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      Characterization of NADPH Oxidase Expression and Activity in Acute Myeloid Leukemia Cell Lines: A Correlation with the Differentiation Status

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          Abstract

          In acute myeloid leukemia (AML), a low level of reactive oxygen species (ROS) is associated with leukemic stem cell (LSC) quiescence, whereas a high level promotes blast proliferation. ROS homeostasis relies on a tightly-regulated balance between the antioxidant and oxidant systems. Among the oxidants, NADPH oxidases (NOX) generate ROS as a physiological function. Although it has been reported in AML initiation and development, the contribution of NOX to the ROS production in AML remains to be clarified. The aim of this study was to investigate the NOX expression and function in AML, and to examine the role of NOX in blast proliferation and differentiation. First, we interrogated the NOX expression in primary cells from public datasets, and investigated their association with prognostic markers. Next, we explored the NOX expression and activity in AML cell lines, and studied the impact of NOX knockdown on cell proliferation and differentiation. We found that NOX2 is ubiquitously expressed in AML blasts, and particularly in cells from the myelomonocytic (M4) and monocytic (M5) stages; however, it is less expressed in LSCs and in relapsed AML. This is consistent with an increased expression throughout normal hematopoietic differentiation, and is reflected in AML cell lines. Nevertheless, no endogenous NOX activity could be detected in the absence of PMA stimulation. Furthermore, CYBB knockdown, although hampering induced NOX2 activity, did not affect the proliferation and differentiation of THP-1 and HL-60 cells. In summary, our data suggest that NOX2 is a marker of AML blast differentiation, while AML cell lines lack any NOX2 endogenous activity.

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          Complex heatmaps reveal patterns and correlations in multidimensional genomic data.

          Parallel heatmaps with carefully designed annotation graphics are powerful for efficient visualization of patterns and relationships among high dimensional genomic data. Here we present the ComplexHeatmap package that provides rich functionalities for customizing heatmaps, arranging multiple parallel heatmaps and including user-defined annotation graphics. We demonstrate the power of ComplexHeatmap to easily reveal patterns and correlations among multiple sources of information with four real-world datasets.
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            The PRIDE database and related tools and resources in 2019: improving support for quantification data

            Abstract The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world’s largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.
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              Regression Models and Life-Tables

              D R Cox (1972)
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                Author and article information

                Contributors
                Role: Academic Editor
                Role: Academic Editor
                Role: Academic Editor
                Journal
                Antioxidants (Basel)
                Antioxidants (Basel)
                antioxidants
                Antioxidants
                MDPI
                2076-3921
                23 March 2021
                March 2021
                : 10
                : 3
                : 498
                Affiliations
                [1 ]University of Tours EA 7501, CNRS ERL 7001, LNOx Team, F-37032 Tours, France; maya.el-dor@ 123456etu.univ-tours.fr (M.E.D.); leclerc_joan@ 123456yahoo.fr (J.L.); farah.kouzi@ 123456etu.univ-tours.fr (F.K.); ali.nehme2@ 123456mcgill.ca (A.N.); margaux.deynoux@ 123456etu.univ-tours.fr (M.D.); christelle.debeissat@ 123456u-bordeaux.fr (C.D.); georges.khamis@ 123456univ-tours.fr (G.K.); elfi.ducrocq@ 123456univ-tours.fr (E.D.); fabrice.gouilleux@ 123456univ-tours.fr (F.G.); olivier.herault@ 123456univ-tours.fr (O.H.)
                [2 ]PRASE, Lebanese University, 6573/14 Beirut, Lebanon; aida.ibrik@ 123456ul.edu.lb
                [3 ]University Grenoble Alpes, CEA, CNRS, IBS, F-38044 Grenoble, France; MJStasia@ 123456chu-grenoble.fr
                [4 ]CDiReC, Pôle Biologie, CHU de Grenoble, F-38043 Grenoble, France
                [5 ]University of Bordeaux, INSERM U1035, F-33000 Bordeaux, France; houssam.raad@ 123456ul.edu.lb (H.R.); hamid-reza.rezvani@ 123456u-bordeaux.fr (H.R.R.)
                [6 ]Biology Department, Faculty of Sciences-I, Lebanese University, 90656 Beirut, Lebanon
                [7 ]CNRS GDR 3697 MicroNiT, F-37032 Tours, France
                [8 ]CHRU de Tours, Service d’Hématologie Biologique, F-37000 Tours, France
                Author notes
                [†]

                These authors contributed equally to the work.

                Author information
                https://orcid.org/0000-0003-0270-8195
                https://orcid.org/0000-0003-4466-4880
                https://orcid.org/0000-0001-6047-1718
                https://orcid.org/0000-0002-9887-072X
                https://orcid.org/0000-0002-7419-1124
                https://orcid.org/0000-0002-6984-7096
                Article
                antioxidants-10-00498
                10.3390/antiox10030498
                8004739
                b9ca70ad-bf85-42f8-a87a-60c3f82ae96b
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 07 February 2021
                : 11 March 2021
                Categories
                Article

                leukemia,aml,transcriptomics,nadph oxidase
                leukemia, aml, transcriptomics, nadph oxidase

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