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Al-Khafaji AS, Wang LM, Alabdei HH, Liloglou T. Effect of valproic acid on histone deacetylase expression in oral cancer (Review). Oncol Lett 2024; 27:197. [PMID: 38516679 PMCID: PMC10955681 DOI: 10.3892/ol.2024.14330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/04/2024] [Indexed: 03/23/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a frequent human malignancy that demonstrates a range of genetic and epigenetic alterations. Histone deacetylases (HDACs) are key epigenetic regulators of cell-cycle progression, differentiation and apoptosis and their dysregulation is implicated in cancer development. HDACs are promising targets for anticancer therapy through the utilisation of HDAC inhibitors (HDACis). OSCC cells have been shown to have low levels of histone acetylation, suggesting that HDACis may produce beneficial effects in patients with OSCC. Valproic acid (VPA) is a class I and IIa HDACi and, therefore, may be useful in anticancer therapy. VPA has been reported as a chemo-preventive epigenetic agent in individuals with high-risk oral dysplasia (OD) and thus associated with a reduced risk of HNSCC. It is hypothesised that HDAC inhibition by VPA triggers a change in the expression levels of different HDAC family gene-members. The present review summarises the current literature on HDAC expression changes in response to VPA in oral cancer patients and in vitro studies in an effort to better understand the potential epigenetic impact of VPA treatment. The present review outlined the need for exploring supportive evidence of the chemo-preventive role played by VPA-based epigenetic modification in treating oral pre-cancerous lesions and, thus, providing a novel tolerable chemotherapeutic strategy for patients with oral cancer.
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Affiliation(s)
- Ahmed S.K. Al-Khafaji
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L7 8TX, UK
- Department of Biology, College of Science, University of Baghdad, Baghdad 10071, Iraq
- College of Medicine, University of Warith Al-Anbiyaa, Karbala 56001, Iraq
| | - Lydia M. Wang
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Haidar H. Alabdei
- College of Medicine, University of Warith Al-Anbiyaa, Karbala 56001, Iraq
| | - Triantafillos Liloglou
- Cardiorespiratory Research Centre, Medical School, Faculty of Health, Social Care and Medicine, Edge Hill University, Ormskirk, Lancashire L39 4QP, UK
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Karandikar PV, Suh L, Gerstl JVE, Blitz SE, Qu QR, Won SY, Gessler FA, Arnaout O, Smith TR, Peruzzi PP, Yang W, Friedman GK, Bernstock JD. Positioning SUMO as an immunological facilitator of oncolytic viruses for high-grade glioma. Front Cell Dev Biol 2023; 11:1271575. [PMID: 37860820 PMCID: PMC10582965 DOI: 10.3389/fcell.2023.1271575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
Oncolytic viral (OV) therapies are promising novel treatment modalities for cancers refractory to conventional treatment, such as glioblastoma, within the central nervous system (CNS). Although OVs have received regulatory approval for use in the CNS, efficacy is hampered by obstacles related to delivery, under-/over-active immune responses, and the "immune-cold" nature of most CNS malignancies. SUMO, the Small Ubiquitin-like Modifier, is a family of proteins that serve as a high-level regulator of a large variety of key physiologic processes including the host immune response. The SUMO pathway has also been implicated in the pathogenesis of both wild-type viruses and CNS malignancies. As such, the intersection of OV biology with the SUMO pathway makes SUMOtherapeutics particularly interesting as adjuvant therapies for the enhancement of OV efficacy alone and in concert with other immunotherapeutic agents. Accordingly, the authors herein provide: 1) an overview of the SUMO pathway and its role in CNS malignancies; 2) describe the current state of CNS-targeted OVs; and 3) describe the interplay between the SUMO pathway and the viral lifecycle and host immune response.
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Affiliation(s)
- Paramesh V. Karandikar
- T. H. Chan School of Medicine, University of Massachusetts, Worcester, MA, United States
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Lyle Suh
- T. H. Chan School of Medicine, University of Massachusetts, Worcester, MA, United States
| | - Jakob V. E. Gerstl
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Sarah E. Blitz
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Qing Rui Qu
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Sae-Yeon Won
- Department of Neurosurgery, University of Rostock, Rostock, Germany
| | | | - Omar Arnaout
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Timothy R. Smith
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Pier Paolo Peruzzi
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Wei Yang
- Department of Anesthesiology, Multidisciplinary Brain Protection Program, Duke University Medical Center, Durham, NC, United States
| | - Gregory K. Friedman
- Department of Neuro-Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX, United States
| | - Joshua D. Bernstock
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
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Vatsa PP, Jindal Y, Bhadwalkar J, Chamoli A, Upadhyay V, Mandoli A. Role of epigenetics in OSCC: an understanding above genetics. Med Oncol 2023; 40:122. [PMID: 36941511 DOI: 10.1007/s12032-023-01992-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/08/2023] [Indexed: 03/22/2023]
Abstract
Oral cavity cancer is categorized under head and neck cancer that frequently develops from squamous cells hence also known as oral squamous cell carcinoma (OSCC). Although molecular markers for oral cavity cancer are already known, epigenetic signatures for the same haven't been explored much. Epigenetic and genetic alterations were initially thought to be discrete mechanisms driving the tumour but the whole exome sequencing of various cancers has revealed the interdependency of epigenetics and genetic alterations. The reversible nature of these epigenetic changes makes them an alluring target for cancer therapeutics. The primary epigenetic alterations in cancer include DNA methylation and histone modifications. These alterations are useful for patient early detection and prognostication. This review summarizes the epigenetic perspective to understand the etiology, epigenetic biomarkers, and epi-drugs for better predictive diagnosis and treatment of OSCC.
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Affiliation(s)
- Priyanka P Vatsa
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Yogita Jindal
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Janhavi Bhadwalkar
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Ambika Chamoli
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Vinal Upadhyay
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Amit Mandoli
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India.
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Advances in the Histone Acetylation Modification in the Oral Squamous Cell Carcinoma. JOURNAL OF ONCOLOGY 2023. [DOI: 10.1155/2023/4616682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is one of the common malignant tumors in the head and neck, characterized by high malignancy, rapid growth and metastasis, high invasive ability, and high mortality. In recent years, surgery combined with chemotherapy or radiotherapy remains the preferred clinical treatment for OSCC, despite considerable advances in diagnostic and therapeutic techniques. Hence, new targeted therapy is urgently needed. Histone modification affects the function of massive cells through histone acetyltransferase and histone deacetylase. Accompanied by the progress of some diseases, especially tumors, these proteins often show abnormal functions, and by reversing these abnormalities with drugs or gene therapy, the cancer phenotype can even be restored to normal. As a result, they are potential drug targets. This article reviewed the role of the histone dynamic process of acetylation modifications and their associated active modifying enzymes in the pathogenesis and progress of OSCC. Moreover, we explored the value of histone acetylation modification as a potential therapeutic target and the new progress of related drugs in clinical treatment.
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Meng Y, Li X. Expression and Prognosis Analysis of SUMOylation Regulators in Oral Squamous Cell Carcinoma Based on High-Throughput Sequencing. Front Genet 2021; 12:671392. [PMID: 34267779 PMCID: PMC8277238 DOI: 10.3389/fgene.2021.671392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
Introduction Oral squamous cell carcinoma (OSCC) originates from oral mucosal epithelial cells, accounting for more than 90% of oral cancers. The relationship between the expression and prognostic role of SUMOylation regulators in OSCC is rarely studied. Materials and methods The expression and survival data of OSCC were derived from TCGA and GEO databases. Wilcoxon test was used to determine the differential expression of the SUMOylation regulators. A prognostic model based on SUMOylation regulator-related genes was constructed by Cox regression. Gene set enrichment analysis was applied to predict the potential biological functions that the genes might be involved in. Results RANBP2 and SENP6 had the highest SNV frequency. Eleven genes including PIAS3, RANBP2, USPL1, SENP6, SENP2, SENP5, SAE1, UBA2, PIAS4, UBE2I, and SENP3 were highly expressed in OSCC. The prognostic model based on nine SUMOylation-regulated genes (TRIM37, UFM1, FUBP1, CCNT1, FXR1, HMG20A, RANBP3, SPATA5, and DDX23) had a strong ability to predict the prognosis of OSCC. Conclusion This study might provide targets for prognostic evaluation and targeted therapy of patients with OSCC.
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Affiliation(s)
- Yutong Meng
- Department of Stomatology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaozhi Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
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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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Cristóbal-Luna JM, Correa-Basurto J, Mendoza-Figueroa HL, Chamorro-Cevallos G. Anti-epileptic activity, toxicity and teratogenicity in CD1 mice of a novel valproic acid arylamide derivative, N-(2-hydroxyphenyl)-2-propylpentanamide. Toxicol Appl Pharmacol 2020; 399:115033. [PMID: 32387339 DOI: 10.1016/j.taap.2020.115033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/07/2020] [Accepted: 05/04/2020] [Indexed: 12/20/2022]
Abstract
N-(2-hydroxyphenyl)-2-propylpentamide (HO-AAVPA) is a novel arylamide derivative of valproic acid (VPA) designed in silico, with better antioxidant and antiproliferative effect on cancer cell lines than VPA. This study was aimed to evaluate the anticonvulsant activity, the toxicity and teratogenicity produced in HO-AAVPA-treated CD1 mice using VPA as positive control. With the maximal electroshock (MES)- and pentylenetetrazole (PTZ)-induced seizure models, HO-AAVPA reduced the time of hind limb extension, stupor and recovery, the number of clonic and tonic seizures and the mortality rate in a dose-dependent manner, obtaining an ED50 of 370 and 348 mg/kg for MES and PTZ, respectively. On the rotarod test, mice administered with 600 mg/kg HO-AAVPA manifested reduced locomotor activity (2.78%); while HO-AAVPA at 300 mg/kg and VPA at 500 mg/kg gave a similar outcome (∼60%). The LD50 of 936.80 mg/kg herein found for HO-AAVPA reflects moderate toxicity. Concerning teratogenicity, the administration of HO-AAVPA to pregnant females at 300 and 600 mg/kg on gestation day (GD) 8.5 generated less visceral and skeletal alterations in the fetuses, as well as, minor rate of modifications in the expression pattern of the neuronal marker Tuj1 and endothelial marker PECAM1 in embryos, that those induced by VPA administration. Altered embryonic development occurred with less frequency and severity with HO-AAVPA at 600 mg/kg than VPA at 500 mg/kg. In conclusion, the protective effect against convulsions provided by HO-AAVPA was comparable to that of VPA in the MES and PZT seizure models, showed lower toxicity and less damage to embryonic and fetal development.
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Affiliation(s)
- José Melesio Cristóbal-Luna
- Laboratorio de Toxicología Preclínica, Departamento de Farmacia, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu, Col. Zacatenco, Del. Gustavo A. Madero, Ciudad de México 07738, Mexico.
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Farmacos e Innovación Biotecnológica, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomás, Del. Miguel Hidalgo, Ciudad de México 11340, Mexico
| | - Humberto L Mendoza-Figueroa
- Laboratorio de Diseño y Desarrollo de Nuevos Farmacos e Innovación Biotecnológica, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomás, Del. Miguel Hidalgo, Ciudad de México 11340, Mexico
| | - Germán Chamorro-Cevallos
- Laboratorio de Toxicología Preclínica, Departamento de Farmacia, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu, Col. Zacatenco, Del. Gustavo A. Madero, Ciudad de México 07738, Mexico
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Zhang Z, Zhang R, Hao C, Pei X, Li J, Wang L. GANT61 and Valproic Acid Synergistically Inhibited Multiple Myeloma Cell Proliferation via Hedgehog Signaling Pathway. Med Sci Monit 2020; 26:e920541. [PMID: 32054823 PMCID: PMC7034399 DOI: 10.12659/msm.920541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Multiple myeloma is featured by the proliferation of malignant plasma cell in bone marrow. We aimed to demonstrate the effects of valproic acid combined with GANT61 on multiple myeloma cell proliferation and clarify its mechanism. Material/Methods Multiple myeloma cells were exposed to valproic acid, GANT61, or the combination of valproic acid and GANT61, respectively. MTT assay was performed to detect the cell viability. Quantitative reverse transcriptase polymerase chain reaction and western blotting were used to detect mRNA and expression levels of proteins in Hedgehog signaling pathway. The Q-value of the combination regime was calculated to evaluate the drug combination effect. Results Both valproic acid and GANT61 alone inhibited multiple myeloma cell proliferation in a dose-dependent manner compared to the control. In the presence of GANT61 or not, valproic acid inhibited multiple myeloma cell proliferation in a time-dependent manner. These 2 drugs had a synergistic effect at valproic acid concentration of ≥4 mM. Expression analysis showed that valproic acid significantly inhibited the expression levels of PTCH1, GLI1, and HES-1. GANT61 enhanced the inhibition of Hedgehog signaling pathway mediated by valproic acid. Conclusions GANT61 and valproic acid inhibited multiple myeloma cell proliferation synergistically by inhibiting the Hedgehog signaling pathway. The present study may provide a combination regime for the therapy of multiple myeloma.
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Affiliation(s)
- Zhihua Zhang
- Department of Hematology, Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China (mainland)
| | - Rongjuan Zhang
- Department of Hematology, Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China (mainland)
| | - Changlai Hao
- Department of Hematology, Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China (mainland)
| | - Xiaochuan Pei
- Department of Hematology, Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China (mainland)
| | - Jundong Li
- Department of Hematology, Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China (mainland)
| | - Lihong Wang
- Department of Hematology, Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China (mainland)
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Kuijpers TJM, Wolters JEJ, Kleinjans JCS, Jennen DGJ. DynOVis: a web tool to study dynamic perturbations for capturing dose-over-time effects in biological networks. BMC Bioinformatics 2019; 20:417. [PMID: 31409281 PMCID: PMC6693283 DOI: 10.1186/s12859-019-2995-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/16/2019] [Indexed: 01/11/2023] Open
Abstract
Background The development of high throughput sequencing techniques provides us with the possibilities to obtain large data sets, which capture the effect of dynamic perturbations on cellular processes. However, because of the dynamic nature of these processes, the analysis of the results is challenging. Therefore, there is a great need for bioinformatics tools that address this problem. Results Here we present DynOVis, a network visualization tool that can capture dynamic dose-over-time effects in biological networks. DynOVis is an integrated work frame of R packages and JavaScript libraries and offers a force-directed graph network style, involving multiple network analysis methods such as degree threshold, but more importantly, it allows for node expression animations as well as a frame-by-frame view of the dynamic exposure. Valuable biological information can be highlighted on the nodes in the network, by the integration of various databases within DynOVis. This information includes pathway-to-gene associations from ConsensusPathDB, disease-to-gene associations from the Comparative Toxicogenomics databases, as well as Entrez gene ID, gene symbol, gene synonyms and gene type from the NCBI database. Conclusions DynOVis could be a useful tool to analyse biological networks which have a dynamic nature. It can visualize the dynamic perturbations in biological networks and allows the user to investigate the changes over time. The integrated data from various online databases makes it easy to identify the biological relevance of nodes in the network. With DynOVis we offer a service that is easy to use and does not require any bioinformatics skills to visualize a network.
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Affiliation(s)
- T J M Kuijpers
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, Maastricht, 6200 MD, The Netherlands.
| | - J E J Wolters
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, Maastricht, 6200 MD, The Netherlands.,Present Address: School for Mental Health and Neuroscience (MHeNS), University Eye clinic Maastricht, Maastricht University Medical Centre + (MUMC+), P.O. Box 5800, Maastricht, 6229 HX, The Netherlands
| | - J C S Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, Maastricht, 6200 MD, The Netherlands
| | - D G J Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, Maastricht, 6200 MD, The Netherlands
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10
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Yang H, Jin X, Dan H, Chen Q. Histone modifications in oral squamous cell carcinoma and oral potentially malignant disorders. Oral Dis 2019; 26:719-732. [PMID: 31056829 DOI: 10.1111/odi.13115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 04/17/2019] [Accepted: 04/29/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Huamei Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Medicine of Carcinogenesis and Management West China Hospital of Stomatology, Sichuan University Chengdu China
| | - Xin Jin
- College of Stomatology Chongqing Medical University Chongqing China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences Chongqing China
| | - Hongxia Dan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Medicine of Carcinogenesis and Management West China Hospital of Stomatology, Sichuan University Chengdu China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Medicine of Carcinogenesis and Management West China Hospital of Stomatology, Sichuan University Chengdu China
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Ma XJ, Wang YS, Gu WP, Zhao X. The role and possible molecular mechanism of valproic acid in the growth of MCF-7 breast cancer cells. Croat Med J 2017; 58:349-357. [PMID: 29094813 PMCID: PMC5733376 DOI: 10.3325/cmj.2017.58.349] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Aim To investigate the role of valproic acid (VPA), a class I selective histone deacetylase inhibitor, on Michigan Cancer Foundation (MCF)-7 breast cancer cells, named and explore its possible molecular mechanism. Methods MCF-7 cells were cultured with sodium valproate (0. 5-4.0 mmol/L) for 24 h, 48 h, and 72 h in vitro, respectively. The cell viability, apoptosis, and cell cycle were examined. The activities and protein expressions of caspase-3, caspase-8, and caspase-9 were subsequently assayed. Finally, mRNA and protein expressions of cyclin A, cyclin D1, cyclin E, and p21 were analyzed. Results Sodium valproate suppressed MCF-7 cell growth, induced cell apoptosis, and arrested G1 phase in a time- and concentration- dependent manner, with the relative cell viabilities decreased, cell apoptosis ratios increased, and percentage of G1 phase enhanced (P < 0.05). Increased activity of caspase-3 and caspase-9, but not caspase-8, and increased protein levels were found under sodium valproate (2.0 mmol/L, 48h). P21 was up-regulated and cyclin D1 was down-regulated at both mRNA and protein levels under sodium valproate (2.0 mmol/L, 48h)(P < 0.05), although cyclin E and cyclin A remained changed. Conclusion These results indicate that VPA can suppress the growth of breast cancer MCF-7 cells by inducing apoptosis and arresting G1 phase. Intrinsic apoptotic pathway is dominant for VPA-induced apoptosis. For G1 phase arrest, p21 up-regulation and down-regulation of cyclin D1 may be the main molecular mechanism.
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Affiliation(s)
| | | | | | - Xia Zhao
- Xia Zhao, Department of Laboratory Medicine, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P. R. China,
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HDAC inhibition as a treatment concept to combat temsirolimus-resistant bladder cancer cells. Oncotarget 2017; 8:110016-110028. [PMID: 29299126 PMCID: PMC5746361 DOI: 10.18632/oncotarget.22454] [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: 06/01/2017] [Accepted: 10/12/2017] [Indexed: 12/16/2022] Open
Abstract
Introduction Although the mechanistic target of rapamycin (mTOR) might be a promising molecular target to treat advanced bladder cancer, resistance develops under chronic exposure to an mTOR inhibitor (everolimus, temsirolimus). Based on earlier studies, we proposed that histone deacetylase (HDAC) blockade might circumvent resistance and investigated whether HDAC inhibition has an impact on growth of bladder cancer cells with acquired resistance towards temsirolimus. Results The HDAC inhibitor valproic acid (VPA) significantly inhibited growth, proliferation and caused G0/G1 phase arrest in RT112res and UMUC-3res. cdk1, cyclin B, cdk2, cyclin A and Skp1 p19 were down-regulated, p27 was elevated. Akt-mTOR signaling was deactivated, whereas acetylation of histone H3 and H4 in RT112res and UMUC-3res increased in the presence of VPA. Knocking down cdk2 or cyclin A resulted in a significant growth blockade of RT112res and UMUC-3res. Materials And Methods Parental (par) and resistant (res) RT112 and UMUC-3 cells were exposed to the HDAC inhibitor VPA. Tumor cell growth, proliferation, cell cycling and expression of cell cycle regulating proteins were then evaluated. siRNA blockade was used to investigate the functional impact of the proteins. Conclusions HDAC inhibition induced a strong response of temsirolimus-resistant bladder cancer cells. Therefore, the temsirolimus-VPA-combination might be an innovative strategy for bladder cancer treatment.
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