1
|
Lucchini S, Constantinou M, Marino S. Unravelling the mosaic: Epigenetic diversity in glioblastoma. Mol Oncol 2024. [PMID: 39148319 DOI: 10.1002/1878-0261.13706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 06/21/2024] [Accepted: 07/23/2024] [Indexed: 08/17/2024] Open
Abstract
Glioblastoma is the most common primary malignant brain tumour. Despite decades of intensive research in the disease, its prognosis remains poor, with an average survival of only 14 months after diagnosis. The remarkable level of intra- and interpatient heterogeneity is certainly contributing to the lack of progress in tackling this tumour. Epigenetic dysregulation plays an important role in glioblastoma biology and significantly contributes to intratumour heterogeneity. However, it is becoming increasingly clear that it also contributes to intertumour heterogeneity, which historically had mainly been linked to diverse genetic events occurring in different patients. In this review, we explore how DNA methylation, chromatin remodelling, microRNA (miRNA) dysregulation, and long noncoding RNA (lncRNA) alterations contribute to intertumour heterogeneity in glioblastoma, including its implications for advanced tumour stratification, which is the essential first step for developing more effective patient-specific therapeutic approaches.
Collapse
Affiliation(s)
- Sara Lucchini
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
| | - Myrianni Constantinou
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
| | - Silvia Marino
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
- Barts Brain Tumour Centre, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
- Barts Health NHS Trust, London, UK
| |
Collapse
|
2
|
Okamoto T, Mizuta R, Takahashi Y, Otani Y, Sasaki E, Horio Y, Kuroda H, Matsushita H, Date I, Hashimoto N, Masago K. Genomic landscape of glioblastoma without IDH somatic mutation in 42 cases: a comprehensive analysis using RNA sequencing data. J Neurooncol 2024; 167:489-499. [PMID: 38653957 DOI: 10.1007/s11060-024-04628-z] [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: 01/16/2024] [Accepted: 02/29/2024] [Indexed: 04/25/2024]
Abstract
PURPOSE Glioblastoma is a malignant brain tumor with a poor prognosis. Genetic mutations associated with this disease are complex are not fully understood and require further elucidation for the development of new treatments. The purpose of this study was to comprehensively analyze genetic mutations in glioblastomas and evaluate the usefulness of RNA sequencing. PATIENTS AND METHODS We analyzed 42 glioblastoma specimens that were resected in routine clinical practice and found wild-type variants of the IDH1 and IDH2 genes. RNA was extracted from frozen specimens and sequenced, and genetic analyses were performed using the CLC Genomics Workbench. RESULTS The most common genetic alterations in the 42 glioblastoma specimens were TP53 mutation (28.6%), EGFR splicing variant (16.7%), EGFR mutation (9.5%), and FGFR3 fusion (9.5%). Novel genetic mutations were detected in 8 patients (19%). In 12 cases (28.6%), driver gene mutations were not detected, suggesting an association with PPP1R14A overexpression. Our findings suggest the transcription factors SOX10 and NKX6-2 are potential markers in glioblastoma. CONCLUSION RNA sequencing is a promising approach for genotyping glioblastomas because it provides comprehensive information on gene expression and is relatively cost-effective.
Collapse
Affiliation(s)
- Takanari Okamoto
- Department of Neurosurgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Ryo Mizuta
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Yoshinobu Takahashi
- Department of Neurosurgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshihiro Otani
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Eiichi Sasaki
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Yoshitsugu Horio
- Department of Thoracic oncology, Aichi Cancer Center Hospital, Aichi, Japan
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Hiroaki Kuroda
- Department of Thoracic Surgery, Teikyo University Mizonokuchi Hospital, Kanagawa, Japan
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Hirokazu Matsushita
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Isao Date
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Naoya Hashimoto
- Department of Neurosurgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Katsuhiro Masago
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan.
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Aichi, Japan.
| |
Collapse
|
3
|
Maleszewska M, Wojnicki K, Mieczkowski J, Król SK, Jacek K, Śmiech M, Kocyk M, Ciechomska IA, Bujko M, Siedlecki J, Kotulska K, Grajkowska W, Zawadzka M, Kaminska B. DMRTA2 supports glioma stem-cell mediated neovascularization in glioblastoma. Cell Death Dis 2024; 15:228. [PMID: 38509074 PMCID: PMC10954651 DOI: 10.1038/s41419-024-06603-y] [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: 09/26/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
Glioblastoma (GBM) is the most common and lethal brain tumor in adults. Due to its fast proliferation, diffusive growth and therapy resistance survival times are less than two years for patients with IDH-wildtype GBM. GBM is noted for the considerable cellular heterogeneity, high stemness indices and abundance of the glioma stem-like cells known to support tumor progression, therapeutic resistance and recurrence. Doublesex- and mab-3-related transcription factor a2 (DMRTA2) is involved in maintaining neural progenitor cells (NPC) in the cell cycle and its overexpression suppresses NPC differentiation. Despite the reports showing that primary GBM originates from transformed neural stem/progenitors cells, the role of DMRTA2 in gliomagenesis has not been elucidated so far. Here we show the upregulation of DMRTA2 expression in malignant gliomas. Immunohistochemical staining showed the protein concentrated in small cells with high proliferative potential and cells localized around blood vessels, where it colocalizes with pericyte-specific markers. Knock-down of DMRTA2 in human glioma cells impairs proliferation but not viability of the cells, and affects the formation of the tumor spheres, as evidenced by strong decrease in the number and size of spheres in in vitro cultures. Moreover, the knockdown of DMRTA2 in glioma spheres affects the stabilization of the glioma stem-like cell-dependent tube formation in an in vitro angiogenesis assay. We conclude that DMRTA2 is a new player in gliomagenesis and tumor neovascularization and due to its high expression in malignant gliomas could be a biomarker and potential target for new therapeutic strategies in glioblastoma.
Collapse
Affiliation(s)
- Marta Maleszewska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
- Department of Animal Physiology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Kamil Wojnicki
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Jakub Mieczkowski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- 3P-Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland
| | - Sylwia K Król
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Karol Jacek
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena Śmiech
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Marta Kocyk
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Iwona A Ciechomska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Janusz Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Katarzyna Kotulska
- Department of Pathology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Wiesława Grajkowska
- Department of Pathology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Małgorzata Zawadzka
- Laboratory of Neuromuscular Plasticity, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| |
Collapse
|
4
|
Kiel K, Król SK, Bronisz A, Godlewski J. MiR-128-3p - a gray eminence of the human central nervous system. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102141. [PMID: 38419943 PMCID: PMC10899074 DOI: 10.1016/j.omtn.2024.102141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
MicroRNA-128-3p (miR-128-3p) is a versatile molecule with multiple functions in the physiopathology of the human central nervous system. Perturbations of miR-128-3p, which is enriched in the brain, contribute to a plethora of neurodegenerative disorders, brain injuries, and malignancies, as this miRNA is a crucial regulator of gene expression in the brain, playing an essential role in the maintenance and function of cells stemming from neuronal lineage. However, the differential expression of miR-128-3p in pathologies underscores the importance of the balance between its high and low levels. Significantly, numerous reports pointed to miR-128-3p as one of the most depleted in glioblastoma, implying it is a critical player in the disease's pathogenesis and thus may serve as a therapeutic agent for this most aggressive form of brain tumor. In this review, we summarize the current knowledge of the diverse roles of miR-128-3p. We focus on its involvement in the neurogenesis and pathophysiology of malignant and neurodegenerative diseases. We also highlight the promising potential of miR-128-3p as an antitumor agent for the future therapy of human cancers, including glioblastoma, and as the linchpin of brain development and function, potentially leading to the development of new therapies for neurological conditions.
Collapse
Affiliation(s)
- Klaudia Kiel
- Tumor Microenvironment Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
| | - Sylwia Katarzyna Król
- Department of Neurooncology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
| | - Agnieszka Bronisz
- Tumor Microenvironment Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
| | - Jakub Godlewski
- Department of Neurooncology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
| |
Collapse
|
5
|
Chakraborty C, Nissen I, Vincent CA, Hägglund AC, Hörnblad A, Remeseiro S. Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying neurogliomal synaptic communication. Nat Commun 2023; 14:6446. [PMID: 37833281 PMCID: PMC10576091 DOI: 10.1038/s41467-023-41919-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Chromatin organization controls transcription by modulating 3D-interactions between enhancers and promoters in the nucleus. Alterations in epigenetic states and 3D-chromatin organization result in gene expression changes contributing to cancer. Here, we map the promoter-enhancer interactome and regulatory landscape of glioblastoma, the most aggressive primary brain tumour. Our data reveals profound rewiring of promoter-enhancer interactions, chromatin accessibility and redistribution of histone marks in glioblastoma. This leads to loss of long-range regulatory interactions and overall activation of promoters, which orchestrate changes in the expression of genes associated to glutamatergic synapses, axon guidance, axonogenesis and chromatin remodelling. SMAD3 and PITX1 emerge as major transcription factors controlling genes related to synapse organization and axon guidance. Inhibition of SMAD3 and neuronal activity stimulation cooperate to promote proliferation of glioblastoma cells in co-culture with glutamatergic neurons, and in mice bearing patient-derived xenografts. Our findings provide mechanistic insight into the regulatory networks that mediate neurogliomal synaptic communication.
Collapse
Affiliation(s)
- Chaitali Chakraborty
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Itzel Nissen
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Craig A Vincent
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Anna-Carin Hägglund
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Andreas Hörnblad
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
| | - Silvia Remeseiro
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden.
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
| |
Collapse
|
6
|
Gillette JS, Wang EJ, Dowd RS, Toms SA. Barriers to overcoming immunotherapy resistance in glioblastoma. Front Med (Lausanne) 2023; 10:1175507. [PMID: 37275361 PMCID: PMC10232794 DOI: 10.3389/fmed.2023.1175507] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/12/2023] [Indexed: 06/07/2023] Open
Abstract
Glioblastoma multiforme (GBM) is the most common malignant primary brain tumor, known for its poor prognosis and high recurrence rate. Current standard of care includes surgical resection followed by combined radiotherapy and chemotherapy. Although immunotherapies have yielded promising results in hematological malignancies, their successful application in GBM remains limited due to a host of immunosuppressive factors unique to GBM. As a result of these roadblocks, research efforts have focused on utilizing combinatorial immunotherapies that target networks of immune processes in GBM with promising results in both preclinical and clinical trials, although limitations in overcoming the immunosuppressive factors within GBM remain. In this review, we aim to discuss the intrinsic and adaptive immune resistance unique to GBM and to summarize the current evidence and outcomes of engineered and non-engineered treatments targeted at overcoming GBM resistance to immunotherapy. Additionally, we aim to highlight the most promising strategies of targeted GBM immunotherapy combinatorial treatments and the insights that may directly improve the current patient prognosis and clinical care.
Collapse
|
7
|
Improvements in Quality Control and Library Preparation for Targeted Sequencing Allowed Detection of Potentially Pathogenic Alterations in Circulating Cell-Free DNA Derived from Plasma of Brain Tumor Patients. Cancers (Basel) 2022; 14:cancers14163902. [PMID: 36010895 PMCID: PMC9405692 DOI: 10.3390/cancers14163902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
Malignant gliomas are the most frequent primary brain tumors in adults. They are genetically heterogenous and invariably recur due to incomplete surgery and therapy resistance. Circulating tumor DNA (ctDNA) is a component of circulating cell-free DNA (ccfDNA) and represents genetic material that originates from the primary tumor or metastasis. Brain tumors are frequently located in the eloquent brain regions, which makes biopsy difficult or impossible due to severe postoperative complications. The analysis of ccfDNA from a patient's blood presents a plausible and noninvasive alternative. In this study, freshly frozen tumors and corresponding blood samples were collected from 84 brain tumor patients and analyzed by targeted next-generation sequencing (NGS). The cohort included 80 glioma patients, 2 metastatic cancer patients, and 2 primary CNS lymphoma (PCNSL) patients. We compared the pattern of genetic alterations in the tumor DNA (tDNA) with that of ccfDNA. The implemented technical improvements in quality control and library preparation allowed for the detection of ctDNA in 8 out of 84 patients, including 5 out of 80 glioma patients. In 32 out of 84 patients, we found potentially pathogenic genetic alterations in ccfDNA that were not detectable in tDNA. While sequencing ccfDNA from plasma has a low efficacy as a diagnostic tool for glioma patients, we concluded that further improvements in sample processing and library preparation can make liquid biopsy a valuable diagnostic tool for glioma patients.
Collapse
|
8
|
Thakur A, Faujdar C, Sharma R, Sharma S, Malik B, Nepali K, Liou JP. Glioblastoma: Current Status, Emerging Targets, and Recent Advances. J Med Chem 2022; 65:8596-8685. [PMID: 35786935 PMCID: PMC9297300 DOI: 10.1021/acs.jmedchem.1c01946] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Glioblastoma (GBM) is a highly malignant
brain tumor characterized
by a heterogeneous population of genetically unstable and highly infiltrative
cells that are resistant to chemotherapy. Although substantial efforts
have been invested in the field of anti-GBM drug discovery in the
past decade, success has primarily been confined to the preclinical
level, and clinical studies have often been hampered due to efficacy-,
selectivity-, or physicochemical property-related issues. Thus, expansion
of the list of molecular targets coupled with a pragmatic design of
new small-molecule inhibitors with central nervous system (CNS)-penetrating
ability is required to steer the wheels of anti-GBM drug discovery
endeavors. This Perspective presents various aspects of drug discovery
(challenges in GBM drug discovery and delivery, therapeutic targets,
and agents under clinical investigation). The comprehensively covered
sections include the recent medicinal chemistry campaigns embarked
upon to validate the potential of numerous enzymes/proteins/receptors
as therapeutic targets in GBM.
Collapse
Affiliation(s)
- Amandeep Thakur
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei 11031, Taiwan
| | - Chetna Faujdar
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida 201307, India
| | - Ram Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei 11031, Taiwan
| | - Sachin Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei 11031, Taiwan
| | - Basant Malik
- Department of Sterile Product Development, Research and Development-Unit 2, Jubiliant Generics Ltd., Noida 201301, India
| | - Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei 11031, Taiwan
| | - Jing Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei 11031, Taiwan
| |
Collapse
|
9
|
Alexanian AR, Brannon A. Unique combinations of epigenetic modifiers synergistically impair the viability of the U87 glioblastoma cell line while exhibiting minor or moderate effects on normal stem cell growth. Med Oncol 2022; 39:86. [PMID: 35478054 DOI: 10.1007/s12032-022-01683-2] [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: 11/11/2021] [Accepted: 02/15/2022] [Indexed: 11/29/2022]
Abstract
Discoveries made over the last decade have shown that critical changes in cancer cells, such as activation of oncogenes and silencing of tumor suppressor genes are caused not only by genetic but also by epigenetic mechanisms. While epigenetic alterations are somatically heritable, in contrast to genetic changes, they are potentially reversible, making them perfect targets for therapeutic intervention. Covalent modifications of chromatin, such as methylation of DNA and acetylation and methylation of histones, are important components of epigenetic machinery. Multiple recent studies have shown that epigenetic modifiers are candidates for potent new drugs in multiple cancers' therapies, including gliomas, and several clinical trials are ongoing. However, as with other chemotherapeutic drugs, toxicity is one of the main concerns with some of the potent epigenetic drugs. Synergistic combinations of these agents are one approach to overcoming toxicity issues while enhancing efficacy. In this study, we demonstrated that while individually BIX01294, an inhibitor of histone methyltransferase G9a, DZNep, an inhibitor of lysine methyltransferase EZH2, and Trichostatin A (TSA), an inhibitor of histone deacetylase at their low concentrations showed a moderate effect on the viability of U87 glioblastoma cells, in combinations they exhibited a synergistic effect. Importantly, these combinations exhibited minimal effect on adipose mesenchymal stem cells (AD-MSCs) growth. Thus, unique combinations and concentrations of epigenetic modifiers, that synergistically attenuated the U87 glioblastoma cells while exhibiting minor or moderate effects on normal stem cell growth, have been discovered.
Collapse
Affiliation(s)
- Arshak R Alexanian
- Cell Reprogramming & Therapeutics LLC, 10437 W Innovation Dr, Wauwatosa (Milwaukee county), WI, 53226, USA.
| | - Avonlea Brannon
- Cell Reprogramming & Therapeutics LLC, 10437 W Innovation Dr, Wauwatosa (Milwaukee county), WI, 53226, USA
| |
Collapse
|
10
|
Sox2 induces glioblastoma cell stemness and tumor propagation by repressing TET2 and deregulating 5hmC and 5mC DNA modifications. Signal Transduct Target Ther 2022; 7:37. [PMID: 35136034 PMCID: PMC8826438 DOI: 10.1038/s41392-021-00857-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 12/01/2021] [Accepted: 12/05/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is a reversible process catalyzed by the ten–eleven translocation (TET) family of enzymes (TET1, TET2, TET3) that convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Altered patterns of 5hmC and 5mC are widely reported in human cancers and loss of 5hmC correlates with poor prognosis. Understanding the mechanisms leading to 5hmC loss and its role in oncogenesis will advance the development of epigenetic-based therapeutics. We show that TET2 loss associates with glioblastoma (GBM) stem cells and correlates with poor survival of GBM patients. We further identify a SOX2:miR-10b-5p:TET2 axis that represses TET2 expression, represses 5hmC, increases 5mC levels, and induces GBM cell stemness and tumor-propagating potential. In vivo delivery of a miR-10b-5p inhibitor that normalizes TET2 expression and 5hmC levels inhibits tumor growth and prolongs survival of animals bearing pre-established orthotopic GBM xenografts. These findings highlight the importance of TET2 and 5hmC loss in Sox2-driven oncogenesis and their potential for therapeutic targeting.
Collapse
|
11
|
Jiang L, Hao Y, Shao C, Wu Q, Prager BC, Gimple RC, Sulli G, Kim LJ, Zhang G, Qiu Z, Zhu Z, Fu XD, Rich JN. ADAR1-mediated RNA editing links ganglioside catabolism to glioblastoma stem cell maintenance. J Clin Invest 2022; 132:143397. [PMID: 35133980 PMCID: PMC8920333 DOI: 10.1172/jci143397] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/03/2022] [Indexed: 11/17/2022] Open
Abstract
Glioblastoma (GBM) is the most common and lethal primary malignant brain tumor, containing GBM stem cells (GSCs) that contribute to therapeutic resistance and relapse. Exposing potential GSC vulnerabilities may provide therapeutic strategies against GBM. Here, we interrogated the role of Adenosine-to-Inosine (A-to-I) RNA editing mediated by ADAR1 (adenosine deaminase acting on RNA 1) in GSCs and found that both ADAR1 and global RNA editomes were elevated in GSCs compared to normal neural stem cells (NSCs). ADAR1 inactivation or blocking the upstream JAK/STAT pathway through TYK2 inhibition impaired GSC self-renewal and stemness. Downstream of ADAR1, RNA editing of the 3'UTR of GM2A, a key ganglioside catabolism activator, proved to be critical, as interfering with ganglioside catabolism showed similar functional impact on GSCs as ADAR1 disruption. These findings reveal RNA editing links ganglioside catabolism to GSC self-renewal and stemness, exposing a potential vulnerability of GBM for therapeutic intervention.
Collapse
Affiliation(s)
- Li Jiang
- Department of Medicine, University of California, San Diego, San Diego, United States of America
| | - Yajing Hao
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States of America
| | - Changwei Shao
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States of America
| | - Qiulian Wu
- Hillman Cancer Center, Cancer Institute, University of Pittsburgh, Pittsburgh, United States of America
| | - Briana C Prager
- Stem Cell Biology, Cleveland Clinic, Cleveland, United States of America
| | - Ryan C Gimple
- Department of Medicine, University of California, San Diego, San Diego, United States of America
| | - Gabriele Sulli
- Department of Medicine, University of California, San Diego, San Diego, United States of America
| | - Leo Jk Kim
- Department of Medicine, University of California, San Diego, San Diego, United States of America
| | - Guoxin Zhang
- Department of Medicine, University of California, San Diego, San Diego, United States of America
| | - Zhixin Qiu
- Hillman Cancer Center, Cancer Institute, University of Pittsburgh, Pittsburgh, United States of America
| | - Zhe Zhu
- Department of Medicine, University of California, San Diego, San Diego, United States of America
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States of America
| | - Jeremy N Rich
- Hillman Cancer Center, Cancer Institute, University of Pittsburgh, Pittsburgh, United States of America
| |
Collapse
|
12
|
Dushanan R, Weerasinghe S, Dissanayake DP, Senthilnithy R. An In-Silico Approach to Evaluate the Inhibitory Potency of Selected Hydroxamic Acid Derivatives on Zinc-Dependent Histone Deacetylase Enzyme. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Histone deacetylase (HDAC) enzymes modify the histone by removing the acetyl group from the lysine residues, known as histone deacetylation. HDACs have been involved in altering gene expressions, resulting in cancer cells in the body. This study focuses on HDAC inhibitors’ impact on histone deacetylase-like protein (HDLP) stability through computational techniques. Molecular dynamics (MD) analyses were used to examine the atomic-level description of drug binding sites and how the HDAC inhibitors change the HDLP enzyme environment. In this study, two hydroxamic acid-derived inhibitors, such as [Formula: see text]-Carboxycinnamic acid bis-hydroxamide (CBHA) and scriptaid (GCK1026), were selected to examine the inhibition ability in terms with suberanilohydroxamic acid (SAHA) as a reference drug. The crystal structure of the HDLP was downloaded from the Protein Data Bank. The structures of inhibitors were optimized using the G09W package. Docking studies were done by AutoDock-Vina, and the resultant complex was used to initiate MD studies. The trajectories obtained from MD simulation were used to perform the structural analysis. Root-mean-square deviation (RMSD), radius of gyration, hydrogen bond, binding free energy and interaction energy studies revealed that the stability of HDLP-SAHA and HDLP-CBHA is higher than the free HDLP enzyme. The HDLP-CBHA complex shows an increased number of hydrogen bonds (5), high MM-PBSA binding free energy ([Formula: see text][Formula: see text]kJ/mol), high interaction energy ([Formula: see text][Formula: see text]kJ/mol), and an increased number of alpha-helical amino acids (130) compared with HDLP-SAHA. It concluded that the CBHA has the relatively same potential as SAHA to inhibit the HDLP. Consequently, the use of CBHA in clinical application is recommended through this in-silico method.
Collapse
Affiliation(s)
- R. Dushanan
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Nugegoda 10250, Sri Lanka
| | - S. Weerasinghe
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo 00700, Sri Lanka
| | - D. P. Dissanayake
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo 00700, Sri Lanka
| | - R. Senthilnithy
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Nugegoda 10250, Sri Lanka
| |
Collapse
|
13
|
Klomp MJ, Dalm SU, de Jong M, Feelders RA, Hofland J, Hofland LJ. Epigenetic regulation of somatostatin and somatostatin receptors in neuroendocrine tumors and other types of cancer. Rev Endocr Metab Disord 2021; 22:495-510. [PMID: 33085037 PMCID: PMC8346415 DOI: 10.1007/s11154-020-09607-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/09/2020] [Indexed: 12/15/2022]
Abstract
Both somatostatin (SST) and somatostatin receptors (SSTRs) are proteins with important functions in both physiological tissue and in tumors, particularly in neuroendocrine tumors (NETs). NETs are frequently characterized by high SSTRs expression levels. SST analogues (SSAs) that bind and activate SSTR have anti-proliferative and anti-secretory activity, thereby reducing both the growth as well as the hormonal symptoms of NETs. Moreover, the high expression levels of SSTR type-2 (SSTR2) in NETs is a powerful target for therapy with radiolabeled SSAs. Due to the important role of both SST and SSTRs, it is of great importance to elucidate the mechanisms involved in regulating their expression in NETs, as well as in other types of tumors. The field of epigenetics recently gained interest in NET research, highlighting the importance of this process in regulating the expression of gene and protein expression. In this review we will discuss the role of the epigenetic machinery in controlling the expression of both SSTRs and the neuropeptide SST. Particular attention will be given to the epigenetic regulation of these proteins in NETs, whereas the involvement of the epigenetic machinery in other types of cancer will be discussed as well. In addition, we will discuss the possibility to target enzymes involved in the epigenetic machinery to modify the expression of the SST-system, thereby possibly improving therapeutic options.
Collapse
Affiliation(s)
- M J Klomp
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, Rotterdam, The Netherlands
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - S U Dalm
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - M de Jong
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - R A Feelders
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, Rotterdam, The Netherlands
| | - J Hofland
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, Rotterdam, The Netherlands
| | - L J Hofland
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, Rotterdam, The Netherlands.
| |
Collapse
|
14
|
Khotimchenko R, Bryukhovetskiy I, Khotimchenko M, Khotimchenko Y. Bioactive Compounds with Antiglioma Activity from Marine Species. Biomedicines 2021; 9:biomedicines9080886. [PMID: 34440090 PMCID: PMC8389718 DOI: 10.3390/biomedicines9080886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/21/2022] Open
Abstract
The search for new chemical compounds with antitumor pharmacological activity is a necessary process for creating more effective drugs for each specific malignancy type. This review presents the outcomes of screening studies of natural compounds with high anti-glioma activity. Despite significant advances in cancer therapy, there are still some tumors currently considered completely incurable including brain gliomas. This review covers the main problems of the glioma chemotherapy including drug resistance, side effects of common anti-glioma drugs, and genetic diversity of brain tumors. The main emphasis is made on the characterization of natural compounds isolated from marine organisms because taxonomic diversity of organisms in seawaters significantly exceeds that of terrestrial species. Thus, we should expect greater chemical diversity of marine compounds and greater likelihood of finding effective molecules with antiglioma activity. The review covers at least 15 classes of organic compounds with their chemical formulas provided as well as semi-inhibitory concentrations, mechanisms of action, and pharmacokinetic profiles. In conclusion, the analysis of the taxonomic diversity of marine species containing bioactives with antiglioma activity is performed noting cytotoxicity indicators and to the tumor cells in comparison with similar indicators of antitumor agents approved for clinical use as antiglioblastoma chemotherapeutics.
Collapse
Affiliation(s)
- Rodion Khotimchenko
- School of Biomedicine, Far Eastern Federal University, 690090 Vladivostok, Russia; (R.K.); (I.B.); (M.K.)
| | - Igor Bryukhovetskiy
- School of Biomedicine, Far Eastern Federal University, 690090 Vladivostok, Russia; (R.K.); (I.B.); (M.K.)
| | - Maksim Khotimchenko
- School of Biomedicine, Far Eastern Federal University, 690090 Vladivostok, Russia; (R.K.); (I.B.); (M.K.)
| | - Yuri Khotimchenko
- School of Biomedicine, Far Eastern Federal University, 690090 Vladivostok, Russia; (R.K.); (I.B.); (M.K.)
- Laboratory of Pharmacology, A. V. Zhirmunsky National Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690950 Vladivostok, Russia
- Correspondence:
| |
Collapse
|
15
|
Stępniak K, Machnicka MA, Mieczkowski J, Macioszek A, Wojtaś B, Gielniewski B, Poleszak K, Perycz M, Król SK, Guzik R, Dąbrowski MJ, Dramiński M, Jardanowska M, Grabowicz I, Dziedzic A, Kranas H, Sienkiewicz K, Diamanti K, Kotulska K, Grajkowska W, Roszkowski M, Czernicki T, Marchel A, Komorowski J, Kaminska B, Wilczyński B. Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas. Nat Commun 2021; 12:3621. [PMID: 34131149 PMCID: PMC8206121 DOI: 10.1038/s41467-021-23922-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/19/2021] [Indexed: 12/15/2022] Open
Abstract
Chromatin structure and accessibility, and combinatorial binding of transcription factors to regulatory elements in genomic DNA control transcription. Genetic variations in genes encoding histones, epigenetics-related enzymes or modifiers affect chromatin structure/dynamics and result in alterations in gene expression contributing to cancer development or progression. Gliomas are brain tumors frequently associated with epigenetics-related gene deregulation. We perform whole-genome mapping of chromatin accessibility, histone modifications, DNA methylation patterns and transcriptome analysis simultaneously in multiple tumor samples to unravel epigenetic dysfunctions driving gliomagenesis. Based on the results of the integrative analysis of the acquired profiles, we create an atlas of active enhancers and promoters in benign and malignant gliomas. We explore these elements and intersect with Hi-C data to uncover molecular mechanisms instructing gene expression in gliomas.
Collapse
Affiliation(s)
- Karolina Stępniak
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena A Machnicka
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Jakub Mieczkowski
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
- Medical University of Gdansk, International Research Agenda 3P Medicine Laboratory, Gdansk, Poland
| | - Anna Macioszek
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Bartosz Wojtaś
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Bartłomiej Gielniewski
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Poleszak
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Malgorzata Perycz
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Sylwia K Król
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Rafał Guzik
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Michał J Dąbrowski
- Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Michał Dramiński
- Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Marta Jardanowska
- Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Ilona Grabowicz
- Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Agata Dziedzic
- Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Hanna Kranas
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Karolina Sienkiewicz
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Klev Diamanti
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Katarzyna Kotulska
- Departments of Neurology, Neurosurgery, Neuropathology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Wiesława Grajkowska
- Departments of Neurology, Neurosurgery, Neuropathology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Marcin Roszkowski
- Departments of Neurology, Neurosurgery, Neuropathology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Tomasz Czernicki
- Department of Neurosurgery, Medical University of Warsaw, Warsaw, Poland
| | - Andrzej Marchel
- Department of Neurosurgery, Medical University of Warsaw, Warsaw, Poland
| | - Jan Komorowski
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Bozena Kaminska
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland.
| | - Bartek Wilczyński
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland.
| |
Collapse
|
16
|
Li Y, Wu Y, Hu Y. Metabolites in the Tumor Microenvironment Reprogram Functions of Immune Effector Cells Through Epigenetic Modifications. Front Immunol 2021; 12:641883. [PMID: 33927716 PMCID: PMC8078775 DOI: 10.3389/fimmu.2021.641883] [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: 12/15/2020] [Accepted: 03/15/2021] [Indexed: 12/29/2022] Open
Abstract
Cellular metabolism of both cancer and immune cells in the acidic, hypoxic, and nutrient-depleted tumor microenvironment (TME) has attracted increasing attention in recent years. Accumulating evidence has shown that cancer cells in TME could outcompete immune cells for nutrients and at the same time, producing inhibitory products that suppress immune effector cell functions. Recent progress revealed that metabolites in the TME could dysregulate gene expression patterns in the differentiation, proliferation, and activation of immune effector cells by interfering with the epigenetic programs and signal transduction networks. Nevertheless, encouraging studies indicated that metabolic plasticity and heterogeneity between cancer and immune effector cells could provide us the opportunity to discover and target the metabolic vulnerabilities of cancer cells while potentiating the anti-tumor functions of immune effector cells. In this review, we will discuss the metabolic impacts on the immune effector cells in TME and explore the therapeutic opportunities for metabolically enhanced immunotherapy.
Collapse
Affiliation(s)
- Yijia Li
- Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China.,Biomedical Translational Research Institute, Jinan University, Guangzhou, China
| | - Yangzhe Wu
- Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China.,Biomedical Translational Research Institute, Jinan University, Guangzhou, China
| | - Yi Hu
- Microbiology and Immunology Department, School of Medicine, Jinan University, Guangzhou, China
| |
Collapse
|
17
|
Zhang L, Liu Z, Dong Y, Kong L. Epigenetic targeting of SLC30A3 by HDAC1 is related to the malignant phenotype of glioblastoma. IUBMB Life 2021; 73:784-799. [PMID: 33715270 DOI: 10.1002/iub.2463] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/24/2022]
Abstract
The epigenetic abnormality is believed as a major driver for cancer initiation. Histone modification plays a vital role in tumor formation and progression. Particularly, alteration in histone acetylation has been highly associated with gene expression, cell cycle, as well as carcinogenesis. By analyzing glioblastoma (GBM)-related microarray from the GEO database and conducting chromatin immunoprecipitation-sequencing (ChIP-seq), we discovered that solute carrier family 30 member 3 (SLC30A3), a super enhancer (SE)-regulated factor, was significantly reduced in GBM tissues. Furthermore, histone deacetylase 1 (HDAC1), overexpressed in GBM tissues, could inhibit SLC30A3 expression by promoting histone H3K27ac deacetylation modification of the SE region of SLC30A3. Our functional validation revealed that SLC30A3 can inhibit the growth and metastatic spread of GBM cells in vitro and in vivo, and can activate the MAPK signaling pathway to promote apoptosis of GBM cells. Moreover, overexpression of HDAC1 resulted in a significant increase in DNA replication activity, a significant decline in apoptosis and cell cycle arrest in GBM cells. In a word, these findings indicate that combined epigenetic targeting of SLC30A3 by HDAC1 and SE is potentially therapeutically feasible in GBM.
Collapse
Affiliation(s)
- Longzhou Zhang
- Department of Neurosurgery, First Hospital Affiliated to Zhengzhou University, Zhengzhou, P.R. China
| | - Zengjin Liu
- Department of Neurosurgery, First Hospital Affiliated to Zhengzhou University, Zhengzhou, P.R. China
| | - Yang Dong
- Department of Neurosurgery, First Hospital Affiliated to Zhengzhou University, Zhengzhou, P.R. China
| | - Lingchang Kong
- Department of Neurosurgery, Zhengzhou Traditional Chinese Medicine Hospital, Zhengzhou, P.R. China
| |
Collapse
|
18
|
Pratap UP, Sareddy GR, Liu Z, Venkata PP, Liu J, Tang W, Altwegg KA, Ebrahimi B, Li X, Tekmal RR, Viswanadhapalli S, McHardy S, Brenner AJ, Vadlamudi RK. Histone deacetylase inhibitors enhance estrogen receptor beta expression and augment agonist-mediated tumor suppression in glioblastoma. Neurooncol Adv 2021; 3:vdab099. [PMID: 34485908 PMCID: PMC8412056 DOI: 10.1093/noajnl/vdab099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Glioblastomas (GBMs) are the most lethal primary brain tumors. Estrogen receptor β (ESR2/ERβ) function as a tumor suppressor in GBM, however, ERβ expression is commonly suppressed during glioma progression. In this study, we examined whether drugs that reverse epigenetic modifications will enhance ERβ expression and augment ERβ agonist-mediated tumor suppression. METHODS We tested the utility of epigenetic drugs which act as an inhibitor of histone deacetylases (HDACs), histone methylases, and BET enzymes. Mechanistic studies utilized RT-qPCR, chromatin immunoprecipitation (ChIP), and western blotting. Cell viability, apoptosis, colony formation, and invasion were measured using in vitro assays. An orthotopic GBM model was used to test the efficacy of in vivo. RESULTS Of all inhibitors tested, HDACi (panobinostat and romidepsin) showed the potential to increase the expression of ERβ in GBM cells. Treatment with HDACi uniquely upregulated ERβ isoform 1 expression that functions as a tumor suppressor but not ERβ isoform 5 that drives oncogenic functions. Further, combination therapy of HDACi with the ERβ agonist, LY500307, potently reduced cell viability, invasion, colony formation, and enhanced apoptosis. Mechanistic studies showed that HDACi induced ERβ is functional, as it enhanced ERβ reporter activities and ERβ target genes expression. ChIP analysis confirmed alterations in the histone acetylation at the ERβ and its target gene promoters. In orthotopic GBM model, combination therapy of panobinostat and LY500307 enhanced survival of tumor-bearing mice. CONCLUSIONS Our results suggest that the combination therapy of HDACi and LY500307 provides therapeutic utility in overcoming the suppression of ERβ expression that commonly occurs in GBM progression.
Collapse
Affiliation(s)
- Uday P Pratap
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Gangadhara R Sareddy
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Zexuan Liu
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Prabhakar Pitta Venkata
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Junhao Liu
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Weiwei Tang
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Department of Obstetrics and Gynecology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, PR China
| | - Kristin A Altwegg
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Behnam Ebrahimi
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Xiaonan Li
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Rajeshwar R Tekmal
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Suryavathi Viswanadhapalli
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Stanton McHardy
- Department of Chemistry, University of Texas San Antonio, San Antonio, Texas, USA
| | - Andrew J Brenner
- Hematology & Oncology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Ratna K Vadlamudi
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, Texas, USA
| |
Collapse
|
19
|
Dushanan R, Weerasinghe S, Dissanayake DP, Senthilinithy R. Cracking a cancer code histone deacetylation in epigenetic: the implication from molecular dynamics simulations on efficacy assessment of histone deacetylase inhibitors. J Biomol Struct Dyn 2020; 40:2352-2368. [PMID: 33131428 DOI: 10.1080/07391102.2020.1838328] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Epigenetic changes, histone acetylation and deacetylation in chromatin have been intensively studied due to their significance in regulating the gene expression. According to the type of tumor, the levels of histone deacetylases (HDAC) are varied. HDAC inhibitors are a new promising class of compounds that inhibit the proliferation of tumor cells. In this study, the inhibitory efficacy of some HDAC inhibitors such as vorinostat, panobinostat, abexinostat, belinostat, resminostat, dacinostat and pracinostat was studied using molecular dynamics simulation. The inhibitory efficacy was estimated by computing the enzyme's stability, positional stability of the individual amino acids and interaction energies of HDLP-inhibitor complexes. It is hoped that this investigation may improve our understanding of the atomic-level description of the inhibitor binding site and how the HDAC inhibitors change the environment of the enzyme's active site. The results obtained from the root-mean-square deviation, the radius of gyration, solvent-accessible surface area, root-mean-square fluctuation, stride server and Ramachandran plot have revealed that the stability of HDLP enzyme with vorinostat, panobinostat and abexinostat is higher than the other studied complexes. According to the calculated values for MM-PBSA, LIE, semi-LIE binding free energies and interaction energies, the stability of the HDLP enzyme varies as panobinostat > abexinostat > vorinostat where resminostat complex showed relatively low stability. The ligandability and drugability values also give the same trend as above. The findings revealed that the panobinostat and abexinostat are potential lead compounds as reference inhibitor vorinostat. Therefore, it is possible to use these drugs as HDAC inhibitors in clinical practices. Also, the outcomes of this study could be utilized to identify new inhibitors for clinical research.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ramachandren Dushanan
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka
| | - Samantha Weerasinghe
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | | | - Rajendram Senthilinithy
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka
| |
Collapse
|
20
|
Green AL, DeSisto J, Flannery P, Lemma R, Knox A, Lemieux M, Sanford B, O'Rourke R, Ramkissoon S, Jones K, Perry J, Hui X, Moroze E, Balakrishnan I, O'Neill AF, Dunn K, DeRyckere D, Danis E, Safadi A, Gilani A, Hubbell-Engler B, Nuss Z, Levy JMM, Serkova N, Venkataraman S, Graham DK, Foreman N, Ligon K, Jones K, Kung AL, Vibhakar R. BPTF regulates growth of adult and pediatric high-grade glioma through the MYC pathway. Oncogene 2020; 39:2305-2327. [PMID: 31844250 PMCID: PMC7071968 DOI: 10.1038/s41388-019-1125-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023]
Abstract
High-grade gliomas (HGG) afflict both children and adults and respond poorly to current therapies. Epigenetic regulators have a role in gliomagenesis, but a broad, functional investigation of the impact and role of specific epigenetic targets has not been undertaken. Using a two-step, in vitro/in vivo epigenomic shRNA inhibition screen, we determine the chromatin remodeler BPTF to be a key regulator of adult HGG growth. We then demonstrate that BPTF knockdown decreases HGG growth in multiple pediatric HGG models as well. BPTF appears to regulate tumor growth through cell self-renewal maintenance, and BPTF knockdown leads these glial tumors toward more neuronal characteristics. BPTF's impact on growth is mediated through positive effects on expression of MYC and MYC pathway targets. HDAC inhibitors synergize with BPTF knockdown against HGG growth. BPTF inhibition is a promising strategy to combat HGG through epigenetic regulation of the MYC oncogenic pathway.
Collapse
Affiliation(s)
- Adam L Green
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA.
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA.
| | - John DeSisto
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | - Patrick Flannery
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | - Rakeb Lemma
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | - Aaron Knox
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | | | - Bridget Sanford
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | - Rebecca O'Rourke
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | | | | | | | - Xu Hui
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erin Moroze
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | - Ilango Balakrishnan
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | | | | | - Deborah DeRyckere
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA, USA
| | - Etienne Danis
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | - Aaron Safadi
- Department of Radiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ahmed Gilani
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Zachary Nuss
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | - Jean M Mulcahy Levy
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA
| | - Natalie Serkova
- Department of Radiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sujatha Venkataraman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | - Douglas K Graham
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA, USA
| | - Nicholas Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA
| | - Keith Ligon
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ken Jones
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | - Andrew L Kung
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rajeev Vibhakar
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-N, Mail Stop 8302 12800 E. 19th Ave., Aurora, CO, 80045, USA
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA
| |
Collapse
|
21
|
Duforestel M, Briand J, Bougras-Cartron G, Heymann D, Frenel JS, Vallette FM, Cartron PF. Cell-free circulating epimarks in cancer monitoring. Epigenomics 2020; 12:145-155. [DOI: 10.2217/epi-2019-0170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cancer numbers increasing, cases heterogeneity and the drug resistance emergence have pushed scientists to search for innovative solutions for patients and epimutations can be one. Methylated DNA, modified nucleosomes and noncoding RNAs are found in all cells, including tumor cells. They are intracellular actors but also have intercellular communication roles, being released in extracellular environment and in different body fluids. Here, we reviewed current literature on the use of these blood circulating epimarks in cancer monitoring. What stands out is that epimarkers must be considered as ‘real time’ images of the tumor, and can be isolated without invasive methods. In the future, the real challenge lies in the development of specific, sensitive, fast and clinically applicable detection and analysis methods of epimarkers.
Collapse
Affiliation(s)
- Manon Duforestel
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
| | - Joséphine Briand
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
| | - Gwenola Bougras-Cartron
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
| | - Dominique Heymann
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
| | - Jean-Sébastien Frenel
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
- Department of Medical Oncology, Institut de Cancérologie de l'Ouest Site René Gauducheau, Saint Herblain, France
| | - François M Vallette
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
- LabEX IGO, Université de Nantes, France
| | - Pierre-François Cartron
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
- LabEX IGO, Université de Nantes, France
| |
Collapse
|
22
|
Abramczyk H, Brozek-Pluska B, Jarota A, Surmacki J, Imiela A, Kopec M. A look into the use of Raman spectroscopy for brain and breast cancer diagnostics: linear and non-linear optics in cancer research as a gateway to tumor cell identity. Expert Rev Mol Diagn 2020; 20:99-115. [PMID: 32013616 DOI: 10.1080/14737159.2020.1724092] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Introduction: Currently, intensely developing of linear and non-linear optical methods for cancer detection provides a valuable tool to improve sensitivity and specificity. One of the main reasons for insufficient progress in cancer diagnostics is related to the fact that most cancer types are not only heterogeneous in their genetic composition but also reside in varying microenvironments and interact with different cell types. Until now, no technology has been fully proven for effective detecting of invasive cancer, which infiltrating the extracellular matrix.Areas covered: This review investigates the current status of Raman spectroscopy and Raman imaging for brain and breast cancer diagnostics. Moreover, the review provides a comprehensive overview of the applicability of atomic force microscopy (AFM), linear and non-linear optics in cancer research as a gateway to tumor cell identity.Expert commentary: A combination of linear and non-linear optics, particularly Raman-driven methods, has many additional advantages to identify alterations in cancer cells that are crucial for their proliferation and that distinguish them from normal cells.
Collapse
Affiliation(s)
- Halina Abramczyk
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| | - Beata Brozek-Pluska
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| | - Arkadiusz Jarota
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| | - Jakub Surmacki
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| | - Anna Imiela
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| | - Monika Kopec
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| |
Collapse
|
23
|
Ozyerli-Goknar E, Sur-Erdem I, Seker F, Cingöz A, Kayabolen A, Kahya-Yesil Z, Uyulur F, Gezen M, Tolay N, Erman B, Gönen M, Dunford J, Oppermann U, Bagci-Onder T. The fungal metabolite chaetocin is a sensitizer for pro-apoptotic therapies in glioblastoma. Cell Death Dis 2019; 10:894. [PMID: 31772153 PMCID: PMC6879621 DOI: 10.1038/s41419-019-2107-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 09/12/2019] [Accepted: 10/16/2019] [Indexed: 01/19/2023]
Abstract
Glioblastoma Multiforme (GBM) is the most common and aggressive primary brain tumor. Despite recent developments in surgery, chemo- and radio-therapy, a currently poor prognosis of GBM patients highlights an urgent need for novel treatment strategies. TRAIL (TNF Related Apoptosis Inducing Ligand) is a potent anti-cancer agent that can induce apoptosis selectively in cancer cells. GBM cells frequently develop resistance to TRAIL which renders clinical application of TRAIL therapeutics inefficient. In this study, we undertook a chemical screening approach using a library of epigenetic modifier drugs to identify compounds that could augment TRAIL response. We identified the fungal metabolite chaetocin, an inhibitor of histone methyl transferase SUV39H1, as a novel TRAIL sensitizer. Combining low subtoxic doses of chaetocin and TRAIL resulted in very potent and rapid apoptosis of GBM cells. Chaetocin also effectively sensitized GBM cells to further pro-apoptotic agents, such as FasL and BH3 mimetics. Chaetocin mediated apoptosis sensitization was achieved through ROS generation and consequent DNA damage induction that involved P53 activity. Chaetocin induced transcriptomic changes showed induction of antioxidant defense mechanisms and DNA damage response pathways. Heme Oxygenase 1 (HMOX1) was among the top upregulated genes, whose induction was ROS-dependent and HMOX1 depletion enhanced chaetocin mediated TRAIL sensitization. Finally, chaetocin and TRAIL combination treatment revealed efficacy in vivo. Taken together, our results provide a novel role for chaetocin as an apoptosis priming agent and its combination with pro-apoptotic therapies might offer new therapeutic approaches for GBMs.
Collapse
Affiliation(s)
- Ezgi Ozyerli-Goknar
- Brain Cancer Research and Therapy Laboratory, Koç University School of Medicine, 34450, Istanbul, Turkey
| | - Ilknur Sur-Erdem
- Brain Cancer Research and Therapy Laboratory, Koç University School of Medicine, 34450, Istanbul, Turkey
| | - Fidan Seker
- Brain Cancer Research and Therapy Laboratory, Koç University School of Medicine, 34450, Istanbul, Turkey
| | - Ahmet Cingöz
- Brain Cancer Research and Therapy Laboratory, Koç University School of Medicine, 34450, Istanbul, Turkey
| | - Alisan Kayabolen
- Brain Cancer Research and Therapy Laboratory, Koç University School of Medicine, 34450, Istanbul, Turkey
| | - Zeynep Kahya-Yesil
- Brain Cancer Research and Therapy Laboratory, Koç University School of Medicine, 34450, Istanbul, Turkey
| | - Fırat Uyulur
- Department of Computational Biology, Koç University, 34450, Istanbul, Turkey
| | - Melike Gezen
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Nazife Tolay
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Batu Erman
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Mehmet Gönen
- Department of Industrial Engineering, College of Engineering, Koç University, İstanbul, Turkey
| | - James Dunford
- Botnar Research Centre, NIHR Biomedical Research Centre Oxford, University of Oxford, Oxford, OX3 7LD, UK
| | - Udo Oppermann
- Botnar Research Centre, NIHR Biomedical Research Centre Oxford, University of Oxford, Oxford, OX3 7LD, UK
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK
- FRIAS, Freiburg Institute of Advanced Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Tugba Bagci-Onder
- Brain Cancer Research and Therapy Laboratory, Koç University School of Medicine, 34450, Istanbul, Turkey.
| |
Collapse
|
24
|
Live Cell Imaging Supports a Key Role for Histone Deacetylase as a Molecular Target during Glioblastoma Malignancy Downgrade through Tumor Competence Modulation. JOURNAL OF ONCOLOGY 2019; 2019:9043675. [PMID: 31531023 PMCID: PMC6720048 DOI: 10.1155/2019/9043675] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/03/2019] [Indexed: 11/21/2022]
Abstract
Glioblastoma (GBM) is the most aggressive tumor of the central nervous system, and the identification of the mechanisms underlying the biological basis of GBM aggressiveness is essential to develop new therapies. Due to the low prognosis of GBM treatment, different clinical studies are in course to test the use of histone deacetylase inhibitors (iHDACs) in anticancer cocktails. Here, we seek to investigate the impact of HDAC activity on GBM cell behavior and plasticity by live cell imaging. We pharmacologically knock down HDAC activity using two different inhibitors (TSA and SAHA) in two different tumor cell types: a commercial GBM cell line (U87-MG) and primary tumor (GBM011). Upon 72 hours of in vitro iHDAC treatment, GBM cells presented a very unusual elongated cell shape due to tunneling tube formation and independent on TGF-β signaling epithelial to mesenchymal transition. Live cell imaging revealed that voltage-sensitive Ca++ signaling was disrupted upon HDAC activity blockade. This behavior was coupled to vimentin and connexin 43 gene expression downregulation, suggesting that HDAC activity blockade downgrades GBM aggressiveness mostly due to tumor cell competence and plasticity modulation in vitro. To test this hypothesis and access whether iHDACs would modulate tumor cell behavior and plasticity to properly respond to environmental cues in vivo, we xenografted GBM oncospheres in the chick developing the neural tube. Remarkably, upon 5 days in the developing neural tube, iHDAC-treated GBM cells ectopically expressed HNK-1, a tumor-suppressor marker tightly correlated to increased survivor of patients. These results describe, for the first time in the literature, the relevance of iHDACs for in vivo tumor cell morphology and competence to properly respond to environmental cues. Ultimately, our results highlight the relevance of chromatin remodeling for tumor cell plasticity and shed light on clinical perspectives aiming the epigenome as a relevant therapeutic target for GBM therapy.
Collapse
|
25
|
Wojtas B, Gielniewski B, Wojnicki K, Maleszewska M, Mondal SS, Nauman P, Grajkowska W, Glass R, Schüller U, Herold-Mende C, Kaminska B. Gliosarcoma Is Driven by Alterations in PI3K/Akt, RAS/MAPK Pathways and Characterized by Collagen Gene Expression Signature. Cancers (Basel) 2019; 11:cancers11030284. [PMID: 30818875 PMCID: PMC6468745 DOI: 10.3390/cancers11030284] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 01/15/2023] Open
Abstract
Gliosarcoma is a very rare brain tumor reported to be a variant of glioblastoma (GBM), IDH-wildtype. While differences in molecular and histological features between gliosarcoma and GBM were reported, detailed information on the genetic background of this tumor is lacking. We intend to fill in this knowledge gap by the complex analysis of somatic mutations, indels, copy number variations, translocations and gene expression patterns in gliosarcomas. Using next generation sequencing, we determined somatic mutations, copy number variations (CNVs) and translocations in 10 gliosarcomas. Six tumors have been further subjected to RNA sequencing analysis and gene expression patterns have been compared to those of GBMs. We demonstrate that gliosarcoma bears somatic alterations in gene coding for PI3K/Akt (PTEN, PI3K) and RAS/MAPK (NF1, BRAF) signaling pathways that are crucial for tumor growth. Interestingly, the frequency of PTEN alterations in gliosarcomas was much higher than in GBMs. Aberrations of PTEN were the most frequent and occurred in 70% of samples. We identified genes differentially expressed in gliosarcoma compared to GBM (including collagen signature) and confirmed a difference in the protein level by immunohistochemistry. We found several novel translocations (including translocations in the RABGEF1 gene) creating potentially unfavorable combinations. Collected results on genetic alterations and transcriptomic profiles offer new insights into gliosarcoma pathobiology, highlight differences in gliosarcoma and GBM genetic backgrounds and point out to distinct molecular cues for targeted treatment.
Collapse
Affiliation(s)
- Bartosz Wojtas
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland.
| | - Bartlomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland.
| | - Kamil Wojnicki
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland.
| | - Marta Maleszewska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland.
| | - Shamba S Mondal
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, Warsaw 02-093, Poland.
| | - Pawel Nauman
- Department of Neurosurgery, Institute of Psychiatry and Neurology, Warsaw 02-957, Poland.
| | - Wieslawa Grajkowska
- Department of Pathology, The Children's Memorial Health Institute, Warsaw 04-730, Poland.
| | - Rainer Glass
- Neurosurgical Research, University Clinics, LMU Munich 80539, Germany.
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center, Hamburg-Eppendorf 20251, Germany.
- Research Institute Children's Cancer Center Hamburg, Hamburg 20251, Germany.
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany.
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University of Heidelberg, Heidelberg 69120, Germany.
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland.
| |
Collapse
|
26
|
From Genotype to Phenotype: Through Chromatin. Genes (Basel) 2019; 10:genes10020076. [PMID: 30678090 PMCID: PMC6410296 DOI: 10.3390/genes10020076] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/16/2019] [Accepted: 01/21/2019] [Indexed: 02/07/2023] Open
Abstract
Advances in sequencing technologies have enabled the exploration of the genetic basis for several clinical disorders by allowing identification of causal mutations in rare genetic diseases. Sequencing technology has also facilitated genome-wide association studies to gather single nucleotide polymorphisms in common diseases including cancer and diabetes. Sequencing has therefore become common in the clinic for both prognostics and diagnostics. The success in follow-up steps, i.e., mapping mutations to causal genes and therapeutic targets to further the development of novel therapies, has nevertheless been very limited. This is because most mutations associated with diseases lie in inter-genic regions including the so-called regulatory genome. Additionally, no genetic causes are apparent for many diseases including neurodegenerative disorders. A complementary approach is therefore gaining interest, namely to focus on epigenetic control of the disease to generate more complete functional genomic maps. To this end, several recent studies have generated large-scale epigenetic datasets in a disease context to form a link between genotype and phenotype. We focus DNA methylation and important histone marks, where recent advances have been made thanks to technology improvements, cost effectiveness, and large meta-scale epigenome consortia efforts. We summarize recent studies unravelling the mechanistic understanding of epigenetic processes in disease development and progression. Moreover, we show how methodology advancements enable causal relationships to be established, and we pinpoint the most important issues to be addressed by future research.
Collapse
|
27
|
Was H, Krol SK, Rotili D, Mai A, Wojtas B, Kaminska B, Maleszewska M. Histone deacetylase inhibitors exert anti-tumor effects on human adherent and stem-like glioma cells. Clin Epigenetics 2019; 11:11. [PMID: 30654849 PMCID: PMC6337817 DOI: 10.1186/s13148-018-0598-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 12/17/2018] [Indexed: 12/29/2022] Open
Abstract
Background The diagnosis of glioblastoma (GBM), a most aggressive primary brain tumor with a median survival of 14.6 months, carries a dismal prognosis. GBMs are characterized by numerous genetic and epigenetic alterations, affecting patient survival and treatment response. Epigenetic mechanisms are deregulated in GBM as a result of aberrant expression/activity of epigenetic enzymes, including histone deacetylases (HDAC) which remove acetyl groups from histones regulating chromatin accessibility. Nevertheless, the impact of class/isoform-selective HDAC inhibitors (HDACi) on glioma cells, including glioma stem cells, had not been systematically determined. Results Comprehensive analysis of the public TCGA dataset revealed the increased expression of HDAC 1, 2, 3, and 7 in malignant gliomas. Knockdown of HDAC 1 and 2 in human GBM cells significantly decreased cell proliferation. We tested the activity of 2 new and 3 previously described HDACi with different class/isoform selectivity on human GBM cells. All tested compounds exerted antiproliferative properties on glioma cells. However, the HDACi 1 and 4 blocked proliferation of glioblastoma cells leading to G2/M growth arrest without affecting astrocyte survival. Moreover, 1 and 4 at low micromolar concentrations displayed cytotoxic and antiproliferative effects on sphere cultures enriched in glioma stem cells. Conclusions We identified two selective HDAC inhibitors that blocked proliferation of glioblastoma cells, but did not affect astrocyte survival. These new and highly effective inhibitors should be considered as promising candidates for further investigation in preclinical GBM models. Electronic supplementary material The online version of this article (10.1186/s13148-018-0598-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Halina Was
- Laboratory of Molecular Neurobiology, Neurobiology Center, The Nencki Institute of Experimental Biology, 3 Pasteur Str, 02-093, Warsaw, Poland.,Laboratory of Molecular Oncology, Military Institute of Medicine, 128 Szaserow Str, 04-141, Warsaw, Poland
| | - Sylwia K Krol
- Laboratory of Molecular Neurobiology, Neurobiology Center, The Nencki Institute of Experimental Biology, 3 Pasteur Str, 02-093, Warsaw, Poland
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Roma, P.le A. Moro 5, 00185, Rome, Italy.,Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, 00185, Rome, Italy
| | - Bartosz Wojtas
- Laboratory of Molecular Neurobiology, Neurobiology Center, The Nencki Institute of Experimental Biology, 3 Pasteur Str, 02-093, Warsaw, Poland
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Neurobiology Center, The Nencki Institute of Experimental Biology, 3 Pasteur Str, 02-093, Warsaw, Poland
| | - Marta Maleszewska
- Laboratory of Molecular Neurobiology, Neurobiology Center, The Nencki Institute of Experimental Biology, 3 Pasteur Str, 02-093, Warsaw, Poland.
| |
Collapse
|
28
|
Ferreira J, Ramos AA, Almeida T, Azqueta A, Rocha E. Drug resistance in glioblastoma and cytotoxicity of seaweed compounds, alone and in combination with anticancer drugs: A mini review. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2018; 48:84-93. [PMID: 30195884 DOI: 10.1016/j.phymed.2018.04.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/19/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Glioblastomas (GBM) are one of the most aggressive tumor of the central nervous system with an average life expectancy of only 1-2 years after diagnosis, even with the use of advanced treatments with surgery, radiation, and chemotherapy. There are several anticancer drugs with alkylating properties that have been used in the therapy of malignant gliomas. Temozolomide (TMZ) is one of them, widely used even in combination with ionizing radiation. However, the main disadvantage of using these types of drugs in the treatment of GBM is the development of cancer drug resistance. Research of bioactive compounds with anticancer activity has been heavily explored. PURPOSE This review focuses on a carotenoid and a phlorotannin present in seaweed, namely fucoxanthin and phloroglucinol, and their anticancer activity against glioblastoma. The combination of natural compounds with conventional drugs is also discussed. CONCLUSION Several natural compounds existing in seaweeds, such as fucoxanthin and phoroglucinol, have shown cytotoxic activity in models in vitro and in vivo, acting through different molecular mechanisms, such as antioxidant, antiproliferative, DNA damage/DNA repair, proapoptotic, antiangiogenic and antimetastic. Within the scope of interactions with conventional drugs, there are evidences that some seaweed compounds could be used to potentiate the action of anticancer drugs. However, their effects and mechanisms of action, alone or in combination with anticancer drugs, namely TMZ, in glioblastoma cell, still few explored and require more attention due to the unquestionable high potential of these marine compounds.
Collapse
Affiliation(s)
- Joana Ferreira
- Team of Histomorphology, Physiopathology and Applied Toxicology, CIIMAR - Interdisciplinary Center for Marine and Environmental Research, U.Porto - University of Porto, Avenida General Norton de Matos s/n, Matosinhos 4450-208, Portugal; Laboratory of Histology and Embryology, Department of Microscopy, ICBAS - Institute of Biomedical Sciences Abel Salazar, U.Porto - University of Porto, Rua de Jorge Viterbo Ferreira, n° 228, Porto 4050-313, Portugal; FCUP - Faculty of Sciences, U.Porto - University of Porto (U.Porto), Rua do Campo Alegre, Porto 4169-007, Portugal
| | - Alice Abreu Ramos
- Team of Histomorphology, Physiopathology and Applied Toxicology, CIIMAR - Interdisciplinary Center for Marine and Environmental Research, U.Porto - University of Porto, Avenida General Norton de Matos s/n, Matosinhos 4450-208, Portugal; Laboratory of Histology and Embryology, Department of Microscopy, ICBAS - Institute of Biomedical Sciences Abel Salazar, U.Porto - University of Porto, Rua de Jorge Viterbo Ferreira, n° 228, Porto 4050-313, Portugal.
| | - Tânia Almeida
- Team of Histomorphology, Physiopathology and Applied Toxicology, CIIMAR - Interdisciplinary Center for Marine and Environmental Research, U.Porto - University of Porto, Avenida General Norton de Matos s/n, Matosinhos 4450-208, Portugal; Laboratory of Histology and Embryology, Department of Microscopy, ICBAS - Institute of Biomedical Sciences Abel Salazar, U.Porto - University of Porto, Rua de Jorge Viterbo Ferreira, n° 228, Porto 4050-313, Portugal; FCUP - Faculty of Sciences, U.Porto - University of Porto (U.Porto), Rua do Campo Alegre, Porto 4169-007, Portugal
| | - Amaya Azqueta
- Department of Pharmacology and Toxicology, University of Navarra, C/ Irunlarrea, CP 31008 Pamplona, Navarra, Spain
| | - Eduardo Rocha
- Team of Histomorphology, Physiopathology and Applied Toxicology, CIIMAR - Interdisciplinary Center for Marine and Environmental Research, U.Porto - University of Porto, Avenida General Norton de Matos s/n, Matosinhos 4450-208, Portugal; Laboratory of Histology and Embryology, Department of Microscopy, ICBAS - Institute of Biomedical Sciences Abel Salazar, U.Porto - University of Porto, Rua de Jorge Viterbo Ferreira, n° 228, Porto 4050-313, Portugal
| |
Collapse
|
29
|
Velpula KK, Guda MR, Sahu K, Tuszynski J, Asuthkar S, Bach SE, Lathia JD, Tsung AJ. Metabolic targeting of EGFRvIII/PDK1 axis in temozolomide resistant glioblastoma. Oncotarget 2018; 8:35639-35655. [PMID: 28410193 PMCID: PMC5482605 DOI: 10.18632/oncotarget.16767] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 02/28/2017] [Indexed: 01/15/2023] Open
Abstract
Glioblastomas are characterized by amplification of EGFR. Approximately half of tumors with EGFR over-expression also express a constitutively active ligand independent EGFR variant III (EGFRvIII). While current treatments emphasize surgery followed by radiation and chemotherapy with Temozolomide (TMZ), acquired chemoresistance is a universal feature of recurrent GBMs. To mimic the GBM resistant state, we generated an in vitro TMZ resistant model and demonstrated that dichloroacetate (DCA), a metabolic inhibitor of pyruvate dehydrogenase kinase 1 (PDK1), reverses the Warburg effect. Microarray analysis conducted on the TMZ resistant cells with their subsequent treatment with DCA revealed PDK1 as its sole target. DCA treatment also induced mitochondrial membrane potential change and apoptosis as evidenced by JC-1 staining and electron microscopic studies. Computational homology modeling and docking studies confirmed DCA binding to EGFR, EGFRvIII and PDK1 with high affinity. In addition, expression of EGFRvIII was comparable to PDK1 when compared to EGFR in GBM surgical specimens supporting our in silico prediction data. Collectively our current study provides the first in vitro proof of concept that DCA reverses the Warburg effect in the setting of EGFRvIII positivity and TMZ resistance leading to GBM cytotoxicity, implicating cellular tyrosine kinase signaling in cancer cell metabolism.
Collapse
Affiliation(s)
- Kiran K Velpula
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA.,Department of Neurosurgery, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Maheedhara R Guda
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Kamlesh Sahu
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Jack Tuszynski
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Swapna Asuthkar
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Sarah E Bach
- Department of Pathology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Justin D Lathia
- Department of Cellular and Molecular medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Andrew J Tsung
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA.,Department of Neurosurgery, University of Illinois College of Medicine at Peoria, Peoria, IL, USA.,Illinois Neurological Institute, Peoria, IL, USA
| |
Collapse
|
30
|
Staberg M, Rasmussen RD, Michaelsen SR, Pedersen H, Jensen KE, Villingshøj M, Skjoth-Rasmussen J, Brennum J, Vitting-Seerup K, Poulsen HS, Hamerlik P. Targeting glioma stem-like cell survival and chemoresistance through inhibition of lysine-specific histone demethylase KDM2B. Mol Oncol 2018; 12:406-420. [PMID: 29360266 PMCID: PMC5830623 DOI: 10.1002/1878-0261.12174] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/18/2017] [Accepted: 01/03/2018] [Indexed: 12/30/2022] Open
Abstract
Glioblastoma (GBM) ranks among the most lethal cancers, with current therapies offering only palliation. Inter‐ and intrapatient heterogeneity is a hallmark of GBM, with epigenetically distinct cancer stem‐like cells (CSCs) at the apex. Targeting GSCs remains a challenging task because of their unique biology, resemblance to normal neural stem/progenitor cells, and resistance to standard cytotoxic therapy. Here, we find that the chromatin regulator, JmjC domain histone H3K36me2/me1 demethylase KDM2B, is highly expressed in glioblastoma surgical specimens compared to normal brain. Targeting KDM2B function genetically or pharmacologically impaired the survival of patient‐derived primary glioblastoma cells through the induction of DNA damage and apoptosis, sensitizing them to chemotherapy. KDM2B loss decreased the GSC pool, which was potentiated by coadministration of chemotherapy. Collectively, our results demonstrate KDM2B is crucial for glioblastoma maintenance, with inhibition causing loss of GSC survival, genomic stability, and chemoresistance.
Collapse
Affiliation(s)
- Mikkel Staberg
- Department of Radiation Biology, The Finsen Center, Copenhagen University Hospital, Denmark.,Brain Tumor Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Signe Regner Michaelsen
- Department of Radiation Biology, The Finsen Center, Copenhagen University Hospital, Denmark.,Brain Tumor Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Henriette Pedersen
- Brain Tumor Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Mette Villingshøj
- Department of Radiation Biology, The Finsen Center, Copenhagen University Hospital, Denmark
| | | | - Jannick Brennum
- Department of Neurosurgery, Copenhagen University Hospital, Denmark
| | | | - Hans Skovgaard Poulsen
- Department of Radiation Biology, The Finsen Center, Copenhagen University Hospital, Denmark
| | - Petra Hamerlik
- Brain Tumor Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| |
Collapse
|
31
|
Mendez FM, Núñez FJ, Zorrilla-Veloz RI, Lowenstein PR, Castro MG. Native Chromatin Immunoprecipitation Using Murine Brain Tumor Neurospheres. J Vis Exp 2018. [PMID: 29443090 DOI: 10.3791/57016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Epigenetic modifications may be involved in the development and progression of glioma. Changes in methylation and acetylation of promoters and regulatory regions of oncogenes and tumor suppressors can lead to changes in gene expression and play an important role in the pathogenesis of brain tumors. Native chromatin immunoprecipitation (ChIP) is a popular technique that allows the detection of modifications or other proteins tightly bound to DNA. In contrast to cross-linked ChIP, in native ChIP, cells are not treated with formaldehyde to covalently link protein to DNA. This is advantageous because sometimes crosslinking may fix proteins that only transiently interact with DNA and do not have functional significance in gene regulation. In addition, antibodies are generally raised against unfixed peptides. Therefore, antibody specificity is increased in native ChIP. However, it is important to keep in mind that native ChIP is only applicable to study histones or other proteins that bind tightly to DNA. This protocol describes the native chromatin immunoprecipitation on murine brain tumor neurospheres.
Collapse
Affiliation(s)
- Flor M Mendez
- Department of Cell and Developmental Biology, University of Michigan Medical School
| | - Felipe J Núñez
- Department of Cell and Developmental Biology, University of Michigan Medical School; Department of Neurosurgery, University of Michigan Medical School
| | - Rocío I Zorrilla-Veloz
- Cancer Research Summer Internship Program (CARSIP), Cancer Biology Program, University of Michigan Medical School; Department of Biology, University of Puerto Rico-Río Piedras Campus
| | - Pedro R Lowenstein
- Department of Cell and Developmental Biology, University of Michigan Medical School; Department of Neurosurgery, University of Michigan Medical School
| | - Maria G Castro
- Department of Cell and Developmental Biology, University of Michigan Medical School; Department of Neurosurgery, University of Michigan Medical School;
| |
Collapse
|
32
|
Cai X, Sughrue ME. Glioblastoma: new therapeutic strategies to address cellular and genomic complexity. Oncotarget 2017; 9:9540-9554. [PMID: 29507709 PMCID: PMC5823664 DOI: 10.18632/oncotarget.23476] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 12/08/2017] [Indexed: 01/19/2023] Open
Abstract
Glioblastoma (GBM) is the most invasive and devastating primary brain tumor with a median overall survival rate about 18 months with aggressive multimodality therapy. Its unique characteristics of heterogeneity, invasion, clonal populations maintaining stem cell-like cells and recurrence, have limited responses to a variety of therapeutic approaches, and have made GBM the most difficult brain cancer to treat. A great effort and progress has been made to reveal promising molecular mechanisms to target therapeutically. Especially with the emerging of new technologies, the mechanisms underlying the pathology of GBM are becoming more clear. The purpose of this review is to summarize the current knowledge of molecular mechanisms of GBM and highlight the novel strategies and concepts for the treatment of GBM.
Collapse
Affiliation(s)
- Xue Cai
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Michael E Sughrue
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| |
Collapse
|
33
|
KDM2B, an H3K36-specific demethylase, regulates apoptotic response of GBM cells to TRAIL. Cell Death Dis 2017; 8:e2897. [PMID: 28661478 PMCID: PMC5520939 DOI: 10.1038/cddis.2017.288] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/16/2017] [Accepted: 05/23/2017] [Indexed: 12/11/2022]
Abstract
Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) can selectively kill tumor cells. TRAIL resistance in cancers is associated with aberrant expression of the key components of the apoptotic program. However, how these components are regulated at the epigenetic level is not understood. In this study, we investigated novel epigenetic mechanisms regulating TRAIL response in glioblastoma multiforme (GBM) cells by a short-hairpin RNA loss-of-function screen. We interrogated 48 genes in DNA and histone modification pathways and identified KDM2B, an H3K36-specific demethylase, as a novel regulator of TRAIL response. Accordingly, silencing of KDM2B significantly enhanced TRAIL sensitivity, the activation of caspase-8, -3 and -7 and PARP cleavage. KDM2B knockdown also accelerated the apoptosis, as revealed by live-cell imaging experiments. To decipher the downstream molecular pathways regulated by KDM2B, levels of apoptosis-related genes were examined by RNA-sequencing upon KDM2B loss, which revealed derepression of proapoptotic genes Harakiri (HRK), caspase-7 and death receptor 4 (DR4) and repression of antiapoptotic genes. The apoptosis phenotype was partly dependent on HRK upregulation, as HRK knockdown significantly abrogated the sensitization. KDM2B-silenced tumors exhibited slower growth in vivo. Taken together, our findings suggest a novel mechanism, where the key apoptosis components are under epigenetic control of KDM2B in GBM cells.
Collapse
|
34
|
Dilillo M, Ait-Belkacem R, Esteve C, Pellegrini D, Nicolardi S, Costa M, Vannini E, Graaf ELD, Caleo M, McDonnell LA. Ultra-High Mass Resolution MALDI Imaging Mass Spectrometry of Proteins and Metabolites in a Mouse Model of Glioblastoma. Sci Rep 2017; 7:603. [PMID: 28377615 PMCID: PMC5429601 DOI: 10.1038/s41598-017-00703-w] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/08/2017] [Indexed: 01/27/2023] Open
Abstract
MALDI mass spectrometry imaging is able to simultaneously determine the spatial distribution of hundreds of molecules directly from tissue sections, without labeling and without prior knowledge. Ultra-high mass resolution measurements based on Fourier-transform mass spectrometry have been utilized to resolve isobaric lipids, metabolites and tryptic peptides. Here we demonstrate the potential of 15T MALDI-FTICR MSI for molecular pathology in a mouse model of high-grade glioma. The high mass accuracy and resolving power of high field FTICR MSI enabled tumor specific proteoforms, and tumor-specific proteins with overlapping and isobaric isotopic distributions to be clearly resolved. The protein ions detected by MALDI MSI were assigned to proteins identified by region-specific microproteomics (0.8 mm2 regions isolated using laser capture microdissection) on the basis of exact mass and isotopic distribution. These label free quantitative experiments also confirmed the protein expression changes observed by MALDI MSI and revealed changes in key metabolic proteins, which were supported by in-situ metabolite MALDI MSI.
Collapse
Affiliation(s)
- M Dilillo
- Fondazione Pisana per la Scienza ONLUS - Via Panfilo Castaldi 2, 56121, Pisa, Italy
- Department of Chemistry and Industrial Chemistry - Università di Pisa - Via Giuseppe Moruzzi 13, 56124, Pisa, Italy
| | - R Ait-Belkacem
- Fondazione Pisana per la Scienza ONLUS - Via Panfilo Castaldi 2, 56121, Pisa, Italy
| | - C Esteve
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - D Pellegrini
- Fondazione Pisana per la Scienza ONLUS - Via Panfilo Castaldi 2, 56121, Pisa, Italy
- NEST, Istituto Nanoscienze-National Research Council, 56127, Pisa, Italy
| | - S Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - M Costa
- CNR Neuroscience Institute, Via Moruzzi 1, 56124, Pisa, Italy
| | - E Vannini
- CNR Neuroscience Institute, Via Moruzzi 1, 56124, Pisa, Italy
| | - E L de Graaf
- Fondazione Pisana per la Scienza ONLUS - Via Panfilo Castaldi 2, 56121, Pisa, Italy
| | - M Caleo
- CNR Neuroscience Institute, Via Moruzzi 1, 56124, Pisa, Italy
| | - L A McDonnell
- Fondazione Pisana per la Scienza ONLUS - Via Panfilo Castaldi 2, 56121, Pisa, Italy.
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
| |
Collapse
|
35
|
Long noncoding RNA FTX is upregulated in gliomas and promotes proliferation and invasion of glioma cells by negatively regulating miR-342-3p. J Transl Med 2017; 97:447-457. [PMID: 28112756 DOI: 10.1038/labinvest.2016.152] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 12/23/2022] Open
Abstract
Gliomas remain a major public health challenge, posing a high risk for brain tumor-related morbidity and mortality. However, the mechanisms that drive the development of gliomas remain largely unknown. Emerging evidence has shown that long noncoding RNAs are key factors in glioma pathogenesis. qRT-PCR analysis was used to assess the expression of FTX and miR-342-3p in the different stages of gliomas in tissues. Bioinformatics tool DIANA and TargetSCan were used to predict the targets of FTX and miR-342-3p, respectively. Pearson's correlation analysis was performed to test the correlation between the expression levels of FTX, miR-342-3p, and astrocyte-elevated gene-1 (AEG-1). To examine the role of FTX in regulating proliferation and invasion of glioma cells, specific siRNA was used to knockdown FTX, and MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) and transwell assays were performed. Furthermore, rescue experiments were performed to further confirm the regulation of miR-342-3p by FTX. We then found that the expression of FTX and miR-342-3p was associated with progression of gliomas. FTX directly inhibited the expression of miR-342-3p, which subsequently regulates the expression of AEG-1. Collectively, FTX is critical for proliferation and invasion of glioma cells by regulating miR-342-3p and AEG-1. Our findings indicate that FTX and miR-342-3p may serve as a biomarker of glioma diagnosis, and offer potential novel therapeutic targets of treatment of gliomas.
Collapse
|
36
|
Inhibition of histone deacetylases sensitizes glioblastoma cells to lomustine. Cell Oncol (Dordr) 2016; 40:21-32. [PMID: 27766591 DOI: 10.1007/s13402-016-0301-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2016] [Indexed: 12/22/2022] Open
Abstract
PURPOSE Glioblastoma (GBM) ranks among the deadliest solid cancers worldwide and its prognosis has remained dismal, despite the use of aggressive chemo-irradiation treatment regimens. Limited drug delivery into the brain parenchyma and frequent resistance to currently available therapies are problems that call for a prompt development of novel therapeutic strategies. While only displaying modest efficacies as mono-therapy in pre-clinical settings, histone deacetylase inhibitors (HDACi) have shown promising sensitizing effects to a number of cytotoxic agents. Here, we sought to investigate the sensitizing effect of the HDACi trichostatin A (TSA) to the alkylating agent lomustine (CCNU), which is used in the clinic for the treatment of GBM. METHODS Twelve primary GBM cell cultures grown as neurospheres were used in this study, as well as one established GBM-derived cell line (U87 MG). Histone deacetylase (HDAC) expression levels were determined using quantitative real-time PCR and Western blotting. The efficacy of either CCNU alone or its combination with TSA was assessed using various assays, i.e., cell viability assays (MTT), cell cycle assays (flow cytometry, FACS), double-strand DNA break (DSB) quantification assays (microscopy/immunofluorescence) and expression profiling assays of proteins involved in apoptosis and cell stress (Western blotting and protein array). RESULTS We found that the HDAC1, 3 and 6 expression levels were significantly increased in GBM samples compared to non-neoplastic brain control samples. Additionally, we found that pre-treatment of GBM cells with TSA resulted in an enhancement of their sensitivity to CCNU, possibly via the accumulation of DSBs, decreased cell proliferation and viability rates, and an increased apoptotic rate. CONCLUSION From our data we conclude that the combined administration of TSA and CCNU eradicates GBM cells with a higher efficacy than either drug alone, thereby opening a novel avenue for the treatment of GBM.
Collapse
|
37
|
Ferreira WAS, Pinheiro DDR, Costa Junior CAD, Rodrigues-Antunes S, Araújo MD, Leão Barros MB, Teixeira ACDS, Faro TAS, Burbano RR, Oliveira EHCD, Harada ML, Borges BDN. An update on the epigenetics of glioblastomas. Epigenomics 2016; 8:1289-305. [PMID: 27585647 DOI: 10.2217/epi-2016-0040] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Glioblastomas, also known as glioblastoma multiforme (GBM), are the most aggressive and malignant type of primary brain tumor in adults, exhibiting notable variability at the histopathological, genetic and epigenetic levels. Recently, epigenetic alterations have emerged as a common hallmark of many tumors, including GBM. Considering that a deeper understanding of the epigenetic modifications that occur in GBM may increase the knowledge regarding the tumorigenesis, progression and recurrence of this disease, in this review we discuss the recent major advances in GBM epigenetics research involving histone modification, glioblastoma stem cells, DNA methylation, noncoding RNAs expression, including their main alterations and the use of epigenetic therapy as a valid option for GBM treatment.
Collapse
Affiliation(s)
- Wallax Augusto Silva Ferreira
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Danilo do Rosário Pinheiro
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Carlos Antonio da Costa Junior
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Symara Rodrigues-Antunes
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Mariana Diniz Araújo
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Mariceli Baia Leão Barros
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Adriana Corrêa de Souza Teixeira
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Thamirys Aline Silva Faro
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | | | | | - Maria Lúcia Harada
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Bárbara do Nascimento Borges
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| |
Collapse
|
38
|
Erasimus H, Gobin M, Niclou S, Van Dyck E. DNA repair mechanisms and their clinical impact in glioblastoma. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 769:19-35. [PMID: 27543314 DOI: 10.1016/j.mrrev.2016.05.005] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/04/2016] [Indexed: 12/18/2022]
Abstract
Despite surgical resection and genotoxic treatment with ionizing radiation and the DNA alkylating agent temozolomide, glioblastoma remains one of the most lethal cancers, due in great part to the action of DNA repair mechanisms that drive resistance and tumor relapse. Understanding the molecular details of these mechanisms and identifying potential pharmacological targets have emerged as vital tasks to improve treatment. In this review, we introduce the various cellular systems and animal models that are used in studies of DNA repair in glioblastoma. We summarize recent progress in our knowledge of the pathways and factors involved in the removal of DNA lesions induced by ionizing radiation and temozolomide. We introduce the therapeutic strategies relying on DNA repair inhibitors that are currently being tested in vitro or in clinical trials, and present the challenges raised by drug delivery across the blood brain barrier as well as new opportunities in this field. Finally, we review the genetic and epigenetic alterations that help shape the DNA repair makeup of glioblastoma cells, and discuss their potential therapeutic impact and implications for personalized therapy.
Collapse
Affiliation(s)
- Hélène Erasimus
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - Matthieu Gobin
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - Simone Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - Eric Van Dyck
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg.
| |
Collapse
|
39
|
Choudhury SR, Cui Y, Milton JR, Li J, Irudayaraj J. Selective increase in subtelomeric DNA methylation: an epigenetic biomarker for malignant glioma. Clin Epigenetics 2015; 7:107. [PMID: 26451167 PMCID: PMC4597615 DOI: 10.1186/s13148-015-0140-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/22/2015] [Indexed: 01/12/2023] Open
Abstract
Background Subtelomeric regions dynamically change their epigenetic pattern during development and progression of several malignancies and degenerative disorders. However, DNA methylation of human subtelomeres and their correlation to telomere length (TL) remain undetermined in glioma. Results Herein, we report on the selective changes in subtelomeric DNA methylation at the end of five chromosomes (Chr.) (7q, 8q. 18p, 21q, and XpYp) and ascertain their correlation with TL in patients with glioma. Subtelomeric methylation level was invariably higher in glioma patients compared to the control group, irrespective of their age and tumor grade. In particular, a significant increase in methylation was observed at the subtelomeric CpG sites of Chr. 8q, 21q, and XpYp in tissues, obtained from the brain tumor of glioma patients. In contrast, no significant change in methylation was observed at the subtelomere of Chr. 7q and 18p. Selective changes in the subtelomeric methylation level, however, did not show any significant correlation to the global TL. This observed phenomenon was validated in vitro by inducing demethylation in a glioblastoma cell line (SF-767) using 5-azacytidine (AZA) treatment. AZA treatment caused significant changes in the subtelomeric methylation pattern but did not alter the TL, which supports our hypothesis. Conclusions DNA methylation level dramatically increased at the subtelomere of Chr.8q, 21q, and XpYp in malignant glioma, which could be used as an early epigenetic diagnostic biomarker of the disease. Alterations in subtelomeric methylation, however, have no effects on the TL. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0140-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Samrat Roy Choudhury
- Department of Biological Engineering, Center for Cancer Research, Purdue University, West Lafayette, IN 47906 USA
| | - Yi Cui
- Department of Biological Engineering, Center for Cancer Research, Purdue University, West Lafayette, IN 47906 USA
| | - Jacob R Milton
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47906 USA
| | - Jian Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008 China
| | - Joseph Irudayaraj
- Department of Biological Engineering, Center for Cancer Research, Purdue University, West Lafayette, IN 47906 USA
| |
Collapse
|
40
|
Sherwani SI, Khan HA. Role of 5-hydroxymethylcytosine in neurodegeneration. Gene 2015; 570:17-24. [PMID: 26115768 DOI: 10.1016/j.gene.2015.06.052] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 05/18/2015] [Accepted: 06/18/2015] [Indexed: 02/05/2023]
Abstract
The recent discovery of 5-hydroxymethylcytosine (5hmC), an epigenetic modifier and oxidation product of 5-methylcytosine (5mC), has broadened the scope and understanding of neural development and neurodegenerative diseases. By virtue of their functional groups, 5mC and 5hmC exert opposite effects on gene expression; the former is generally associated with gene silencing whereas the latter is mainly involved in up-regulation of gene expression affecting the cellular processes such as differentiation, development, and aging. Although DNA methylation plays an important role in normal neural development and neuroprotection, an altered pathway due to complex interaction with environmental and genetic factors may cause severe neurodegeneration. The levels of 5hmC in brain increase progressively from birth until death, while in patients with neurodegenerative disorders, the levels are found to be highly compromised. This article discusses the recent developments in the area of hydroxymethylation, with particular emphasis on the role of 5hmC in neurodegenerative diseases including Alzheimer's disease, Parkinson's diseases and Huntington's disease. We have also included recent findings on the role of 5hmC in brain tumors (gliomas). Despite compelling evidence on the involvement of 5hmC in neurodegeneration, it is yet to be established whether this epigenetic molecule is the cause or the effect of the onset and progression of neurodegenerative diseases.
Collapse
Affiliation(s)
- Shariq I Sherwani
- Department of Internal Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Haseeb A Khan
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| |
Collapse
|
41
|
Maleszewska M, Kaminska B. Deregulation of histone-modifying enzymes and chromatin structure modifiers contributes to glioma development. Future Oncol 2015; 11:2587-601. [PMID: 26289459 DOI: 10.2217/fon.15.171] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The epigenetic landscape is deregulated in cancer due to aberrant activation or inactivation of enzymes maintaining and modifying the epigenome. Histone modifications and global aberrations at the histone level may result in distorted patterns of gene expression, and malfunction of proteins that regulate chromatin modification and remodeling. Recent whole genome studies demonstrated that histones and chaperone proteins harbor mutations that may result in gross alterations of the epigenome leading to genome instability. Glioma development is a multistep process, involving genetic and epigenetic alterations. This review summarizes newly identified mechanisms affecting expression/functions of histone-modifying enzymes and chromatin modifiers in gliomas. We discuss recent approaches to overcome epigenetic alterations with histone-modifying enzyme inhibitors and their prospects for glioma therapy.
Collapse
Affiliation(s)
- Marta Maleszewska
- Laboratory of Molecular Neurobiology, Neurobiology Center, Nencki Institute of Experimental Biology, 3 Pasteur Str., 02-093 Warsaw, Poland
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Neurobiology Center, Nencki Institute of Experimental Biology, 3 Pasteur Str., 02-093 Warsaw, Poland
| |
Collapse
|
42
|
Alexanian AR, Huang YW. Specific combinations of the chromatin-modifying enzyme modulators significantly attenuate glioblastoma cell proliferation and viability while exerting minimal effect on normal adult stem cells growth. Tumour Biol 2015; 36:9067-72. [PMID: 26084611 DOI: 10.1007/s13277-015-3654-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/09/2015] [Indexed: 02/06/2023] Open
Abstract
The discoveries of recent decade showed that all critical changes in cancer cells, such as silencing of tumor-suppressor genes and activation of oncogenes, are caused not only by genetic but also by epigenetic mechanisms. Although epigenetic changes are somatically heritable, in contrast to genetic changes, they are potentially reversible, making them good targets for therapeutic intervention. Covalent modifications of chromatin such as methylation and acetylation of histones and methylation of DNA are the important components of epigenetic machinery. In this study, we investigated the effect of different modulators of DNA and histone covalent-modifying enzymes on the proliferation and viability of normal adult stem cells, such as human bone marrow mesenchymal stem cells (hMSCs), and on malignant tumor cells, such as glioblastoma (GB) D54 cells. Results demonstrated that specific combinations of histone methyltransferases and deacetylases inhibitors significantly attenuated D54 cells viability but having only a small effect on hMSCs growth. Taken together, these studies suggest that specific combinations of histone covalent modifiers could be an effective treatment option for the most aggressive type of primary brain tumors such as glioblastoma multiforme.
Collapse
Affiliation(s)
- Arshak R Alexanian
- Cell Reprogramming & Therapeutics LLC, W229 N1870 Westwood Drive, Waukesha, WI, 53186, USA.
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, 9200 West Wisconsin Ave., Milwaukee, WI, 53226-3522, USA.
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, 9200 West Wisconsin Ave., Milwaukee, WI, 53226-3522, USA.
| |
Collapse
|
43
|
Lee P, Murphy B, Miller R, Menon V, Banik NL, Giglio P, Lindhorst SM, Varma AK, Vandergrift WA, Patel SJ, Das A. Mechanisms and clinical significance of histone deacetylase inhibitors: epigenetic glioblastoma therapy. Anticancer Res 2015; 35:615-625. [PMID: 25667438 PMCID: PMC6052863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Glioblastoma is the most common and deadliest of malignant primary brain tumors (Grade IV astrocytoma) in adults. Current standard treatments have been improving but patient prognosis still remains unacceptably devastating. Glioblastoma recurrence is linked to epigenetic mechanisms and cellular pathways. Thus, greater knowledge of the cellular, genetic and epigenetic origin of glioblastoma is the key for advancing glioblastoma treatment. One rapidly growing field of treatment, epigenetic modifiers; histone deacetylase inhibitors (HDACis), has now shown much promise for improving patient outcomes through regulation of the acetylation states of histone proteins (a form of epigenetic modulation) and other non-histone protein targets. HDAC inhibitors have been shown, in a pre-clinical setting, to be effective anticancer agents via multiple mechanisms, by up-regulating expression of tumor suppressor genes, inhibiting oncogenes, inhibiting tumor angiogenesis and up-regulating the immune system. There are many HDAC inhibitors that are currently in pre-clinical and clinical stages of investigation for various types of cancers. This review will explain the theory of epigenetic cancer therapy, identify HDAC inhibitors that are being investigated for glioblastoma therapy, explain the mechanisms of therapeutic effects as demonstrated by pre-clinical and clinical studies and describe the current status of development of these drugs as they pertain to glioblastoma therapy.
Collapse
Affiliation(s)
- Philip Lee
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - Ben Murphy
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - Rickey Miller
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - Vivek Menon
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - Naren L Banik
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A. Ralph H. Johnson VA Medical Center, Charleston, SC, U.S.A
| | - Pierre Giglio
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A. Department of Neurological Surgery Ohio State University Wexner Medical College, Columbus, OH, U.S.A
| | - Scott M Lindhorst
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - Abhay K Varma
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - William A Vandergrift
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - Sunil J Patel
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - Arabinda Das
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A.
| |
Collapse
|
44
|
Yao Y, Des Marais TL, Costa M. Chromatin Memory in the Development of Human Cancers. GENE TECHNOLOGY 2014; 3:114. [PMID: 25606572 PMCID: PMC4297643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cancer is a complex disease with acquired genomic and epigenomic alterations that affect cell proliferation, viability and invasiveness. Almost all the epigenetic mechanisms including cytosine methylation and hydroxymethylation, chromatin remodeling and non-coding RNAs have been found associate with carcinogenesis and cancer specific expression profile. Altered histone modification as an epigenetic hallmark is frequently found in tumors. Understanding the epigenetic alterations induced by carcinogens or infectious agents may help us understand early epigenetic changes prior to the development of cancer. In this review, we focus on chromatin remodeling and the associated histone modifiers in the development of cancer; the application of these modifiers as a cancer therapy target in different clinical trial phases is also discussed.
Collapse
Affiliation(s)
- Yixin Yao
- Department of Environmental Medicine New York University, New York, USA,Corresponding author: Yixin Yao, Department of Environmental Medicine, New York University, New York, USA; Tel: 845-731-3517;
| | | | - Max Costa
- Department of Environmental Medicine New York University, New York, USA,Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, Tuxedo, New York, USA
| |
Collapse
|
45
|
Palani M, Arunkumar R, Vanisree AJ. Methylation and expression patterns of tropomyosin-related kinase genes in different grades of glioma. Neuromolecular Med 2014; 16:529-39. [PMID: 24840578 DOI: 10.1007/s12017-014-8303-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 04/08/2014] [Indexed: 10/25/2022]
Abstract
Tropomyosin-related kinase family (NTRK1, NTRK2 and NTRK3) is well known to play an important role in the pathogenesis of brain tumour, which exhibit heterogeneity in its biological and clinical behaviour. However, the mechanism that regulates NTRKs in glioma is not well understood. The present study investigates the epigenetic status (methylation) of NTRKs and their expression in different grades of glioma. Promoter methylation and structural relationship of NTRKs was assessed using methylation-specific PCR followed by chromatin immunoprecipitation in brain tissue samples from 220 subjects with different grades of glioma. Control brain samples were also assessed similarly. Reverse transcriptase PCR was performed to analyse the expressions of NTRK mRNAs in the grades of glioma. In addition, the expression level of p75(NTR) protein was analysed using immunofluorescent technique in all of the samples. The overall percentage of NTRK3 gene methylation frequency with subsequent loss of mRNA expression was significantly higher in glioma compared with control samples (p < 0.05). No such significance was observed in other NTRK1 and NTRK2 genes. Further, mRNA expression pattern of NTRK1 and NTRK2 genes was found to be significantly higher in low grades as compared with high grades (HG) and control samples (p < 0.05). Survival rate of HG patients with negative expressions of NTRK1 and NTRK2 was poor than those with the positive expressions of both NTRK1 and NTRK2. Further, a significant correlation was observed with reduced expression of p75(NTR) and the expression pattern of NTRK family in glioma as compared with the control samples (p < 0.05). There exists a correlation between the expression of NTRK family and different grades of glioma with a significant suggestion that the promoter methylation does not play role in the regulation of these genes in glioma. Further, poor survival could be associated with NTRK mRNAs 1 and 2. Hence, NTRKs are potential probes for assessing the behaviour of different grades of glioma, which could also function as significant prognostic factors and thus deserve wider attention for an effective management of the grades.
Collapse
Affiliation(s)
- Mahalakshmi Palani
- Department of Biochemistry, University of Madras, Guindy Campus, Chennai, Tamil Nadu, India
| | | | | |
Collapse
|