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      The MDM2 inducible promoter folds into four-tetrad antiparallel G-quadruplexes targetable to fight malignant liposarcoma

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          Abstract

          Well-differentiated liposarcoma (WDLPS) is a malignant neoplasia hard to diagnose and treat. Its main molecular signature is amplification of the MDM2-containing genomic region. The MDM2 oncogene is the master regulator of p53: its overexpression enhances p53 degradation and inhibits apoptosis, leading to the tumoral phenotype. Here, we show that the MDM2 inducible promoter G-rich region folds into stable G-quadruplexes both in vitro and in vivo and it is specifically recognized by cellular helicases. Cell treatment with G-quadruplex-ligands reduces MDM2 expression and p53 degradation, thus stimulating cancer cell cycle arrest and apoptosis. Structural characterization of the MDM2 G-quadruplex revealed an extraordinarily stable, unique four-tetrad antiparallel dynamic conformation, amenable to selective targeting. These data indicate the feasibility of an out-of-the-box G-quadruplex-targeting approach to defeat WDLPS and all tumours where restoration of wild-type p53 is sought. They also point to G-quadruplex-dependent genomic instability as possible cause of MDM2 expansion and WDLPS tumorigenesis.

          Graphical Abstract

          Graphical Abstract

          Scheme representing how G4-ligand-induced stabilization of MDM2 P2 promoter G4 leads to accumulation of p53 and hnRNP-K proteins, resulting in stimulation of apoptosis and cell cycle arrest.

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          Most cited references76

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          BEDTools: a flexible suite of utilities for comparing genomic features

          Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools Contact: aaronquinlan@gmail.com; imh4y@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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            Putting p53 in Context.

            TP53 is the most frequently mutated gene in human cancer. Functionally, p53 is activated by a host of stress stimuli and, in turn, governs an exquisitely complex anti-proliferative transcriptional program that touches upon a bewildering array of biological responses. Despite the many unveiled facets of the p53 network, a clear appreciation of how and in what contexts p53 exerts its diverse effects remains unclear. How can we interpret p53's disparate activities and the consequences of its dysfunction to understand how cell type, mutation profile, and epigenetic cell state dictate outcomes, and how might we restore its tumor-suppressive activities in cancer?
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              In vivo activation of the p53 pathway by small-molecule antagonists of MDM2.

              MDM2 binds the p53 tumor suppressor protein with high affinity and negatively modulates its transcriptional activity and stability. Overexpression of MDM2, found in many human tumors, effectively impairs p53 function. Inhibition of MDM2-p53 interaction can stabilize p53 and may offer a novel strategy for cancer therapy. Here, we identify potent and selective small-molecule antagonists of MDM2 and confirm their mode of action through the crystal structures of complexes. These compounds bind MDM2 in the p53-binding pocket and activate the p53 pathway in cancer cells, leading to cell cycle arrest, apoptosis, and growth inhibition of human tumor xenografts in nude mice.
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                Author and article information

                Contributors
                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                25 January 2021
                07 January 2021
                07 January 2021
                : 49
                : 2
                : 847-863
                Affiliations
                Department of Molecular Medicine, University of Padua , via A. Gabelli 63, 35121 Padua, Italy
                Department of Molecular Medicine, University of Padua , via A. Gabelli 63, 35121 Padua, Italy
                Department of Molecular Medicine, University of Padua , via A. Gabelli 63, 35121 Padua, Italy
                Department of Molecular Medicine, University of Padua , via A. Gabelli 63, 35121 Padua, Italy
                Slovenian NMR center, National Institute of Chemistry , Hajdrihova, 19, Ljubljana SI-1000, Slovenia
                Department of Molecular Medicine, University of Padua , via A. Gabelli 63, 35121 Padua, Italy
                Department of Molecular Medicine, University of Padua , via A. Gabelli 63, 35121 Padua, Italy
                Division of Molecular Biology, Biomedical Center, Faculty of Medicine , LMU Munich, Germany
                Department of Chemistry, University of Pavia , V. le Taramelli 10, 27100, Pavia, Italy
                Department of Chemistry, University of Pavia , V. le Taramelli 10, 27100, Pavia, Italy
                Slovenian NMR center, National Institute of Chemistry , Hajdrihova, 19, Ljubljana SI-1000, Slovenia
                Division of Molecular Biology, Biomedical Center, Faculty of Medicine , LMU Munich, Germany
                Department of Molecular Medicine, University of Padua , via A. Gabelli 63, 35121 Padua, Italy
                Author notes
                To whom correspondence should be addressed. Tel: +39 0498272346; Email: sara.richter@ 123456unipd.it
                Author information
                http://orcid.org/0000-0001-5179-550X
                http://orcid.org/0000-0003-0989-4074
                http://orcid.org/0000-0002-3965-9334
                http://orcid.org/0000-0001-6595-193X
                http://orcid.org/0000-0001-5135-5707
                http://orcid.org/0000-0003-2814-3436
                http://orcid.org/0000-0002-6683-1726
                http://orcid.org/0000-0002-1308-1060
                http://orcid.org/0000-0003-1570-8602
                http://orcid.org/0000-0003-4940-6135
                http://orcid.org/0000-0002-5446-9029
                Article
                gkaa1273
                10.1093/nar/gkaa1273
                7826256
                33410915
                e0934884-654b-4ba6-bb58-87f638c3b23f
                © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 21 December 2020
                : 18 December 2020
                : 29 February 2020
                Page count
                Pages: 17
                Funding
                Funded by: Italian Foundation for Cancer Research, DOI 10.13039/501100007076;
                Award ID: 21850
                Funded by: European Research Council, DOI 10.13039/100010663;
                Award ID: 615879
                Funded by: Deutsche Forschungsgemeinschaft, DOI 10.13039/501100001659;
                Award ID: SFB1064 – A11
                Award ID: SFB1243 – A03
                Categories
                AcademicSubjects/SCI00010
                Gene regulation, Chromatin and Epigenetics

                Genetics
                Genetics

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