - Tian Tian
- New Jersey Institute of Technology, Newark, NJ, USA
| | - Zhi Wei
- New Jersey Institute of Technology, Newark, NJ, USA
| | - Benchun Miao
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Nishanth Ulhas Nair
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Olga Ponomarova
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Adam A Friedman
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Arnaud Amzallag
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Tabea Moll
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Gyulnara Kasumova
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Patricia Greninger
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Regina K Egan
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Leah J Damon
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Dennie T Frederick
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Livnat Jerby-Arnon
- Schools of Computer Science & Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Allon Wagner
- Department of Electrical Engineering and Computer Science, the Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Kuoyuan Cheng
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Seung Gu Park
- Department of Biostatistics and Computational Biology, Harvard School of Public Health, Boston, MA, USA
| | - Welles Robinson
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Kevin Gardner
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Genevieve Boland
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Sridhar Hannenhalli
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - Cyril Benes
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Keith Flaherty
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Ji Luo
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - J Silvio Gutkind
- Department of Pharmacology & Moores Cancer Center, University of California, San Diego La Jolla, CA, USA
| | - Eytan Ruppin
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Schools of Computer Science & Medicine, Tel-Aviv University, Tel-Aviv, Israel
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6
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McDonald AJ, Curt KM, Patel RP, Kozlowski H, Sackett DL, Robey RW, Gottesman MM, Bates SE. Targeting mitochondrial hexokinases increases efficacy of histone deacetylase inhibitors in solid tumor models. Exp Cell Res 2018; 375:106-112. [PMID: 30579954 DOI: 10.1016/j.yexcr.2018.12.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/12/2018] [Accepted: 12/15/2018] [Indexed: 02/06/2023]
Abstract
Hexokinase 1 and 2 have been shown to inhibit Bak- and Bax-mediated apoptosis, leading us to combine the histone deacetylase inhibitor romidepsin with clotrimazole or bifonazole, two compounds that reportedly decrease mitochondrial localization of hexokinases. Cancer cell lines derived from breast, kidney, lung, colon or ovarian cancers were treated with a short-term exposure to 25 ng/ml romidepsin combined with either clotrimazole or bifonazole. The combination of romidepsin with 25 µM clotrimazole or bifonazole resulted in increased annexin staining compared to cells treated with any of the drugs alone. Cell death was caspase-mediated, as the pan-caspase inhibitor Q-VD-OPh was found to inhibit apoptosis induced by the combination. A549 lung cancer cells or HCT-116 cells deficient in Bak and Bax were also resistant to apoptosis with the combination implicating the intrinsic apoptotic pathway. We found that a 24 h treatment with clotrimazole or bifonazole decreased total hexokinase 2 expression, resulting in a 76% or 60% decrease, respectively, of mitochondrial expression of hexokinase 2. Mitochondrial hexokinase 1 levels increased 2-fold or less. Our work suggests that the combination of a short-term romidepsin treatment with bifonazole or clotrimazole leads to increased apoptosis, most likely due to decreased mitochondrial expression of hexokinase 2.
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Affiliation(s)
- Andrew J McDonald
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Katherine M Curt
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Ruchi P Patel
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Hanna Kozlowski
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Dan L Sackett
- Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Robert W Robey
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States; Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Michael M Gottesman
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Susan E Bates
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States; Columbia University Medical Center, Division of Hematology/Oncology, New York, NY 10032, United States.
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7
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Sabol M, Trnski D, Musani V, Ozretić P, Levanat S. Role of GLI Transcription Factors in Pathogenesis and Their Potential as New Therapeutic Targets. Int J Mol Sci 2018; 19:E2562. [PMID: 30158435 PMCID: PMC6163343 DOI: 10.3390/ijms19092562] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/17/2018] [Accepted: 08/25/2018] [Indexed: 02/05/2023] Open
Abstract
GLI transcription factors have important roles in intracellular signaling cascade, acting as the main mediators of the HH-GLI signaling pathway. This is one of the major developmental pathways, regulated both canonically and non-canonically. Deregulation of the pathway during development leads to a number of developmental malformations, depending on the deregulated pathway component. The HH-GLI pathway is mostly inactive in the adult organism but retains its function in stem cells. Aberrant activation in adult cells leads to carcinogenesis through overactivation of several tightly regulated cellular processes such as proliferation, angiogenesis, EMT. Targeting GLI transcription factors has recently become a major focus of potential therapeutic protocols.
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Affiliation(s)
- Maja Sabol
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Diana Trnski
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Vesna Musani
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Petar Ozretić
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Sonja Levanat
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
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8
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Williams SP, Barthorpe AS, Lightfoot H, Garnett MJ, McDermott U. High-throughput RNAi screen for essential genes and drug synergistic combinations in colorectal cancer. Sci Data 2017; 4:170139. [PMID: 28972570 PMCID: PMC5625556 DOI: 10.1038/sdata.2017.139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/14/2017] [Indexed: 12/19/2022] Open
Abstract
Metastatic colorectal cancer is a leading cause of cancer death. However, current therapy options are limited to chemotherapy, with the addition of anti-EGFR antibodies for patients with RAS wild-type tumours. Novel drug targets, or drug combinations that induce a synergistic response, would be of great benefit to patients. The identification of genes that are essential for cell survival can be undertaken using functional genomics screens. Furthermore, performing such screens in the presence of a targeted agent would allow the identification of combinations that result in a synthetic lethal interaction. Here, we present a dataset containing the results of a large scale RNAi screen (815 genes) to detect essential genes as well as synergistic combinations with targeted therapeutic agents using a panel of 27 colorectal cancer cell lines. These data identify genes that are essential for colorectal cancer cell survival as well as synthetic lethal treatment combinations using novel computational approaches. Moreover, this dataset could be utilised in combination with genomic profiling to identify predictive biomarkers of response.
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9
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The emerging field of epigenetics in neurodegeneration and neuroprotection. Nat Rev Neurosci 2017; 18:347-361. [PMID: 28515491 DOI: 10.1038/nrn.2017.46] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Epigenetic mechanisms - including DNA methylation, histone post-translational modifications and changes in nucleosome positioning - regulate gene expression, cellular differentiation and development in almost all tissues, including the brain. In adulthood, changes in the epigenome are crucial for higher cognitive functions such as learning and memory. Striking new evidence implicates the dysregulation of epigenetic mechanisms in neurodegenerative disorders and diseases. Although these disorders differ in their underlying causes and pathophysiologies, many involve the dysregulation of restrictive element 1-silencing transcription factor (REST), which acts via epigenetic mechanisms to regulate gene expression. Although not somatically heritable, epigenetic modifications in neurons are dynamic and reversible, which makes them good targets for therapeutic intervention.
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Williams SP, Gould CM, Nowell CJ, Karnezis T, Achen MG, Simpson KJ, Stacker SA. Systematic high-content genome-wide RNAi screens of endothelial cell migration and morphology. Sci Data 2017; 4:170009. [PMID: 28248931 PMCID: PMC5332011 DOI: 10.1038/sdata.2017.9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/30/2016] [Indexed: 02/08/2023] Open
Abstract
Many cell types undergo migration during embryogenesis and disease. Endothelial cells line blood vessels and lymphatics, which migrate during development as part of angiogenesis, lymphangiogenesis and other types of vessel remodelling. These processes are also important in wound healing, cancer metastasis and cardiovascular conditions. However, the molecular control of endothelial cell migration is poorly understood. Here, we present a dataset containing siRNA screens that identify known and novel components of signalling pathways regulating migration of lymphatic endothelial cells. These components are compared to signalling in blood vascular endothelial cells. Further, using high-content microscopy, we captured a dataset of images of migrating cells following transfection with a genome-wide siRNA library. These datasets are suitable for the identification and analysis of genes involved in endothelial cell migration and morphology, and for computational approaches to identify signalling networks controlling the migratory response and integration of cell morphology, gene function and cell signaling. This may facilitate identification of protein targets for therapeutically modulating angiogenesis and lymphangiogenesis in the context of human disease.
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Affiliation(s)
- Steven P Williams
- Tumour Angiogenesis Program, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, Victoria 3000, Australia.,Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia
| | - Cathryn M Gould
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, Victoria 3000, Australia
| | - Cameron J Nowell
- Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia.,The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Tara Karnezis
- Tumour Angiogenesis Program, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, Victoria 3000, Australia.,Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Marc G Achen
- Tumour Angiogenesis Program, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, Victoria 3000, Australia.,Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, Victoria 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Pathology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Steven A Stacker
- Tumour Angiogenesis Program, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, Victoria 3000, Australia.,Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia
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Carbone C, Di Gennaro E, Piro G, Milone MR, Pucci B, Caraglia M, Budillon A. Tissue transglutaminase (TG2) is involved in the resistance of cancer cells to the histone deacetylase (HDAC) inhibitor vorinostat. Amino Acids 2016; 49:517-528. [PMID: 27761756 DOI: 10.1007/s00726-016-2338-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/20/2016] [Indexed: 12/22/2022]
Abstract
Vorinostat demonstrated preclinical and clinical efficacy in human cancers and is the first histone deacetylase inhibitor (HDACi) approved for cancer treatment. Tissue transglutaminase (TG2) is a multifunctional enzyme that catalyzes a Ca2+ dependent transamidating reaction resulting in covalent cross-links between proteins. TG2 acts also as G-protein in trans-membrane signaling and as a cell surface adhesion mediator. TG2 up-regulation has been demonstrated in several cancers and its expression levels correlate with resistance to chemotherapy and metastatic potential. We demonstrated that the anti-proliferative effect of the HDACi vorinostat is paralleled by the induction of TG2 mRNA and protein expression in cancer cells but not in ex vivo treated peripheral blood lymphocytes. This effect was also shared by other pan-HDACi and resulted in increased TG2 transamidating activity. Notably, high TG2 basal levels in a panel of cancer cell lines correlated with lower vorinostat antiproliferative activity. Notably, in TG2-knockdown cancer cells vorinostat anti-proliferative and pro-apoptotic effects were enhanced, whereas in TG2-full-length transfected cells were impaired, suggesting that TG2 could represent a mechanism of intrinsic or acquired resistance to vorinostat. In fact, co-treatment of tumor cells with inhibitors of TG2 transamidating activity potentiated the antitumor effect of vorinostat. Moreover, vorinostat-resistant MCF7 cells selected by stepwise increasing concentrations of the drug, significantly overexpressed TG2 protein compared to parental cells, and co-treatment of these cells with TG2 inhibitors reversed vorinostat-resistance. Taken together, our data demonstrated that TG2 is involved in the resistance of cancer cells to vorinostat, as well as to other HDACi.
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Affiliation(s)
- Carmine Carbone
- Experimental Pharmacology Unit, Istituto Nazionale Tumori Fondazione G. Pascale-IRCCS, 80131, Naples, Italy.,Digestive Molecular Clinical Oncology Research Unit, Department of Medicine, University of Verona, Verona, Italy
| | - Elena Di Gennaro
- Experimental Pharmacology Unit, Istituto Nazionale Tumori Fondazione G. Pascale-IRCCS, 80131, Naples, Italy
| | - Geny Piro
- Centro Ricerche Oncologiche Mercogliano, Istituto Nazionale Tumori Fondazione G. Pascale-IRCCS, Naples, Italy.,Laboratory of Oncology and Molecular Therapy, Department of Medicine, University of Verona, Verona, Italy
| | - Maria Rita Milone
- Centro Ricerche Oncologiche Mercogliano, Istituto Nazionale Tumori Fondazione G. Pascale-IRCCS, Naples, Italy
| | - Biagio Pucci
- Centro Ricerche Oncologiche Mercogliano, Istituto Nazionale Tumori Fondazione G. Pascale-IRCCS, Naples, Italy
| | - Michele Caraglia
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy
| | - Alfredo Budillon
- Experimental Pharmacology Unit, Istituto Nazionale Tumori Fondazione G. Pascale-IRCCS, 80131, Naples, Italy. .,Centro Ricerche Oncologiche Mercogliano, Istituto Nazionale Tumori Fondazione G. Pascale-IRCCS, Naples, Italy.
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