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Yu X, Li S. Specific regulation of epigenome landscape by metabolic enzymes and metabolites. Biol Rev Camb Philos Soc 2024; 99:878-900. [PMID: 38174803 DOI: 10.1111/brv.13049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Metabolism includes anabolism and catabolism, which play an essential role in many biological processes. Chromatin modifications are post-translational modifications of histones and nucleic acids that play important roles in regulating chromatin-associated processes such as gene transcription. There is a tight connection between metabolism and chromatin modifications. Many metabolic enzymes and metabolites coordinate cellular activities with alterations in nutrient availability by regulating gene expression through epigenetic mechanisms such as DNA methylation and histone modifications. The dysregulation of gene expression by metabolism and epigenetic modifications may lead to diseases such as diabetes and cancer. Recent studies reveal that metabolic enzymes and metabolites specifically regulate chromatin modifications, including modification types, modification residues and chromatin regions. This specific regulation has been implicated in the development of human diseases, yet the underlying mechanisms are only beginning to be uncovered. In this review, we summarise recent studies of the molecular mechanisms underlying the metabolic regulation of histone and DNA modifications and discuss how they contribute to pathogenesis. We also describe recent developments in technologies used to address the key questions in this field. We hope this will inspire further in-depth investigations of the specific regulatory mechanisms involved, and most importantly will shed lights on the development of more effective disease therapies.
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Affiliation(s)
- Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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2
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Zhao T, Fan J, Abu-Zaid A, Burley SK, Zheng XS. Nuclear mTOR Signaling Orchestrates Transcriptional Programs Underlying Cellular Growth and Metabolism. Cells 2024; 13:781. [PMID: 38727317 PMCID: PMC11083943 DOI: 10.3390/cells13090781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
mTOR is a central regulator of cell growth and metabolism in response to mitogenic and nutrient signals. Notably, mTOR is not only found in the cytoplasm but also in the nucleus. This review highlights direct involvement of nuclear mTOR in regulating transcription factors, orchestrating epigenetic modifications, and facilitating chromatin remodeling. These effects intricately modulate gene expression programs associated with growth and metabolic processes. Furthermore, the review underscores the importance of nuclear mTOR in mediating the interplay between metabolism and epigenetic modifications. By integrating its functions in nutrient signaling and gene expression related to growth and metabolism, nuclear mTOR emerges as a central hub governing cellular homeostasis, malignant transformation, and cancer progression. Better understanding of nuclear mTOR signaling has the potential to lead to novel therapies against cancer and other growth-related diseases.
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Affiliation(s)
- Tinghan Zhao
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Jialin Fan
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Ahmed Abu-Zaid
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Stephen K. Burley
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - X.F. Steven Zheng
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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3
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Dupouy G, Dong Y, Herzog E, Chabouté ME, Berr A. Nuclear envelope dynamics in connection to chromatin remodeling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:963-981. [PMID: 37067011 DOI: 10.1111/tpj.16246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/29/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
The nucleus is a central organelle of eukaryotic cells undergoing dynamic structural changes during cellular fundamental processes such as proliferation and differentiation. These changes rely on the integration of developmental and stress signals at the nuclear envelope (NE), orchestrating responses at the nucleo-cytoplasmic interface for efficient genomic functions such as DNA transcription, replication and repair. While in animals, correlation has already been established between NE dynamics and chromatin remodeling using last-generation tools and cutting-edge technologies, this topic is just emerging in plants, especially in response to mechanical cues. This review summarizes recent data obtained in this field with more emphasis on the mechanical stress response. It also highlights similarities/differences between animal and plant cells at multiples scales, from the structural organization of the nucleo-cytoplasmic continuum to the functional impacts of NE dynamics.
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Affiliation(s)
- Gilles Dupouy
- Institut de Biologie Moléculaire des Plantes du CNRS- Université de Strasbourg, 12 rue du Général Zimmer,, F-67084, Strasbourg, France
| | - Yihan Dong
- Institut de Biologie Moléculaire des Plantes du CNRS- Université de Strasbourg, 12 rue du Général Zimmer,, F-67084, Strasbourg, France
| | - Etienne Herzog
- Institut de Biologie Moléculaire des Plantes du CNRS- Université de Strasbourg, 12 rue du Général Zimmer,, F-67084, Strasbourg, France
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes du CNRS- Université de Strasbourg, 12 rue du Général Zimmer,, F-67084, Strasbourg, France
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du CNRS- Université de Strasbourg, 12 rue du Général Zimmer,, F-67084, Strasbourg, France
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4
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Kim H, Lebeau B, Papadopoli D, Jovanovic P, Russo M, Avizonis D, Morita M, Afzali F, Ursini-Siegel J, Postovit LM, Witcher M, Topisirovic I. MTOR modulation induces selective perturbations in histone methylation which influence the anti-proliferative effects of mTOR inhibitors. iScience 2024; 27:109188. [PMID: 38433910 PMCID: PMC10904987 DOI: 10.1016/j.isci.2024.109188] [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: 11/08/2023] [Revised: 01/11/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024] Open
Abstract
Emerging data suggest a significant cross-talk between metabolic and epigenetic programs. However, the relationship between the mechanistic target of rapamycin (mTOR), which is a pivotal metabolic regulator, and epigenetic modifications remains poorly understood. Our results show that mTORC1 activation caused by the abrogation of its negative regulator tuberous sclerosis complex 2 (TSC2) coincides with increased levels of the histone modification H3K27me3 but not H3K4me3 or H3K9me3. This selective H3K27me3 induction was mediated via 4E-BP-dependent increase in EZH2 protein levels. Surprisingly, mTOR inhibition also selectively induced H3K27me3. This was independent of TSC2, and was paralleled by reduced EZH2 and increased EZH1 protein levels. Notably, the ability of mTOR inhibitors to induce H3K27me3 levels was positively correlated with their anti-proliferative effects. Collectively, our findings demonstrate that both activation and inhibition of mTOR selectively increase H3K27me3 by distinct mechanisms, whereby the induction of H3K27me3 may potentiate the anti-proliferative effects of mTOR inhibitors.
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Affiliation(s)
- HaEun Kim
- Department of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada
| | - Benjamin Lebeau
- Department of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - David Papadopoli
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Predrag Jovanovic
- Department of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada
| | - Mariana Russo
- Goodman Cancer Research Centre, Montréal, QC H3A 1A3, Canada
| | - Daina Avizonis
- Goodman Cancer Research Centre, Montréal, QC H3A 1A3, Canada
| | - Masahiro Morita
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Farzaneh Afzali
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Josie Ursini-Siegel
- Department of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
- Department of Biochemistry, McGill University, Montreal, QC H3A 0G4, Canada
| | - Lynne-Marie Postovit
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Michael Witcher
- Department of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Ivan Topisirovic
- Department of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
- Department of Biochemistry, McGill University, Montreal, QC H3A 0G4, Canada
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5
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Harachi M, Masui K, Shimizu E, Murakami K, Onizuka H, Muragaki Y, Kawamata T, Nakayama H, Miyata M, Komori T, Cavenee WK, Mischel PS, Kurata A, Shibata N. DNA hypomethylator phenotype reprograms glutamatergic network in receptor tyrosine kinase gene-mutated glioblastoma. Acta Neuropathol Commun 2024; 12:40. [PMID: 38481314 PMCID: PMC10935831 DOI: 10.1186/s40478-024-01750-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/25/2024] [Indexed: 03/17/2024] Open
Abstract
DNA methylation is crucial for chromatin structure and gene expression and its aberrancies, including the global "hypomethylator phenotype", are associated with cancer. Here we show that an underlying mechanism for this phenotype in the large proportion of the highly lethal brain tumor glioblastoma (GBM) carrying receptor tyrosine kinase gene mutations, involves the mechanistic target of rapamycin complex 2 (mTORC2), that is critical for growth factor signaling. In this scenario, mTORC2 suppresses the expression of the de novo DNA methyltransferase (DNMT3A) thereby inducing genome-wide DNA hypomethylation. Mechanistically, mTORC2 facilitates a redistribution of EZH2 histone methyltransferase into the promoter region of DNMT3A, and epigenetically represses the expression of DNA methyltransferase. Integrated analyses in both orthotopic mouse models and clinical GBM samples indicate that the DNA hypomethylator phenotype consistently reprograms a glutamate metabolism network, eventually driving GBM cell invasion and survival. These results nominate mTORC2 as a novel regulator of DNA hypomethylation in cancer and an exploitable target against cancer-promoting epigenetics.
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Affiliation(s)
- Mio Harachi
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Kenta Masui
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan.
| | - Erika Shimizu
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Kumiko Murakami
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Hiromi Onizuka
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Yoshihiro Muragaki
- Department of Neurosurgery, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
- Center for Advanced Medical Engineering Research and Development, Kobe University, Kobe, Hyogo, 650-0047, Japan
| | - Takakazu Kawamata
- Department of Neurosurgery, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Hisako Nakayama
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Mariko Miyata
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Takashi Komori
- Department of Neuropathology, Tokyo Metropolitan Neurological Hospital, Musashinodai, Tokyo, 156-8506, Japan
| | - Webster K Cavenee
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Atsushi Kurata
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Noriyuki Shibata
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
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6
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Saleh Z, Moccia MC, Ladd Z, Joneja U, Li Y, Spitz F, Hong YK, Gao T. Pancreatic Neuroendocrine Tumors: Signaling Pathways and Epigenetic Regulation. Int J Mol Sci 2024; 25:1331. [PMID: 38279330 PMCID: PMC10816436 DOI: 10.3390/ijms25021331] [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: 12/20/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
Pancreatic neuroendocrine tumors (PNETs) are characterized by dysregulated signaling pathways that are crucial for tumor formation and progression. The efficacy of traditional therapies is limited, particularly in the treatment of PNETs at an advanced stage. Epigenetic alterations profoundly impact the activity of signaling pathways in cancer development, offering potential opportunities for drug development. There is currently a lack of extensive research on epigenetic regulation in PNETs. To fill this gap, we first summarize major signaling events that are involved in PNET development. Then, we discuss the epigenetic regulation of these signaling pathways in the context of both PNETs and commonly occurring-and therefore more extensively studied-malignancies. Finally, we will offer a perspective on the future research direction of the PNET epigenome and its potential applications in patient care.
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Affiliation(s)
- Zena Saleh
- Department of Surgery, Cooper University Health Care, Camden, NJ 08103, USA; (Z.S.); (Z.L.)
| | - Matthew C. Moccia
- Department of Surgery, Cooper University Health Care, Camden, NJ 08103, USA; (Z.S.); (Z.L.)
| | - Zachary Ladd
- Department of Surgery, Cooper University Health Care, Camden, NJ 08103, USA; (Z.S.); (Z.L.)
| | - Upasana Joneja
- Department of Pathology, Cooper University Health Care, Camden, NJ 08103, USA
| | - Yahui Li
- Department of Surgery, Cooper University Health Care, Camden, NJ 08103, USA; (Z.S.); (Z.L.)
| | - Francis Spitz
- Department of Surgery, Cooper University Health Care, Camden, NJ 08103, USA; (Z.S.); (Z.L.)
| | - Young Ki Hong
- Department of Surgery, Cooper University Health Care, Camden, NJ 08103, USA; (Z.S.); (Z.L.)
| | - Tao Gao
- Department of Surgery, Cooper University Health Care, Camden, NJ 08103, USA; (Z.S.); (Z.L.)
- Camden Cancer Research Center, Camden, NJ 08103, USA
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7
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Serizawa M, Serizawa K, Masui K, Toguchi M, Murakami K, Yamamoto T, Nagashima Y, Takagi T, Kurata A. Metabolic and Epigenetic Reprogramming in a Case of Nuclear Protein in Testis (NUT) Carcinoma of the Retroperitoneum. Cureus 2024; 16:e52814. [PMID: 38389647 PMCID: PMC10883765 DOI: 10.7759/cureus.52814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2024] [Indexed: 02/24/2024] Open
Abstract
Nuclear protein in testis (NUT) carcinoma is a rare but highly aggressive carcinoma, driven by genetic rearrangement of the NUT midline carcinoma family member 1 (NUTM1) gene on chromosome 15q14. Recently, a tight link has been suggested between genetic abnormalities and subsequent metabolic and epigenetic dysregulation to drive the progression of malignant tumors. However, it remains elusive whether such reprogramming could contribute to the pathogenesis of NUT carcinoma. We herein report an autopsy case of NUT carcinoma arising in the retroperitoneum of a 31-year-old male. Notably, reprogramming of glycolytic metabolism and epigenetic histone modifications was observed in this unusual NUT carcinoma case, and this phenomenon was further confirmed by an in vitro cell culture model with bromodomain containing 4 (BRD4)-NUT overexpression. The rationale for documenting the case is based on our findings to reveal that metabolic and epigenetic reprogramming could be one of the contributing factors to the pathogenesis of NUT carcinoma, which could be exploitable as a novel therapeutic target for this rare and aggressive cancer type.
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Affiliation(s)
- Mika Serizawa
- Department of Pathology, Tokyo Women's Medical University, Tokyo, JPN
| | - Kaho Serizawa
- Department of Pathology, Tokyo Women's Medical University, Tokyo, JPN
| | - Kenta Masui
- Department of Pathology, Tokyo Women's Medical University, Tokyo, JPN
| | - Makoto Toguchi
- Department of Urology, Tokyo Women's Medical University Hospital, Tokyo, JPN
| | - Kumiko Murakami
- Department of Pathology, Tokyo Women's Medical University, Tokyo, JPN
| | - Tomoko Yamamoto
- Department of Surgical Pathology, Tokyo Women's Medical University Hospital, Tokyo, JPN
| | - Yoji Nagashima
- Department of Surgical Pathology, Tokyo Women's Medical University Hospital, Tokyo, JPN
| | - Toshio Takagi
- Department of Urology, Tokyo Women's Medical University Hospital, Tokyo, JPN
| | - Atsushi Kurata
- Department of Pathology, Tokyo Women's Medical University, Tokyo, JPN
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Masui K, Mischel PS. Metabolic and epigenetic reprogramming in the pathogenesis of glioblastoma: Toward the establishment of "metabolism-based pathology". Pathol Int 2023; 73:533-541. [PMID: 37755062 DOI: 10.1111/pin.13379] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/03/2023] [Indexed: 09/28/2023]
Abstract
Molecular genetic approaches are now mandatory for cancer diagnostics, especially for brain tumors. Genotype-based diagnosis has predominated over the phenotype-based approach, with its prognostic and predictive powers. However, comprehensive genetic testing would be difficult to perform in the clinical setting, and translational research is required to histologically decipher the peculiar biology of cancer. Of interest, recent studies have demonstrated discrete links between oncogenotypes and the resultant metabolic phenotypes, revealing cancer metabolism as a promising histologic surrogate to reveal specific characteristics of each cancer type and indicate the best way to manage cancer patients. Here, we provide an overview of our research progress to work on cancer metabolism, with a particular focus on the genomically well-characterized malignant tumor glioblastoma. With the use of clinically relevant animal models and human tissue, we found that metabolic reprogramming plays a major role in the aggressive cancer biology by conferring therapeutic resistance to cancer cells and rewiring their epigenomic landscapes. We further discuss our future endeavor to establish "metabolism-based pathology" on how the basic knowledge of cancer metabolism could be leveraged to improve the management of patients by linking cancer cell genotype, epigenotype, and phenotype through metabolic reprogramming.
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Affiliation(s)
- Kenta Masui
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Paul S Mischel
- Department of Pathology, Stanford University, Stanford, California, USA
- Department of Neurosurgery, Stanford University, Stanford, California, USA
- Sarafan ChEM-H, Stanford University, Stanford, California, USA
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9
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Chen M, Fan L, Wu G, Wang H, Gu S. Histone methyltransferase enzyme enhancer of zeste homolog 2 counteracts ischemic brain injury via H3K27me3-mediated regulation of PI3K/AKT/mTOR signaling pathway. ENVIRONMENTAL TOXICOLOGY 2023; 38:2240-2255. [PMID: 37334851 DOI: 10.1002/tox.23863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND Epigenetic histone methylation plays a crucial role in cerebral ischemic injury, particularly in the context of ischemic stroke. However, the complete understanding of regulators involved in histone methylation, such as Enhancer of Zeste Homolog 2 (EZH2), along with their functional effects and underlying mechanisms, remains incomplete. METHODS Here, we employed a rat model of MCAO (Middle cerebral artery occlusion) and an OGD (Oxygen-Glucose Deprivation) model of primary cortical neurons to study the role of EZH2 and H3K27me3 in cerebral ischemia-reperfusion injury. The infarct volume was measured through TTC staining, while cell apoptosis was detected using TUNEL staining. The mRNA expression levels were quantified through quantitative real-time polymerase chain reaction (qPCR), whereas protein expressions were evaluated via western blotting and immunofluorescence experiments. RESULTS The expression levels of EZH2 and H3K27me3 were upregulated in OGD; these expression levels were further enhanced by GSK-J4 but reduced by EPZ-6438 and AKT inhibitor (LY294002) under OGD conditions. Similar trends were observed for mTOR, AKT, and PI3K while contrasting results were noted for UTX and JMJD3. The phosphorylation levels of mTOR, AKT, and PI3K were activated by OGD, further stimulated by GSK-J4, but inhibited by EPZ-6438 and AKT inhibitor. Inhibition of EZH2 or AKT effectively counteracted OGD-/MCAO-induced cell apoptosis. Additionally, inhibition of EZH2 or AKT mitigated MCAO-induced infarct size and neurological deficit in vivo. CONCLUSIONS Collectively, our results demonstrate that EZH2 inhibition exerts a protective effect against ischemic brain injury by modulating the H3K27me3/PI3K/AKT/mTOR signaling pathway. The results provide novel insights into potential therapeutic mechanisms for stroke treatment.
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Affiliation(s)
- Miao Chen
- Department of Emergency, The First Affiliated Hospital of Hainan Medical University, Haikou, People's Republic of China
| | - Limin Fan
- The Institute for Biomedical Engineering and Nano Science, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Guoping Wu
- Department of Emergency, Sansha People's Hospital, Sansha, People's Republic of China
| | - Hairong Wang
- Department of Emergency, Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Shuo Gu
- Department of Pediatric Neurosurgery, The First Affiliated Hospital of Hainan Medical University, Haikou, People's Republic of China
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10
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Duan W, Yu M, Chen J. BRD4: New Hope in the Battle Against Glioblastoma. Pharmacol Res 2023; 191:106767. [PMID: 37061146 DOI: 10.1016/j.phrs.2023.106767] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 04/17/2023]
Abstract
The BET family proteins, comprising BRD2, BRD3 and BRD4, represent epigenetic readers of acetylated histone marks that play pleiotropic roles in the tumorigenesis and growth of multiple human malignancies, including glioblastoma (GBM). A growing body of investigation has proven BET proteins as valuable therapeutic targets for cancer treatment. Recently, several BRD4 inhibitors and degraders have been reported to successfully suppress GBM in preclinical and clinical studies. However, the precise role and mechanism of BRD4 in the pathogenesis of GBM have not been fully elucidated or summarized. This review focuses on summarizing the roles and mechanisms of BRD4 in the context of the initiation and development of GBM. In addition, several BRD4 inhibitors have been evaluated for therapeutic purposes as monotherapy or in combination with chemotherapy, radiotherapy, and immune therapies. Here, we provide a critical appraisal of studies evaluating various BRD4 inhibitors and degraders as novel treatment strategies against GBM.
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Affiliation(s)
- Weichen Duan
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Miao Yu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Jiajia Chen
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
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11
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Zhu J, Wang H, Jiang X. mTORC1 beyond anabolic metabolism: Regulation of cell death. J Biophys Biochem Cytol 2022; 221:213609. [PMID: 36282248 PMCID: PMC9606688 DOI: 10.1083/jcb.202208103] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 12/13/2022] Open
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1), a multi-subunit protein kinase complex, interrogates growth factor signaling with cellular nutrient and energy status to control metabolic homeostasis. Activation of mTORC1 promotes biosynthesis of macromolecules, including proteins, lipids, and nucleic acids, and simultaneously suppresses catabolic processes such as lysosomal degradation of self-constituents and extracellular components. Metabolic regulation has emerged as a critical determinant of various cellular death programs, including apoptosis, pyroptosis, and ferroptosis. In this article, we review the expanding knowledge on how mTORC1 coordinates metabolic pathways to impinge on cell death regulation. We focus on the current understanding on how nutrient status and cellular signaling pathways connect mTORC1 activity with ferroptosis, an iron-dependent cell death program that has been implicated in a plethora of human diseases. In-depth understanding of the principles governing the interaction between mTORC1 and cell death pathways can ultimately guide the development of novel therapies for the treatment of relevant pathological conditions.
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Affiliation(s)
- Jiajun Zhu
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China,Tsinghua-Peking Center for Life Sciences, Beijing, China,Correspondence to Jiajun Zhu:
| | - Hua Wang
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xuejun Jiang
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY,Xuejun Jiang:
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12
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Yu B, Wang F, Wang Y. Advances in the Structural and Physiological Functions of SHARPIN. Front Immunol 2022; 13:858505. [PMID: 35547743 PMCID: PMC9084887 DOI: 10.3389/fimmu.2022.858505] [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: 01/20/2022] [Accepted: 03/28/2022] [Indexed: 11/29/2022] Open
Abstract
SHARPIN was initially found as a SHANK-associated protein. SHARPIN can be used as an important component to form the linear ubiquitin chain assembly complex (LUBAC) with HOIL-1L, HOIP to produce a linear ubiquitin chain connected N-terminal Met1, playing a critical role in various cellular processes including NF-κB signaling, inflammation, embryogenesis and apoptosis. SHARPIN alone can also participate in many critical physiological activities and cause various disorders such as chronic dermatitis, tumor, and Alzheimer’s disease. Mice with spontaneous autosomal recessive mutations in the SHARPIN protein mainly exhibit chronic dermatitis and immunodeficiency with elevated IgM. Additionally, SHARPIN alone also plays a key role in various cellular events, such as B cells activation and platelet aggregation. Structural studies of the SHARPIN or LUBAC have been reported continuously, advancing our understanding of it at the molecular level. However, the full-length structure of the SHARPIN or LUBAC was lagging, and the molecular mechanism underlying these physiological processes is also unclear. Herein, we summarized the currently resolved structure of SHARPIN as well as the emerging physiological role of SHARPIN alone or in LUBAC. Further structural and functional study of SHARPIN will provide insight into the role and underlying mechanism of SHARPIN in disease, as well as its potential application in therapeutic.
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Affiliation(s)
- Beiming Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Feng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yanfeng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
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13
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Masui K, Cavenee WK, Mischel PS, Shibata N. The metabolomic landscape plays a critical role in glioma oncogenesis. Cancer Sci 2022; 113:1555-1563. [PMID: 35271755 PMCID: PMC9128185 DOI: 10.1111/cas.15325] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/24/2022] [Accepted: 03/04/2022] [Indexed: 12/01/2022] Open
Abstract
Cancer cells depend on metabolic reprogramming for survival, undergoing profound shifts in nutrient sensing, nutrient uptake and flux through anabolic pathways, in order to drive nucleotide, lipid, and protein synthesis and provide key intermediates needed for those pathways. Although metabolic enzymes themselves can be mutated, including to generate oncometabolites, this is a relatively rare event in cancer. Usually, gene amplification, overexpression, and/or downstream signal transduction upregulate rate‐limiting metabolic enzymes and limit feedback loops, to drive persistent tumor growth. Recent molecular‐genetic advances have revealed discrete links between oncogenotypes and the resultant metabolic phenotypes. However, more comprehensive approaches are needed to unravel the dynamic spatio‐temporal regulatory map of enzymes and metabolites that enable cancer cells to adapt to their microenvironment to maximize tumor growth. Proteomic and metabolomic analyses are powerful tools for analyzing a repertoire of metabolic enzymes as well as intermediary metabolites, and in conjunction with other omics approaches could provide critical information in this regard. Here, we provide an overview of cancer metabolism, especially from an omics perspective and with a particular focus on the genomically well characterized malignant brain tumor, glioblastoma. We further discuss how metabolomics could be leveraged to improve the management of patients, by linking cancer cell genotype, epigenotype, and phenotype through metabolic reprogramming.
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Affiliation(s)
- Kenta Masui
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Webster K Cavenee
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Noriyuki Shibata
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
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14
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M JR, Ramalingam PS, Mathavan S, B.R.D. Yamajala R, Moparthi NR, Kurappalli RK, Manyam RR. Synthesis, in vitro and structural aspects of cap substituted Suberoylanilide hydroxamic acid analogs as potential inducers of apoptosis in Glioblastoma cancer cells via HDAC /microRNA regulation. Chem Biol Interact 2022; 357:109876. [DOI: 10.1016/j.cbi.2022.109876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/04/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023]
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15
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Pinker B, Barciszewska AM. mTOR Signaling and Potential Therapeutic Targeting in Meningioma. Int J Mol Sci 2022; 23:ijms23041978. [PMID: 35216092 PMCID: PMC8876623 DOI: 10.3390/ijms23041978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/30/2022] [Indexed: 12/30/2022] Open
Abstract
Meningiomas are the most frequent primary tumors arising in the central nervous system. They typically follow a benign course, with an excellent prognosis for grade I lesions through surgical intervention. Although radiotherapy is a good option for recurrent, progressive, or inoperable tumors, alternative treatments are very limited. mTOR is a protein complex with increasing therapeutical potential as a target in cancer. The current understanding of the mTOR pathway heavily involves it in the development of meningioma. Its activation is strongly dependent on PI3K/Akt signaling and the merlin protein. Both factors are commonly defective in meningioma cells, which indicates their likely function in tumor growth. Furthermore, regarding molecular tumorigenesis, the kinase activity of the mTORC1 complex inhibits many components of the autophagosome, such as the ULK1 or Beclin complexes. mTOR contributes to redox homeostasis, a vital component of neoplasia. Recent clinical trials have investigated novel chemotherapeutic agents for mTOR inhibition, showing promising results in resistant or recurrent meningiomas.
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Affiliation(s)
- Benjamin Pinker
- Medical Faculty, Karol Marcinkowski University of Medical Sciences, Fredry 10, 61-701 Poznan, Poland
- Correspondence:
| | - Anna-Maria Barciszewska
- Intraoperative Imaging Unit, Chair and Department of Neurosurgery and Neurotraumatology, Karol Marcinkowski University of Medical Sciences, Przybyszewskiego 49, 60-355 Poznan, Poland;
- Department of Neurosurgery and Neurotraumatology, Heliodor Swiecicki Clinical Hospital, Przybyszewskiego 49, 60-355 Poznan, Poland
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16
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EZH2 as a new therapeutic target in brain tumors: Molecular landscape, therapeutic targeting and future prospects. Biomed Pharmacother 2021; 146:112532. [PMID: 34906772 DOI: 10.1016/j.biopha.2021.112532] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 12/20/2022] Open
Abstract
Brain tumors are responsible for high mortality and morbidity worldwide. The brain tumor treatment depends on identification of molecular pathways involved in progression and malignancy. Enhancer of zeste homolog 2 (EZH2) has obtained much attention in recent years in field of cancer therapy due to its aberrant expression and capacity in modulating expression of genes by binding to their promoter and affecting methylation status. The present review focuses on EZH2 signaling in brain tumors including glioma, glioblastoma, astrocytoma, ependymomas, medulloblastoma and brain rhabdoid tumors. EZH2 signaling mainly participates in increasing proliferation and invasion of cancer cells. However, in medulloblastoma, EZH2 demonstrates tumor-suppressor activity. Furthermore, EZH2 can regulate response of brain tumors to chemotherapy and radiotherapy. Various molecular pathways can function as upstream mediators of EZH2 in brain tumors including lncRNAs and miRNAs. Owing to its enzymatic activity, EZH2 can bind to promoter of target genes to induce methylation and affects their expression. EZH2 can be considered as an independent prognostic factor in brain tumors that its upregulation provides undesirable prognosis. Both anti-tumor agents and gene therapies such as siRNA have been developed for targeting EZH2 in cancer therapy.
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17
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Agarwal D, Kumari R, Ilyas A, Tyagi S, Kumar R, Poddar NK. Crosstalk between epigenetics and mTOR as a gateway to new insights in pathophysiology and treatment of Alzheimer's disease. Int J Biol Macromol 2021; 192:895-903. [PMID: 34662652 DOI: 10.1016/j.ijbiomac.2021.10.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 09/19/2021] [Accepted: 10/04/2021] [Indexed: 12/17/2022]
Abstract
Epigenetics in the current times has become a gateway to acquire answers to questions that were left unanswered by classical and modern genetics, be it resolving the complex mystery behind neurodegenerative disorders or understanding the complexity behind life-threatening cancers. It has presented to the world an entirely new dimension and has added a dynamic angle to an otherwise static field of genetics. Alzheimer's disease is one of the most prevalent neurodegenerative disorders is largely found to be a result of alterations in epigenetic pathways. These changes majorly comprise an imbalance in DNA methylation levels and altered acetylation and methylation of histones. They are often seen to cross-link with metabolic regulatory pathways such as that of mTOR, contributing significantly to the pathophysiology of AD. This review focusses on the study of the interplay of the mTOR regulatory pathway with that of epigenetic machinery that may elevate the rate of early diagnosis and prove to be a gateway to the development of an efficient and novel therapeutic strategy for the treatment of Alzheimer's disease at an early stage.
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Affiliation(s)
- Disha Agarwal
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India
| | - Ruchika Kumari
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India
| | - Ashal Ilyas
- Department of Biotechnology, Invertis University, Bareilly 243 123, India
| | - Shweta Tyagi
- HNo-88, Ranjit Avenue, Bela Chowk, Kota Nihang, Punjab 140001, India
| | - Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Uttar Pradesh. India
| | - Nitesh Kumar Poddar
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India.
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18
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The Bumpy Road towards mTOR Inhibition in Glioblastoma: Quo Vadis? Biomedicines 2021; 9:biomedicines9121809. [PMID: 34944625 PMCID: PMC8698473 DOI: 10.3390/biomedicines9121809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023] Open
Abstract
Glioblastoma multiforme (GBM), a grade IV astrocytoma, is a lethal brain tumor with a poor prognosis. Despite recent advances in the molecular biology of GBM, neuro-oncologists have very limited treatment options available to improve the survival of GBM patients. A prominent signaling pathway implicated in GBM pathogenesis is that of the mechanistic target of rapamycin (mTOR). Attempts to target the mTOR pathway with first-generation mTOR inhibitors appeared promising in the preclinical stage; however, results have been disappointing in clinical trials, owing to the heterogeneous nature of GBM, escape mechanisms against treatment, the blood–brain barrier, drug-related toxicities, and the imperfect design of clinical trials, among others. The development of next-generation mTOR inhibitors and their current evaluation in clinical trials have sparked new hope to realize the clinical potential of mTOR inhibitors in GBM. Meanwhile, studies are continuously furthering our understanding of mTOR signaling dysregulation, its downstream effects, and interplay with other signaling pathways in GBM tumors. Therefore, it remains to be seen whether targeting mTOR in GBM will eventually prove to be fruitful or futile.
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19
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Yang Y, Luan Y, Yuan RX, Luan Y. Histone Methylation Related Therapeutic Challenge in Cardiovascular Diseases. Front Cardiovasc Med 2021; 8:710053. [PMID: 34568453 PMCID: PMC8458636 DOI: 10.3389/fcvm.2021.710053] [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: 05/17/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
The epidemic of cardiovascular diseases (CVDs) is predicted to spread rapidly in advanced countries accompanied by the high prevalence of risk factors. In terms of pathogenesis, the pathophysiology of CVDs is featured by multiple disorders, including vascular inflammation accompanied by simultaneously perturbed pathways, such as cell death and acute/chronic inflammatory reactions. Epigenetic alteration is involved in the regulation of genome stabilization and cellular homeostasis. The association between CVD progression and histone modifications is widely known. Among the histone modifications, histone methylation is a reversible process involved in the development and homeostasis of the cardiovascular system. Abnormal methylation can promote CVD progression. This review discusses histone methylation and the enzymes involved in the cardiovascular system and determine the effects of histone methyltransferases and demethylases on the pathogenesis of CVDs. We will further demonstrate key proteins mediated by histone methylation in blood vessels and review histone methylation-mediated cardiomyocytes and cellular functions and pathways in CVDs. Finally, we will summarize the role of inhibitors of histone methylation and demethylation in CVDs and analyze their therapeutic potential, based on previous studies.
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Affiliation(s)
- Yang Yang
- Department of Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Luan
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Rui-Xia Yuan
- Department of Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yi Luan
- Department of Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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20
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Onizuka H, Masui K, Amano K, Kawamata T, Yamamoto T, Nagashima Y, Shibata N. Metabolic Reprogramming Drives Pituitary Tumor Growth through Epigenetic Regulation of TERT. Acta Histochem Cytochem 2021; 54:87-96. [PMID: 34276102 PMCID: PMC8275863 DOI: 10.1267/ahc.21-00007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
Pituitary adenomas are common, benign brain tumors. Some tumors show aggressive phenotypes including early recurrence, local invasion and distant metastasis, but the underlying mechanism to drive the progression of pituitary tumors has remained to be clarified. Aerobic glycolysis known as the Warburg effect is one of the emerging hallmarks of cancer, which has an impact on the tumor biology partly through epigenetic regulation of the tumor-promoting genes. Here, we demonstrate metabolic reprogramming in pituitary tumors contributes to tumor cell growth with epigenetic changes such as histone acetylation. Notably, a shift in histone acetylation increases the expression of telomerase reverse transcriptase (TERT) oncogene, which drives metabolism-dependent cell proliferation in pituitary tumors. These indicate that epigenetic changes could be the specific biomarker for predicting the behavior of pituitary tumors and exploitable as a novel target for the aggressive types of the pituitary tumors.
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Affiliation(s)
- Hiromi Onizuka
- Department of Surgical Pathology, Tokyo Women’s Medical University
- Division of Pathological Neuroscience, Department of Pathology, Tokyo Women’s Medical University
| | - Kenta Masui
- Division of Pathological Neuroscience, Department of Pathology, Tokyo Women’s Medical University
| | - Kosaku Amano
- Department of Neurosurgery, Tokyo Women’s Medical University
| | | | - Tomoko Yamamoto
- Department of Surgical Pathology, Tokyo Women’s Medical University
- Division of Pathological Neuroscience, Department of Pathology, Tokyo Women’s Medical University
| | - Yoji Nagashima
- Department of Surgical Pathology, Tokyo Women’s Medical University
| | - Noriyuki Shibata
- Division of Pathological Neuroscience, Department of Pathology, Tokyo Women’s Medical University
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21
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Uthamacumaran A. A review of dynamical systems approaches for the detection of chaotic attractors in cancer networks. PATTERNS (NEW YORK, N.Y.) 2021; 2:100226. [PMID: 33982021 PMCID: PMC8085613 DOI: 10.1016/j.patter.2021.100226] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cancers are complex dynamical systems. They remain the leading cause of disease-related pediatric mortality in North America. To overcome this burden, we must decipher the state-space attractor dynamics of gene expression patterns and protein oscillations orchestrated by cancer stemness networks. The review provides an overview of dynamical systems theory to steer cancer research in pattern science. While most of our current tools in network medicine rely on statistical correlation methods, causality inference remains primitively developed. As such, a survey of attractor reconstruction methods and machine algorithms for the detection of causal structures applicable in experimentally derived time series cancer datasets is presented. A toolbox of complex systems approaches are discussed for reconstructing the signaling state space of cancer networks, interpreting causal relationships in their time series gene expression patterns, and assisting clinical decision making in computational oncology. As a proof of concept, the applicability of some algorithms are demonstrated on pediatric brain cancer datasets and the requirement of their time series analysis is highlighted.
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22
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Harachi M, Masui K, Cavenee WK, Mischel PS, Shibata N. Protein Acetylation at the Interface of Genetics, Epigenetics and Environment in Cancer. Metabolites 2021; 11:216. [PMID: 33916219 PMCID: PMC8066013 DOI: 10.3390/metabo11040216] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 02/07/2023] Open
Abstract
Metabolic reprogramming is an emerging hallmark of cancer and is driven by abnormalities of oncogenes and tumor suppressors. Accelerated metabolism causes cancer cell aggression through the dysregulation of rate-limiting metabolic enzymes as well as by facilitating the production of intermediary metabolites. However, the mechanisms by which a shift in the metabolic landscape reshapes the intracellular signaling to promote the survival of cancer cells remain to be clarified. Recent high-resolution mass spectrometry-based proteomic analyses have spotlighted that, unexpectedly, lysine residues of numerous cytosolic as well as nuclear proteins are acetylated and that this modification modulates protein activity, sublocalization and stability, with profound impact on cellular function. More importantly, cancer cells exploit acetylation as a post-translational protein for microenvironmental adaptation, nominating it as a means for dynamic modulation of the phenotypes of cancer cells at the interface between genetics and environments. The objectives of this review were to describe the functional implications of protein lysine acetylation in cancer biology by examining recent evidence that implicates oncogenic signaling as a strong driver of protein acetylation, which might be exploitable for novel therapeutic strategies against cancer.
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Affiliation(s)
- Mio Harachi
- Department of Pathology, Division of Pathological Neuroscience, Tokyo Women’s Medical University, Tokyo 162-8666, Japan; (M.H.); (N.S.)
| | - Kenta Masui
- Department of Pathology, Division of Pathological Neuroscience, Tokyo Women’s Medical University, Tokyo 162-8666, Japan; (M.H.); (N.S.)
| | - Webster K. Cavenee
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA;
| | - Paul S. Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA;
| | - Noriyuki Shibata
- Department of Pathology, Division of Pathological Neuroscience, Tokyo Women’s Medical University, Tokyo 162-8666, Japan; (M.H.); (N.S.)
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