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Lin DL, Magnaye KM, Porsche CE, Levan SR, Rackaityte E, Özçam M, Lynch SV. 12,13-diHOME Promotes Inflammatory Macrophages and Epigenetically Modifies Their Capacity to Respond to Microbes and Allergens. J Immunol Res 2024; 2024:2506586. [PMID: 38974097 PMCID: PMC11227377 DOI: 10.1155/2024/2506586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 05/10/2024] [Accepted: 05/25/2024] [Indexed: 07/09/2024] Open
Abstract
Elevated infant fecal concentrations of the bacterial-derived lipid 12,13-dihydroxy-9Z-octadecenoic acid (12,13-diHOME) increase the risk for childhood atopy and asthma. However, the mechanisms by which this lipid contributes to disease development are largely unknown. We hypothesized that macrophages, which are key to both antimicrobial and antigen responses, are functionally and epigenetically modified by 12,13-diHOME leading to short- and long-term dysfunction with consequences for both antimicrobial and antigenic responses. Macrophages exposed to 12,13-diHOME are skewed toward inflammatory IL-1β highCD206low cells, a phenomenon that is further amplified in the presence of common microbial-, aero-, and food-allergens. These IL-1β highCD206low macrophages also exhibit reduced bacterial phagocytic capacity. In primary immune cell coculture assays involving peanut allergen stimulation, 12,13-diHOME promotes both IL-1β and IL-6 production, memory B cell expansion, and increased IgE production. Exposure to 12,13-diHOME also induces macrophage chromatin remodeling, specifically diminishing access to interferon-stimulated response elements resulting in reduced interferon-regulated gene expression upon bacterial lipopolysaccharide stimulation. Thus 12,13-diHOME reprograms macrophage effector function, B-cell interactions and promotes epigenetic modifications that exacerbate inflammatory response to allergens and mutes antimicrobial response along the interferon axis. These observations offer plausible mechanisms by which this lipid promotes early-life pathogenic microbiome development and innate immune dysfunction associated with childhood allergic sensitization.
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Affiliation(s)
- Din L. Lin
- Division of GastroenterologyDepartment of MedicineUniversity of California, San Francisco, CA 94143, USA
| | - Kevin M. Magnaye
- Division of GastroenterologyDepartment of MedicineUniversity of California, San Francisco, CA 94143, USA
| | - Cara E. Porsche
- Division of GastroenterologyDepartment of MedicineUniversity of California, San Francisco, CA 94143, USA
| | - Sophia R. Levan
- Division of GastroenterologyDepartment of MedicineUniversity of California, San Francisco, CA 94143, USA
| | - Elze Rackaityte
- Division of GastroenterologyDepartment of MedicineUniversity of California, San Francisco, CA 94143, USA
| | - Mustafa Özçam
- Division of GastroenterologyDepartment of MedicineUniversity of California, San Francisco, CA 94143, USA
| | - Susan V. Lynch
- Division of GastroenterologyDepartment of MedicineUniversity of California, San Francisco, CA 94143, USA
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Fouladvandi R, Masoudi AA, Totonchi M, Hezavehei M, Sharafi M. Effects of different extenders on epigenetic patterns and functional parameters of bull sperm during cryopreservation process. Reprod Domest Anim 2024; 59:e14570. [PMID: 38700367 DOI: 10.1111/rda.14570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/27/2024] [Accepted: 04/09/2024] [Indexed: 05/05/2024]
Abstract
The cryopreservation process induces alterations in cellular parameters and epigenetic patterns in bull sperm, which can be prevented by adding cryoprotectants in the freezing extenders. The purpose of this study was to compare the protective effects of two extenders based on soybean lecithin (SLE) and egg yolk (EYE) on epigenetic patterns and quality parameters of sperm such as motility parameters, mitochondrial membrane integrity, DNA fragmentation, viability, and apoptotic-like changes of bull sperm after cryopreservation. Results demonstrated that cryopreservation significantly (p < .05) reduced the level of DNA global methylation, H3K9 histone acetylation, and H3K4 histone methylation in both frozen groups compared to the fresh sperm. Also, the level of H3K9 acetylation was lower in the frozen SLE group (21.2 ± 1.86) compared to EYE group (15.2 ± 1.86). In addition, the SLE frozen group had a higher percentage of viability, progressive motility, and linearity (LIN) in SLE frozen group compared to EYE frozen group. However, no difference was observed in mitochondrial membrane integrity and DNA fragmentation between SLE and EYE frozen groups. While soybean-lecithin-based extender showed some initial positive impacts of epigenetics and semen parameters, further investigations can provide useful information for better freezing.
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Affiliation(s)
- Razieh Fouladvandi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Ali Akbar Masoudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Mehdi Totonchi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Maryam Hezavehei
- Department of Embryology at Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
- Research Center for Reproduction and Fertility, Faculty of Veterinary Medicine, Montreal University, Quebec, Canada
| | - Mohsen Sharafi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
- Semex Alliance, Guelph, Ontario, Canada
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Effects of 5-Aza on neurogenesis contribute to learning and memory in the mouse hippocampus. Biomed Pharmacother 2022; 154:113623. [PMID: 36081289 DOI: 10.1016/j.biopha.2022.113623] [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: 06/01/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND 5-Aza-2'-deoxycytidine (5-Aza-CdR) is a demethylating agent that has various biological effects related to DNA methylation. DNA methylation plays important roles in learning and memory. We have reported that 5-Aza-CdR improved the performance of mice in the water maze and step-down tests. Some behaviours have been well recognized to be mediated by neurogenesis in the hippocampus. The Notch signalling pathway plays a key role in adult hippocampal neurogenesis. In this study, we examined whether 5-Aza-CdR (DNA methyltransferase inhibitor) affects neurogenesis and Notch1 expression. METHODS The learning and memory behaviour of mice was evaluated by a conditioned avoidance learning 24 h after 5-Aza-CdR treatment. The mRNA and protein expression levels of Notch1 and HES1 were measured by real-time PCR and Western blotting. The 5-bromo-2'-deoxyuridine (BrdU)-positive cells and the expression of Notch1 in the hippocampal DG were observed through laser confocal microscopy. To further clarify whether 5-Aza-CdR affects behaviour through neurogenesis, the expression level of Notch1, cell viability and cell cycle were analysed using the HT22 cell line. RESULTS The behaviour in conditioned avoidance learning was improved, while neurogenesis and the Notch1 pathway were increased in the hippocampus of mice that were injected with 5-Aza-CdR. In vitro experiments showed that 5-Aza-CdR increased the expression of the Notch1 pathway and upregulated S-phase in the cell cycle and cell viability. CONCLUSIONS Our results suggest that the effect of 5-Aza-CdR on behaviour may be related to an increase in neurogenesis with upregulation of the Notch1 pathway in the hippocampus.
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Untargeted Metabolomics Showed Accumulation of One-Carbon Metabolites to Facilitate DNA Methylation during Extracellular Matrix Detachment of Cancer Cells. Metabolites 2022; 12:metabo12030267. [PMID: 35323710 PMCID: PMC8951017 DOI: 10.3390/metabo12030267] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 02/01/2023] Open
Abstract
Tumor cells detached from the extracellular matrix (ECM) undergo anoikis resistance and metabolic reprogramming to facilitate cancer cell survival and promote metastasis. During ECM detachment, cancer cells utilize genomic methylation to regulate transcriptional events. One-carbon (1C) metabolism is a well-known contributor of SAM, a global substrate for methylation reactions, especially DNA methylation. DNA methylation-mediated repression of NK cell ligands MICA and MICB during ECM detachment has been overlooked. In the current work, we quantitated the impact of ECM detachment on one-carbon metabolites, expression of 1C regulatory pathway genes, and total methylation levels. Our results showed that ECM detachment promotes the accumulation of one-carbon metabolites and induces regulatory pathway genes and total DNA methylation. Furthermore, we measured the expression of well-known targets of DNA methylation in NK cell ligands in cancer cells, namely, MICA/B, during ECM detachment and observed low expression compared to ECM-attached cancer cells. Finally, we treated the ECM-detached cancer cells with vitamin C (a global methylation inhibitor) and observed a reduction in the promoter methylation of NK cell ligands, resulting in MICA/B re-expression. Treatment with vitamin C was also found to reduce global DNA methylation levels in ECM-detached cancer cells.
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Mendonca A, Sánchez O, Zhao H, Lin L, Min A, Yuan C. Development and application of novel BiFC probes for cell sorting based on epigenetic modification. Cytometry A 2022; 101:339-350. [PMID: 35001539 DOI: 10.1002/cyto.a.24530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022]
Abstract
The epigenetic signature of cancer cells varies with disease progression and drug treatment, necessitating the study of these modifications with single cell resolution over time. The rapid detection and sorting of cells based on their underlying epigenetic modifications by flow cytometry can enable single cell measurement and tracking to understand tumor heterogeneity and progression warranting the development of a live-cell compatible epigenome probes. In this work, we developed epigenetic probes based on bimolecular fluorescence complementation (BiFC) and demonstrated their capabilities in quantifying and sorting cells based on their epigenetic modification contents. The sorted cells are viable and exhibit distinctive responses to chemo-therapy drugs. Notably, subpopulations of MCF7 cells with higher H3K9me3 levels are more likely to develop resistance to Doxorubicin. Subpopulations with higher 5mC levels, on the other hand, tend to be more responsive. Overall, we report for the first time, the application of novel split probes in flow cytometry application and elucidated the potential role of 5mC and H3K9me3 in determining drug responses.
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Affiliation(s)
- Agnes Mendonca
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Oscar Sánchez
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Han Zhao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Li Lin
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Alan Min
- Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana, USA.,Purdue University Center for Cancer Research, West Lafayette, Indiana, USA
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Meier R, Nissen E, Koestler DC. Low variability in the underlying cellular landscape adversely affects the performance of interaction-based approaches for conducting cell-specific analyses of DNA methylation in bulk samples. Stat Appl Genet Mol Biol 2021; 20:73-84. [PMID: 34378875 PMCID: PMC9125800 DOI: 10.1515/sagmb-2021-0004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/19/2021] [Indexed: 11/15/2022]
Abstract
Statistical methods that allow for cell type specific DNA methylation (DNAm) analyses based on bulk-tissue methylation data have great potential to improve our understanding of human disease and have created unprecedented opportunities for new insights using the wealth of publicly available bulk-tissue methylation data. These methodologies involve incorporating interaction terms formed between the phenotypes/exposures of interest and proportions of the cell types underlying the bulk-tissue sample used for DNAm profiling. Despite growing interest in such "interaction-based" methods, there has been no comprehensive assessment how variability in the cellular landscape across study samples affects their performance. To answer this question, we used numerous publicly available whole-blood DNAm data sets along with extensive simulation studies and evaluated the performance of interaction-based approaches in detecting cell-specific methylation effects. Our results show that low cell proportion variability results in large estimation error and low statistical power for detecting cell-specific effects of DNAm. Further, we identified that many studies targeting methylation profiling in whole-blood may be at risk to be underpowered due to low variability in the cellular landscape across study samples. Finally, we discuss guidelines for researchers seeking to conduct studies utilizing interaction-based approaches to help ensure that their studies are adequately powered.
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Affiliation(s)
- Richard Meier
- Department of Biostatistics & Data Science, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City66160, KS, USA
| | - Emily Nissen
- Department of Biostatistics & Data Science, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City66160, KS, USA
| | - Devin C. Koestler
- Department of Biostatistics & Data Science, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City66160, KS, USA
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7
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Somasundaram S, Satheesh V, Singh M, Anandhan S. A simple flow cytometry-based assay to study global methylation levels in onion, a non-model species. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1859-1865. [PMID: 34539120 PMCID: PMC8405793 DOI: 10.1007/s12298-021-01047-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED DNA methylation is an important epigenetic mark and global methylation dynamics regulate plant developmental processes. Even though genome sequencing technologies have made DNA methylation studies easier, it is difficult in non-model species where genome information is not available. Therefore in this study, we developed a simple assay for analysing global methylation levels in plants by washless immunolabelling of unfixed nuclei using flow cytometry. Onion leaf tissue was used as a model system, and mean fluorescence intensity due to anti-5- methyl cytosine (5-mC) antibodies were used as a measure of global methylation levels. Among three nuclear isolation buffers evaluated, the highest nuclear yield with the low background was obtained with LB01. To maintain a balance between high DNA fluorescence value and low coefficient of variation of DNA peaks, 45 min of hydrolysis with 0.2 N hydrochloric acid was used for chromatin denaturation resulting in six-fold increase in 5-mC fluorescence compared to control. This method was used successfully to detect 5-Azacytidine induced DNA hypomethylation in onion leaf tissues. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01047-6.
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Affiliation(s)
- Saravanakumar Somasundaram
- ICAR-Directorate of Onion and Garlic Research, Pune, 410505 India
- Present Address: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Major Singh
- ICAR-Directorate of Onion and Garlic Research, Pune, 410505 India
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Seddon AR, Liau Y, Pace PE, Miller AL, Das AB, Kennedy MA, Hampton MB, Stevens AJ. Genome-wide impact of hydrogen peroxide on maintenance DNA methylation in replicating cells. Epigenetics Chromatin 2021; 14:17. [PMID: 33761969 PMCID: PMC7992848 DOI: 10.1186/s13072-021-00388-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/01/2021] [Indexed: 12/22/2022] Open
Abstract
Background Environmental factors, such as oxidative stress, have the potential to modify the epigenetic landscape of cells. We have previously shown that DNA methyltransferase (DNMT) activity can be inhibited by sublethal doses of hydrogen peroxide (H2O2). However, site-specific changes in DNA methylation and the reversibility of any changes have not been explored. Using bead chip array technology, differential methylation was assessed in Jurkat T-lymphoma cells following exposure to H2O2. Results Sublethal H2O2 exposure was associated with an initial genome-wide decrease in DNA methylation in replicating cells, which was largely corrected 72 h later. However, some alterations were conserved through subsequent cycles of cell division. Significant changes to the variability of DNA methylation were also observed both globally and at the site-specific level. Conclusions This research indicates that increased exposure to H2O2 can result in long-term alterations to DNA methylation patterns, providing a mechanism for environmental factors to have prolonged impact on gene expression. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00388-6.
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Affiliation(s)
- Annika R Seddon
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand.
| | - Yusmiati Liau
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Paul E Pace
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Allison L Miller
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Andrew B Das
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Mark B Hampton
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Aaron J Stevens
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand.
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Deshpande SS, Nemani H, Arumugam G, Ravichandran A, Balasinor NH. High-fat diet-induced and genetically inherited obesity differentially alters DNA methylation profile in the germline of adult male rats. Clin Epigenetics 2020; 12:179. [PMID: 33213487 PMCID: PMC7678167 DOI: 10.1186/s13148-020-00974-7] [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: 05/19/2020] [Accepted: 11/10/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Paternal obesity has been associated with reduced live birth rates. It could lead to inheritance of metabolic disturbances to the offspring through epigenetic mechanisms. However, obesity is a multifactorial disorder with genetic or environmental causes. Earlier we had demonstrated differential effects of high-fat diet-induced obesity (DIO) and genetically inherited obesity (GIO) on metabolic, hormonal profile, male fertility, and spermatogenesis using two rat models. The present study aimed to understand the effect of DIO and GIO on DNA methylation in male germline, and its subsequent effects on the resorbed (post-implantation embryo loss) and normal embryos. First, we assessed the DNA methylation enzymatic machinery in the testis by Real-Time PCR, followed global DNA methylation levels in spermatozoa and testicular cells by ELISA and flow cytometry, respectively. Further, we performed Methylation Sequencing in spermatozoa for both the groups. Sequencing data in spermatozoa from both the groups were validated using Pyrosequencing. Expression of the differentially methylated genes was assessed in the resorbed and normal embryos sired by the DIO group using Real-Time PCR for functional validation. RESULTS We noted a significant decrease in Dnmt transcript and global DNA methylation levels in the DIO group and an increase in the GIO group. Sequencing analysis showed 16,966 and 9113 differentially methylated regions in the spermatozoa of the DIO and GIO groups, respectively. Upon pathway analysis, we observed genes enriched in pathways involved in embryo growth and development namely Wnt, Hedgehog, TGF-beta, and Notch in spermatozoa for both the groups, the methylation status of which partially correlated with the gene expression pattern in resorbed and normal embryos sired by the DIO group. CONCLUSION Our study reports the mechanism by which diet-induced and genetically inherited obesity causes differential effects on the DNA methylation in the male germline that could be due to a difference in the white adipose tissue accumulation. These differences could either lead to embryo loss or transmit obesity-related traits to the offspring in adult life.
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Affiliation(s)
- Sharvari S. Deshpande
- Department of Neuroendocrinology, ICMR-National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai 400012 India
| | - Harishankar Nemani
- National Institute of Nutrition Animal Facility, ICMR-National Institute of Nutrition, Jamai-Osmania PO, Hyderabad 500 007 India
| | - Gandhimathi Arumugam
- Genome Informatics Department, Genotypic Technologies Pvt. Ltd., #2/13, Balaji Complex, Poojari Layout, 80 Feet Road, R.M.V. 2nd stage, Bengaluru, India
| | - Avinash Ravichandran
- Genome Informatics Department, Genotypic Technologies Pvt. Ltd., #2/13, Balaji Complex, Poojari Layout, 80 Feet Road, R.M.V. 2nd stage, Bengaluru, India
| | - Nafisa H. Balasinor
- Department of Neuroendocrinology, ICMR-National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai 400012 India
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Li S, Ren C, Stone C, Chandra A, Xu J, Li N, Han C, Ding Y, Ji X, Shao G. Hamartin: An Endogenous Neuroprotective Molecule Induced by Hypoxic Preconditioning. Front Genet 2020; 11:582368. [PMID: 33193709 PMCID: PMC7556298 DOI: 10.3389/fgene.2020.582368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/08/2020] [Indexed: 11/23/2022] Open
Abstract
Hypoxic/ischemic preconditioning (HPC/IPC) is an innate neuroprotective mechanism in which a number of endogenous molecules are known to be involved. Tuberous sclerosis complex 1 (TSC1), also known as hamartin, is thought to be one such molecule. It is also known that hamartin is involved as a target in the rapamycin (mTOR) signaling pathway, which functions to integrate a variety of environmental triggers in order to exert control over cellular metabolism and homeostasis. Understanding the role of hamartin in ischemic/hypoxic neuroprotection will provide a novel target for the treatment of hypoxic-ischemic disease. Therefore, the proposed molecular mechanisms of this neuroprotective role and its preconditions are reviewed in this paper, with emphases on the mTOR pathway and the relationship between the expression of hamartin and DNA methylation.
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Affiliation(s)
- Sijie Li
- Beijing Key Laboratory of Hypoxic Conditioning Translational Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China.,Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, China
| | - Changhong Ren
- Beijing Key Laboratory of Hypoxic Conditioning Translational Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China.,Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, China
| | - Christopher Stone
- Department of Neurosurgery, Wayne State University School of Medicine, Detroit, MI, United States
| | - Ankush Chandra
- Department of Neurosurgery, Wayne State University School of Medicine, Detroit, MI, United States
| | - Jiali Xu
- Beijing Key Laboratory of Hypoxic Conditioning Translational Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Ning Li
- Beijing Key Laboratory of Hypoxic Conditioning Translational Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Cong Han
- Department of Neurosurgery, The Fifth Medical Centre of PLA General Hospital, Beijing, China
| | - Yuchuan Ding
- Department of Neurosurgery, Wayne State University School of Medicine, Detroit, MI, United States
| | - Xunming Ji
- Beijing Key Laboratory of Hypoxic Conditioning Translational Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Guo Shao
- Beijing Key Laboratory of Hypoxic Conditioning Translational Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China.,Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, China.,Public Health Department, Biomedicine Research Center, Basic Medical College, Baotou, China.,Baotou Medical College of Neuroscience Institute, Baotou Medical College, Baotou, China
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11
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Lou M, Li R, Lang TY, Zhang LY, Zhou Q, Li L. Aberrant methylation of GADD45A is associated with decreased radiosensitivity in cervical cancer through the PI3K/AKT signaling pathway. Oncol Lett 2020; 21:8. [PMID: 33240414 PMCID: PMC7681222 DOI: 10.3892/ol.2020.12269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022] Open
Abstract
Epigenetic inactivation of GADD45A is a common occurrence in different types of cancer. However, little is known regarding its association with radiosensitivity in cervical cancer (CC). Thus, the present study aimed to investigate the association between aberrant GADD45A methylation and radiosensitivity in CC. SiHa, HeLa and CaSki CC cells were treated with 5-azacytidine (5-azaC), with or without irradiation. The expression levels of GADD45A and AKT related molecules were detected via reverse transcription-quantitative PCR and western blot analyses. The methylation status of GADD45A was assessed via methylation-specific PCR and cell proliferation assays, while clonogenic assays and flow cytometric analysis were performed to assess the function of the genes (GADD45A and AKT) in the CC cell lines. The results demonstrated that methylation of GADD45A was significantly higher in the radioresistant tissues (63.16%) compared with the radiosensitive samples (33.33%). In addition, the surviving fraction of SiHa cells following irradiation with 2 Gy was demonstrated to be highest amongst the three CC cells (CaSki, 57±9.5%; HeLa, 70±4% and SiHa, 75±10%). The survival rate of SiHa cells following treatment with 5-azaC and ionizing radiation (IR) significantly decreased as the radiation dose increased, compared with treatment with IR alone. Following overexpression of GADD45A or treatment with 5-azaC, the radiosensitivity of SiHa cells significantly increased compared with both the control vector and PBS treated groups. In addition, the AKT inhibitor, MK-2206, increased the radiosensitivity of SiHa cells. Notably, aberrant methylation of GADD45A was associated with decreased radiosensitivity in CC, and the PI3K/AKT signaling pathway was essential for radioresistance, which was mediated through downregulation of GADD45A.
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Affiliation(s)
- Meng Lou
- Department of Gynecologic Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Rong Li
- Department of Gynecologic Oncology, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing 400030, P.R. China
| | - Ting-Yuan Lang
- Department of Gynecologic Oncology, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing 400030, P.R. China
| | - Li-Ying Zhang
- Department of Gynecology, The Second Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi 530000, P.R. China
| | - Qi Zhou
- Department of Gynecologic Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China.,Department of Gynecologic Oncology, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing 400030, P.R. China.,Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing 400030, P.R. China.,Key Laboratory for Biorheological Science and Technology of Ministry of Education, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing 400030, P.R. China
| | - Li Li
- Department of Gynecologic Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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Mudla A, Jiang Y, Arimoto KI, Xu B, Rajesh A, Ryan AP, Wang W, Daugherty MD, Zhang DE, Hao N. Cell-cycle-gated feedback control mediates desensitization to interferon stimulation. eLife 2020; 9:58825. [PMID: 32945770 PMCID: PMC7500952 DOI: 10.7554/elife.58825] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/02/2020] [Indexed: 12/13/2022] Open
Abstract
Cells use molecular circuits to interpret and respond to extracellular cues, such as hormones and cytokines, which are often released in a temporally varying fashion. In this study, we combine microfluidics, time-lapse microscopy, and computational modeling to investigate how the type I interferon (IFN)-responsive regulatory network operates in single human cells to process repetitive IFN stimulation. We found that IFN-α pretreatments lead to opposite effects, priming versus desensitization, depending on input durations. These effects are governed by a regulatory network composed of a fast-acting positive feedback loop and a delayed negative feedback loop, mediated by upregulation of ubiquitin-specific peptidase 18 (USP18). We further revealed that USP18 upregulation can only be initiated at the G1/early S phases of cell cycle upon the treatment onset, resulting in heterogeneous and delayed induction kinetics in single cells. This cell cycle gating provides a temporal compartmentalization of feedback loops, enabling duration-dependent desensitization to repetitive stimulations.
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Affiliation(s)
- Anusorn Mudla
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Yanfei Jiang
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Kei-Ichiro Arimoto
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Bingxian Xu
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Adarsh Rajesh
- Department of Bioengineering, University of California, San Diego, La Jolla, United States
| | - Andy P Ryan
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, United States
| | - Matthew D Daugherty
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Dong-Er Zhang
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States.,Department of Pathology, Moores UCSD Cancer Center, University of California, San Diego, La Jolla, United States
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
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Bhowmick S, AlFaris NA, ALTamimi JZ, ALOthman ZA, Aldayel TS, Wabaidur SM, Islam MA. Screening and analysis of bioactive food compounds for modulating the CDK2 protein for cell cycle arrest: Multi-cheminformatics approaches for anticancer therapeutics. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128316] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Mitochondrial DNA methylation misleads global DNA methylation detected by antibody-based methods. Anal Biochem 2020; 601:113789. [PMID: 32473121 DOI: 10.1016/j.ab.2020.113789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/12/2020] [Accepted: 05/17/2020] [Indexed: 12/27/2022]
Abstract
Cytosine methylation is the leading epigenetic modification on DNA playing a role in gene regulation. Methylation can occur in cytosines of any nucleic acids in cytosol (as mitochondrial DNA, mtDNA) and in nuclear DNA (ncDNA). mtDNA exists as multiple copies within numerous mitochondria. This suggests that the number of mitochondria and mtDNA copy number can indicate the presence of a significant amount of DNA methylation within total DNA methylation detected. However, immunofluorescence method does not have a step to discriminate the staining between ncDNA and mtDNA. Antibodies used in immunological methods are methylation-specific but not selective for DNA type and they can bind to methylated cytosines in any DNA within the specimen. Current study aimed to understand whether mtDNA methylation interferes with the detection of nuclear DNA methylation by immunofluorescence and affinity enrichment (ELISA) in different mammalian cells. Experiments were performed to distinguish methylation between mtDNA and ncDNA. Immunofluorescence showed that there was no significant difference in the detected amount of methylation between mitochondrial and nuclear DNA. But ELISA revealed that up to 25% of cellular methylation was derived from mitochondria. This suggests that significant contamination of mtDNA methylation with ncDNA methylation can result in overestimation of the quantitative level of nuclear methylation.
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Enzyme-mediated depletion of serum l-Met abrogates prostate cancer growth via multiple mechanisms without evidence of systemic toxicity. Proc Natl Acad Sci U S A 2020; 117:13000-13011. [PMID: 32434918 PMCID: PMC7293657 DOI: 10.1073/pnas.1917362117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Extensive studies in prostate cancer and other malignancies have revealed that l-methionine (l-Met) and its metabolites play a critical role in tumorigenesis. Preclinical and clinical studies have demonstrated that systemic restriction of serum l-Met, either via partial dietary restriction or with bacterial l-Met-degrading enzymes exerts potent antitumor effects. However, administration of bacterial l-Met-degrading enzymes has not proven practical for human therapy because of problems with immunogenicity. As the human genome does not encode l-Met-degrading enzymes, we engineered the human cystathionine-γ-lyase (hMGL-4.0) to catalyze the selective degradation of l-Met. At therapeutically relevant dosing, hMGL-4.0 reduces serum l-Met levels to >75% for >72 h and significantly inhibits the growth of multiple prostate cancer allografts/xenografts without weight loss or toxicity. We demonstrate that in vitro, hMGL-4.0 causes tumor cell death, associated with increased reactive oxygen species, S-adenosyl-methionine depletion, global hypomethylation, induction of autophagy, and robust poly(ADP-ribose) polymerase (PARP) cleavage indicative of DNA damage and apoptosis.
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Jiménez-Hernández E, Duarte-Rodríguez DA, Núñez-Enriquez JC, Flores-Lujano J, Martín-Trejo JA, Espinoza-Hernández LE, Arellano-Galindo J, Medina-Sanson A, García-Jiménez X, Paredes-Aguilera R, Flores-Villegas LV, Peñaloza-González JG, Torres-Nava JR, Espinosa-Elizondo RM, Amador-Sánchez R, Dosta-Herrera JJ, Mondragón-García JA, Valdés-Guzmán H, Mejía-Pérez L, Espinoza-Anrubio G, Paz-Bribiesca MM, Salcedo-Lozada P, Landa-García RÁ, Ramírez-Colorado R, Hernández-Mora L, Pérez-Saldivar ML, Santamaría-Ascencio M, López-Loyola A, Godoy-Esquivel AH, García-López LR, Anguiano-Ávalos AI, Mora-Rico K, Castañeda-Echevarría A, Rodríguez-Jiménez R, Cibrian-Cruz JA, Cárdenas-Cardos R, Altamirano-García MB, Sánchez-Ruiz M, Rivera-Luna R, Rodríguez-Villalobos LR, Hernández-Pérez F, Olvera-Durán JÁ, García-Cortés LR, Mata-Rocha M, Sepúlveda-Robles OA, Bekker-Méndez VC, Jiménez-Morales S, Rosas-Vargas H, Mejía-Aranguré JM. Maternal and paternal ages at conception of index child and risk of childhood acute leukaemia: A multicentre case-control study in Greater Mexico City. Cancer Epidemiol 2020; 67:101731. [PMID: 32447241 DOI: 10.1016/j.canep.2020.101731] [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: 07/17/2019] [Revised: 04/15/2020] [Accepted: 04/19/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND The parental age at conception has been reported to be a risk factor for childhood acute leukaemia (AL); however, the relationship is controversial. The aim of the present study was to investigate the association between parental age at conception and the risk of AL in Mexican children, a population with a high incidence of the disease and a high prevalence of pregnancies in adolescents and young adults. METHODS A multicentre case-control study was conducted. Incident AL cases younger than 17 years of age diagnosed between 2010 and 2015 were included. Controls were matched with cases according to age, sex, and health institution. Using logistic regression analysis, adjusted odds ratios (aOR) and 95 % confidence intervals (95 % CI) were calculated for each maternal stratum after adjusting for paternal age at conception of index child. The maternal age between 25 and 29.99 years was selected as the reference category. RESULTS In most strata where maternal and paternal ages were assessed, no association was found with the risk of developing acute lymphoblastic leukaemia (ALL) and acute myeloid leukaemia (AML) in their offspring. An increased risk for AML was observed when the mother was between 20 and 24.99 years of age and the father aged 25-29.99 years (aOR, 1.94; 95 % CI, 1.03-3.67). In addition, there was a positive association for ALL when the mother´s age was between 20 and 24.99 years and the father was <20 years of age, however, a very wide confidence interval was noted (aOR, 12.26; 95 % CI, 1.41-106.83). CONCLUSION In the present study, maternal and paternal ages assessed in different strata showed little association with risk of developing ALL and AML in children. Positive associations between risk of both types of childhood AL were observed with younger paternal and maternal ages.
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Affiliation(s)
- Elva Jiménez-Hernández
- Coordinación de Investigación en Salud, CMN "Siglo XXI", IMSS. Av. Cuauhtemoc 330, Delegación Cuauhtémoc, Mexico City, 06720, Mexico; Servicio de Hematología Pediátrica, Hospital General "Gaudencio González Garza", CMN "La Raza", IMSS. Calzada Vallejo y Jacarandas S/N Col. La Raza, Delegación Azcapotzalco, Mexico City, 02990, Mexico.
| | - David Aldebarán Duarte-Rodríguez
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de AltaEspecialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS). Av. Cuauhtemoc 330, Delegación Cuauhtémoc, Mexico City, 06720, Mexico.
| | - Juan Carlos Núñez-Enriquez
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de AltaEspecialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS). Av. Cuauhtemoc 330, Delegación Cuauhtémoc, Mexico City, 06720, Mexico.
| | - Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de AltaEspecialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS). Av. Cuauhtemoc 330, Delegación Cuauhtémoc, Mexico City, 06720, Mexico.
| | - Jorge Alfonso Martín-Trejo
- Servicio de Hematología, UMAE Hospital de Pediatría, CMN "Siglo XXI", IMSS.Av. Cuauhtemoc 330, Delegación Cuauhtémoc, Mexico City, 06720, Mexico.
| | - Laura Eugenia Espinoza-Hernández
- Servicio de Hematología Pediátrica, Hospital General "Gaudencio González Garza", CMN "La Raza", IMSS. Calzada Vallejo y Jacarandas S/N Col. La Raza, Delegación Azcapotzalco, Mexico City, 02990, Mexico.
| | - José Arellano-Galindo
- Hospital Infantil de México Federico Gómez, Secretaria de Salud (SS). Calle Doctor Márquez 162, Col. Doctores, Delegación Cuauhtémoc, Mexico City, 06720, Mexico.
| | - Aurora Medina-Sanson
- Hospital Infantil de México Federico Gómez, Secretaria de Salud (SS). Calle Doctor Márquez 162, Col. Doctores, Delegación Cuauhtémoc, Mexico City, 06720, Mexico.
| | - Xochiketzalli García-Jiménez
- Servicio de Hematología, UMAE Hospital de Pediatría, CMN "Siglo XXI", IMSS.Av. Cuauhtemoc 330, Delegación Cuauhtémoc, Mexico City, 06720, Mexico.
| | - Rogelio Paredes-Aguilera
- Servicio de Hematología, Instituto Nacional de Pediatría (INP), SS. Insurgentes Sur 3700, Letra C, Col. Insurgentes Cuicuilco, Delegación Coyoacán, Mexico City, 04530, Mexico.
| | - Luz Victoria Flores-Villegas
- Servicio de Hematología Pediátrica, CMN "20 de Noviembre", Instituto de Seguridad Social al Servicio de los Trabajadores del Estado (ISSSTE). Félix Cuevas 540, Col. Del Valle, Delegación Benito Juárez, Mexico City, 03229, Mexico.
| | - José Gabriel Peñaloza-González
- Servicio de Onco-Pediatría, Hospital Juárez de México, SS. Av. Instituto Politécnico Nacional 5160, Col. Magdalena de las Salinas, Delegación Gustavo A. Madero, Mexico City, 07760, Mexico.
| | - José Refugio Torres-Nava
- Servicio de Oncología, Hospital Pediátrico "Moctezuma", Secretaría de Salud de la Ciudad de México (SSCDMX). Oriente 158-189, Col. Moctezuma 2a Sección, Delegación Venustiano Carranza, Mexico City, 15530, Mexico.
| | - Rosa Martha Espinosa-Elizondo
- Servicio de Hematología Pediátrica, Hospital General de México, SSa. Eje 2A Sur (Dr. Balmis) 148, Col. Doctores, Delegación Cuauhtémoc, Mexico City, 06726, Mexico.
| | - Raquel Amador-Sánchez
- Servicio de Hematología Pediátrica, Hospital General Regional (HGR), No. 1 "Dr. Carlos Mac Gregor Sánchez Navarro" IMSS. Av. Gabriel Mancera No. 222, Col. Del Valle, Mexico City, 03100, Mexico.
| | - Juan José Dosta-Herrera
- Servicio de Cirugía Pediátrica, Hospital General "Gaudencio González Garza", CMN "La Raza", IMSS. Calzada Vallejo y Jacarandas S/N Col. La Raza, Delegación Azcapotzalco, Mexico City, 02990, Mexico.
| | - Javier Anastacio Mondragón-García
- Servicio de Cirugía Pediátrica, HGR No. 1 "Dr. Carlos Mac Gregor Sánchez Navarro" IMSS. Av. Gabriel Mancera No. 222, Col. Del Valle, Mexico City, 03100, Mexico.
| | - Heriberto Valdés-Guzmán
- Hospital Pediátrico de Iztacalco, SSCDMX. Av. Coyuya y Terraplén de Rio Frio S/N, Col. La Cruz. Iztacalco, Mexico City, 08310 Mexico.
| | - Laura Mejía-Pérez
- Hospital Pediátrico de Iztapalapa, SSCDMX. Av. Ermita Iztapalapa 780, Col. Granjas San Antonio. Delegación Iztapalapa, Mexico City, 09070. Mexico.
| | - Gilberto Espinoza-Anrubio
- Servicio de Pediatría, Hospital General Zona (HGZ) No. 8 "Dr. Gilberto Flores Izquierdo"IMSS. Av. Rio Magdalena 289 Ciudad De México, Col.Tizapan San Angel, Delegación Álvaro Obregón, Mexico City, 1090, Mexico.
| | - María Minerva Paz-Bribiesca
- Servicio de Pediatría, Hospital Juárez del Centro, SS. Jesus María 13, Col Centro, Delegación Cuahtemoc, Mexico City, 06000, Mexico.
| | - Perla Salcedo-Lozada
- Hospital General de Ecatepec "Las Américas", Instituto de Salud del Estado de México (ISEM). Av. Simón Bolivar 1, Fraccionamiento Las Américas, Municipio Ecatepec de Morelos. State of Mexico, 55076. Mexico.
| | - Rodolfo Ángel Landa-García
- Hospital General "Dr. Manuel Gea González" SS. Calz. de Tlalpan 4800, Tlalpan Centro I, Belisario Domínguez Secc 16, Delegación Tlalpan, Mexico City,14080, Mexico.
| | - Rosario Ramírez-Colorado
- Hospital Pediátrico "La Villa", SSCDMX. Av. Cantera, Esq. Av. Hidalgo S/n, Col. Estanzuela. Delegación Gustavo A. Madero, Mexico City, 07050, Mexico.
| | - Luis Hernández-Mora
- Hospital Pediátrico "San Juan de Aragón", SSCDMX. Av. 506, S/N San Juan de Aragón 1A. Delegación Gustavo A. Madero, 07969, Mexico.
| | - María Luisa Pérez-Saldivar
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de AltaEspecialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS). Av. Cuauhtemoc 330, Delegación Cuauhtémoc, Mexico City, 06720, Mexico.
| | - Marlene Santamaría-Ascencio
- Servicio de Pediatría, HGR No. 72 "Lic. Vicente Santos Guajardo", IMSS. Calle Filiberto Gómez; S/N, Tlalnepantla, Edo. de Mexico, CP54030. México.
| | - Anselmo López-Loyola
- Servicio de Cirugía Pediátrica, HGZ No. 32, IMSS. Clzd. del Hueso S/N, Col. EX-Ex Hacienda Coapa, Delegación Coyoacán, Mexico City, 14310, Mexico.
| | - Arturo Hermilo Godoy-Esquivel
- Servicio de Cirugía Pediátrica, Hospital Pediátrico de Moctezuma, SSCDMX. Oriente 158-189, Col. Moctezuma 2a Sección, Delegación Venustiano Carranza, Mexico City, 15530, Mexico.
| | - Luis Ramiro García-López
- Servicio de Pediatría, Hospital Pediátrico de Tacubaya, SSCDMX. Carlos Lazo 25, Col. Tacubaya, Delegación Miguel Hidalgo, México City, 11870, Mexico.
| | - Alison Ireri Anguiano-Ávalos
- Urgencias Pediátricas, HGZ No. 47, IMSS. Av. Campaña de Ébano S/N Col. Unidad Vicente Guerrero, Dlegación Iztapalapa, México City, 09200. Mexico.
| | - Karina Mora-Rico
- Servicio de Cirugía Pediátrica, Hospital Regional "1° Octubre", ISSSTE. Av Instituto Politécnico Nacional 1669, Revolución IMSS, Delegación Gustavo A Madero, 07300 Mexico.
| | - Alejandro Castañeda-Echevarría
- Servicio de Pediatría, HGR No. 25 IMSS.Clzd. Ignacio Zaragoza 1840, Col. Juan Escutia, Delegación Iztapalapa, Mexico City, 09100 Mexico.
| | - Roberto Rodríguez-Jiménez
- Servicio de Pediatría, Hospital General de Zona con Medicina Familiar (HGZMF) No. 29, IMSS. AV. 510, S/N, Col. Unidad San Juan de Aragón. Delegación Gustavo A. Madero, Mexico City, 07950, Mexico.
| | - José Alberto Cibrian-Cruz
- Servicio de Cirugía Pediátrica, HGZ No. 27, IMSS. AV. Lázaro Cárdenas, S/N Tlaltelolco, Delegación Cuauhtémoc, México City, 06900 Mexico.
| | - Rocío Cárdenas-Cardos
- Servicio de Oncología, INP, SSa. Insurgentes Sur 3700, Letra C, Col. Insurgentes Cuicuilco, Delegación Coyoacán, Mexico City, 04530, Mexico.
| | - Martha Beatriz Altamirano-García
- Servicio de Pediatría, Hospital General Zona (HGZ) No. 8 "Dr. Gilberto Flores Izquierdo"IMSS. Av. Rio Magdalena 289 Ciudad De México, Col.Tizapan San Angel, Delegación Álvaro Obregón, Mexico City, 1090, Mexico.
| | - Martin Sánchez-Ruiz
- Hospital General de Ecatepec "Las Américas", Instituto de Salud del Estado de México (ISEM). Av. Simón Bolivar 1, Fraccionamiento Las Américas, Municipio Ecatepec de Morelos. State of Mexico, 55076. Mexico.
| | - Roberto Rivera-Luna
- Servicio de Oncología, INP, SSa. Insurgentes Sur 3700, Letra C, Col. Insurgentes Cuicuilco, Delegación Coyoacán, Mexico City, 04530, Mexico.
| | - Luis Rodolfo Rodríguez-Villalobos
- Servicio de Pediatría, Hospital Pediátrico de Tacubaya, SSCDMX. Carlos Lazo 25, Col. Tacubaya, Delegación Miguel Hidalgo, México City, 11870, Mexico.
| | - Francisco Hernández-Pérez
- Urgencias Pediátricas, HGZ No. 47, IMSS. Av. Campaña de Ébano S/N Col. Unidad Vicente Guerrero, Dlegación Iztapalapa, México City, 09200. Mexico.
| | - Jaime Ángel Olvera-Durán
- Servicio de Cirugía Pediátrica, Hospital Regional "1° Octubre", ISSSTE. Av Instituto Politécnico Nacional 1669, Revolución IMSS, Delegación Gustavo A Madero, 07300 Mexico.
| | - Luis Rey García-Cortés
- Delegación Regional Estado de México Oriente, IMSS. Calle 4 25, Fracc. Industrial Alce Blanco, Municipio de Naucalpan de Juárez, State of Mexico, 53370, Mexico.
| | - Minerva Mata-Rocha
- Laboratorio de Biología Molecular de las Leucemias, Unidad de Investigación en Genética Humana, UMAE, Hospital de Pediatría, CMN "Siglo XXI", IMSS. Av. Cuauhtemoc 330, Delegación Cuauhtémoc, Mexico City, 06720, Mexico.
| | - Omar Alejandro Sepúlveda-Robles
- Laboratorio de Biología Molecular de las Leucemias, Unidad de Investigación en Genética Humana, UMAE, Hospital de Pediatría, CMN "Siglo XXI", IMSS. Av. Cuauhtemoc 330, Delegación Cuauhtémoc, Mexico City, 06720, Mexico.
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr.Daniel Méndez Hernández", CMN "La Raza", IMSS. Address. Av. Río Consulado, Col La Raza S/N. Delegación Azcapotzalco, Mexico City, 02990 Mexico.
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Mexico City,14610 Mexico.
| | - Haydee Rosas-Vargas
- Unidad de Investigación Médica en Genética Humana, UMAE, Hospital de Pediatría, CMN "Siglo XXI", IMSS. Av. Cuauhtemoc 330, Delegación Cuauhtémoc, Mexico City, 06720, Mexico.
| | - Juan Manuel Mejía-Aranguré
- Coordinación de Investigación en Salud, CMN "Siglo XXI", IMSS. Av. Cuauhtemoc 330, Delegación Cuauhtémoc, Mexico City, 06720, Mexico; Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de AltaEspecialidad (UMAE) Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS). Av. Cuauhtemoc 330, Delegación Cuauhtémoc, Mexico City, 06720, Mexico; Laboratorio de Biología Molecular de las Leucemias, Unidad de Investigación en Genética Humana, UMAE, Hospital de Pediatría, CMN "Siglo XXI", IMSS. Av. Cuauhtemoc 330, Delegación Cuauhtémoc, Mexico City, 06720, Mexico.
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Zhang W, Klinkebiel D, Barger CJ, Pandey S, Guda C, Miller A, Akers SN, Odunsi K, Karpf AR. Global DNA Hypomethylation in Epithelial Ovarian Cancer: Passive Demethylation and Association with Genomic Instability. Cancers (Basel) 2020; 12:cancers12030764. [PMID: 32213861 PMCID: PMC7140107 DOI: 10.3390/cancers12030764] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 03/19/2020] [Indexed: 02/08/2023] Open
Abstract
A hallmark of human cancer is global DNA hypomethylation (GDHO), but the mechanisms accounting for this defect and its pathological consequences have not been investigated in human epithelial ovarian cancer (EOC). In EOC, GDHO was associated with advanced disease and reduced overall and disease-free survival. GDHO (+) EOC tumors displayed a proliferative gene expression signature, including FOXM1 and CCNE1 overexpression. Furthermore, DNA hypomethylation in these tumors was enriched within genomic blocks (hypomethylated blocks) that overlapped late-replicating regions, lamina-associated domains, PRC2 binding sites, and the H3K27me3 histone mark. Increased proliferation coupled with hypomethylated blocks at late-replicating regions suggests a passive hypomethylation mechanism. This hypothesis was further supported by our observation that cytosine DNA methyltransferases (DNMTs) and UHRF1 showed significantly reduced expression in GDHO (+) EOC after normalization to canonical proliferation markers, including MKI67. Finally, GDHO (+) EOC tumors had elevated chromosomal instability (CIN), and copy number alterations (CNA) were enriched at the DNA hypomethylated blocks. Together, these findings implicate a passive DNA demethylation mechanism in ovarian cancer that is associated with genomic instability and poor prognosis.
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Affiliation(s)
- Wa Zhang
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198, USA; (W.Z.); (C.J.B.)
| | - David Klinkebiel
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; (D.K.); (C.G.)
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Carter J. Barger
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198, USA; (W.Z.); (C.J.B.)
| | - Sanjit Pandey
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Chittibabu Guda
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; (D.K.); (C.G.)
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Austin Miller
- Department of Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Stacey N. Akers
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (S.N.A.); (K.O.)
| | - Kunle Odunsi
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (S.N.A.); (K.O.)
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Adam R. Karpf
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198, USA; (W.Z.); (C.J.B.)
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; (D.K.); (C.G.)
- Correspondence: ; Tel.: +1-402-559-6115; Fax: +1-402-599-4651
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Rocha MA, Veronezi GMB, Felisbino MB, Gatti MSV, Tamashiro WMSC, Mello MLS. Sodium valproate and 5-aza-2'-deoxycytidine differentially modulate DNA demethylation in G1 phase-arrested and proliferative HeLa cells. Sci Rep 2019; 9:18236. [PMID: 31796828 PMCID: PMC6890691 DOI: 10.1038/s41598-019-54848-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023] Open
Abstract
Sodium valproate/valproic acid (VPA), a histone deacetylase inhibitor, and 5-aza-2-deoxycytidine (5-aza-CdR), a DNA methyltransferase 1 (DNMT1) inhibitor, induce DNA demethylation in several cell types. In HeLa cells, although VPA leads to decreased DNA 5-methylcytosine (5mC) levels, the demethylation pathway involved in this effect is not fully understood. We investigated this process using flow cytometry, ELISA, immunocytochemistry, Western blotting and RT-qPCR in G1 phase-arrested and proliferative HeLa cells compared to the presumably passive demethylation promoted by 5-aza-CdR. The results revealed that VPA acts predominantly on active DNA demethylation because it induced TET2 gene and protein overexpression, decreased 5mC abundance, and increased 5-hydroxy-methylcytosine (5hmC) abundance, in both G1-arrested and proliferative cells. However, because VPA caused decreased DNMT1 gene expression levels, it may also act on the passive demethylation pathway. 5-aza-CdR attenuated DNMT1 gene expression levels but increased TET2 and 5hmC abundance in replicating cells, although it did not affect the gene expression of TETs at any stage of the cell cycle. Therefore, 5-aza-CdR may also function in the active pathway. Because VPA reduces DNA methylation levels in non-replicating HeLa cells, it could be tested as a candidate for the therapeutic reversal of DNA methylation in cells in which cell division is arrested.
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Affiliation(s)
- Marina Amorim Rocha
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (UNICAMP), 13083-862, Campinas, SP, Brazil
| | - Giovana Maria Breda Veronezi
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (UNICAMP), 13083-862, Campinas, SP, Brazil
| | - Marina Barreto Felisbino
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (UNICAMP), 13083-862, Campinas, SP, Brazil
| | - Maria Silvia Viccari Gatti
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), 13083-862, Campinas, SP, Brazil
| | - Wirla M S C Tamashiro
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), 13083-862, Campinas, SP, Brazil
| | - Maria Luiza Silveira Mello
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (UNICAMP), 13083-862, Campinas, SP, Brazil.
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19
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Borchiellini M, Ummarino S, Di Ruscio A. The Bright and Dark Side of DNA Methylation: A Matter of Balance. Cells 2019; 8:cells8101243. [PMID: 31614870 PMCID: PMC6830319 DOI: 10.3390/cells8101243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/06/2019] [Accepted: 10/10/2019] [Indexed: 12/11/2022] Open
Abstract
DNA methylation controls several cellular processes, from early development to old age, including biological responses to endogenous or exogenous stimuli contributing to disease transition. As a result, minimal DNA methylation changes during developmental stages drive severe phenotypes, as observed in germ-line imprinting disorders, while genome-wide alterations occurring in somatic cells are linked to cancer onset and progression. By summarizing the molecular events governing DNA methylation, we focus on the methods that have facilitated mapping and understanding of this epigenetic mark in healthy conditions and diseases. Overall, we review the bright (health-related) and dark (disease-related) side of DNA methylation changes, outlining how bulk and single-cell genomic analyses are moving toward the identification of new molecular targets and driving the development of more specific and less toxic demethylating agents.
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Affiliation(s)
- Marta Borchiellini
- Department of Health Sciences, University of Eastern Piedmont, 28100 Novara, Italy.
- Department of Translational Medicine, University of Eastern Piedmont, 28100 Novara, Italy.
| | - Simone Ummarino
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Annalisa Di Ruscio
- Department of Translational Medicine, University of Eastern Piedmont, 28100 Novara, Italy.
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA.
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20
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Tsuji S, Imanishi M. Modified nucleobase-specific gene regulation using engineered transcription activator-like effectors. Adv Drug Deliv Rev 2019; 147:59-65. [PMID: 31513826 DOI: 10.1016/j.addr.2019.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 01/10/2023]
Abstract
Epigenetic modification, as typified by cytosine methylation, is a key aspect of gene regulation that affects many biological processes. However, the biological roles of individual methylated cytosines are poorly understood. Sequence-specific DNA recognition tools can be used to investigate the roles of individual instances of DNA methylation. Transcription activator-like effectors (TALEs), which are DNA-binding proteins, are promising candidate tools with designable sequence specificity and sensitivity to DNA methylation. In this review, we describe the bases of DNA recognition of TALEs, including methylated cytosine recognition, and the applications of TALEs for the study of methylated DNA. In addition, we discuss TALE-based epigenome editing and oxidized methylated cytosine recognition.
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21
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Effects of 5-Aza on p-Y1472 NR2B related to learning and memory in the mouse hippocampus. Biomed Pharmacother 2018; 109:701-707. [PMID: 30551522 DOI: 10.1016/j.biopha.2018.10.090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND We have previously reported that 5-Aza-2-deoxycytidine (5-Aza-cdR) can repress protein serine/threonine phosphatase-1γ (PP1γ) expression and activity in the mouse hippocampus and affect the behaviour of mice in a water maze. It is well known that the phosphorylation of N-methyl-d-aspartate receptor 2B subunit (NR2B) plays a role in behaviour. In this study, we examined whether 5-Aza-cdR affects NR2B phosphorylation at tyrosine 1472 (p-Y1472 NR2B) and whether it affected the responses of the mice in a passive avoidance test. METHODS 5-Aza-cdR (10 μM) was administered to mice via intracerebroventricular injection (i.c.v). The learning and memory behaviour of the mice were evaluated by measuring their response in a step-down type passive avoidance test 24 h after the injection. The mRNA level of NR2B was measured by real-time PCR. NR2B and p-Y1472 NR2B protein expression in the mouse hippocampus was detected by western blot and immunofluorescence. CDK5 activity was detected by the ADP-Glo™ + CDK5/p35 Kinase Enzyme System. To further clarify whether the 5-Aza-cdR effects on behaviour were dependent on cellular proliferation or not, the effect of 5-Aza-cdR on the expression level of NR2B, the phosphorylation level of p-Y1472 NR2B, cell viability and the cell cycle were analysed using the immortalized mouse hippocampal neuronal cells neural cell line HT22 treated with 10 μM 5-Aza-cdR compared with an untreated control group. RESULTS After injection with 5-Aza-cdR, the behaviour of the mice in the step-down test was improved, while their phosphorylation level of p-Y1472 NR2B was increased and their CDK5 activity was decreased in the hippocampus. In vitro experiments showed 10 μM 5-Aza-cdR increased the p-Y1472 NR2B phosphorylation level with inhibition of cell viability and cell cycle arrest. CONCLUSIONS Our results suggested that the effect of 5-Aza-cdR on behaviour may be related to the increase in phosphorylation of p-Y1472 NR2B in the hippocampus.
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22
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Navalta JW, Ciulei MA, Tibana RA, Voltarelli FA, Prestes J, Young JC. Global DNA methylation is stable across time and following acute exercise. GAZZETTA MEDICA ITALIANA ARCHIVIO PER LE SCIENZE MEDICHE 2018. [DOI: 10.23736/s0393-3660.17.03671-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Dmitrijeva M, Ossowski S, Serrano L, Schaefer MH. Tissue-specific DNA methylation loss during ageing and carcinogenesis is linked to chromosome structure, replication timing and cell division rates. Nucleic Acids Res 2018; 46:7022-7039. [PMID: 29893918 PMCID: PMC6101545 DOI: 10.1093/nar/gky498] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/16/2018] [Accepted: 05/23/2018] [Indexed: 12/15/2022] Open
Abstract
DNA methylation is an epigenetic mechanism known to affect gene expression and aberrant DNA methylation patterns have been described in cancer. However, only a small fraction of differential methylation events target genes with a defined role in cancer, raising the question of how aberrant DNA methylation contributes to carcinogenesis. As recently a link has been suggested between methylation patterns arising in ageing and those arising in cancer, we asked which aberrations are unique to cancer and which are the product of normal ageing processes. We therefore compared the methylation patterns between ageing and cancer in multiple tissues. We observed that hypermethylation preferentially occurs in regulatory elements, while hypomethylation is associated with structural features of the chromatin. Specifically, we observed consistent hypomethylation of late-replicating, lamina-associated domains. The extent of hypomethylation was stronger in cancer, but in both ageing and cancer it was proportional to the replication timing of the region and the cell division rate of the tissue. Moreover, cancer patients who displayed more hypomethylation in late-replicating, lamina-associated domains had higher expression of cell division genes. These findings suggest that different cell division rates contribute to tissue- and cancer type-specific DNA methylation profiles.
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Affiliation(s)
- Marija Dmitrijeva
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - Martin H Schaefer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
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24
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Tsuji S, Futaki S, Imanishi M. Sequence-specific recognition of methylated DNA by an engineered transcription activator-like effector protein. Chem Commun (Camb) 2018; 52:14238-14241. [PMID: 27872906 DOI: 10.1039/c6cc06824c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A 5mC-selective TALE-repeat was created by screening a TALE repeat library containing randomized amino acids at repeat variable diresidues and their neighboring residues. The new repeat showed high 5mC discrimination ability. An artificial TALE containing the new repeat activated an endogenous gene in a genomic methylation status-dependent manner.
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Affiliation(s)
- Shogo Tsuji
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
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25
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Tsuji S, Shinoda K, Futaki S, Imanishi M. Sequence-specific 5mC detection in live cells based on the TALE-split luciferase complementation system. Analyst 2018; 143:3793-3797. [DOI: 10.1039/c8an00562a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The newly developed TALE-split luciferase complementation system enabled sequence-specific 5mC detection of genomic DNA in live cells.
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Affiliation(s)
- Shogo Tsuji
- Institute for Chemical Research
- Kyoto University
- Uji
- Japan
| | - Kouki Shinoda
- Institute for Chemical Research
- Kyoto University
- Uji
- Japan
| | - Shiroh Futaki
- Institute for Chemical Research
- Kyoto University
- Uji
- Japan
| | - Miki Imanishi
- Institute for Chemical Research
- Kyoto University
- Uji
- Japan
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26
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Li H, Guo A, Xie Z, Tu W, Yu J, Wang H, Zhao J, Zhong C, Kang J, Li J, Huang S, Shen L. Stabilization of mouse haploid embryonic stem cells with combined kinase and signal modulation. Sci Rep 2017; 7:13222. [PMID: 29038567 PMCID: PMC5643530 DOI: 10.1038/s41598-017-13471-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 09/22/2017] [Indexed: 12/19/2022] Open
Abstract
Mammalian haploid embryonic stem cells (haESCs) provide new possibilities for large-scale genetic screens because they bear only one copy of each chromosome. However, haESCs are prone to spontaneous diploidization through unknown mechanisms. Here, we report that a small molecule combination could restrain mouse haESCs from diploidization by impeding exit from naïve pluripotency and by shortening the S-G2/M phases. Combined with 2i and PD166285, our chemical cocktail could maintain haESCs in the haploid state for at least five weeks without fluorescence-activated cell sorting (FACS) enrichment of haploid cells. Taken together, we established an effective chemical approach for long-term maintenance of haESCs, and highlighted that proper cell cycle progression was critical for the maintenance of haploid state.
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Affiliation(s)
- Haisen Li
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell biology, Chinese Academy of Sciences, Shanghai, 200031, China.,Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis, and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Ao Guo
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhenfei Xie
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Wanzhi Tu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jiali Yu
- Life Sciences Institute, Zhejiang University, Hangzhou, 310000, China
| | - Huihan Wang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310000, China
| | - Jian Zhao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cuiqing Zhong
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shichao Huang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell biology, Chinese Academy of Sciences, Shanghai, 200031, China. .,Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-based Bio-medicine, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Li Shen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310000, China.
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27
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Luo H, Xi Y, Li W, Li J, Li Y, Dong S, Peng L, Liu Y, Yu W. Cell identity bookmarking through heterogeneous chromatin landscape maintenance during the cell cycle. Hum Mol Genet 2017; 26:4231-4243. [DOI: 10.1093/hmg/ddx312] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/02/2017] [Indexed: 12/29/2022] Open
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28
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Bai J, Zhang X, Liu B, Wang H, Du Z, Song J. Silencing DNA methyltransferase 1 leads to the activation of the esophageal suppressor gene p16 in vitro and in vivo. Oncol Lett 2017; 14:3077-3081. [PMID: 28927055 DOI: 10.3892/ol.2017.6535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 11/25/2017] [Indexed: 11/06/2022] Open
Abstract
Previous studies have demonstrated that DNA methyltransferase 1 (DNMT1) is required for the maintenance of DNA methylation and epigenetic changes that may lead to the development of esophageal squamous cell carcinoma (ESCC). In order to investigate whether the silencing of DNMT1 protects tumor suppressor genes, including p16, and is able to be used as a potential therapy for human ESCC, short hairpin RNA targeting DNMT1 (shRNA-DNMT1) was synthesized and transfected into the human ESCC lines KYSE150 and KYSE410, which were then injected into the backs of nude mice prior to harvesting. Results from the reverse transcription-quantitative polymerase chain reaction (PCR) and western blotting demonstrated that p16 mRNA expression was increased in the shRNA-DNMT1-transfected ESCC cell lines in vitro and in vivo. Consistent with the immunohistochemistry results, p16 was expressed in tumor tissue from nude mice that had been transplanted with the modified human ESCC lines. It was also observed that p16 methylation was inhibited following transfection with shRNA-DNMT1 as detected using methylation-specific PCR analysis. The results of the present study suggest that silencing DNMT1 serves a protective role through the demethylation and subsequent activation of p16 in vitro and in vivo.
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Affiliation(s)
- Jian Bai
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi 710000, P.R. China
| | - Xue Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi 710000, P.R. China
| | - Bangqing Liu
- Department of Thoracic and Cardiovascular Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Zhuang 541100, P.R. China
| | - Haiyong Wang
- Department of Thoracic and Cardiovascular Surgery, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Zhuang 541001, P.R. China
| | - Zhenzong Du
- Department of Thoracic Surgery, Nanxi Shan Hospital of Guangxi Zhuang Autonomous Region, Guilin, Guangxi Zhuang 541002, P.R. China
| | - Jianfei Song
- Department of Thoracic and Cardiovascular Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Zhuang 541100, P.R. China
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29
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Pechalrieu D, Etievant C, Arimondo PB. DNA methyltransferase inhibitors in cancer: From pharmacology to translational studies. Biochem Pharmacol 2016; 129:1-13. [PMID: 27956110 DOI: 10.1016/j.bcp.2016.12.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/07/2016] [Indexed: 12/31/2022]
Abstract
DNA methylation is a mammalian epigenetic mark that participates to define where and when genes are expressed, both in normal cells and in the context of diseases. Like other epigenetic marks, it is reversible and can be modulated by chemical agents. Because it plays an important role in cancer by silencing certain genes, such as tumour suppressor genes, it is a promising therapeutic target. Two compounds are already approved to treat haematological cancers, and many efforts have been carried out to discover new molecules that inhibit DNA methyltransferases, the enzymes responsible for DNA methylation. Here, we analyse the molecular mechanisms and cellular pharmacology of these inhibitors, pointing out the necessity for new pharmacological models and paradigms. The parameters of pharmacological responses need to be redefined: the aim is cellular reprogramming rather than general cytotoxicity. Thus, "epigenetic" rather than cytotoxic dosages are defined. Another issue is the delay of the response: cellular reprogramming can take several generations to produce observable phenotypes. Is this compatible with laboratory scale experiments? Finally, it is important to consider the specificity for cancer cells compared to normal cells and the appearance of resistance. We also discuss different techniques that are used and the selection of pharmacological models.
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Affiliation(s)
- Dany Pechalrieu
- Unité de Service et de Recherche CNRS-Pierre Fabre USR3388, CNRS FRE3600, ETaC, Epigenetic Targeting of Cancer, Toulouse, France
| | - Chantal Etievant
- Unité de Service et de Recherche CNRS-Pierre Fabre USR3388, CNRS FRE3600, ETaC, Epigenetic Targeting of Cancer, Toulouse, France
| | - Paola B Arimondo
- Unité de Service et de Recherche CNRS-Pierre Fabre USR3388, CNRS FRE3600, ETaC, Epigenetic Targeting of Cancer, Toulouse, France.
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30
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Zhang Z, Yang J, Liu X, Jia X, Xu S, Gong K, Yan S, Zhang C, Shao G. Effects of 5-Aza-2′-deoxycytidine on expression of PP1γ in learning and memory. Biomed Pharmacother 2016; 84:277-283. [DOI: 10.1016/j.biopha.2016.09.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 12/22/2022] Open
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31
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Extensive Epigenetic Changes Accompany Terminal Differentiation of Mouse Hepatocytes After Birth. G3-GENES GENOMES GENETICS 2016; 6:3701-3709. [PMID: 27652892 PMCID: PMC5100869 DOI: 10.1534/g3.116.034785] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
DNA methylation is traditionally thought to be established during early development and to remain mostly unchanged thereafter in healthy tissues, although recent studies have shown that this epigenetic mark can be more dynamic. Epigenetic changes occur in the liver after birth, but the timing and underlying biological processes leading to DNA methylation changes are not well understood. We hypothesized that this epigenetic reprogramming was the result of terminal differentiation of hepatocyte precursors. Using genomic approaches, we characterized the DNA methylation patterns in mouse liver from E18.5 until adulthood to determine if the timing of the DNA methylation change overlaps with hepatocyte terminal differentiation, and to examine the genomic context of these changes and identify the regulatory elements involved. Out of 271,325 CpGs analyzed throughout the genome, 214,709 CpGs changed DNA methylation by more than 5% (e.g., from 5 to 10% methylation) between E18.5 and 9 wk of age, and 18,863 CpGs changed DNA methylation by more than 30%. Genome-scale data from six time points between E18.5 and P20 show that DNA methylation changes coincided with the terminal differentiation of hepatoblasts into hepatocytes. We also showed that epigenetic reprogramming occurred primarily in intergenic enhancer regions while gene promoters were less affected. Our data suggest that normal postnatal hepatic development and maturation involves extensive epigenetic remodeling of the genome, and that enhancers play a key role in controlling the transition from hepatoblasts to fully differentiated hepatocytes. Our study provides a solid foundation to support future research aimed at further revealing the role of epigenetics in stem cell biology.
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32
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TU ZHENBO, HE DU, DENG XINZHOU, XIONG MENG, HUANG XIAOXING, LI XINRAN, HAO LING, DING QIANSHAN, ZHANG QIUPING. An eight-long non-coding RNA signature as a candidate prognostic biomarker for lung cancer. Oncol Rep 2016; 36:215-22. [DOI: 10.3892/or.2016.4817] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/22/2016] [Indexed: 11/05/2022] Open
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33
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Vandiver AR, Idrizi A, Rizzardi L, Feinberg AP, Hansen KD. DNA methylation is stable during replication and cell cycle arrest. Sci Rep 2015; 5:17911. [PMID: 26648411 PMCID: PMC4673417 DOI: 10.1038/srep17911] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/09/2015] [Indexed: 01/15/2023] Open
Abstract
DNA methylation is an epigenetic modification with important functions in development. Large-scale loss of DNA methylation is a hallmark of cancer. Recent work has identified large genomic blocks of hypomethylation associated with cancer, EBV transformation and replicative senescence, all of which change the proportion of actively proliferating cells within the population measured. We asked if replication or cell-cycle arrest affects the global levels of methylation or leads to hypomethylated blocks as observed in other settings. We used fluorescence activated cell sorting to isolate primary dermal fibroblasts in G0, G1 and G2 based on DNA content and Ki67 staining. We additionally examined G0 cells arrested by contact inhibition for one week to determine the effects of extended arrest. We analyzed genome wide DNA methylation from sorted cells using whole genome bisulfite sequencing. This analysis demonstrated no global changes or large-scale hypomethylated blocks in any of the examined cell cycle phases, indicating that global levels of methylation are stable with replication and arrest.
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Affiliation(s)
- Amy R Vandiver
- Center for Epigenetics, Johns Hopkins University School of Medicine
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine
| | - Lindsay Rizzardi
- Center for Epigenetics, Johns Hopkins University School of Medicine
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine.,Department of Medicine, Johns Hopkins University School of Medicine
| | - Kasper D Hansen
- Center for Epigenetics, Johns Hopkins University School of Medicine.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
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34
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Tao H, Shi KH, Yang JJ, Li J. Epigenetic mechanisms in atrial fibrillation: New insights and future directions. Trends Cardiovasc Med 2015; 26:306-18. [PMID: 26475117 DOI: 10.1016/j.tcm.2015.08.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 08/23/2015] [Accepted: 08/28/2015] [Indexed: 11/28/2022]
Abstract
Atrial fibrillation (AF) is the most common sustained arrhythmia. AF is a complex disease that results from genetic and environmental factors and their interactions. In recent years, numerous studies have shown that epigenetic mechanisms significantly participate in AF pathogenesis. Even though a poor understanding of the molecular and electrophysiologic mechanisms of AF, accumulated evidence has suggested that the relevance of epigenetic changes in the development of AF. The aim of this review is to describe the present knowledge about the epigenetic regulatory features significantly participates in AF, and look ahead on new perspectives of epigenetic mechanisms research. Epigenetic regulatory features such as DNA methylation, histone modification, and microRNA influence gene expression by epigenetic mechanisms and by directly binding to various factor response elements in the target gene promoters. Given the role of epigenetic alterations in regulating genes, there is potential for the integration of factors-induced epigenetic alterations as informative factors in the risk assessment process. In this review, new insight into the epigenetic mechanisms in AF pathogenesis is discussed, with special emphasis on DNA methylation, histone modification, and microRNA. Further studies are needed to reveal the potential targets of epigenetic mechanisms, and it can be developed as a therapeutic target for AF.
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Affiliation(s)
- Hui Tao
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei, China; Cardiovascular Research Center, Anhui Medical University, Hefei, China
| | - Kai-Hu Shi
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei, China; Cardiovascular Research Center, Anhui Medical University, Hefei, China.
| | - Jing-Jing Yang
- Department of Pharmacology, The Second Hospital of Anhui Medical University, Hefei, China.
| | - Jun Li
- School of Pharmacy, Anhui Medical University, Hefei, China
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Loiseau C, Ali A, Itzykson R. New therapeutic approaches in myelodysplastic syndromes: Hypomethylating agents and lenalidomide. Exp Hematol 2015; 43:661-72. [PMID: 26123365 DOI: 10.1016/j.exphem.2015.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 01/17/2023]
Abstract
Recent advances in the treatment of myelodysplastic syndromes have come from the use of the hypomethylating agents decitabine and azacitidine as well as the immunomodulatory drug lenalidomide. Their clinical benefit has been demonstrated by randomized phase III clinical trials, mostly in high-risk and del(5q) myelodysplastic syndromes, respectively. Neither drug, however, appears to eradicate myelodysplastic stem cells, and thus they currently do not represent curative options. Here, we review data from both clinical and translational research on those drugs to identify their molecular and cellular mechanisms of action and to delineate paths for improved treatment allocation and further therapeutic advances in myelodysplastic syndromes.
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Affiliation(s)
- Clémence Loiseau
- Department of Hematology, Saint-Louis Hospital, Assistance Publique, Hopitaux de Paris, Paris Diderot University, Paris, France
| | - Ashfaq Ali
- Institut National de la Santé et de la Recherche Médicale, Saint-Louis Institute, Paris, France
| | - Raphael Itzykson
- Department of Hematology, Saint-Louis Hospital, Assistance Publique, Hopitaux de Paris, Paris Diderot University, Paris, France; Institut National de la Santé et de la Recherche Médicale, Saint-Louis Institute, Paris, France.
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