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      Sox2 induces glioblastoma cell stemness and tumor propagation by repressing TET2 and deregulating 5hmC and 5mC DNA modifications

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          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.

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          Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

          Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic and epigenetic feature sets derived from non-transformed pluripotent stem cells and their differentiated progeny. Using OCLR, we were able to identify previously undiscovered biological mechanisms associated with the dedifferentiated oncogenic state. Analyses of the tumor microenvironment revealed unanticipated correlation of cancer stemness with immune checkpoint expression and infiltrating immune cells. We found that the dedifferentiated oncogenic phenotype was generally most prominent in metastatic tumors. Application of our stemness indices to single-cell data revealed patterns of intra-tumor molecular heterogeneity. Finally, the indices allowed for the identification of novel targets and possible targeted therapies aimed at tumor differentiation.
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            Glioma stem cells promote radioresistance by preferential activation of the DNA damage response.

            Ionizing radiation represents the most effective therapy for glioblastoma (World Health Organization grade IV glioma), one of the most lethal human malignancies, but radiotherapy remains only palliative because of radioresistance. The mechanisms underlying tumour radioresistance have remained elusive. Here we show that cancer stem cells contribute to glioma radioresistance through preferential activation of the DNA damage checkpoint response and an increase in DNA repair capacity. The fraction of tumour cells expressing CD133 (Prominin-1), a marker for both neural stem cells and brain cancer stem cells, is enriched after radiation in gliomas. In both cell culture and the brains of immunocompromised mice, CD133-expressing glioma cells survive ionizing radiation in increased proportions relative to most tumour cells, which lack CD133. CD133-expressing tumour cells isolated from both human glioma xenografts and primary patient glioblastoma specimens preferentially activate the DNA damage checkpoint in response to radiation, and repair radiation-induced DNA damage more effectively than CD133-negative tumour cells. In addition, the radioresistance of CD133-positive glioma stem cells can be reversed with a specific inhibitor of the Chk1 and Chk2 checkpoint kinases. Our results suggest that CD133-positive tumour cells represent the cellular population that confers glioma radioresistance and could be the source of tumour recurrence after radiation. Targeting DNA damage checkpoint response in cancer stem cells may overcome this radioresistance and provide a therapeutic model for malignant brain cancers.
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              Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1.

              DNA cytosine methylation is crucial for retrotransposon silencing and mammalian development. In a computational search for enzymes that could modify 5-methylcytosine (5mC), we identified TET proteins as mammalian homologs of the trypanosome proteins JBP1 and JBP2, which have been proposed to oxidize the 5-methyl group of thymine. We show here that TET1, a fusion partner of the MLL gene in acute myeloid leukemia, is a 2-oxoglutarate (2OG)- and Fe(II)-dependent enzyme that catalyzes conversion of 5mC to 5-hydroxymethylcytosine (hmC) in cultured cells and in vitro. hmC is present in the genome of mouse embryonic stem cells, and hmC levels decrease upon RNA interference-mediated depletion of TET1. Thus, TET proteins have potential roles in epigenetic regulation through modification of 5mC to hmC.
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                Author and article information

                Contributors
                Lopezbertoni@kennedykrieger.org
                Laterra@kennedykrieger.org
                Journal
                Signal Transduct Target Ther
                Signal Transduct Target Ther
                Signal Transduction and Targeted Therapy
                Nature Publishing Group UK (London )
                2095-9907
                2059-3635
                9 February 2022
                9 February 2022
                2022
                : 7
                : 37
                Affiliations
                [1 ]GRID grid.240023.7, ISNI 0000 0004 0427 667X, Hugo W. Moser Research Institute at Kennedy Krieger, ; Baltimore, MD USA
                [2 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Department of Neurology, , Johns Hopkins University School of Medicine, ; Baltimore, MD USA
                [3 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Department of Biomedical Engineering, Institute for NanoBioTechnology, and the Translational Tissue Engineering Center, , Johns Hopkins University School of Medicine, ; Baltimore, MD USA
                [4 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Bloomberg School of Public Health, Department of Environmental Health and Engineering, , The Johns Hopkins University School of Medicine, ; Baltimore, MD USA
                [5 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, The Department of Radiation Oncology and Molecular Radiation Sciences, , The Johns Hopkins University School of Medicine, ; Baltimore, MD USA
                [6 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Department of Ophthalmology, , Johns Hopkins University School of Medicine, ; Baltimore, MD USA
                [7 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Department of Oncology, , Johns Hopkins University School of Medicine, ; Baltimore, MD USA
                [8 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Departments of Materials Science & Engineering and Chemical & Biomolecular Engineering, , Johns Hopkins University, ; Baltimore, MD USA
                [9 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Department of Neurosurgery, , Johns Hopkins University School of Medicine, ; Baltimore, MD USA
                [10 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Department of Neuroscience, , Johns Hopkins University School of Medicine, ; Baltimore, MD USA
                Author information
                http://orcid.org/0000-0001-6618-1092
                http://orcid.org/0000-0002-3055-945X
                http://orcid.org/0000-0002-1962-3844
                http://orcid.org/0000-0003-4176-3808
                Article
                857
                10.1038/s41392-021-00857-0
                8826438
                35136034
                1401f997-17ea-47ee-93d1-b08d22571e82
                © The Author(s) 2022

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 24 May 2021
                : 1 December 2021
                : 5 December 2021
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000065, U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS);
                Award ID: NS120949-01
                Award ID: 1R01NS110087-01A1
                Award Recipient :
                Funded by: Intellectual & Developmental Disabilities Research Center (IDDRC) - 5P50HD103538-02
                Funded by: FundRef https://doi.org/10.13039/100007316, Division of Cancer Prevention, National Cancer Institute (NCI Division of Cancer Prevention);
                Award ID: 2R01CA228133-06A1
                Award Recipient :
                Funded by: U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)
                Categories
                Article
                Custom metadata
                © The Author(s) 2022

                cancer stem cells,epigenetics
                cancer stem cells, epigenetics

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