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Yadav C, Yadav R, Nanda S, Ranga S, Ahuja P, Tanwar M. Role of HOX genes in cancer progression and their therapeutical aspects. Gene 2024; 919:148501. [PMID: 38670395 DOI: 10.1016/j.gene.2024.148501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/28/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
HOX genes constitute a family of evolutionarily conserved transcription factors that play pivotal roles in embryonic development, tissue patterning, and cell differentiation. These genes are essential for the precise spatial and temporal control of body axis formation in vertebrates. In addition to their developmental functions, HOX genes have garnered significant attention for their involvement in various diseases, including cancer. Deregulation of HOX gene expression has been observed in numerous malignancies, where they can influence tumorigenesis, progression, and therapeutic responses. This review provides an overview of the diverse roles of HOX genes in development, disease, and potential therapeutic targets, highlighting their significance in understanding biological processes and their potential clinical implications.
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Affiliation(s)
- Chetna Yadav
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Ritu Yadav
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana 124001, India.
| | - Smiti Nanda
- Retd. Senior Professor and Head, Department of Gynaecology and Obstetrics, Pt. B.D. Sharma University of Health Sciences, Rohtak 124001, India
| | - Shalu Ranga
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Parul Ahuja
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Mukesh Tanwar
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana 124001, India
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2
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Zarate-Lopez D, Torres-Chávez AL, Gálvez-Contreras AY, Gonzalez-Perez O. Three Decades of Valproate: A Current Model for Studying Autism Spectrum Disorder. Curr Neuropharmacol 2024; 22:260-289. [PMID: 37873949 PMCID: PMC10788883 DOI: 10.2174/1570159x22666231003121513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 10/25/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder with increased prevalence and incidence in recent decades. Its etiology remains largely unclear, but it seems to involve a strong genetic component and environmental factors that, in turn, induce epigenetic changes during embryonic and postnatal brain development. In recent decades, clinical studies have shown that inutero exposure to valproic acid (VPA), a commonly prescribed antiepileptic drug, is an environmental factor associated with an increased risk of ASD. Subsequently, prenatal VPA exposure in rodents has been established as a reliable translational model to study the pathophysiology of ASD, which has helped demonstrate neurobiological changes in rodents, non-human primates, and brain organoids from human pluripotent stem cells. This evidence supports the notion that prenatal VPA exposure is a valid and current model to replicate an idiopathic ASD-like disorder in experimental animals. This review summarizes and describes the current features reported with this animal model of autism and the main neurobiological findings and correlates that help elucidate the pathophysiology of ASD. Finally, we discuss the general framework of the VPA model in comparison to other environmental and genetic ASD models.
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Affiliation(s)
- David Zarate-Lopez
- Laboratory of Neuroscience, School of Psychology, University of Colima, Colima 28040, México
- Physiological Science Ph.D. Program, School of Medicine, University of Colima, Colima 28040, Mexico
| | - Ana Laura Torres-Chávez
- Laboratory of Neuroscience, School of Psychology, University of Colima, Colima 28040, México
- Physiological Science Ph.D. Program, School of Medicine, University of Colima, Colima 28040, Mexico
| | - Alma Yadira Gálvez-Contreras
- Department of Neuroscience, Centro Universitario de Ciencias de la Salud, University of Guadalajara, Guadalajara 44340, México
| | - Oscar Gonzalez-Perez
- Laboratory of Neuroscience, School of Psychology, University of Colima, Colima 28040, México
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3
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Chen A, Wang M, Xu C, Zhao Y, Xian P, Li Y, Zheng W, Yi X, Wu S, Wang Y. Glycolysis mediates neuron specific histone acetylation in valproic acid-induced human excitatory neuron differentiation. Front Mol Neurosci 2023; 16:1151162. [PMID: 37089691 PMCID: PMC10118002 DOI: 10.3389/fnmol.2023.1151162] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
Pregnancy exposure of valproic acid (VPA) is widely adopted as a model of environmental factor induced autism spectrum disorder (ASD). Increase of excitatory/inhibitory synaptic transmission ratio has been proposed as the mechanism of VPA induced ASD. How this happened, particularly at the level of excitatory neuron differentiation in human neural progenitor cells (NPCs) remains largely unclear. Here, we report that VPA exposure remarkably inhibited human NPC proliferation and induced excitatory neuronal differentiation without affecting inhibitory neurons. Following VPA treatment, mitochondrial dysfunction was observed before neuronal differentiation, as showed by ultrastructural changes, respiratory complex activity, mitochondrial membrane potential and oxidation levels. Meanwhile, extracellular acidification assay revealed an elevation of glycolysis by VPA stimulation. Interestingly, inhibiting glycolysis by 2-deoxy-d-glucose-6-phosphate (2-DG) efficiently blocked the excitatory neuronal differentiation of human NPCs induced by VPA. Furthermore, 2-DG treatment significantly compromised the VPA-induced expression of H3ac and H3K9ac, and the VPA-induced binding of H3K9ac on the promoter of Ngn2 and Mash1, two key transcription factors of excitatory neuron fate determination. These data, for the first time, demonstrated that VPA biased excitatory neuron differentiation by glycolysis-mediated histone acetylation of neuron specific transcription factors.
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Affiliation(s)
- Andi Chen
- Department of Neurobiology, School of Basic Medicine, Institute of Neurosciences, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Mengmeng Wang
- Department of Neurobiology, School of Basic Medicine, Institute of Neurosciences, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Chao Xu
- Department of Neurobiology, School of Basic Medicine, Institute of Neurosciences, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Youyi Zhao
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Engineering Research, Center for Dental Materials and Advanced Manufacture, Department of Anesthesiology, School of Stomatology, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Panpan Xian
- Department of Neurobiology, School of Basic Medicine, Institute of Neurosciences, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Yuqian Li
- Department of Neurobiology, School of Basic Medicine, Institute of Neurosciences, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Weian Zheng
- Department of Neurobiology, School of Basic Medicine, Institute of Neurosciences, Fourth Military Medical University, Xi’an, Shaanxi, China
- School of Life Sciences and Research Center for Natural Peptide Drugs, Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan’an University, Yan’an, China
| | - Xuyang Yi
- Department of Neurobiology, School of Basic Medicine, Institute of Neurosciences, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Shengxi Wu
- Department of Neurobiology, School of Basic Medicine, Institute of Neurosciences, Fourth Military Medical University, Xi’an, Shaanxi, China
- Shengxi Wu,
| | - Yazhou Wang
- Department of Neurobiology, School of Basic Medicine, Institute of Neurosciences, Fourth Military Medical University, Xi’an, Shaanxi, China
- *Correspondence: Yazhou Wang,
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4
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Rocha MA, de Campos Vidal B, Mello MLS. Sodium Valproate Modulates the Methylation Status of Lysine Residues 4, 9 and 27 in Histone H3 of HeLa Cells. Curr Mol Pharmacol 2023; 16:197-210. [PMID: 35297358 DOI: 10.2174/1874467215666220316110405] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/27/2021] [Accepted: 01/12/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Valproic acid/sodium valproate (VPA), a well-known anti-epileptic agent, inhibits histone deacetylases, induces histone hyperacetylation, promotes DNA demethylation, and affects the histone methylation status in some cell models. Histone methylation profiles have been described as potential markers for cervical cancer prognosis. However, histone methylation markers that can be studied in a cervical cancer cell line, like HeLa cells, have not been investigated following treatment with VPA. METHODS In this study, the effect of 0.5 mM and 2.0 mM VPA for 24 h on H3K4me2/me3, H3K9me/me2 and H3K27me/me3 signals as well as on KMT2D, EZH2, and KDM3A gene expression was investigated using confocal microscopy, Western blotting, and RT-PCR. Histone methylation changes were also investigated by Fourier-transform infrared spectroscopy (FTIR). RESULTS We found that VPA induces increased levels of H3K4me2/me3 and H3K9me, which are indicative of chromatin activation. Particularly, H3K4me2 markers appeared intensified close to the nuclear periphery, which may suggest their implication in increased transcriptional memory. The abundance of H3K4me2/me3 in the presence of VPA was associated with increased methyltransferase KMT2D gene expression. VPA induced hypomethylation of H3K9me2, which is associated with gene silencing, and concomitant with the demethylase KDM3A, it increased gene expression. Although VPA induces increased H3K27me/me3 levels, it is suggested that the role of the methyltransferase EZH2 in this context could be affected by interactions with this drug. CONCLUSION Histone FTIR spectra were not affected by VPA under present experimental conditions. Whether our epigenetic results are consistent with VPA affecting the aggressive tumorous state of HeLa cells, further investigation is required.
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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
| | - Benedicto de Campos Vidal
- Department of Structural and Functional Biology, 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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Feng Y, Zhang T, Wang Y, Xie M, Ji X, Luo X, Huang W, Xia L. Homeobox Genes in Cancers: From Carcinogenesis to Recent Therapeutic Intervention. Front Oncol 2021; 11:770428. [PMID: 34722321 PMCID: PMC8551923 DOI: 10.3389/fonc.2021.770428] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/28/2021] [Indexed: 12/11/2022] Open
Abstract
The homeobox (HOX) genes encoding an evolutionarily highly conserved family of homeodomain-containing transcriptional factors are essential for embryogenesis and tumorigenesis. HOX genes are involved in cell identity determination during early embryonic development and postnatal processes. The deregulation of HOX genes is closely associated with numerous human malignancies, highlighting the indispensable involvement in mortal cancer development. Since most HOX genes behave as oncogenes or tumor suppressors in human cancer, a better comprehension of their upstream regulators and downstream targets contributes to elucidating the function of HOX genes in cancer development. In addition, targeting HOX genes may imply therapeutic potential. Recently, novel therapies such as monoclonal antibodies targeting tyrosine receptor kinases, small molecular chemical inhibitors, and small interfering RNA strategies, are difficult to implement for targeting transcriptional factors on account of the dual function and pleiotropic nature of HOX genes-related molecular networks. This paper summarizes the current state of knowledge on the roles of HOX genes in human cancer and emphasizes the emerging importance of HOX genes as potential therapeutic targets to overcome the limitations of present cancer therapy.
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Affiliation(s)
- Yangyang Feng
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tongyue Zhang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yijun Wang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meng Xie
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu Ji
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiangyuan Luo
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjie Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Limin Xia
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Parodi C, Di Fede E, Peron A, Viganò I, Grazioli P, Castiglioni S, Finnell RH, Gervasini C, Vignoli A, Massa V. Chromatin Imbalance as the Vertex Between Fetal Valproate Syndrome and Chromatinopathies. Front Cell Dev Biol 2021; 9:654467. [PMID: 33959609 PMCID: PMC8093873 DOI: 10.3389/fcell.2021.654467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022] Open
Abstract
Prenatal exposure to valproate (VPA), an antiepileptic drug, has been associated with fetal valproate spectrum disorders (FVSD), a clinical condition including congenital malformations, developmental delay, intellectual disability as well as autism spectrum disorder, together with a distinctive facial appearance. VPA is a known inhibitor of histone deacetylase which regulates the chromatin state. Interestingly, perturbations of this epigenetic balance are associated with chromatinopathies, a heterogeneous group of Mendelian disorders arising from mutations in components of the epigenetic machinery. Patients affected from these disorders display a plethora of clinical signs, mainly neurological deficits and intellectual disability, together with distinctive craniofacial dysmorphisms. Remarkably, critically examining the phenotype of FVSD and chromatinopathies, they shared several overlapping features that can be observed despite the different etiologies of these disorders, suggesting the possible existence of a common perturbed mechanism(s) during embryonic development.
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Affiliation(s)
- Chiara Parodi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Elisabetta Di Fede
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Angela Peron
- Human Pathology and Medical Genetics, ASST Santi Paolo e Carlo, San Paolo Hospital, Milan, Italy.,Child Neuropsychiatry Unit-Epilepsy Center, Department of Health Sciences, San Paolo Hospital, ASST Santi Paolo e Carlo, Università degli Studi di Milano, Milan, Italy.,Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Ilaria Viganò
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Paolo Grazioli
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Silvia Castiglioni
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Richard H Finnell
- Departments of Molecular and Cellular Biology, Molecular and Human Genetics and Medicine, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Cristina Gervasini
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy.,"Aldo Ravelli" Center for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy
| | - Aglaia Vignoli
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Valentina Massa
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy.,"Aldo Ravelli" Center for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy
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Krasic J, Skara L, Ulamec M, Katusic Bojanac A, Dabelic S, Bulic-Jakus F, Jezek D, Sincic N. Teratoma Growth Retardation by HDACi Treatment of the Tumor Embryonal Source. Cancers (Basel) 2020; 12:cancers12113416. [PMID: 33217978 PMCID: PMC7698704 DOI: 10.3390/cancers12113416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/09/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Testicular germ cell tumors are the most common neoplasms in young male populations, with a rising incidence. Among them, teratomas may often be very aggressive and resistant to therapy. Our aim was to investigate the impact of two potential anti-tumor epigenetic drugs (Valproate and Trichostatin A) in a mammalian model of teratoma development from an early trilaminar mouse embryo. Both drugs applied to the embryonic tissue had a significant negative impact on the teratoma growth in a three-dimensional in vitro culture. However, Trichostatin A did not diminish some potentially dangerous features of teratomas in contrast to Valproate. This research is an original contribution to the basic knowledge of the origin and development of teratomas. Such knowledge is necessary for envisioning therapeutic strategies against human testicular tumors. Abstract Among testicular germ cell tumors, teratomas may often be very aggressive and therapy-resistant. Our aim was to investigate the impact of histone deacetylase inhibitors (HDACi) on the in vitro growth of experimental mouse teratoma by treating their embryonic source, the embryo-proper, composed only of the three germ layers. The growth of teratomas was measured for seven days, and histopathological analysis, IHC/morphometry quantification, gene enrichment analysis, and qPCR analysis on a selected panel of pluripotency and early differentiation genes followed. For the first time, within teratomas, we histopathologically assessed the undifferentiated component containing cancer stem cell-like cells (CSCLCs) and differentiated components containing numerous lymphocytes. Mitotic indices were higher than apoptotic indices in both components. Both HDACi treatments of the embryos-proper significantly reduced teratoma growth, although this could be related neither to apoptosis nor proliferation. Trichostatin A increased the amount of CSCLCs, and upregulated the mRNA expression of pluripotency/stemness genes as well as differentiation genes, e.g., T and Eomes. Valproate decreased the amount of CSCLCs, and downregulated the expressions of pluripotency/stemness and differentiation genes. In conclusion, both HDACi treatments diminished the inherent tumorigenic growth potential of the tumor embryonal source, although Trichostatin A did not diminish the potentially dangerous expression of cancer-related genes and the amount of CSCLC.
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Affiliation(s)
- Jure Krasic
- Department of Medical Biology, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia; (J.K.); (L.S.); (A.K.B.); (F.B.-J.)
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia;
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia;
| | - Lucija Skara
- Department of Medical Biology, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia; (J.K.); (L.S.); (A.K.B.); (F.B.-J.)
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia;
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia;
| | - Monika Ulamec
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia;
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia;
- Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre Milosrdnice University Hospital Center, 10 000 Zagreb, Croatia
- Department of Pathology, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia
| | - Ana Katusic Bojanac
- Department of Medical Biology, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia; (J.K.); (L.S.); (A.K.B.); (F.B.-J.)
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia;
| | - Sanja Dabelic
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, University of Zagreb, 10 000 Zagreb, Croatia;
| | - Floriana Bulic-Jakus
- Department of Medical Biology, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia; (J.K.); (L.S.); (A.K.B.); (F.B.-J.)
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia;
| | - Davor Jezek
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia;
- Department of Histology and Embryology, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia
| | - Nino Sincic
- Department of Medical Biology, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia; (J.K.); (L.S.); (A.K.B.); (F.B.-J.)
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia;
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10 000 Zagreb, Croatia;
- Correspondence: ; Tel.: +385-1-45-66-806; Fax: +385-45-960-199
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Deepika VB, Vohra M, Mishra S, Dorai K, Rai P, Satyamoorthy K, Murali TS. DNA demethylation overcomes attenuation of colchicine biosynthesis in an endophytic fungus Diaporthe. J Biotechnol 2020; 323:33-41. [PMID: 32745507 DOI: 10.1016/j.jbiotec.2020.07.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/27/2020] [Accepted: 07/27/2020] [Indexed: 10/23/2022]
Abstract
Fungal endophytes, a major component of the plant host microbiome, are known to synthesize plant-derived metabolites in vitro. However, attenuation of metabolite production upon repeated sub-culturing is a major drawback towards utilizing them as an alternative for plant-derived metabolites. In this study, we isolated Diaporthe perseae, a fungal endophyte from Gloriosa superba tubers, which showed the production of colchicine in axenic cultures. Mass spectrometry, Nuclear Magnetic Resonance spectroscopy, and tubulin polymerization assays confirmed the compound to be colchicine. Repeated sub-culturing of the endophyte for 10 generations led to a reduction in the yield of the metabolite from 55.25 μg/g to 2.32 μg/g of mycelial dry weight. Treatment of attenuated cultures with DNA methylation inhibitor 5-azacytidine resulted in increased metabolite concentration (39.68 μg/g mycelial dry weight) in treated samples compared to control (2.61 μg/g mycelial dry weight) suggesting that 5-azacytidine can induce demethylation of the fungal genome to overcome the phenomenon of attenuation of metabolite synthesis. Reduced levels of global methylation were observed upon 5-azacytidine treatment in attenuated cultures (0.41 % of total cytosines methylated) as compared to untreated control (0.78 % of total cytosines methylated). The results provide a significant breakthrough in utilizing fungal endophytes as a veritable source of plant-derived metabolites from critically endangered plants.
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Affiliation(s)
- Vishwanath Bhat Deepika
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India.
| | - Manik Vohra
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India.
| | - Sumit Mishra
- Department of Physical Sciences, Indian Institute of Science Education & Research (IISER) Mohali, Sector 81, SAS Nagar, Manauli PO, 140306 Punjab, India.
| | - Kavita Dorai
- Department of Physical Sciences, Indian Institute of Science Education & Research (IISER) Mohali, Sector 81, SAS Nagar, Manauli PO, 140306 Punjab, India.
| | - Padmalatha Rai
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India.
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India.
| | - Thokur Sreepathy Murali
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India.
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Hajikazemi M, Sohrabi H, Yamchi A, Saeedi M. The effects of valproic acid on the mRNA expression of Natriuretic Peptide Receptor A and KQT-like subfamily Q-1 in human colon cancer cell lines. ALEXANDRIA JOURNAL OF MEDICINE 2019. [DOI: 10.1016/j.ajme.2017.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Mona Hajikazemi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Hoda Sohrabi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ahad Yamchi
- Department of Plant Breeding and Biotechnology, College of Plant Production Gorgan University of Agriculture Science and Natural Recourses, Gorgan, Iran
| | - Mohsen Saeedi
- Stem Cell Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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10
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Dai X, Yan X, Xie P, Lian J. [Sodium valprovate suppresses autophagy in SH-SY5Y cells via activating miR-34c-5p/ATG4B signaling pathway]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2018; 38:1415-1420. [PMID: 30613007 DOI: 10.12122/j.issn.1673-4254.2018.12.03] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the effect of sodium valproate (VPA) on activation of miR-34c-5p/ATG4B signaling pathway and autophagy in SH-SY5Y cells. METHODS Routinely cultured SH-SY5Y cells were treated with VPA at different doses for 24 h, and the changes in the mRNA levels of ATG4B and miR-34c-5p and the protein expression of ATG4B were assessed using qRTPCR and immunoblotting, respectively. The effect of transfection with a plasmid containing ATG4B promoter on the promoter activity of ATG4B in VPA-treated SH-SY5Y cells was assessed using the reporter gene assay. The stability of ATG4B mRNA was analyzed with qPCR in SH-SY5Y cells treated with VPA alone or with VPA combined with the transcription inhibitor actinomycin D. The expression level of miR-34c-5p was detected using qPCR in SH-SY5Y cells treated with VPA alone or with VPA combined with miR-34c-5p mimics or antagonist, and the role of miR-34c-5p in VPA-induced ATG4B down-regulation was evaluated. The changes in the level of autophagy were evaluated by detecting LC3-Ⅱ expression in the cells after treatment with VPA or VPA combined with miR-34c-5p antagonist. RESULTS VPA dose-dependently down-regulated the expression of ATG4B at both the mRNA and protein levels in SH-SY5Y cells. VPA treatment did not significantly affect the promoter activity of ATG4B, but obviously lowered the mRNA stability of ATG4B in SH-SY5Y cells. VPA treatment up-regulated the expression of miR-34c-5p, and the miR-34c-5p antagonist reversed VPA-induced down-regulation of ATG4B in SH-SY5Y cells. VPA also down-regulated the expression level of LC3-Ⅱ in SH-SY5Y cells. CONCLUSIONS VPA suppresses autophagy in SH-SY5Y cells possibly via activating miR-34c-5p/ATG4B signaling pathway.
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Affiliation(s)
- Xufang Dai
- Chongqing Key Laboratory of Psychological Diagnosis and Educational Technology for Children with Special Needs.,Facultiy of Educationfor Children with Special Needs, College of Education Science, Chongqing Normal University, Chongqing 400047, China
| | - Xiaojing Yan
- Department ofBiochemistry and Molecular Biology, Army Medical University, Chongqing 400038, China
| | - Peng Xie
- Department ofBiochemistry and Molecular Biology, Army Medical University, Chongqing 400038, China
| | - Jiqin Lian
- Department ofBiochemistry and Molecular Biology, Army Medical University, Chongqing 400038, China
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11
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Balasubramanian D, Pearson JF, Kennedy MA. Gene expression effects of lithium and valproic acid in a serotonergic cell line. Physiol Genomics 2018; 51:43-50. [PMID: 30576260 DOI: 10.1152/physiolgenomics.00069.2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Valproic acid (VPA) and lithium are widely used in the treatment of bipolar disorder. However, the underlying mechanism of action of these drugs is not clearly understood. We used RNA-Seq analysis to examine the global profile of gene expression in a rat serotonergic cell line (RN46A) after exposure to these two mood stabilizer drugs. Numerous genes were differentially regulated in response to VPA (log2 fold change ≥ 1.0; i.e., odds ratio of ≥2, at false discovery rate <5%), but only two genes ( Dynlrb2 and Cdyl2) showed significant differential regulation after exposure of the cells to lithium, with the same analysis criteria. Both of these genes were also regulated by VPA. Many of the differentially expressed genes had functions of potential relevance to mood disorders or their treatment, such as several serpin family genes (including neuroserpin), Nts (neurotensin), Maob (monoamine oxidase B), and Ap2b1, which is important for synaptic vesicle function. Pathway analysis revealed significant enrichment of Gene Ontology terms such as extracellular matrix remodeling, cell adhesion, and chemotaxis. This study in a cell line derived from the raphe nucleus has identified a range of genes and pathways that provide novel insights into potential therapeutic actions of the commonly used mood stabilizer drugs.
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Affiliation(s)
- Diana Balasubramanian
- Carney Centre for Pharmacogenomics, Department of Pathology and Biomedical Science, University of Otago , Christchurch , New Zealand
| | - John F Pearson
- Carney Centre for Pharmacogenomics, Department of Pathology and Biomedical Science, University of Otago , Christchurch , New Zealand.,Biostatistics and Computational Biology Unit, University of Otago , Christchurch , New Zealand
| | - Martin A Kennedy
- Carney Centre for Pharmacogenomics, Department of Pathology and Biomedical Science, University of Otago , Christchurch , New Zealand
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12
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Alternative SET/TAFI Promoters Regulate Embryonic Stem Cell Differentiation. Stem Cell Reports 2017; 9:1291-1303. [PMID: 28966118 PMCID: PMC5639460 DOI: 10.1016/j.stemcr.2017.08.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/27/2017] [Accepted: 08/28/2017] [Indexed: 01/21/2023] Open
Abstract
Embryonic stem cells (ESCs) are regulated by pluripotency-related transcription factors in concert with chromatin regulators. To identify additional stem cell regulators, we screened a library of endogenously labeled fluorescent fusion proteins in mouse ESCs for fluorescence loss during differentiation. We identified SET, which displayed a rapid isoform shift during early differentiation from the predominant isoform in ESCs, SETα, to the primary isoform in differentiated cells, SETβ, through alternative promoters. SETα is selectively bound and regulated by pluripotency factors. SET depletion causes proliferation slowdown and perturbed neuronal differentiation in vitro and developmental arrest in vivo, and photobleaching methods demonstrate SET's role in maintaining a dynamic chromatin state in ESCs. This work identifies an important regulator of pluripotency and early differentiation, which is controlled by alternative promoter usage. We identify SETα to be rapidly downregulated during ESC differentiation SETα is regulated by pluripotency factors and replaced by SETβ during differentiation SETα/SETβ switch is crucial for ESC differentiation SETα regulates chromatin plasticity in ESCs
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13
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Bhushal S, Wolfsmüller M, Selvakumar TA, Kemper L, Wirth D, Hornef MW, Hauser H, Köster M. Cell Polarization and Epigenetic Status Shape the Heterogeneous Response to Type III Interferons in Intestinal Epithelial Cells. Front Immunol 2017; 8:671. [PMID: 28659914 PMCID: PMC5467006 DOI: 10.3389/fimmu.2017.00671] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/23/2017] [Indexed: 11/13/2022] Open
Abstract
Type I and type III interferons (IFNs) are crucial components of the first-line antiviral host response. While specific receptors for both IFN types exist, intracellular signaling shares the same Jak-STAT pathway. Due to its receptor expression, IFN-λ responsiveness is restricted mainly to epithelial cells. Here, we display IFN-stimulated gene induction at the single cell level to comparatively analyze the activities of both IFN types in intestinal epithelial cells and mini-gut organoids. Initially, we noticed that the response to both types of IFNs at low concentrations is based on a single cell decision-making determining the total cell intrinsic antiviral activity. We identified histone deacetylase (HDAC) activity as a crucial restriction factor controlling the cell frequency of IFN-stimulated gene (ISG) induction upon IFN-λ but not IFN-β stimulation. Consistently, HDAC blockade confers antiviral activity to an elsewise non-responding subpopulation. Second, in contrast to the type I IFN system, polarization of intestinal epithelial cells strongly enhances their ability to respond to IFN-λ signaling and raises the kinetics of gene induction. Finally, we show that ISG induction in mini-gut organoids by low amounts of IFN is characterized by a scattered heterogeneous responsiveness of the epithelial cells and HDAC activity fine-tunes exclusively IFN-λ activity. This study provides a comprehensive description of the differential response to type I and type III IFNs and demonstrates that cell polarization in gut epithelial cells specifically increases IFN-λ activity.
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Affiliation(s)
- Sudeep Bhushal
- Research Group Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Markus Wolfsmüller
- Research Group Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Tharini A Selvakumar
- Research Group Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Lucas Kemper
- Research Group Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Dagmar Wirth
- Research Group Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Mathias W Hornef
- Institute for Medical Microbiology, RWTH Aachen University Hospital, Aachen, Germany
| | - Hansjörg Hauser
- Research Group Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Mario Köster
- Research Group Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
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Duncan HF, Smith AJ, Fleming GJP, Partridge NC, Shimizu E, Moran GP, Cooper PR. The Histone-Deacetylase-Inhibitor Suberoylanilide Hydroxamic Acid Promotes Dental Pulp Repair Mechanisms Through Modulation of Matrix Metalloproteinase-13 Activity. J Cell Physiol 2017; 231:798-816. [PMID: 26264761 DOI: 10.1002/jcp.25128] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 08/07/2015] [Indexed: 12/23/2022]
Abstract
Direct application of histone-deacetylase-inhibitors (HDACis) to dental pulp cells (DPCs) induces chromatin changes, promoting gene expression and cellular-reparative events. We have previously demonstrated that HDACis (valproic acid, trichostatin A) increase mineralization in dental papillae-derived cell-lines and primary DPCs by stimulation of dentinogenic gene expression. Here, we investigated novel genes regulated by the HDACi, suberoylanilide hydroxamic acid (SAHA), to identify new pathways contributing to DPC differentiation. SAHA significantly compromised DPC viability only at relatively high concentrations (5 μM); while low concentrations (1 μM) SAHA did not increase apoptosis. HDACi-exposure for 24 h induced mineralization-per-cell dose-dependently after 2 weeks; however, constant 14d SAHA-exposure inhibited mineralization. Microarray analysis (24 h and 14 days) of SAHA exposed cultures highlighted that 764 transcripts showed a significant >2.0-fold change at 24 h, which reduced to 36 genes at 14 days. 59% of genes were down-regulated at 24 h and 36% at 14 days, respectively. Pathway analysis indicated SAHA increased expression of members of the matrix metalloproteinase (MMP) family. Furthermore, SAHA-supplementation increased MMP-13 protein expression (7 d, 14 days) and enzyme activity (48 h, 14 days). Selective MMP-13-inhibition (MMP-13i) dose-dependently accelerated mineralization in both SAHA-treated and non-treated cultures. MMP-13i-supplementation promoted expression of several mineralization-associated markers, however, HDACi-induced cell migration and wound healing were impaired. Data demonstrate that short-term low-dose SAHA-exposure promotes mineralization in DPCs by modulating gene pathways and tissue proteases. MMP-13i further increased mineralization-associated events, but decreased HDACi cell migration indicating a specific role for MMP-13 in pulpal repair processes. Pharmacological inhibition of HDAC and MMP may provide novel insights into pulpal repair processes with significant translational benefit. J. Cell. Physiol. 231: 798-816, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Henry F Duncan
- Division of Restorative Dentistry and Periodontology, Dublin Dental University Hospital, Trinity College Dublin, Lincoln Place, Dublin 2, Ireland
| | - Anthony J Smith
- Oral Biology, School of Dentistry, University of Birmingham, Birmingham, UK
| | - Garry J P Fleming
- Material Science Unit, Dublin Dental University Hospital, Trinity College Dublin, Ireland
| | - Nicola C Partridge
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York
| | - Emi Shimizu
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York
| | - Gary P Moran
- Division of Oral Biosciences, Dublin Dental University Hospital, Trinity College Dublin, Ireland
| | - Paul R Cooper
- Oral Biology, School of Dentistry, University of Birmingham, Birmingham, UK
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Veronezi GMB, Felisbino MB, Gatti MSV, Mello MLS, Vidal BDC. DNA Methylation Changes in Valproic Acid-Treated HeLa Cells as Assessed by Image Analysis, Immunofluorescence and Vibrational Microspectroscopy. PLoS One 2017; 12:e0170740. [PMID: 28114349 PMCID: PMC5256918 DOI: 10.1371/journal.pone.0170740] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 01/10/2017] [Indexed: 12/18/2022] Open
Abstract
Valproic acid (VPA), a well-known histone deacetylase inhibitor, has been reported to affect the DNA methylation status in addition to inducing histone hyperacetylation in several cell types. In HeLa cells, VPA promotes histone acetylation and chromatin remodeling. However, DNA demethylation was not checked in this cell model for standing effects longer than those provided by histone acetylation, which is a rapid and transient phenomenon. Demonstration of VPA-induced DNA demethylation in HeLa cells would contribute to understanding the effect of VPA on an aggressive tumor cell line. In the present work, DNA demethylation in VPA-treated HeLa cells was assessed by image analysis of chromatin texture, the abundance of 5-methylcytosine (5mC) immunofluorescence signals and Fourier transform-infrared (FT-IR) microspectroscopy centered on spectral regions related to the vibration of–CH3 groups. Image analysis indicated that increased chromatin unpacking promoted by a 4-h-treatment with 1.0 mM VPA persisted for 24 h in the absence of the drug, suggesting the occurrence of DNA demethylation that was confirmed by decreased 5mC immunofluorescence signals. FT-IR spectra of DNA samples from 1 mM or 20 mM VPA-treated cells subjected to a peak fitting analysis of the spectral window for–CH3 stretching vibrations showed decreased vibrations and energy of these groups as a function of the decreased abundance of 5mC induced by increased VPA concentrations. Only the 20 mM-VPA treatment caused an increase in the ratio of -CH3 bending vibrations evaluated at 1375 cm-1 in relation to in-plane vibrations of overall cytosines evaluated at 1492 cm-1. CH3 stretching vibrations showed to be more sensitive than–CH3 bending vibrations, as detected with FT-IR microspectroscopy, for studies aiming to associate vibrational spectroscopy and changes in DNA 5mC abundance.
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Affiliation(s)
- Giovana M. B. Veronezi
- Department of Structural and Functional Biology and, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Marina Barreto Felisbino
- Department of Structural and Functional Biology and, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Maria Sílvia V. Gatti
- Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Maria Luiza S. Mello
- Department of Structural and Functional Biology and, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
- * E-mail:
| | - Benedicto de Campos Vidal
- Department of Structural and Functional Biology and, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
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16
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Stefanovic S, Zaffran S. Mechanisms of retinoic acid signaling during cardiogenesis. Mech Dev 2016; 143:9-19. [PMID: 28007475 DOI: 10.1016/j.mod.2016.12.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/29/2016] [Accepted: 12/12/2016] [Indexed: 10/20/2022]
Abstract
Substantial experimental and epidemiological data have highlighted the interplay between nutritional and genetic factors in the development of congenital heart defects. Retinoic acid (RA), a derivative of vitamin A, plays a key role during vertebrate development including the formation of the heart. Retinoids bind to RA and retinoid X receptors (RARs and RXRs) which then regulate tissue-specific genes. Here, we will focus on the roles of RA signaling and receptors in gene regulation during cardiogenesis, and the consequence of deregulated retinoid signaling on heart formation and congenital heart defects.
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Wiersma M, Bussiere M, Halsall JA, Turan N, Slany R, Turner BM, Nightingale KP. Protein kinase Msk1 physically and functionally interacts with the KMT2A/MLL1 methyltransferase complex and contributes to the regulation of multiple target genes. Epigenetics Chromatin 2016; 9:52. [PMID: 27895715 PMCID: PMC5106815 DOI: 10.1186/s13072-016-0103-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 11/03/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The KMT2A/MLL1 lysine methyltransferase complex is an epigenetic regulator of selected developmental genes, in part through the SET domain-catalysed methylation of H3K4. It is essential for normal embryonic development and haematopoiesis and frequently mutated in cancer. The catalytic properties and targeting of KMT2A/MLL1 depend on the proteins with which it complexes and the post-translational protein modifications which some of these proteins put in place, though detailed mechanisms remain unclear. RESULTS KMT2A/MLL1 (both native and FLAG-tagged) and Msk1 (RPS6KA5) co-immunoprecipitated in various cell types. KMT2A/MLL1 and Msk1 knockdown demonstrated that the great majority of genes whose activity changed on KTM2A/MLL1 knockdown, responded comparably to Msk1 knockdown, as did levels of H3K4 methylation and H3S10 phosphorylation at KTM2A target genes HoxA4, HoxA5. Knockdown experiments also showed that KMT2A/MLL1 is required for the genomic targeting of Msk1, but not vice versa. CONCLUSION The KMT2A/MLL1 complex is associated with, and functionally dependent upon, the kinase Msk1, part of the MAP kinase signalling pathway. We propose that Msk1-catalysed phosphorylation at H3 serines 10 and 28, supports H3K4 methylation by the KMT2A/MLL1 complex both by making H3 a more attractive substrate for its SET domain, and improving target gene accessibility by prevention of HP1- and Polycomb-mediated chromatin condensation.
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Affiliation(s)
- Maaike Wiersma
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Marianne Bussiere
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
- Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 22f, Box 2404, 3001 Louvain, Belgium
| | - John A. Halsall
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Nil Turan
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Robert Slany
- Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Bryan M. Turner
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Karl P. Nightingale
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
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Valproic Acid Increases CD133 Positive Cells that Show Low Sensitivity to Cytostatics in Neuroblastoma. PLoS One 2016; 11:e0162916. [PMID: 27627801 PMCID: PMC5023141 DOI: 10.1371/journal.pone.0162916] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 08/30/2016] [Indexed: 01/26/2023] Open
Abstract
Valproic acid (VPA) is a well-known antiepileptic drug that exhibits antitumor activities through its action as a histone deacetylase inhibitor. CD133 is considered to be a cancer stem cell marker in several tumors including neuroblastoma. CD133 transcription is strictly regulated by epigenetic modifications. We evaluated the epigenetic effects of treatment with 1mM VPA and its influence on the expression of CD133 in four human neuroblastoma cell lines. Chemoresistance and cell cycle of CD133+ and CD133- populations were examined by flow cytometry. We performed bisulfite conversion followed by methylation-sensitive high resolution melting analysis to assess the methylation status of CD133 promoters P1 and P3. Our results revealed that VPA induced CD133 expression that was associated with increased acetylation of histones H3 and H4. On treatment with VPA and cytostatics, CD133+ cells were mainly detected in the S and G2/M phases of the cell cycle and they showed less activated caspase-3 compared to CD133- cells. UKF-NB-3 neuroblastoma cells which express CD133 displayed higher colony and neurosphere formation capacities when treated with VPA, unlike IMR-32 which lacks for CD133 protein. Induction of CD133 in UKF-NB-3 was associated with increased expression of phosphorylated Akt and pluripotency transcription factors Nanog, Oct-4 and Sox2. VPA did not induce CD133 expression in cell lines with methylated P1 and P3 promoters, where the CD133 protein was not detected. Applying the demethylating agent 5-aza-2'-deoxycytidine to the cell lines with methylated promoters resulted in CD133 re-expression that was associated with a drop in P1 and P3 methylation level. In conclusion, CD133 expression in neuroblastoma can be regulated by histone acetylation and/or methylation of its CpG promoters. VPA can induce CD133+ cells which display high proliferation potential and low sensitivity to cytostatics in neuroblastoma. These results give new insight into the possible limitations to use VPA in cancer therapy.
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19
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Epigenetic modulations rendering cell-to-cell variability and phenotypic metastability. J Genet Genomics 2016; 43:503-11. [DOI: 10.1016/j.jgg.2016.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 05/12/2016] [Accepted: 05/25/2016] [Indexed: 02/01/2023]
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Herteleer L, Zwarts L, Hens K, Forero D, Del-Favero J, Callaerts P. Mood stabilizing drugs regulate transcription of immune, neuronal and metabolic pathway genes in Drosophila. Psychopharmacology (Berl) 2016; 233:1751-62. [PMID: 26852229 DOI: 10.1007/s00213-016-4223-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 01/28/2016] [Indexed: 12/29/2022]
Abstract
RATIONALE Lithium and valproate (VPA) are drugs used in the management of bipolar disorder. Even though they reportedly act on various pathways, the transcriptional targets relevant for disease mechanism and therapeutic effect remain unclear. Furthermore, multiple studies used lymphoblasts of bipolar patients as a cellular proxy, but it remains unclear whether peripheral cells provide a good readout for the effects of these drugs in the brain. OBJECTIVES We used Drosophila culture cells and adult flies to analyze the transcriptional effects of lithium and VPA and define mechanistic pathways. METHODS Transcriptional profiles were determined for Drosophila S2-cells and adult fly heads following lithium or VPA treatment. Gene ontology categories were identified using the DAVID functional annotation tool with a cut-off of p < 0.05. Significantly enriched GO terms were clustered using REVIGO and DAVID functional annotation clustering. Significance of overlap between transcript lists was determined with a Fisher's exact hypergeometric test. RESULTS Treatment of cultured cells and adult flies with lithium and VPA induces transcriptional responses in genes with similar ontology, with as most prominent immune response, neuronal development, neuronal function, and metabolism. CONCLUSIONS (i) Transcriptional effects of lithium and VPA in Drosophila S2 cells and heads show significant overlap. (ii) The overlap between transcriptional alterations in peripheral versus neuronal cells at the single gene level is negligible, but at the gene ontology and pathway level considerable overlap can be found. (iii) Lithium and VPA act on evolutionarily conserved pathways in Drosophila and mammalian models.
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Affiliation(s)
- L Herteleer
- Laboratory of Behavioral and Developmental Genetics, VIB-KULeuven, Herestraat 49 bus 602, 3000, Leuven, Belgium
- KULeuven Department of Human Genetics, Leuven, Belgium
- VIB Center for the Biology of Disease, Leuven, Belgium
| | - L Zwarts
- Laboratory of Behavioral and Developmental Genetics, VIB-KULeuven, Herestraat 49 bus 602, 3000, Leuven, Belgium
- KULeuven Department of Human Genetics, Leuven, Belgium
- VIB Center for the Biology of Disease, Leuven, Belgium
| | - K Hens
- Laboratory of Behavioral and Developmental Genetics, VIB-KULeuven, Herestraat 49 bus 602, 3000, Leuven, Belgium
- KULeuven Department of Human Genetics, Leuven, Belgium
- VIB Center for the Biology of Disease, Leuven, Belgium
- Centre for Neural Circuits and Behavior, Oxford University, Oxford, UK
| | - D Forero
- Laboratory of Behavioral and Developmental Genetics, VIB-KULeuven, Herestraat 49 bus 602, 3000, Leuven, Belgium
- KULeuven Department of Human Genetics, Leuven, Belgium
- VIB Center for the Biology of Disease, Leuven, Belgium
- Applied Molecular Genomics Group, VIB Department of Molecular Genetics, Leuven, Belgium
- University of Antwerp, Antwerp, Belgium
- Laboratory of Neuropsychiatric Genetics, School of Medicine, Antonio Narino University, Bogota, Colombia
| | - J Del-Favero
- Applied Molecular Genomics Group, VIB Department of Molecular Genetics, Leuven, Belgium
- University of Antwerp, Antwerp, Belgium
| | - P Callaerts
- Laboratory of Behavioral and Developmental Genetics, VIB-KULeuven, Herestraat 49 bus 602, 3000, Leuven, Belgium.
- KULeuven Department of Human Genetics, Leuven, Belgium.
- VIB Center for the Biology of Disease, Leuven, Belgium.
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Bailey JM, Oliveri AN, Karbhari N, Brooks RAJ, De La Rocha AJ, Janardhan S, Levin ED. Persistent behavioral effects following early life exposure to retinoic acid or valproic acid in zebrafish. Neurotoxicology 2015; 52:23-33. [PMID: 26439099 DOI: 10.1016/j.neuro.2015.10.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND Moderate to severe dysregulation in retinoid signaling during early development is associated with a constellation of physical malformations and/or neural tube defects, including spina bifida. It is thought that more subtle dysregulation of this system, which might be achievable via dietary (i.e. hypervitaminosis A) or pharmacological (i.e. valproic acid) exposure in humans, will manifest on behavioral domains including sociability, without overt physical abnormalities. METHODS During early life, zebrafish were exposed to low doses of two chemicals that disrupt retinoid signaling. From 0 to 5dpf, larvae were reared in aqueous solutions containing retinoic acid (0, 0.02, 0.2 or 2nM) or valproic acid (0, 0.5, 5.0 or 50μM). One cohort of zebrafish was assessed using a locomotor activity screen at 6-dpf; another was reared to adulthood and assessed using a neurobehavioral test battery (startle habituation, novel tank exploration, shoaling, and predator escape/avoidance). RESULTS There was no significant increase in the incidence of physical malformation among exposed fish compared to controls. Both retinoic acid and valproic acid exposures during development disrupted larval activity with persisting behavioral alterations later in life, primarily manifesting as decreased social affiliation. CONCLUSIONS Social behavior and some aspects of motor function were altered in exposed fish; the importance of examining emotional or psychological consequences of early life exposure to retinoid acting chemicals is discussed.
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Affiliation(s)
- Jordan M Bailey
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anthony N Oliveri
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nishika Karbhari
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Roy A J Brooks
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amberlene J De La Rocha
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sheila Janardhan
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Edward D Levin
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA.
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22
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Halsall JA, Turan N, Wiersma M, Turner BM. Cells adapt to the epigenomic disruption caused by histone deacetylase inhibitors through a coordinated, chromatin-mediated transcriptional response. Epigenetics Chromatin 2015; 8:29. [PMID: 26380582 PMCID: PMC4572612 DOI: 10.1186/s13072-015-0021-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/03/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The genome-wide hyperacetylation of chromatin caused by histone deacetylase inhibitors (HDACi) is surprisingly well tolerated by most eukaryotic cells. The homeostatic mechanisms that underlie this tolerance are unknown. Here we identify the transcriptional and epigenomic changes that constitute the earliest response of human lymphoblastoid cells to two HDACi, valproic acid and suberoylanilide hydroxamic acid (Vorinostat), both in widespread clinical use. RESULTS Dynamic changes in transcript levels over the first 2 h of exposure to HDACi were assayed on High Density microarrays. There was a consistent response to the two different inhibitors at several concentrations. Strikingly, components of all known lysine acetyltransferase (KAT) complexes were down-regulated, as were genes required for growth and maintenance of the lymphoid phenotype. Up-regulated gene clusters were enriched in regulators of transcription, development and phenotypic change. In untreated cells, HDACi-responsive genes, whether up- or down-regulated, were packaged in highly acetylated chromatin. This was essentially unaffected by HDACi. In contrast, HDACi induced a strong increase in H3K27me3 at transcription start sites, irrespective of their transcriptional response. Inhibition of the H3K27 methylating enzymes, EZH1/2, altered the transcriptional response to HDACi, confirming the functional significance of H3K27 methylation for specific genes. CONCLUSIONS We propose that the observed transcriptional changes constitute an inbuilt adaptive response to HDACi that promotes cell survival by minimising protein hyperacetylation, slowing growth and re-balancing patterns of gene expression. The transcriptional response to HDACi is mediated by a precisely timed increase in H3K27me3 at transcription start sites. In contrast, histone acetylation, at least at the three lysine residues tested, seems to play no direct role. Instead, it may provide a stable chromatin environment that allows transcriptional change to be induced by other factors, possibly acetylated non-histone proteins.
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Affiliation(s)
- John A Halsall
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Nil Turan
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Maaike Wiersma
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Bryan M Turner
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
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23
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Rakitin A, Kõks S, Reimann E, Prans E, Haldre S. Changes in the Peripheral Blood Gene Expression Profile Induced by 3 Months of Valproate Treatment in Patients with Newly Diagnosed Epilepsy. Front Neurol 2015; 6:188. [PMID: 26379622 PMCID: PMC4553897 DOI: 10.3389/fneur.2015.00188] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/13/2015] [Indexed: 11/24/2022] Open
Abstract
Valproic acid (VPA) is a widely used antiepileptic drug with a broad range of effects and broad clinical efficacy. As a well-known histone deacetylase (HDAC) inhibitor, VPA regulates epigenetic programming by altering the expression of many genes. The aim of study was to analyze differences in gene expression profiles before and after the start of VPA treatment in patients with newly diagnosed epilepsy. RNA sequencing was used to compare whole-genome gene expression patterns of peripheral blood from nine patients with epilepsy before and 3 months after the start of treatment with VPA. Of the 23,099 analyzed genes, only 11 showed statistically significant differential expression with false discovery rate-adjusted p-values below 0.1. Functional annotation and network analyses showed activation of only one genetic network (enrichment score = 30), which included genes for cardiovascular system development and function, cell morphology, and hematological system development and function. The finding of such a small number of differently expressed genes between before and after the start of treatment suggests a lack of HDAC inhibition in these patients, which could be explained by the relatively low doses of VPA that were used. In conclusion, VPA at standard therapeutic dosages modulates the expression of a small number of genes. Therefore, to minimize the potential side effects of HDAC inhibition, it is recommended that the lowest effective dose of VPA be used for treating epilepsy.
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Affiliation(s)
- Aleksei Rakitin
- Department of Neurology and Neurosurgery, University of Tartu , Tartu , Estonia ; Neurology Clinic, Tartu University Hospital , Tartu , Estonia
| | - Sulev Kõks
- Department of Pathophysiology, University of Tartu , Tartu , Estonia ; Centre of Translational Medicine, University of Tartu , Tartu , Estonia
| | - Ene Reimann
- Department of Pathophysiology, University of Tartu , Tartu , Estonia ; Centre of Translational Medicine, University of Tartu , Tartu , Estonia
| | - Ele Prans
- Department of Pathophysiology, University of Tartu , Tartu , Estonia ; Centre of Translational Medicine, University of Tartu , Tartu , Estonia
| | - Sulev Haldre
- Department of Neurology and Neurosurgery, University of Tartu , Tartu , Estonia ; Neurology Clinic, Tartu University Hospital , Tartu , Estonia
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24
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Chu W, Yuan J, Huang L, Xiang X, Zhu H, Chen F, Chen Y, Lin J, Feng H. Valproic Acid Arrests Proliferation but Promotes Neuronal Differentiation of Adult Spinal NSPCs from SCI Rats. Neurochem Res 2015; 40:1472-86. [PMID: 26023063 DOI: 10.1007/s11064-015-1618-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 04/02/2015] [Accepted: 05/18/2015] [Indexed: 11/29/2022]
Abstract
Although the adult spinal cord contains a population of multipotent neural stem/precursor cells (NSPCs) exhibiting the potential to replace neurons, endogenous neurogenesis is very limited after spinal cord injury (SCI) because the activated NSPCs primarily differentiate into astrocytes rather than neurons. Valproic acid (VPA), a histone deacetylase inhibitor, exerts multiple pharmacological effects including fate regulation of stem cells. In this study, we cultured adult spinal NSPCs from chronic compressive SCI rats and treated with VPA. In spite of inhibiting the proliferation and arresting in the G0/G1 phase of NSPCs, VPA markedly promoted neuronal differentiation (β-tubulin III(+) cells) as well as decreased astrocytic differentiation (GFAP(+) cells). Cell cycle regulator p21(Cip/WAF1) and proneural genes Ngn2 and NeuroD1 were increased in the two processes respectively. In vivo, to minimize the possible inhibitory effects of VPA to the proliferation of NSPCs as well as avoid other neuroprotections of VPA in acute phase of SCI, we carried out a delayed intraperitoneal injection of VPA (150 mg/kg/12 h) to SCI rats from day 15 to day 22 after injury. Both of the newborn neuron marker doublecortin and the mature neuron marker neuron-specific nuclear protein were significantly enhanced after VPA treatment in the epicenter and adjacent segments of the injured spinal cord. Although the impaired corticospinal tracks had not significantly improved, Basso-Beattie-Bresnahan scores in VPA treatment group were better than control. Our study provide the first evidence that administration of VPA enhances the neurogenic potential of NSPCs after SCI and reveal the therapeutic value of delayed treatment of VPA to SCI.
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Affiliation(s)
- Weihua Chu
- Department of Neurosurgery, Southwest Hospital, Third Military Medical University, No. 29, Gaotanyan Street, Shapingba District, Chongqing, 400038, China,
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25
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Oronsky B, Oronsky N, Knox S, Fanger G, Scicinski J. Episensitization: therapeutic tumor resensitization by epigenetic agents: a review and reassessment. Anticancer Agents Med Chem 2015; 14:1121-7. [PMID: 24893730 PMCID: PMC4262965 DOI: 10.2174/1871520614666140418144610] [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: 03/30/2014] [Revised: 04/16/2014] [Accepted: 04/18/2014] [Indexed: 11/22/2022]
Abstract
Resistance to chemotherapy, biological and targeted therapies is an important clinical problem. Resistance can arise and/or be selected for multiple mechanisms of action. Unfortunately, acquired resistance to antitumor agents or regimens is nearly inevitable in all patients with metastatic disease. Until recently, it was believed that this resistance was unalterable and irreversible, rendering retreatment with the same or similar drugs futile in most cases. However, the introduction of epigenetic therapies, including HDAC inhibitors and DNA methyltransferase inhibitors (DNMTIs), has provided oncologists with new strategies to potentially overcome this resistance. For example, if chemoresistance is the product of multiple non-genetic alterations, which develop and accumulate over time in response to treatment, then the ability to epigenetically modify the tumor to reconfigure it back to its baseline non-resistant state, holds tremendous promise for the treatment of advanced, metastatic cancer. This minireview aims (1) to explore the potential mechanisms by which a group of small molecule agents including HDACs (entinostat and vorinostat), DNA hypomethylating agents such as the DNMTIs (decitabine (DEC), 5-azacytidine (5-AZA)) and redox modulators (RRx-001) may reprogram the tumors from a refractory to non-refractory state, (2) highlight some recent findings in this area, and (3) discuss the therapeutic potential of resensitization approaches with formerly failed chemotherapies.
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Affiliation(s)
| | | | | | | | - Jan Scicinski
- RadioRx, Inc, 800 W El Camino Real, Suite 180, Mountain View CA 94040.
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26
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Kim YE, Park JA, Park SK, Kang HB, Kwon HJ, Lee Y. Enhancement of Transgene Expression by HDAC Inhibitors in Mouse Embryonic Stem Cells. Dev Reprod 2015; 17:379-87. [PMID: 25949154 PMCID: PMC4382945 DOI: 10.12717/dr.2013.17.4.379] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 12/07/2013] [Accepted: 12/13/2013] [Indexed: 12/04/2022]
Abstract
Embryonic stem (ES) cells can self-renew and differentiate to various cells depending on the culture condition. Although ES cells are a good model for cell type specification and can be useful for application in clinics in the future, studies on ES cells have many experimental restraints including low transfection efficiency and transgene expression. Here, we observed that transgene expression after transfection was enhanced by treatment with histone deacetylse (HDAC) inhibitors such as trichostatin A, sodium butyrate, and valproic acid. Transfection was performed using conventional transfection reagents with a retroviral vector encoding GFP under the control of CMV promoter as a reporter. Treatment of ES cells with HDAC inhibitors after transfection increased population of GFP positive cells up to 180% compared with untreated control. ES cells showed normal expression of stem cell markers after treatment with HDAC inhibitors. Transgene expression was further enhanced by modifying transfection procedure. GFP positive cells selected after transfection were proved to have the stem cell properties. Our improved protocol for enhanced gene delivery and expression in mouse ES cells without hampering ES cell properties will be useful for study and application of ES cells.
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Affiliation(s)
- Young-Eun Kim
- Department of Biochemistry, College of Natural Sciences, Republic of Korea ; Biotechnology Research Institute, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Jeong-A Park
- Department of Biochemistry, College of Natural Sciences, Republic of Korea
| | - Sang-Kyu Park
- Department of Biochemistry, College of Natural Sciences, Republic of Korea
| | - Ho-Bum Kang
- Biotechnology Research Institute, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Hyung-Joo Kwon
- Center for Medical Science Research, Republic of Korea ; Department of Microbiology, College of Medicine, Hallym University, Chuncheon 200-702, Republic of Korea
| | - Younghee Lee
- Department of Biochemistry, College of Natural Sciences, Republic of Korea ; Biotechnology Research Institute, Chungbuk National University, Cheongju 361-763, Republic of Korea
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27
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Alajem A, Biran A, Harikumar A, Sailaja BS, Aaronson Y, Livyatan I, Nissim-Rafinia M, Sommer AG, Mostoslavsky G, Gerbasi VR, Golden DE, Datta A, Sze SK, Meshorer E. Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation. Cell Rep 2015; 10:2019-31. [PMID: 25818293 DOI: 10.1016/j.celrep.2015.02.064] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 01/09/2015] [Accepted: 02/25/2015] [Indexed: 11/19/2022] Open
Abstract
Embryonic stem cells (ESCs) possess a distinct chromatin conformation maintained by specialized chromatin proteins. To identify chromatin regulators in ESCs, we developed a simple biochemical assay named D-CAP (differential chromatin-associated proteins), using brief micrococcal nuclease digestion of chromatin, followed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Using D-CAP, we identified several differentially chromatin-associated proteins between undifferentiated and differentiated ESCs, including the chromatin remodeling protein SMARCD1. SMARCD1 depletion in ESCs led to altered chromatin and enhanced endodermal differentiation. Gene expression and chromatin immunoprecipitation sequencing (ChIP-seq) analyses suggested that SMARCD1 is both an activator and a repressor and is enriched at developmental regulators and that its chromatin binding coincides with H3K27me3. SMARCD1 knockdown caused H3K27me3 redistribution and increased H3K4me3 around the transcription start site (TSS). One of the identified SMARCD1 targets was Klf4. In SMARCD1-knockdown clones, KLF4, as well as H3K4me3 at the Klf4 locus, remained high and H3K27me3 was abolished. These results propose a role for SMARCD1 in restricting pluripotency and activating lineage pathways by regulating H3K27 methylation.
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Affiliation(s)
- Adi Alajem
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alva Biran
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Arigela Harikumar
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Badi Sri Sailaja
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yair Aaronson
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ilana Livyatan
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Malka Nissim-Rafinia
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Andreia Gianotti Sommer
- Section of Gastroenterology, Department of Medicine, Center for Regenerative Medicine (CReM), Boston University School of Medicine, 670 Albany Street, Suite 209, Boston, MA 02118, USA
| | - Gustavo Mostoslavsky
- Section of Gastroenterology, Department of Medicine, Center for Regenerative Medicine (CReM), Boston University School of Medicine, 670 Albany Street, Suite 209, Boston, MA 02118, USA
| | - Vincent R Gerbasi
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA; Naval Medical Research Center, Silver Spring, MD 20910, USA
| | | | - Arnab Datta
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Eran Meshorer
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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28
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Ziyatdinova S, Viswanathan J, Hiltunen M, Tanila H, Pitkänen A. Reduction of epileptiform activity by valproic acid in a mouse model of Alzheimer's disease is not long-lasting after treatment discontinuation. Epilepsy Res 2015; 112:43-55. [PMID: 25847338 DOI: 10.1016/j.eplepsyres.2015.02.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 01/28/2015] [Accepted: 02/04/2015] [Indexed: 12/29/2022]
Abstract
Patients with Alzheimer's disease are at increased risk for unprovoked seizures and epilepsy compared with age-matched controls. Experimental evidence suggests that neuronal hyperexcitability and epilepsy can be triggered by amyloid-β (Aβ), the main component of amyloid plaques. Previous studies demonstrated that the administration of an anticonvulsant and histone deacetylase inhibitor, valproic acid, leads to a long-lasting reduction in Aβ levels. Here we used an APdE9 mouse model of Alzheimer's disease with overproduction of Aβ to assess whether treatment with valproic acid initiated immediately after epilepsy onset modifies the occurrence of epileptiform activity. We also analyzed whether the effect is long-lasting and associated with antiamyloidogenesis and histone-modifications. Male APdE9 mice (15 week old) received daily intraperitoneal injections of 30mg/kg valproic acid for 1 week. After a 3-week wash-out, the same animals received injections of a higher dose of valproic acid (300mg/kg) daily for 1 week. Long-term video-electroencephalography monitoring was performed prior to, during, and after the treatments. Aβ and total histone H3 and H4 acetylation levels were measured at 1 month after the final valproic acid treatment. While 30mg/kg valproic acid reduced spontaneous seizures in APdE9 mice (p<0.05, chi-square), epileptiform discharges were not reduced. Administration of 300mg/kg valproic acid, however, reduced epileptiform discharges in APdE9 mice for at least 1 week after treatment discontinuation (p<0.05, Wilcoxon test), but there was no consistent long-term effects on epileptiform activity after treatment withdrawal. Further, we found no long-lasting effect on Aβ levels (p>0.05, Mann-Whitney test), only a meager increase in global acetylation of histone H3 (p<0.05), and no effects on H4 acetylation (p>0.05). In conclusion, valproic acid treatment of APdE9 mice at the stage when amyloid plaques are beginning to develop and epileptiform activity is detected reduced the amount of epileptiform activity, but the effect disappeared after treatment discontinuation.
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Affiliation(s)
- Sofya Ziyatdinova
- A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland
| | - Jayashree Viswanathan
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | - Mikko Hiltunen
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | - Heikki Tanila
- A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland; Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Asla Pitkänen
- A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland.
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29
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Rochtus A, Izzi B, Vangeel E, Louwette S, Wittevrongel C, Lambrechts D, Moreau Y, Winand R, Verpoorten C, Jansen K, Van Geet C, Freson K. DNA methylation analysis of Homeobox genes implicates HOXB7 hypomethylation as risk factor for neural tube defects. Epigenetics 2015; 10:92-101. [PMID: 25565354 DOI: 10.1080/15592294.2014.998531] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Neural tube defects (NTDs) are common birth defects of complex etiology. Though family- and population-based studies have confirmed a genetic component, the responsible genes for NTDs are still largely unknown. Based on the hypothesis that folic acid prevents NTDs by stimulating methylation reactions, epigenetic factors, such as DNA methylation, are predicted to be involved in NTDs. Homeobox (HOX) genes play a role in spinal cord development and are tightly regulated in a spatiotemporal and collinear manner, partly by epigenetic modifications. We have quantified DNA methylation for the different HOX genes by subtracting values from a genome-wide methylation analysis using leukocyte DNA from 10 myelomeningocele (MMC) patients and 6 healthy controls. From the 1575 CpGs profiled for the 4 HOX clusters, 26 CpGs were differentially methylated (P-value < 0.05; β-difference > 0.05) between MMC patients and controls. Seventy-seven percent of these CpGs were located in the HOXA and HOXB clusters, with the most profound difference for 3 CpGs within the HOXB7 gene body. A validation case-control study including 83 MMC patients and 30 unrelated healthy controls confirmed a significant association between MMC and HOXB7 hypomethylation (-14.4%; 95% CI: 11.9-16.9%; P-value < 0.0001) independent of the MTHFR 667C>T genotype. Significant HOXB7 hypomethylation was also present in 12 unaffected siblings, each related to a MMC patient, suggestive of an epigenetic change induced by the mother. The inclusion of a neural tube formation model using zebrafish showed that Hoxb7a overexpression but not depletion resulted in deformed body axes with dysmorphic neural tube formation. Our results implicate HOXB7 hypomethylation as risk factor for NTDs and highlight the importance for future genome-wide DNA methylation analyses without preselecting candidate pathways.
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Affiliation(s)
- Anne Rochtus
- a Department of Cardiovascular Sciences; Center for Molecular and Vascular Biology ; University of Leuven ; Leuven , Belgium
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30
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Balmer NV, Klima S, Rempel E, Ivanova VN, Kolde R, Weng MK, Meganathan K, Henry M, Sachinidis A, Berthold MR, Hengstler JG, Rahnenführer J, Waldmann T, Leist M. From transient transcriptome responses to disturbed neurodevelopment: role of histone acetylation and methylation as epigenetic switch between reversible and irreversible drug effects. Arch Toxicol 2014; 88:1451-68. [PMID: 24935251 PMCID: PMC4067541 DOI: 10.1007/s00204-014-1279-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 05/19/2014] [Indexed: 01/17/2023]
Abstract
The superordinate principles governing the transcriptome response of differentiating cells exposed to drugs are still unclear. Often, it is assumed that toxicogenomics data reflect the immediate mode of action (MoA) of drugs. Alternatively, transcriptome changes could describe altered differentiation states as indirect consequence of drug exposure. We used here the developmental toxicants valproate and trichostatin A to address this question. Neurally differentiating human embryonic stem cells were treated for 6 days. Histone acetylation (primary MoA) increased quickly and returned to baseline after 48 h. Histone H3 lysine methylation at the promoter of the neurodevelopmental regulators PAX6 or OTX2 was increasingly altered over time. Methylation changes remained persistent and correlated with neurodevelopmental defects and with effects on PAX6 gene expression, also when the drug was washed out after 3-4 days. We hypothesized that drug exposures altering only acetylation would lead to reversible transcriptome changes (indicating MoA), and challenges that altered methylation would lead to irreversible developmental disturbances. Data from pulse-chase experiments corroborated this assumption. Short drug treatment triggered reversible transcriptome changes; longer exposure disrupted neurodevelopment. The disturbed differentiation was reflected by an altered transcriptome pattern, and the observed changes were similar when the drug was washed out during the last 48 h. We conclude that transcriptome data after prolonged chemical stress of differentiating cells mainly reflect the altered developmental stage of the model system and not the drug MoA. We suggest that brief exposures, followed by immediate analysis, are more suitable for information on immediate drug responses and the toxicity MoA.
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Affiliation(s)
- Nina V. Balmer
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Stefanie Klima
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Eugen Rempel
- Department of Statistics, TU Dortmund, Dortmund, Germany
| | - Violeta N. Ivanova
- Chair for Bioinformatics and Information Mining, University of Konstanz, Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | | | - Matthias K. Weng
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Kesavan Meganathan
- Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Margit Henry
- Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Agapios Sachinidis
- Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Michael R. Berthold
- Chair for Bioinformatics and Information Mining, University of Konstanz, Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | - Jan G. Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), 44139 Dortmund, Germany
| | | | - Tanja Waldmann
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Marcel Leist
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
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31
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Seuter S, Pehkonen P, Heikkinen S, Carlberg C. Dynamics of 1α,25-dihydroxyvitamin D3-dependent chromatin accessibility of early vitamin D receptor target genes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1266-75. [PMID: 24185200 DOI: 10.1016/j.bbagrm.2013.10.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 10/01/2013] [Accepted: 10/18/2013] [Indexed: 01/05/2023]
Abstract
The signaling cascade of the transcription factor vitamin D receptor (VDR) is triggered by its specific ligand 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3). In this study we demonstrate that in THP-1 human monocytic leukemia cells 87.4% of the 1034 most prominent genome-wide VDR binding sites co-localize with loci of open chromatin. At 165 of them 1α,25(OH)2D3 strongly increases chromatin accessibility and has at further 217 sites weaker effects. Interestingly, VDR binding sites in 1α,25(OH)2D3-responsive chromatin regions are far more often composed of direct repeats with 3 intervening nucleotides (DR3s) than those in ligand insensitive regions. DR3-containing VDR sites are enriched in the neighborhood of genes that are involved in controling cellular growth, while non-DR3 VDR binding is often found close to genes related to immunity. At the example of six early VDR target genes we show that the slope of their 1α,25(OH)2D3-induced transcription correlates with the basal chromatin accessibility of their major VDR binding regions. However, the chromatin loci controlling these genes are indistinguishable in their VDR association kinetics. Taken together, ligand responsive chromatin loci represent dynamically regulated contact points of VDR with the genome, from where it controls early 1α,25(OH)2D3 target genes.
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Key Words
- 1α,25(OH)(2)D(3) or 1,25D
- 1α,25-dihydroxyvitamin D(3)
- B2M
- CAMP
- CD14
- ChIP
- ChIP sequencing
- ChIP-seq
- DR3
- FAIRE
- FAIRE sequencing
- FAIRE-seq
- FANCE
- FBP1
- FCS
- FDR
- Fanconi anemia, complementation group E
- GAPDH
- GEO
- GREAT
- Gene Expression Omnibus
- Genomic Regions Enrichment of Annotations Tool
- H3K27ac
- HBB
- HBEGF
- HDAC
- HDAC inhibitor
- HPRTI
- IGV
- Integrative Genomics Viewer
- MB
- NFKBIA
- NINJ1
- Open chromatin
- PDCD1LG2
- PPARGC1B
- PSMA6
- SAHA
- SCTR
- SEMA6B
- TMEM37
- TSS
- TsA
- VDR
- VPA
- Vitamin D
- beta-2-microglobulin
- cathelicidin antimicrobial peptide
- chromatin immunoprecipitation
- cluster of differentiation 14 molecule
- direct repeat spaced by 3 nucleotides
- false discovery rate
- fetal calf serum
- formaldehyde-assisted isolation of regulatory elements
- fructose-1,6-bisphosphatase 1
- gylcerinaldehyde-3-phosphate-dehydrogenase
- hemoglobin, beta
- heparin-binding EGF-like growth factor
- histone 3 acetylation at lysine 27
- histone deacetylase
- hypoxanthine phosphoribosyltransferase 1
- myoglobin
- ninjurin 1
- nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha
- peroxisome proliferator-activated receptor γ, co-activator 1β
- programmed cell death 1 ligand 2
- proteasome subunit, alpha type, 6
- qPCR
- real-time quantitative polymerase chain reaction
- secretin receptor
- semaphorin 6B
- suberoylanilide hydroxamic acid
- transcription start site
- transmembrane protein 37
- trichostatin A
- valproic acid
- vitamin D receptor
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Affiliation(s)
- Sabine Seuter
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FIN-70211 Kuopio, Finland
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