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      Mutation of the Cell Cycle Regulator p27kip1 Drives Pseudohypoxic Pheochromocytoma Development

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          Abstract

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          Pheochromocytomas and paragangliomas (PPGLs) can be subdivided into at least three different subgroups associated with different clinical manifestations and depending on the risk to metastasize. A shortage in human tumor material, the lack of a functional human cell line and very limited animal models were major drawbacks for PPGL research and consequently for the development of patient-tailored targeted therapies. We have previously reported that the MENX rat model develops pheochromocytoma with a full penetrance at the age of 8–10 months, however, it was unclear which human group the rat tumors modeled best. In order to characterize the rat pheochromocytomas, we analyzed gene expression, the catecholamine profile, TCA-cycle metabolism, methylation, angiogenesis, histology and mitochondrial ultrastructure. In all aspects, rat MENX pheochromocytomas resemble the features of the human pseudohypoxia group, the most aggressive one and in need of effective therapeutic approaches.

          Abstract

          Background: Pseudohypoxic tumors activate pro-oncogenic pathways typically associated with severe hypoxia even when sufficient oxygen is present, leading to highly aggressive tumors. Prime examples are pseudohypoxic pheochromocytomas and paragangliomas (p-PPGLs), neuroendendocrine tumors currently lacking effective therapy. Previous attempts to generate mouse models for p-PPGLs all failed. Here, we describe that the rat MENX line, carrying a Cdkn1b (p27) frameshift-mutation, spontaneously develops pseudohypoxic pheochromocytoma (p-PCC). Methods: We compared rat p-PCCs with their cognate human tumors at different levels: histology, immunohistochemistry, catecholamine profiling, electron microscopy, transcriptome and metabolome. The vessel architecture and angiogenic potential of pheochromocytomas (PCCs) was analyzed by light-sheet fluorescence microscopy ex vivo and multi-spectral optoacoustic tomography (MSOT) in vivo. Results: The analysis of tissues at various stages, from hyperplasia to advanced grades, allowed us to correlate tumor characteristics with progression. Pathological changes affecting the mitochrondrial ultrastructure where present already in hyperplasias. Rat PCCs secreted high levels of norepinephrine and dopamine. Transcriptomic and metabolomic analysis revealed changes in oxidative phosphorylation that aggravated over time, leading to an accumulation of the oncometabolite 2-hydroxyglutarate, and to hypermethylation, evident by the loss of the epigenetic mark 5-hmC. While rat PCC xenografts showed high oxygenation, induced by massive neoangiogenesis, rat primary PCC transcriptomes possessed a pseudohypoxic signature of high Hif2a, Vegfa, and low Pnmt expression, thereby clustering with human p-PPGL. Conclusion: Endogenous rat PCCs recapitulate key phenotypic features of human p-PPGLs. Thus, MENX rats emerge as the best available animal model of these aggressive tumors. Our study provides evidence of a link between cell cycle dysregulation and pseudohypoxia.

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          TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

          The Cancer Genome Atlas (TCGA) research network has made public a large collection of clinical and molecular phenotypes of more than 10 000 tumor patients across 33 different tumor types. Using this cohort, TCGA has published over 20 marker papers detailing the genomic and epigenomic alterations associated with these tumor types. Although many important discoveries have been made by TCGA's research network, opportunities still exist to implement novel methods, thereby elucidating new biological pathways and diagnostic markers. However, mining the TCGA data presents several bioinformatics challenges, such as data retrieval and integration with clinical data and other molecular data types (e.g. RNA and DNA methylation). We developed an R/Bioconductor package called TCGAbiolinks to address these challenges and offer bioinformatics solutions by using a guided workflow to allow users to query, download and perform integrative analyses of TCGA data. We combined methods from computer science and statistics into the pipeline and incorporated methodologies developed in previous TCGA marker studies and in our own group. Using four different TCGA tumor types (Kidney, Brain, Breast and Colon) as examples, we provide case studies to illustrate examples of reproducibility, integrative analysis and utilization of different Bioconductor packages to advance and accelerate novel discoveries.
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            ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

            The Principal Component Analysis (PCA) is a widely used method of reducing the dimensionality of high-dimensional data, often followed by visualizing two of the components on the scatterplot. Although widely used, the method is lacking an easy-to-use web interface that scientists with little programming skills could use to make plots of their own data. The same applies to creating heatmaps: it is possible to add conditional formatting for Excel cells to show colored heatmaps, but for more advanced features such as clustering and experimental annotations, more sophisticated analysis tools have to be used. We present a web tool called ClustVis that aims to have an intuitive user interface. Users can upload data from a simple delimited text file that can be created in a spreadsheet program. It is possible to modify data processing methods and the final appearance of the PCA and heatmap plots by using drop-down menus, text boxes, sliders etc. Appropriate defaults are given to reduce the time needed by the user to specify input parameters. As an output, users can download PCA plot and heatmap in one of the preferred file formats. This web server is freely available at http://biit.cs.ut.ee/clustvis/.
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              Mitochondrial Cristae: Where Beauty Meets Functionality.

              Mitochondrial cristae are dynamic bioenergetic compartments whose shape changes under different physiological conditions. Recent discoveries have unveiled the relation between cristae shape and oxidative phosphorylation (OXPHOS) function, suggesting that membrane morphology modulates the organization and function of the OXPHOS system, with a direct impact on cellular metabolism. As a corollary, cristae-shaping proteins have emerged as potential modulators of mitochondrial bioenergetics, a concept confirmed by genetic experiments in mouse models of respiratory chain deficiency. Here, we review our knowledge of mitochondrial ultrastructural organization and how it impacts mitochondrial metabolism.
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                Author and article information

                Journal
                Cancers (Basel)
                Cancers (Basel)
                cancers
                Cancers
                MDPI
                2072-6694
                02 January 2021
                January 2021
                : 13
                : 1
                : 126
                Affiliations
                [1 ]Institute for Diabetes and Cancer, Helmholtz Centre Munich, Ingolstaedter Landstr.1, 85764 Neuherberg, Germany; hermine.mohr@ 123456helmholtz-muenchen.de (H.M.); sebastian.gulde@ 123456helmholtz-muenchen.de (S.G.); tobias.wiedemann@ 123456helmholtz-muenchen.de (T.W.)
                [2 ]Joint Heidelberg-IDC Translational Diabetes Program, Heidelberg University Hospital, 69120 Heidelberg, Germany
                [3 ]Institute of Pathology, School of Medicine, Technical University Munich, Trogerstr. 18, 81675 Munich, Germany; simone.ballke@ 123456tum.de (S.B.); katja.steiger@ 123456tum.de (K.S.)
                [4 ]Department of Medicine III, University Hospital Carl Gustav Carus, Technical University Dresden, Fetscherstrasse 74, 01307 Dresden, Germany; Nicole.Bechmann@ 123456uniklinikum-dresden.de
                [5 ]Institute of Clinical Chemistry and Laboratory, University Hospital Carl Gustav Carus, Technical University Dresden, Fetscherstrasse 74, 01307 Dresden, Germany; Mirko.Peitzsch@ 123456uniklinikum-dresden.de
                [6 ]Chair of Biological Imaging, Technical University of Munich, Ismaninger Straße 22, 81675 Munich, Germany; jaber.malekzadeh@ 123456helmholtz-muenchen.de (J.M.-N.); v.ntziachristos@ 123456helmholtz-muenchen.de (V.N.)
                [7 ]Institute for Biomedical Imaging, Helmholtz Centre Munich, Ingolstaedter Landstr.1, 85764 Neuherberg, Germany
                Author notes
                [* ]Correspondence: natalia.pellegata@ 123456helmholtz-muenchen.de ; Tel.: +49-(0)89-3187-2633
                Author information
                https://orcid.org/0000-0002-6932-333X
                https://orcid.org/0000-0002-7269-5433
                Article
                cancers-13-00126
                10.3390/cancers13010126
                7794757
                33401758
                ed8e3fc6-1d98-45d9-b99f-29cd2f526b7d
                © 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
                : 10 November 2020
                : 29 December 2020
                Categories
                Article

                animal model,menx,endogenous pheochromocytoma,pseudohypoxia,ppgls,oncometabolites,mitochondrial dysfunction,2-hydroxyglutarate,5-hmc,cell cycle,hypermethylation,angiogenesis

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