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Wan C, Ma H, Liu J, Liu F, Liu J, Dong G, Zeng X, Li D, Yu Z, Wang X, Li J, Zhang G. Quantitative relationships of FAM50B and PTCHD3 methylation with reduced intelligence quotients in school aged children exposed to lead: Evidence from epidemiological and in vitro studies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167976. [PMID: 37866607 DOI: 10.1016/j.scitotenv.2023.167976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/22/2023] [Accepted: 10/18/2023] [Indexed: 10/24/2023]
Abstract
At present, the application of DNA methylation (DNAm) biomarkers in environmental health risk assessment (EHRA) is more challenging due to the unclearly quantitative relationship between them. We aimed to explore the role of FAM50B and PTCHD3 at the level of signaling pathways, and establish the quantitative relationship between them and children's intelligence quotients (IQs). DNAm of target regions was measured in multiple cell models and was compared with the human population data. Then the dose-response relationships of lead exposure with neurotoxicity and DNAm were established by benchmark dose (BMD) model, followed by potential signaling pathway screening. Results showed that there was a quantitative linear relationship between children's IQs and FAM50B/PTCHD3 DNAm (DNAm between 51.40 % - 78.78 % and 31.41 % - 74.19 % for FAM50B and PTCHD3, respectively), and this relationship was more significant when children's IQs > 90. The receiver operating characteristic (ROC) and calibration curves showed that FAM50B/PTCHD3 DNAm had a satisfying accuracy and consistency in predicting children's IQs, which was confirmed by sensitivity analysis of gender and CpG site grouping data. In cell experiments, there was also a quantitative linear relationship between FAM50B DNAm and reactive oxygen species (ROS) production, which was mediated by PI3K-AKT signaling pathway. In addition, the lead BMD of ROS was close to that of FAM50B DNAm, suggesting that FAM50B DNAm was a suitable biomarker for the risk assessments of adverse outcomes induced by lead. Taken collectively, these results suggest that FAM50B/PTCHD3 can be applied to EHRA and the prevention/intervention of adverse effects of lead on children's IQs.
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Affiliation(s)
- Cong Wan
- State Key Laboratory of Organic Geochemistry, Guangdong Province Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| | - Huimin Ma
- State Key Laboratory of Organic Geochemistry, Guangdong Province Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China.
| | - Jiahong Liu
- State Key Laboratory of Organic Geochemistry, Guangdong Province Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Liu
- School of Business Administration, South China University of Technology, Guangzhou 510641, China
| | - Jing Liu
- Guangzhou First People's Hospital, Guangzhou 510180, China
| | - Guanghui Dong
- Department of Preventive Medicine, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiaowen Zeng
- Department of Preventive Medicine, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Daochuan Li
- Department of Preventive Medicine, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangdong Province Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| | - Xinming Wang
- State Key Laboratory of Organic Geochemistry, Guangdong Province Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| | - Jun Li
- State Key Laboratory of Organic Geochemistry, Guangdong Province Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry, Guangdong Province Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
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Watanabe K, Seki N. Biology and Development of DNA-Targeted Drugs, Focusing on Synthetic Lethality, DNA Repair, and Epigenetic Modifications for Cancer: A Review. Int J Mol Sci 2024; 25:752. [PMID: 38255825 PMCID: PMC10815806 DOI: 10.3390/ijms25020752] [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: 11/27/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
DNA-targeted drugs constitute a specialized category of pharmaceuticals developed for cancer treatment, directly influencing various cellular processes involving DNA. These drugs aim to enhance treatment efficacy and minimize side effects by specifically targeting molecules or pathways crucial to cancer growth. Unlike conventional chemotherapeutic drugs, recent discoveries have yielded DNA-targeted agents with improved effectiveness, and a new generation is anticipated to be even more specific and potent. The sequencing of the human genome in 2001 marked a transformative milestone, contributing significantly to the advancement of targeted therapy and precision medicine. Anticipated progress in precision medicine is closely tied to the continuous development in the exploration of synthetic lethality, DNA repair, and expression regulatory mechanisms, including epigenetic modifications. The integration of technologies like circulating tumor DNA (ctDNA) analysis further enhances our ability to elucidate crucial regulatory factors, promising a more effective era of precision medicine. The combination of genomic knowledge and technological progress has led to a surge in clinical trials focusing on precision medicine. These trials utilize biomarkers for identifying genetic alterations, molecular profiling for potential therapeutic targets, and tailored cancer treatments addressing multiple genetic changes. The evolving landscape of genomics has prompted a paradigm shift from tumor-centric to individualized, genome-directed treatments based on biomarker analysis for each patient. The current treatment strategy involves identifying target genes or pathways, exploring drugs affecting these targets, and predicting adverse events. This review highlights strategies incorporating DNA-targeted drugs, such as PARP inhibitors, SLFN11, methylguanine methyltransferase (MGMT), and ATR kinase.
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Affiliation(s)
- Kiyotaka Watanabe
- Department of Medicine, School of Medicine, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo 173-8605, Japan
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Laganà M, Cremaschi V, Alberti A, Vodopivec Kuri DM, Cosentini D, Berruti A. The Evolving Treatment Landscape of Medullary Thyroid Cancer. Curr Treat Options Oncol 2023; 24:1815-1832. [PMID: 37979019 PMCID: PMC10781862 DOI: 10.1007/s11864-023-01145-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
OPINION STATEMENT Genetic assessment is crucial to address the correct treatment for advanced medullary thyroid cancer (MTC). Multi tyrosine kinase inhibitors (mTKIs) cabozantinib and vandetanib are good first line options, even vandetanib prescription is currently limited to RET mutated patients. Selective RET inhibitors such as pralsetinib could be a preferred upfront treatment in case of RET mutated MTC presenting common or gatekeeper RET mutations (e.g. M918T; V804L/M). Selpercatinib, otherwise, can be prescribed as the second line after disease progression to mTKIs. The best option for subsequent lines is to consider inclusion in clinical trials or alternatively other mTKIs such as sunitinib, sorafenib, lenvatinib, or pazopanib could be evaluated. New perspectives include next-generation RET inhibitors able to overcome resistance mechanisms responsible for disease progression to standard mTKIs and RET inhibitors, and immunotherapy for MTC presenting with high tumor mutational burden.
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Affiliation(s)
- Marta Laganà
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia at ASST Spedali Civili, 25123, Brescia, Italy
| | - Valentina Cremaschi
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia at ASST Spedali Civili, 25123, Brescia, Italy
| | - Andrea Alberti
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia at ASST Spedali Civili, 25123, Brescia, Italy.
| | - Danica M Vodopivec Kuri
- Department of Endocrinology, Diabetes, and Metabolism, University Of Alabama, 619 19Th St S, Birmingham, AL, 35249, USA
| | - Deborah Cosentini
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia at ASST Spedali Civili, 25123, Brescia, Italy
| | - Alfredo Berruti
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia at ASST Spedali Civili, 25123, Brescia, Italy
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Marei HE, Hasan A, Pozzoli G, Cenciarelli C. Cancer immunotherapy with immune checkpoint inhibitors (ICIs): potential, mechanisms of resistance, and strategies for reinvigorating T cell responsiveness when resistance is acquired. Cancer Cell Int 2023; 23:64. [PMID: 37038154 PMCID: PMC10088229 DOI: 10.1186/s12935-023-02902-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/24/2023] [Indexed: 04/12/2023] Open
Abstract
Cancer is still the leading cause of death globally. The approval of the therapeutic use of monoclonal antibodies against immune checkpoint molecules, notably those that target the proteins PD-1 and PD-L1, has changed the landscape of cancer treatment. In particular, first-line PD-1/PD-L1 inhibitor drugs are increasingly common for the treatment of metastatic cancer, significantly prolonging patient survival. Despite the benefits brought by immune checkpoint inhibitors (ICIs)-based therapy, the majority of patients had their diseases worsen following a promising initial response. To increase the effectiveness of ICIs and advance our understanding of the mechanisms causing cancer resistance, it is crucial to find new, effective, and tolerable combination treatments. In this article, we addressed the potential of ICIs for the treatment of solid tumors and offer some insight into the molecular pathways behind therapeutic resistance to ICIs. We also discuss cutting-edge therapeutic methods for reactivating T-cell responsiveness after resistance has been established.
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Affiliation(s)
- Hany E Marei
- Department of Cytology and Histology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35116, Egypt.
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha, Qatar
| | - Giacomo Pozzoli
- Pharmacology Section, Department of Health Care Surveillance and Bioethics, Università Cattolica del Sacro Cuore, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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Zhang Z, Wang G, Li Y, Lei D, Xiang J, Ouyang L, Wang Y, Yang J. Recent progress in DNA methyltransferase inhibitors as anticancer agents. Front Pharmacol 2022; 13:1072651. [PMID: 37077808 PMCID: PMC10107375 DOI: 10.3389/fphar.2022.1072651] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
DNA methylation mediated by DNA methyltransferase is an important epigenetic process that regulates gene expression in mammals, which plays a key role in silencing certain genes, such as tumor suppressor genes, in cancer, and it has become a promising therapeutic target for cancer treatment. Similar to other epigenetic targets, DNA methyltransferase can also be modulated by chemical agents. Four agents have already been approved to treat hematological cancers. In order to promote the development of a DNA methyltransferase inhibitor as an anti-tumor agent, in the current review, we discuss the relationship between DNA methylation and tumor, the anti-tumor mechanism, the research progress and pharmacological properties of DNA methyltransferase inhibitors, and the future research trend of DNA methyltransferase inhibitors.
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Affiliation(s)
- Zhixiong Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Yuyan Li
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Dongsheng Lei
- School of Physical Science and Technology, Electron Microscopy Center of Lanzhou University, Lanzhou University, Lanzhou, China
| | - Jin Xiang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
- Science and Technology Department, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yanyan Wang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
- Science and Technology Department, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Yanyan Wang, ; Jinliang Yang,
| | - Jinliang Yang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
- *Correspondence: Yanyan Wang, ; Jinliang Yang,
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Selective CDK9 Inhibition by Natural Compound Toyocamycin in Cancer Cells. Cancers (Basel) 2022; 14:cancers14143340. [PMID: 35884401 PMCID: PMC9324262 DOI: 10.3390/cancers14143340] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/24/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary By combining drug screens, transcriptomic studies, and in vitro assays, our study identified the natural product toyocamycin as a potent and selective CDK9 inhibitor. Thus, toyocamycin can be used as a new small molecule to modulate CDK9 activity in preclinical research. Through docking simulations, we identified its specific binding sites, which could spark some interest to design novel small molecule CDK9 inhibitors. Abstract Aberrant transcription in cancer cells involves the silencing of tumor suppressor genes (TSGs) and activation of oncogenes. Transcriptomic changes are associated with epigenomic alterations such as DNA-hypermethylation, histone deacetylation, and chromatin condensation in promoter regions of silenced TSGs. To discover novel drugs that trigger TSG reactivation in cancer cells, we used a GFP-reporter system whose expression is silenced by promoter DNA hypermethylation and histone deacetylation. After screening a natural product drug library, we identified that toyocamycin, an adenosine-analog, induces potent GFP reactivation and loss of clonogenicity in human colon cancer cells. Connectivity-mapping analysis revealed that toyocamycin produces a pharmacological signature mimicking cyclin-dependent kinase (CDK) inhibitors. RNA-sequencing revealed that the toyocamycin transcriptomic signature resembles that of a specific CDK9 inhibitor (HH1). Specific inhibition of RNA Pol II phosphorylation level and kinase assays confirmed that toyocamycin specifically inhibits CDK9 (IC50 = 79 nM) with a greater efficacy than other CDKs (IC50 values between 0.67 and 15 µM). Molecular docking showed that toyocamycin efficiently binds the CDK9 catalytic site in a conformation that differs from other CDKs, explained by the binding contribution of specific amino acids within the catalytic pocket and protein backbone. Altogether, we demonstrated that toyocamycin exhibits specific CDK9 inhibition in cancer cells, highlighting its potential for cancer chemotherapy.
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Kawakubo K, Castillo CFD, Liss AS. Epigenetic regulation of pancreatic adenocarcinoma in the era of cancer immunotherapy. J Gastroenterol 2022; 57:819-826. [PMID: 36048239 PMCID: PMC9596544 DOI: 10.1007/s00535-022-01915-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/16/2022] [Indexed: 02/04/2023]
Abstract
Pancreatic adenocarcinoma is a lethal cancer with poor response to chemotherapy and immune checkpoint inhibitors. Recent studies suggest that epigenetic alterations contribute to its aggressive biology and the tumor microenvironment which render it unresponsive to immune checkpoint blockade. Here, we review our current understandings of epigenetic dysregulation in pancreatic adenocarcinoma, its effect on the tumor immune microenvironment, and the potential for epigenetic therapy to be combined with immune checkpoint inhibitors.
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Affiliation(s)
- Kazumichi Kawakubo
- grid.39158.360000 0001 2173 7691Department of Gastroenterology and Hepatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan ,grid.38142.3c000000041936754XDepartment of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Carlos Fernandez-del Castillo
- grid.38142.3c000000041936754XDepartment of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Andrew Scott Liss
- grid.38142.3c000000041936754XDepartment of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
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Azevedo Portilho N, Saini D, Hossain I, Sirois J, Moraes C, Pastor WA. The DNMT1 inhibitor GSK-3484862 mediates global demethylation in murine embryonic stem cells. Epigenetics Chromatin 2021; 14:56. [PMID: 34906184 PMCID: PMC8672470 DOI: 10.1186/s13072-021-00429-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/26/2021] [Indexed: 12/16/2022] Open
Abstract
Background DNA methylation plays an important role in regulating gene expression in mammals. The covalent DNMT1 inhibitors 5-azacytidine and decitabine are widely used in research to reduce DNA methylation levels, but they impart severe cytotoxicity which limits their demethylation capability and confounds interpretation of experiments. Recently, a non-covalent inhibitor of DNMT1 called GSK-3484862 was developed by GlaxoSmithKline. We sought to determine whether GSK-3484862 can induce demethylation more effectively than 5-azanucleosides. Murine embryonic stem cells (mESCs) are an ideal cell type in which to conduct such experiments, as they have a high degree of DNA methylation but tolerate dramatic methylation loss. Results We determined the cytotoxicity and optimal concentration of GSK-3484862 by treating wild-type (WT) or Dnmt1/3a/3b triple knockout (TKO) mESC with different concentrations of the compound, which was obtained from two commercial sources. Concentrations of 10 µM or below were readily tolerated for 14 days of culture. Known DNA methylation targets such as germline genes and GLN-family transposons were upregulated within 2 days of the start of GSK-3484862 treatment. By contrast, 5-azacytidine and decitabine induced weaker upregulation of methylated genes and extensive cell death. Whole-genome bisulfite sequencing showed that treatment with GSK-3484862 induced dramatic DNA methylation loss, with global CpG methylation levels falling from near 70% in WT mESC to less than 18% after 6 days of treatment with GSK-3484862. The treated cells showed a methylation level and pattern similar to that observed in Dnmt1-deficient mESCs. Conclusions GSK-3484862 mediates striking demethylation in mESCs with minimal non-specific toxicity. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00429-0.
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Affiliation(s)
- Nathalia Azevedo Portilho
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada.,Department of Chemical Engineering, McGill University, Montreal, QC, H3A 0C5, Canada
| | - Deepak Saini
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada.,The Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Ishtiaque Hossain
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada.,The Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Jacinthe Sirois
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada.,The Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Christopher Moraes
- Department of Chemical Engineering, McGill University, Montreal, QC, H3A 0C5, Canada.,The Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada
| | - William A Pastor
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada. .,The Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada.
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Huot M, Caron M, Richer C, Djibo R, Najmanovich R, St-Onge P, Sinnett D, Raynal NJM. Repurposing proscillaridin A in combination with decitabine against embryonal rhabdomyosarcoma RD cells. Cancer Chemother Pharmacol 2021; 88:845-856. [PMID: 34331108 DOI: 10.1007/s00280-021-04339-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/15/2021] [Indexed: 12/13/2022]
Abstract
PURPOSE Embryonal rhabdomyosarcoma (eRMS) is the most common type of rhabdomyosarcoma in children. eRMS is characterized by malignant skeletal muscle cells driven by hyperactivation of several oncogenic pathways including the MYC pathway. Targeting MYC in cancer has been extremely challenging. Recently, we have demonstrated that the heart failure drug, proscillaridin A, produced anticancer effects with specificity toward MYC expressing leukemia cells. We also reported that decitabine, a hypomethylating drug, synergizes with proscillaridin A in colon cancer cells. Here, we investigated whether proscillaridin A exhibits epigenetic and anticancer activity against eRMS RD cells, overexpressing MYC oncogene, and its combination with decitabine. METHODS We investigated the anticancer effects of proscillaridin A in eRMS RD cells in vitro. In response to drug treatment, we measured growth inhibition, cell cycle arrest, loss of clonogenicity and self-renewal capacity. We further evaluated the impact of proscillaridin A on MYC expression and its downstream transcriptomic effects by RNA sequencing. Then, we measured protein expression of epigenetic regulators and their associated chromatin post-translational modifications in response to drug treatment. Chromatin immunoprecipitation sequencing data sets were coupled with transcriptomic results to pinpoint the impact of proscillaridin A on gene pathways associated with specific chromatin modifications. Lastly, we evaluated the effect of the combination of proscillaridin A and the DNA demethylating drug decitabine on eRMS RD cell growth and clonogenic potential. RESULTS Clinically relevant concentration of proscillaridin A (5 nM) produced growth inhibition, cell cycle arrest and loss of clonogenicity in eRMS RD cells. Proscillaridin A produced a significant downregulation of MYC protein expression and inhibition of oncogenic transcriptional programs controlled by MYC, involved in cell replication. Interestingly, significant reduction in total histone 3 acetylation and on specific lysine residues (lysine 9, 14, 18, and 27 on histone 3) was associated with significant protein downregulation of a series of lysine acetyltransferases (KAT3A, KAT3B, KAT2A, KAT2B, and KAT5). In addition, proscillaridin A produced synergistic growth inhibition and loss of clonogenicity when combined with the approved DNA demethylating drug decitabine. CONCLUSION Proscillaridin A produces anticancer and epigenetic effects in the low nanomolar range and its combination with decitabine warrants further investigation for the treatment of eRMS.
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Affiliation(s)
- Marielle Huot
- Département de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC, Canada.,Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - Maxime Caron
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - Chantal Richer
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - Rahinatou Djibo
- Département de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC, Canada.,Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - Rafael Najmanovich
- Département de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC, Canada
| | - Pascal St-Onge
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - Daniel Sinnett
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Département de Pédiatrie, Université de Montréal, Montréal, QC, Canada
| | - Noël J M Raynal
- Département de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC, Canada. .,Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.
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Sun M, Cao Y, Yang X, An F, Wu H, Wang J. DNA methylation in the OPG/RANK/RANKL pathway is associated with steroid-induced osteonecrosis of the femoral head. BMC Musculoskelet Disord 2021; 22:599. [PMID: 34187427 PMCID: PMC8240366 DOI: 10.1186/s12891-021-04472-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 06/10/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Dysregulation of the OPG/RANK/RANKL signalling pathway is a key step in the occurrence of steroid-induced osteonecrosis of the femoral head (ONFH). This study aims to understand the degree of methylation of the OPG, RANK, and RANKL genes in steroid-related ONFH. METHODS A case-control study was designed, including 50 patients (25 males and 25 females) and 50 matched controls. The European Molecular Biology Open Software Suite (EMBOSS) was used to predict the existence and location of CpG islands in the OPG, RANK, and RANKL genes. The Agena MassARRAY platform was used to detect the methylation status of the above genes in the blood of subjects. The relationship between the methylation level of CpG sites in each gene and steroid-related ONFH was analysed by the chi-square test, logistic regression analysis, and other statistical methods. RESULTS In the CpG islands of the OPG, RANK, and RANKL genes in patients with steroid-related ONFH, several CpG sites with high methylation rates and high methylation levels were found. Some hypermethylated CpG sites increase the risk of steroid-related ONFH. In addition, a few hypermethylated CpG sites have predictive value for the early diagnosis of steroid-related ONFH. CONCLUSION Methylation of certain sites in the OPG/RANK/RANKL signalling pathway increases the risk of steroid-related ONFH. Some hypermethylated CpG sites may be used as early prediction and diagnostic targets for steroid-related ONFH.
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Affiliation(s)
- Menghu Sun
- Department of Orthopedics and Traumatology, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010030, Inner Mongolia, China
- Inner Mongolia Medical University, Hohhot, 010050, Inner Mongolia, China
| | - Yuju Cao
- Zhengzhou Traditional Chinese Medicine (TCM) Traumatology Hospital, Zhengzhou, 450016, Henan Province, China
| | - Xiaolong Yang
- Department of Orthopedics and Traumatology, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010030, Inner Mongolia, China
| | - Feimeng An
- Inner Mongolia Autonomous Region Hospital of Traditional Chinese Medicine, Hohhot, 010110, Inner Mongolia, China
| | - Huiqiang Wu
- Inner Mongolia Autonomous Region Hospital of Traditional Chinese Medicine, Hohhot, 010110, Inner Mongolia, China
| | - Jianzhong Wang
- Department of Orthopedics and Traumatology, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010030, Inner Mongolia, China.
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11
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Coyne GO'S, Wang L, Zlott J, Juwara L, Covey JM, Beumer JH, Cristea MC, Newman EM, Koehler S, Nieva JJ, Garcia AA, Gandara DR, Miller B, Khin S, Miller SB, Steinberg SM, Rubinstein L, Parchment RE, Kinders RJ, Piekarz RL, Kummar S, Chen AP, Doroshow JH. Intravenous 5-fluoro-2'-deoxycytidine administered with tetrahydrouridine increases the proportion of p16-expressing circulating tumor cells in patients with advanced solid tumors. Cancer Chemother Pharmacol 2020; 85:979-993. [PMID: 32314030 PMCID: PMC7188725 DOI: 10.1007/s00280-020-04073-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/06/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE Following promising responses to the DNA methyltransferase (DNMT) inhibitor 5-fluoro-2'-deoxycytidine (FdCyd) combined with tetrahydrouridine (THU) in phase 1 testing, we initiated a non-randomized phase 2 study to assess response to this combination in patients with advanced solid tumor types for which tumor suppressor gene methylation is potentially prognostic. To obtain pharmacodynamic evidence for DNMT inhibition by FdCyd, we developed a novel method for detecting expression of tumor suppressor protein p16/INK4A in circulating tumor cells (CTCs). METHODS Patients in histology-specific strata (breast, head and neck [H&N], or non-small cell lung cancers [NSCLC] or urothelial transitional cell carcinoma) were administered FdCyd (100 mg/m2) and THU (350 mg/m2) intravenously 5 days/week for 2 weeks, in 28-day cycles, and progression-free survival (PFS) rate and objective response rate (ORR) were evaluated. Blood specimens were collected for CTC analysis. RESULTS Ninety-three eligible patients were enrolled (29 breast, 21 H&N, 25 NSCLC, and 18 urothelial). There were three partial responses. All strata were terminated early due to insufficient responses (H&N, NSCLC) or slow accrual (breast, urothelial). However, the preliminary 4-month PFS rate (42%) in the urothelial stratum exceeded the predefined goal-though the ORR (5.6%) did not. An increase in the proportion of p16-expressing cytokeratin-positive CTCs was detected in 69% of patients evaluable for clinical and CTC response, but was not significantly associated with clinical response. CONCLUSION Further study of FdCyd + THU is potentially warranted in urothelial carcinoma but not NSCLC or breast or H&N cancer. Increase in the proportion of p16-expressing cytokeratin-positive CTCs is a pharmacodynamic marker of FdCyd target engagement.
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Affiliation(s)
- Geraldine O 'Sullivan Coyne
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - Lihua Wang
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jennifer Zlott
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - Lamin Juwara
- Clinical Monitoring Research Program, Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph M Covey
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - Jan H Beumer
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Mihaela C Cristea
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Edward M Newman
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | | | - Jorge J Nieva
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Agustin A Garcia
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
- Louisiana State University, New Orleans, LA, 70112, USA
| | - David R Gandara
- University of California Davis Cancer Center, Sacramento, CA, USA
| | - Brandon Miller
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sonny Khin
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sarah B Miller
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - Seth M Steinberg
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Larry Rubinstein
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - Ralph E Parchment
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert J Kinders
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Richard L Piekarz
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - Shivaani Kummar
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - Alice P Chen
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA.
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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12
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Dan H, Zhang S, Zhou Y, Guan Q. DNA Methyltransferase Inhibitors: Catalysts For Antitumour Immune Responses. Onco Targets Ther 2019; 12:10903-10916. [PMID: 31849494 PMCID: PMC6913319 DOI: 10.2147/ott.s217767] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/02/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetics is a kind of heritable change that involves the unaltered DNA sequence and can have effects on gene expression. The regulatory mechanism mainly includes DNA methylation, histone modification and non-coding RNA regulation. DNA methylation is currently the most studied aspect of epigenetics. It is widely present in eukaryotic cells and is the most important epigenetic mark in the regulation of gene expression in the cell. DNA methyltransferase inhibitors (DNMTi) have been increasingly recognized in the field of cancer immunotherapy, have been approved for the treatment of acute myeloid leukaemia (AML) and are widely being used in clinical trials of cancer immunotherapies. DNMTi promote the reactivation of tumour suppressor genes, enhance tumour immunogenicity, and stimulate a variety of immune cells to secrete cytokines that exert cytotoxic effects, promote tumour cell death, including macrophages, natural killer (NK) cells and CD8+ T cells, and upregulate major histocompatibility complex (MHC) class I expression levels. Here, we mainly summarize the epigenetics related to DNMTi and their regulation of the antitumour immune response and DNMTi combined with immuno-therapeutics or histone deacetylase inhibitors to demonstrate the great development potential and clinical application value of DNMTi.
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Affiliation(s)
- Huimin Dan
- Gansu Province Key Laboratory of Gastrointestinal Diseases, The First Hospital of Lanzhou University, Lanzhou University, Lanzhou, Gansu Province, People's Republic of China
| | - Shanshan Zhang
- Gansu Province Key Laboratory of Gastrointestinal Diseases, The First Hospital of Lanzhou University, Lanzhou University, Lanzhou, Gansu Province, People's Republic of China
| | - Yongning Zhou
- Gansu Province Key Laboratory of Gastrointestinal Diseases, The First Hospital of Lanzhou University, Lanzhou University, Lanzhou, Gansu Province, People's Republic of China
| | - Quanlin Guan
- Gansu Province Key Laboratory of Gastrointestinal Diseases, The First Hospital of Lanzhou University, Lanzhou University, Lanzhou, Gansu Province, People's Republic of China
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13
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Han P, Liu Q, Xiang J. Monitoring methylation-driven genes as prognostic biomarkers in patients with lung squamous cell cancer. Oncol Lett 2019; 19:707-716. [PMID: 31897186 PMCID: PMC6924172 DOI: 10.3892/ol.2019.11163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 10/16/2019] [Indexed: 12/20/2022] Open
Abstract
Aberrant DNA methylations have been reported to be significantly associated with lung squamous cell cancer (LUSC). The aim of this study was to investigate the DNA methylation-driven genes in LUSC by integrative bioinformatics analysis. In the present study, methylation-driven genes in LUSC were screened out, and survival analysis related to these genes was performed to confirm their value in prognostic assessment. Gene expression and methylation data were downloaded from The Cancer Genome Atlas (TCGA), and the MethylMix algorithm was used to identify methylation-driven genes. ConsensusPathDB was used to perform Gene Ontology and pathway enrichment analysis of methylation-driven genes. Survival analysis was performed to investigate the correlation with prognosis. In total, 52 differentially expressed methylation-driven genes were identified in LUSC and adjacent tissues. Survival analysis showed that DQX1, GPR75, STX12, and TRIM61 could serve as independent prognostic biomarkers. In addition, the combined methylation and gene expression survival analysis revealed that the combined expression level of the genes ALG1L, DQX1, and ZNF418 alone can be used as a prognostic marker or drug target. Methylation of four sites of gene ZNF418, four sites of ZNF701, two sites of DQX1, and four sites of DCAF4L2 was significantly associated with survival. The present study provides an important bioinformatic and relevant theoretical basis for subsequent early diagnosis and prognostic assessment of LUSC.
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Affiliation(s)
- Pengkai Han
- Department of Respiratory Medicine, Chongqing Three Gorges Central Hospital, Chongqing 404100, P.R. China
| | - Qiping Liu
- Department of Respiratory Medicine, Chongqing Three Gorges Central Hospital, Chongqing 404100, P.R. China
| | - Jianhua Xiang
- Department of Respiratory Medicine, Chongqing Three Gorges Central Hospital, Chongqing 404100, P.R. China
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14
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Jia D, Lin W, Tang H, Cheng Y, Xu K, He Y, Geng W, Dai Q. Integrative analysis of DNA methylation and gene expression to identify key epigenetic genes in glioblastoma. Aging (Albany NY) 2019; 11:5579-5592. [PMID: 31395792 PMCID: PMC6710056 DOI: 10.18632/aging.102139] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/29/2019] [Indexed: 12/19/2022]
Abstract
Glioblastoma (GBM) ranks the most common and aggressive primary brain malignant tumor worldwide. However, the survival rates of patients remain very poor. Therefore, molecular oncology of GBM are urgently needed. In this study, we performed an integrative analysis of DNA methylation and gene expression to identify key epigenetic genes in GBM. The methylation and gene expression of GBM patients in The Cancer Genome Atlas (TCGA) database were downloaded. After data preprocessing, we identified 4,881 differentially expressed genes (DEGs) between tumor and normal samples, including 1,111 upregulated and 3,770 downregulated genes. Then, we randomly separated all samples into training set (n = 69) and testing set (n = 69). We next obtained 11,269 survival-methylation sites by univariate and multivariate Cox regression analyses. In the correlation analysis, we defined 198 low promoter methylation with high gene expression as epigenetically induced (EI) genes and 111 high promoter methylation with low gene expression as epigenetically suppressed (ES) genes. Key markers including C1orf61 and FAM50B were selected with a Pearson correlation coefficient greater than 0.75. Further, we chose the 20 CpG methylation sites of above two genes in unsupervised clustering analysis using the Euclidean distance. We found that the prognosis of the hypomethylated group was significantly better than that in the hypermethylated group (log-rank test p-value = 0.011). Based on the validation in the TCGA testing set and GEO dataset, we validated the prognostic value of our signature (p-value = 0.02 in TCGA and 0.012 in GEO). In conclusion, our findings provided predictive and prognostic value as methylation-based biomarkers for the diagnosis and treatment of GBM.
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Affiliation(s)
- Danyun Jia
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Wei Lin
- Zhejiang Department of Pediatric Intensive Care Unit, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Hongli Tang
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Yifan Cheng
- Department of Neurology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Kaiwei Xu
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Yanshu He
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Wujun Geng
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Qinxue Dai
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
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15
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Chandhok NS, Prebet T. Insights into novel emerging epigenetic drugs in myeloid malignancies. Ther Adv Hematol 2019; 10:2040620719866081. [PMID: 31431820 PMCID: PMC6685116 DOI: 10.1177/2040620719866081] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/10/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetics has been defined as ‘a stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence’ and several epigenetic regulators are recurrently mutated in hematological malignancies. Epigenetic modifications include changes such as DNA methylation, histone modifications and RNA associated gene silencing. Transcriptional regulation, chromosome stability, DNA replication and DNA repair are all controlled by these modifications. Mutations in genes encoding epigenetic modifiers are a frequent occurrence in hematologic malignancies and important in both the initiation and progression of cancer. Epigenetic modifications are also frequently reversible, allowing excellent opportunities for therapeutic intervention. The goal of epigenetic therapies is to reverse epigenetic dysregulation, restore the epigenetic balance, and revert malignant cells to a more normal condition. The role of epigenetic therapies thus far is most established in hematologic malignancies, with several agents already approved by the US Food and Drug Administration. In this review, we discuss pharmacological agents targeting epigenetic regulators.
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Affiliation(s)
- Namrata S Chandhok
- Division of Hematology/Oncology, Smilow Cancer Center at Yale New Haven Hospital, New Haven, CT, USA
| | - Thomas Prebet
- Division of Hematology/Oncology, Smilow Cancer Center at Yale New Haven Hospital, 35 Park Street, New Haven, CT 06511, USA
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16
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Power M, Das S, Schütze K, Marigo V, Ekström P, Paquet-Durand F. Cellular mechanisms of hereditary photoreceptor degeneration - Focus on cGMP. Prog Retin Eye Res 2019; 74:100772. [PMID: 31374251 DOI: 10.1016/j.preteyeres.2019.07.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/25/2019] [Accepted: 07/29/2019] [Indexed: 12/21/2022]
Abstract
The cellular mechanisms underlying hereditary photoreceptor degeneration are still poorly understood, a problem that is exacerbated by the enormous genetic heterogeneity of this disease group. However, the last decade has yielded a wealth of new knowledge on degenerative pathways and their diversity. Notably, a central role of cGMP-signalling has surfaced for photoreceptor cell death triggered by a subset of disease-causing mutations. In this review, we examine key aspects relevant for photoreceptor degeneration of hereditary origin. The topics covered include energy metabolism, epigenetics, protein quality control, as well as cGMP- and Ca2+-signalling, and how the related molecular and metabolic processes may trigger photoreceptor demise. We compare and integrate evidence on different cell death mechanisms that have been associated with photoreceptor degeneration, including apoptosis, necrosis, necroptosis, and PARthanatos. A special focus is then put on the mechanisms of cGMP-dependent cell death and how exceedingly high photoreceptor cGMP levels may cause activation of Ca2+-dependent calpain-type proteases, histone deacetylases and poly-ADP-ribose polymerase. An evaluation of the available literature reveals that a large group of patients suffering from hereditary photoreceptor degeneration carry mutations that are likely to trigger cGMP-dependent cell death, making this pathway a prime target for future therapy development. Finally, an outlook is given into technological and methodological developments that will with time likely contribute to a comprehensive overview over the entire metabolic complexity of photoreceptor cell death. Building on such developments, new imaging technology and novel biomarkers may be used to develop clinical test strategies, that fully consider the genetic heterogeneity of hereditary retinal degenerations, in order to facilitate clinical testing of novel treatment approaches.
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Affiliation(s)
- Michael Power
- Cell Death Mechanism Group, Institute for Ophthalmic Research, University of Tübingen, Germany; Centre for Integrative Neurosciences (CIN), University of Tübingen, Germany; Graduate Training Centre of Neuroscience (GTC), University of Tübingen, Germany
| | - Soumyaparna Das
- Cell Death Mechanism Group, Institute for Ophthalmic Research, University of Tübingen, Germany; Graduate Training Centre of Neuroscience (GTC), University of Tübingen, Germany
| | | | - Valeria Marigo
- Department of Life Sciences, University of Modena and Reggio Emilia, Italy
| | - Per Ekström
- Ophthalmology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Sweden
| | - François Paquet-Durand
- Cell Death Mechanism Group, Institute for Ophthalmic Research, University of Tübingen, Germany.
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17
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Li F, Wan X, Xing J, Tan X, Li X, Wang Y, Zhao J, Wu X, Liu X, Li Z, Luo X, Lu W, Zheng M. Deep Neural Network Classifier for Virtual Screening Inhibitors of (S)-Adenosyl-L-Methionine (SAM)-Dependent Methyltransferase Family. Front Chem 2019; 7:324. [PMID: 31134191 PMCID: PMC6524412 DOI: 10.3389/fchem.2019.00324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 04/23/2019] [Indexed: 12/15/2022] Open
Abstract
The (S)-adenosyl-L-methionine (SAM)-dependent methyltransferases play essential roles in post-translational modifications (PTMs) and other miscellaneous biological processes, and are implicated in the pathogenesis of various genetic disorders and cancers. Increasing efforts have been committed toward discovering novel PTM inhibitors targeting the (S)-Adenosyl-L-methionine (SAM)-binding site and the substrate-binding site of methyltransferases, among which virtual screening (VS) and structure-based drug design (SBDD) are the most frequently used strategies. Here, we report the development of a target-specific scoring model for compound VS, which predict the likelihood of the compound being a potential inhibitor for the SAM-binding pocket of a given methyltransferase. Protein-ligand interaction characterized by Fingerprinting Triplets of Interaction Pseudoatoms was used as the input feature, and a binary classifier based on deep neural networks is trained to build the scoring model. This model enhances the efficiency of the existing strategies used for discovering novel chemical modulators of methyltransferase, which is crucial for understanding and exploring the complexity of epigenetic target space.
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Affiliation(s)
- Fei Li
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China.,State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiaozhe Wan
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Xing
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI, United States
| | - Xiaoqin Tan
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Xutong Li
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Yulan Wang
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jihui Zhao
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolong Wu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xiaohong Liu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Zhaojun Li
- School of Information Management, Dezhou University, Dezhou, China
| | - Xiaomin Luo
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Wencong Lu
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Mingyue Zheng
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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18
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From Genotype to Phenotype: Through Chromatin. Genes (Basel) 2019; 10:genes10020076. [PMID: 30678090 PMCID: PMC6410296 DOI: 10.3390/genes10020076] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/16/2019] [Accepted: 01/21/2019] [Indexed: 02/07/2023] Open
Abstract
Advances in sequencing technologies have enabled the exploration of the genetic basis for several clinical disorders by allowing identification of causal mutations in rare genetic diseases. Sequencing technology has also facilitated genome-wide association studies to gather single nucleotide polymorphisms in common diseases including cancer and diabetes. Sequencing has therefore become common in the clinic for both prognostics and diagnostics. The success in follow-up steps, i.e., mapping mutations to causal genes and therapeutic targets to further the development of novel therapies, has nevertheless been very limited. This is because most mutations associated with diseases lie in inter-genic regions including the so-called regulatory genome. Additionally, no genetic causes are apparent for many diseases including neurodegenerative disorders. A complementary approach is therefore gaining interest, namely to focus on epigenetic control of the disease to generate more complete functional genomic maps. To this end, several recent studies have generated large-scale epigenetic datasets in a disease context to form a link between genotype and phenotype. We focus DNA methylation and important histone marks, where recent advances have been made thanks to technology improvements, cost effectiveness, and large meta-scale epigenome consortia efforts. We summarize recent studies unravelling the mechanistic understanding of epigenetic processes in disease development and progression. Moreover, we show how methodology advancements enable causal relationships to be established, and we pinpoint the most important issues to be addressed by future research.
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19
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Leroy M, Mélin L, LaPlante SR, Medina-Franco JL, Gagnon A. Synthesis of NSC 106084 and NSC 14778 and evaluation of their DNMT inhibitory activity. Bioorg Med Chem Lett 2019; 29:826-831. [PMID: 30704813 DOI: 10.1016/j.bmcl.2019.01.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 01/01/2023]
Abstract
DNA methylation is an epigenetic modification that is performed by DNA methyltransferases (DNMTs) and that leads to the transfer of a methyl group from S-adenosylmethionine (SAM) to the C5 position of cytosine. This transformation results in hypermethylation and silencing of genes such as tumor suppressor genes. Aberrant DNA methylation has been associated with the development of many diseases, including cancer. Inhibition of DNMTs promotes the demethylation and reactivation of epigenetically silenced genes. NSC 106084 and 14778 have been reported to inhibit DNMTs in the micromolar range. We report herein the synthesis of NSC 106084 and 14778 and the evaluation of their DNMT inhibitory activity. Our results indicate that while commercial NSC 14778 is moderately active against DNMT1, 3A/3L and 3B/3L, resynthesized NSC 14778 is inactive under our assay conditions. Resynthesized 106084 was also found to be inactive.
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Affiliation(s)
- Maxime Leroy
- Département de chimie, Université du Québec à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada
| | - Léa Mélin
- Département de chimie, Université du Québec à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada
| | - Steven R LaPlante
- Centre INRS-Armand Frappier, 531 boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - José L Medina-Franco
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico
| | - Alexandre Gagnon
- Département de chimie, Université du Québec à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada.
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20
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Guo J, Zhao C, Yao R, Sui A, Sun L, Liu X, Wu S, Su Z, Li T, Liu S, Gao Y, Liu J, Feng X, Wang W, Zhao H, Cui Z, Li G, Meng F. 3D culture enhances chemoresistance of ALL Jurkat cell line by increasing DDR1 expression. Exp Ther Med 2019; 17:1593-1600. [PMID: 30783426 PMCID: PMC6364197 DOI: 10.3892/etm.2019.7153] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/30/2018] [Indexed: 12/16/2022] Open
Abstract
Three dimensional (3D) culture has gradually become a research hotspot in the field of drug screening, stem cell research, and tissue engineering due to its more physiological-like morphology and function. In this study, we compared the differences of cell proliferation, population, protein expression and chemoresistance profiles between two dimensional (2D) and 3D culture of acute lymphoblastic leukemia (ALL) Jurkat cell line. Polycaprolactone (PCL) is used for 3D culture owing to its biochemical properties and compatibility. Culturing of ALL Jurkat cell line in collagen type I coated polycaprolactone scaffold for 168 h increased cell proliferation, attachment, as well as the drug resistance to cytarabine (Ara-C) and daunorubicin (DNR) without changing the original CD2+CD3+CD4+dimCD8−CD34−CD45+dim phenotype, compared to uncoated PCL scaffold and tissue culture plate systems. Molecularly, increased chemoresistance is associated with the upregulation of discoidin domain receptor 1 (DDR1) and transcription factor STAT3. Inhibition of DDR1 activity by DDR1-specific inhibitor DDR-IN-1 accelerated cell death in the presence of Ara-C, DNR or their combination. These results demonstrated that 3D culture enhances chemoresistance of ALL Jurkat cell line by increasing DDR1 expression. Importantly, the cell adhesion-mediated drug resistance induced by DDR1 in the scaffold was similar to the clinical situation, indicating the 3D culture of cancer cells recapitulate the in vivo tumor environment and this platform can be used as a promising pre-clinic drug-screen system.
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Affiliation(s)
- Jun Guo
- College of Medicine, Qingdao University, Qingdao, Shandong 266071, P.R. China.,Department of Hematology, People's Hospital of Rizhao, Rizhao, Shandong 276800, P.R. China
| | - Chunting Zhao
- Department of Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266555, P.R. China
| | - Ruyong Yao
- Central Laboratory, Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong 266035, P.R. China
| | - Aihua Sui
- Central Laboratory, Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong 266035, P.R. China
| | - Lingjie Sun
- Department of Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266555, P.R. China
| | - Xiaodan Liu
- Department of Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266555, P.R. China
| | - Shaoling Wu
- Department of Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266555, P.R. China
| | - Zhan Su
- Department of Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266555, P.R. China
| | - Tianlan Li
- Department of Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266555, P.R. China
| | - Shanshan Liu
- Department of Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266555, P.R. China
| | - Yan Gao
- Department of Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266555, P.R. China
| | - Jiaxiu Liu
- Central Laboratory, Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong 266035, P.R. China
| | - Xianqi Feng
- Department of Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266555, P.R. China
| | - Wei Wang
- Department of Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266555, P.R. China
| | - Hongguo Zhao
- Department of Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266555, P.R. China
| | - Zhongguang Cui
- Department of Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266555, P.R. China
| | - Guanglun Li
- Department of Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266555, P.R. China
| | - Fanjun Meng
- Department of Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266555, P.R. China
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Liu X, Li H, Wu ML, Wu J, Sun Y, Zhang KL, Liu J. Resveratrol Reverses Retinoic Acid Resistance of Anaplastic Thyroid Cancer Cells via Demethylating CRABP2 Gene. Front Endocrinol (Lausanne) 2019; 10:734. [PMID: 31736873 PMCID: PMC6828648 DOI: 10.3389/fendo.2019.00734] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 10/10/2019] [Indexed: 12/29/2022] Open
Abstract
Background: Cellular retinoic acid binding protein 2 (CRABP2) mediates retinoic acid/RA anti-cancer pathways. Resveratrol effectively reverses RA tolerance and upregulates CRABP2 expression of anaplastic thyroid cancer cell line THJ-11T. As DNA methylation is responsible for CRABP2 silencing, the CRABP2 methylation status of THJ-11T cells and the demethylating effect of resveratrol on this gene are elucidated. Materials and methods: The statuses of CRABP2 expression and methylation and the levels of DNA methyltransferases (DNMTs) DNMT1, DNMT3A, and DNMT3B of THJ-11T cells were examined before and after resveratrol treatment via multiple experimental methods. The human medulloblastoma UW228-2 cell line was cited as the control of CRABP2 methylation and gemcitabine as the demethylator control. Results: RT-PCR, immunocytochemical staining and Western blotting showed that resveratrol significantly increased the CRABP2 expression and RA sensitivity of THJ-11T and UW228-2 cells. Bisulfite sequencing showed five CpG methylation sites at the CRABP2 promoter region of both cell lines, which were partially (3/5) demethylated by resveratrol and totally (5/5) by gemcitabine. DNMT1, DNMT3A, and DNMT3B were reduced in UW228-2 cells and DNMT1 and DNMT3A were reduced in THJ-11T cells after resveratrol treatment in a time-related fashion. Conclusion: Resveratrol is able to erase CRABP2 methylation and can thereby increase the RA sensitivity of THJ-11T and UW228-2 cells. This study demonstrates the additional value of the natural polyphenolic compound resveratrol as a demethylator in cancer treatments.
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Affiliation(s)
- Xin Liu
- Liaoning Laboratory of Cancer Genetics and Epigenetics, Department of Cell Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Hong Li
- Liaoning Laboratory of Cancer Genetics and Epigenetics, Department of Cell Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Mo-Li Wu
- Liaoning Laboratory of Cancer Genetics and Epigenetics, Department of Cell Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Jiao Wu
- Liaoning Laboratory of Cancer Genetics and Epigenetics, Department of Cell Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yuan Sun
- Liaoning Laboratory of Cancer Genetics and Epigenetics, Department of Cell Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Kai-Li Zhang
- Liaoning Laboratory of Cancer Genetics and Epigenetics, Department of Cell Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
- *Correspondence: Kai-Li Zhang
| | - Jia Liu
- Liaoning Laboratory of Cancer Genetics and Epigenetics, Department of Cell Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
- Research Center, South China University School of Medicine, Guangzhou, China
- Jia Liu
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