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4. Development of a Postpartum Stressor Measure

Author

Park, E. R., Psaros, C., Traeger, L., Stagg, A., Jacquart, J., Willett, J., Alert, M. D., LaRoche, K. L., and Ecker, J. L.

Subjects
Social support -- Research -- Influence, Postpartum depression -- Research -- Risk factors -- Control, Health care industry
Abstract

To develop a brief self-report assessment of the type and magnitude of stressors during the postpartum period. A cross-sectional study of a convenience sample of 138 women at Massachusetts General Hospital in Boston, MA completed a measure of postpartum stressors at their 6-week postpartum visit. Item analyses were conducted; items were eliminated based on low relevance, low endorsement, and cross-loadings, resulting in a 9-item measure. Items were summed to create a total postpartum stressors score. To establish concurrent validity with perceived stress, the total postpartum stressors score was correlated with the 4-item Perceived Stress Scale (PSS-4). The stressors score was tested for bivariate associations with depression (Patient Health Questionnaire-2) and with social support (three items adapted from the MOS Social Support Scale). The 9-item measure, which was comprised of three factors (baby care, well-being, and work) demonstrated good reliability (Cronbach's [alpha] = .74) and concurrent validity with the PSS-4 (r = .53; p < .001) in the current sample. The stressors total score was negatively associated with social support (p < .001) and was positively associated with depression symptoms (p < .001). The early psychometric results on this measure are promising and associated with postpartum social support and depressive symptoms. With additional research to enhance external validity, this measure could be used and tested in an intervention study at the 6-week postpartum visit to identify women at risk for distress., Author(s): E. R. Park[sup.1] [sup.2] [sup.5] , C. Psaros[sup.1] [sup.2] [sup.6] , L. Traeger[sup.1] [sup.2] [sup.6] , A. Stagg[sup.3] [sup.7] , J. Jacquart[sup.1] [sup.8] , J. Willett[sup.1] [sup.8] , M. [...]

Published
2015
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8. P057 Mucosal microbiota adapts to ATF6-induced alterations in host lipid metabolism with prognostic value in colorectal cancer

Author

Bierwirth, S, primary, Sorbie, A, additional, Coleman, O, additional, Reuß, E, additional, Weber, P, additional, Köhler, N, additional, Kacprowski, T, additional, Dunkel, A, additional, Pauling, J, additional, Ecker, J, additional, Baumbach, J, additional, Rosenstiel, P, additional, Steiger, K, additional, Wirbel, J, additional, Zeller, G, additional, Janssen, K P, additional, and Haller, D, additional

Published
2022
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15. PATZ1 fusions define a novel molecularly distinct neuroepithelial tumor entity with a broad histological spectrum

Author

Alhalabi, K.T. Stichel, D. Sievers, P. Peterziel, H. Sommerkamp, A.C. Sturm, D. Wittmann, A. Sill, M. Jäger, N. Beck, P. Pajtler, K.W. Snuderl, M. Jour, G. Delorenzo, M. Martin, A.M. Levy, A. Dalvi, N. Hansford, J.R. Gottardo, N.G. Uro-Coste, E. Maurage, C.-A. Godfraind, C. Vandenbos, F. Pietsch, T. Kramm, C. Filippidou, M. Kattamis, A. Jones, C. Øra, I. Mikkelsen, T.S. Zapotocky, M. Sumerauer, D. Scheie, D. McCabe, M. Wesseling, P. Tops, B.B.J. Kranendonk, M.E.G. Karajannis, M.A. Bouvier, N. Papaemmanuil, E. Dohmen, H. Acker, T. von Hoff, K. Schmid, S. Miele, E. Filipski, K. Kitanovski, L. Krskova, L. Gojo, J. Haberler, C. Alvaro, F. Ecker, J. Selt, F. Milde, T. Witt, O. Oehme, I. Kool, M. von Deimling, A. Korshunov, A. Pfister, S.M. Sahm, F. Jones, D.T.W.

Abstract

Large-scale molecular profiling studies in recent years have shown that central nervous system (CNS) tumors display a much greater heterogeneity in terms of molecularly distinct entities, cellular origins and genetic drivers than anticipated from histological assessment. DNA methylation profiling has emerged as a useful tool for robust tumor classification, providing new insights into these heterogeneous molecular classes. This is particularly true for rare CNS tumors with a broad morphological spectrum, which are not possible to assign as separate entities based on histological similarity alone. Here, we describe a molecularly distinct subset of predominantly pediatric CNS neoplasms (n = 60) that harbor PATZ1 fusions. The original histological diagnoses of these tumors covered a wide spectrum of tumor types and malignancy grades. While the single most common diagnosis was glioblastoma (GBM), clinical data of the PATZ1-fused tumors showed a better prognosis than typical GBM, despite frequent relapses. RNA sequencing revealed recurrent MN1:PATZ1 or EWSR1:PATZ1 fusions related to (often extensive) copy number variations on chromosome 22, where PATZ1 and the two fusion partners are located. These fusions have individually been reported in a number of glial/glioneuronal tumors, as well as extracranial sarcomas. We show here that they are more common than previously acknowledged, and together define a biologically distinct CNS tumor type with high expression of neural development markers such as PAX2, GATA2 and IGF2. Drug screening performed on the MN1:PATZ1 fusion-bearing KS-1 brain tumor cell line revealed preliminary candidates for further study. In summary, PATZ1 fusions define a molecular class of histologically polyphenotypic neuroepithelial tumors, which show an intermediate prognosis under current treatment regimens. © 2021, The Author(s).

Published
2021

16. PATZ1 fusions define a novel molecularly distinct neuroepithelial tumor entity with a broad histological spectrum

Author

Alhalabi, KT, Stichel, D, Sievers, P, Peterziel, H, Sommerkamp, AC, Sturm, D, Wittmann, A, Sill, M, Jaeger, N, Beck, P, Pajtler, KW, Snuderl, M, Jour, G, Delorenzo, M, Martin, AM, Levy, A, Dalvi, N, Hansford, JR, Gottardo, NG, Uro-Coste, E, Maurage, C-A, Godfraind, C, Vandenbos, F, Pietsch, T, Kramm, C, Filippidou, M, Kattamis, A, Jones, C, Ora, I, Mikkelsen, TS, Zapotocky, M, Sumerauer, D, Scheie, D, McCabe, M, Wesseling, P, Tops, BBJ, Kranendonk, MEG, Karajannis, MA, Bouvier, N, Papaemmanuil, E, Dohmen, H, Acker, T, von Hoff, K, Schmid, S, Miele, E, Filipski, K, Kitanovski, L, Krskova, L, Gojo, J, Haberler, C, Alvaro, F, Ecker, J, Selt, F, Milde, T, Witt, O, Oehme, I, Kool, M, von Deimling, A, Korshunov, A, Pfister, SM, Sahm, F, Jones, DTW, Alhalabi, KT, Stichel, D, Sievers, P, Peterziel, H, Sommerkamp, AC, Sturm, D, Wittmann, A, Sill, M, Jaeger, N, Beck, P, Pajtler, KW, Snuderl, M, Jour, G, Delorenzo, M, Martin, AM, Levy, A, Dalvi, N, Hansford, JR, Gottardo, NG, Uro-Coste, E, Maurage, C-A, Godfraind, C, Vandenbos, F, Pietsch, T, Kramm, C, Filippidou, M, Kattamis, A, Jones, C, Ora, I, Mikkelsen, TS, Zapotocky, M, Sumerauer, D, Scheie, D, McCabe, M, Wesseling, P, Tops, BBJ, Kranendonk, MEG, Karajannis, MA, Bouvier, N, Papaemmanuil, E, Dohmen, H, Acker, T, von Hoff, K, Schmid, S, Miele, E, Filipski, K, Kitanovski, L, Krskova, L, Gojo, J, Haberler, C, Alvaro, F, Ecker, J, Selt, F, Milde, T, Witt, O, Oehme, I, Kool, M, von Deimling, A, Korshunov, A, Pfister, SM, Sahm, F, and Jones, DTW

Abstract

Large-scale molecular profiling studies in recent years have shown that central nervous system (CNS) tumors display a much greater heterogeneity in terms of molecularly distinct entities, cellular origins and genetic drivers than anticipated from histological assessment. DNA methylation profiling has emerged as a useful tool for robust tumor classification, providing new insights into these heterogeneous molecular classes. This is particularly true for rare CNS tumors with a broad morphological spectrum, which are not possible to assign as separate entities based on histological similarity alone. Here, we describe a molecularly distinct subset of predominantly pediatric CNS neoplasms (n = 60) that harbor PATZ1 fusions. The original histological diagnoses of these tumors covered a wide spectrum of tumor types and malignancy grades. While the single most common diagnosis was glioblastoma (GBM), clinical data of the PATZ1-fused tumors showed a better prognosis than typical GBM, despite frequent relapses. RNA sequencing revealed recurrent MN1:PATZ1 or EWSR1:PATZ1 fusions related to (often extensive) copy number variations on chromosome 22, where PATZ1 and the two fusion partners are located. These fusions have individually been reported in a number of glial/glioneuronal tumors, as well as extracranial sarcomas. We show here that they are more common than previously acknowledged, and together define a biologically distinct CNS tumor type with high expression of neural development markers such as PAX2, GATA2 and IGF2. Drug screening performed on the MN1:PATZ1 fusion-bearing KS-1 brain tumor cell line revealed preliminary candidates for further study. In summary, PATZ1 fusions define a molecular class of histologically polyphenotypic neuroepithelial tumors, which show an intermediate prognosis under current treatment regimens.

Published
2021

17. Sarcoma classification by DNA methylation profiling

Author

Koelsche, C, Schrimpf, D, Stichel, D, Sill, M, Sahm, F, Reuss, DE, Blattner, M, Worst, B, Heilig, CE, Beck, K, Horak, P, Kreutzfeldt, S, Paff, E, Stark, S, Johann, P, Selt, F, Ecker, J, Sturm, D, Pajtler, K W, Reinhardt, A, Wefers, AK, Sievers, P, Ebrahimi, A, Suwala, A, Fernandez-Klett, F, Casalini, B, Korshunov, A, Hovestadt, V, Kommoss, FKF, Kriegsmann, M, Schick, M, Bewerunge-Hudler, M, Milde, T, Witt, O, Kulozik, AE, Kool, M, Romero-Perez, L, Grunewald, TGP, Kirchner, T, Wick, W, Platten, M, Unterberg, A, Uhl, M, Abdollahi, A, Debus, J, Lehner, B, Thomas, C, Hasselblatt, M, Paulus, W, Hartmann, C, Staszewski, O, Prinz, M, Hench, J, Frank, S, Versleijen-Jonkers, YMH, Weidema, ME, Mentzel, T, Griewank, K, Alava, E, Martin, JD, Gastearena, MAI, Chang, KTE, Low, SYY, Cuevas-Bourdier, A, Mittelbronn, M, Mynarek, M, Rutkowski, S, Schuller, U, Mautner, VF, Schittenhelm, J, Serrano, J, Snuderl, M, Buttner, R, Klingebiel, T, Buslei, R, Gessler, M, Wesseling, P, Dinjens, Winand, Brandner, S, Jaunmuktane, Z, Lyskjaer, I, Schirmacher, P, Stenzinger, A, Brors, B, Glimm, H, Heining, C, Tirado, OM, Sainz-Jaspeado, M, Mora, J, Alonso, J, del Muro, XG, Moran, S, Esteller, M, Benhamida, JK, Ladanyi, M, Wardelmann, E, Antonescu, C, Flanagan, A, Dirksen, U, Hohenberger, P, Baumhoer, D, Hartmann, W, Vokuhl, C, Flucke, U, Petersen, I, Mechtersheimer, G, Capper, D, Jones, DT, Frohling, S, Pfister, SM, von Deimling, A, Koelsche, C, Schrimpf, D, Stichel, D, Sill, M, Sahm, F, Reuss, DE, Blattner, M, Worst, B, Heilig, CE, Beck, K, Horak, P, Kreutzfeldt, S, Paff, E, Stark, S, Johann, P, Selt, F, Ecker, J, Sturm, D, Pajtler, K W, Reinhardt, A, Wefers, AK, Sievers, P, Ebrahimi, A, Suwala, A, Fernandez-Klett, F, Casalini, B, Korshunov, A, Hovestadt, V, Kommoss, FKF, Kriegsmann, M, Schick, M, Bewerunge-Hudler, M, Milde, T, Witt, O, Kulozik, AE, Kool, M, Romero-Perez, L, Grunewald, TGP, Kirchner, T, Wick, W, Platten, M, Unterberg, A, Uhl, M, Abdollahi, A, Debus, J, Lehner, B, Thomas, C, Hasselblatt, M, Paulus, W, Hartmann, C, Staszewski, O, Prinz, M, Hench, J, Frank, S, Versleijen-Jonkers, YMH, Weidema, ME, Mentzel, T, Griewank, K, Alava, E, Martin, JD, Gastearena, MAI, Chang, KTE, Low, SYY, Cuevas-Bourdier, A, Mittelbronn, M, Mynarek, M, Rutkowski, S, Schuller, U, Mautner, VF, Schittenhelm, J, Serrano, J, Snuderl, M, Buttner, R, Klingebiel, T, Buslei, R, Gessler, M, Wesseling, P, Dinjens, Winand, Brandner, S, Jaunmuktane, Z, Lyskjaer, I, Schirmacher, P, Stenzinger, A, Brors, B, Glimm, H, Heining, C, Tirado, OM, Sainz-Jaspeado, M, Mora, J, Alonso, J, del Muro, XG, Moran, S, Esteller, M, Benhamida, JK, Ladanyi, M, Wardelmann, E, Antonescu, C, Flanagan, A, Dirksen, U, Hohenberger, P, Baumhoer, D, Hartmann, W, Vokuhl, C, Flucke, U, Petersen, I, Mechtersheimer, G, Capper, D, Jones, DT, Frohling, S, Pfister, SM, and von Deimling, A

Abstract

Sarcomas are malignant soft tissue and bone tumours affecting adults, adolescents and children. They represent a morphologically heterogeneous class of tumours and some entities lack defining histopathological features. Therefore, the diagnosis of sarcomas is burdened with a high inter-observer variability and misclassification rate. Here, we demonstrate classification of soft tissue and bone tumours using a machine learning classifier algorithm based on array-generated DNA methylation data. This sarcoma classifier is trained using a dataset of 1077 methylation profiles from comprehensively pre-characterized cases comprising 62 tumour methylation classes constituting a broad range of soft tissue and bone sarcoma subtypes across the entire age spectrum. The performance is validated in a cohort of 428 sarcomatous tumours, of which 322 cases were classified by the sarcoma classifier. Our results demonstrate the potential of the DNA methylation-based sarcoma classification for research and future diagnostic applications.

Published
2021

21. Current status of the multinational Arabidopsis community

Author

Parry, Geraint, Provart, Nicholas J., Brady, Siobhan M., Uzilday, Baris, Adams, K., Araújo, W., Aubourg, S., Baginsky, S., Bakker, E., Bärenfaller, K., Batley, J., Beale, M., Beilstein, M., Belkhadir, Y., Berardini, T., Bergelson, J., Blanco-Herrera, F., Brady, S., Braun, Hans-Peter, Briggs, S., Brownfield, L., Cardarelli, M., Castellanos-Uribe, M., Coruzzi, G., Dassanayake, M., Jaeger, G.D., Dilkes, B., Doherty, C., Ecker, J., Edger, P., Edwards, D., Kasmi, F.E., Eriksson, M., Exposito-Alonso, M., Falter-Braun, P., Fernie, A., Ferro, M., Fiehn, O., Friesner, J., Greenham, K., Guo, Y., Hamann, T., Hancock, A., Hauser, M.-T., Heazlewood, J., Ho, C.-H., Hõrak, H., Huala, E., Hwang, I., Iuchi, S., Jaiswal, P., Jakobson, L., Jiang, Y., Jiao, Y., Jones, A., Kadota, Y., Khurana, J., Kliebenstein, D., Knee, E., Kobayashi, M., Koch, M., Krouk, G., Larson, T., Last, R., Lepiniec, L., Li, S., Lurin, C., Lysak, M., Maere, S., Malinowski, R., Maumus, F., May, S., Mayer, K., Mendoza-Cozatl, D., Mendoza-Poudereux, I., Meyers, B., Micol, J.L., Millar, H., Mock, H.-P., Mukhtar, K., Mukhtar, S., Murcha, M., Nakagami, H., Nakamura, Y., Nicolov, L., Nikolau, B., Nowack, M., Nunes-Nesi, A., Palmgren, M., Parry, G., Patron, N., Peck, S., Pedmale, U., Perrot-Rechenmann, C., Pieruschka, R., Pío-Beltrán, J., Pires, J.C., Provart, N., Rajjou, L., Reiser, L., Reumann, S., Rhee, S., Rigas, S., Rolland, N., Romanowski, A., Santoni, V., Savaldi-Goldstein, S., Schmitz, R., Schulze, W., Seki, M., Shimizu, K.K., Slotkin, K., Small, I., Somers, D., Sozzani, R., Spillane, C., Srinivasan, R., Taylor, N., Tello-Ruiz, M.-K., Thelen, J., Tohge, T., Town, C., Toyoda, T., Uzilday, B., Peer, Y.V.D., Wijk, K., Gillhaussen, P.V., Walley, J., Ware, D., Weckwerth, W., Whitelegge, J., Wienkoop, S., Wright, C., Wrzaczek, M., Yamazaki, M., Yanovsky, M., Žárský, V., Zhong, X., Biological Systems Engineering, Organisms and Environment Research Division, Cardiff School of Biosciences, Cardiff University, University of Toronto, University of California [Davis] (UC Davis), University of California, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany, Department of Ecology and Evolution [Chicago], University of Chicago, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), University of Arizona, Gregor Mendel Institute (GMI) - Vienna Biocenter (VBC), Austrian Academy of Sciences (OeAW), University of California (UC), Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Flanders Institute for Biotechnology, National Center for Atmospheric Research [Boulder] (NCAR), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Agricultural Sustainability Institute and Department of Neurobiology, Physiology, and Behavior, Norwegian University of Science and Technology (NTNU), University of Melbourne, King Abdullah University of Science and Technology (KAUST), University of Chinese Academy of Sciences [Beijing] (UCAS), The Sainsbury Laboratory [Norwich] (TSL), IBM Research – Tokyo, University Medical Center Groningen [Groningen] (UMCG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre for Novel Agricultural Products, Department of Biology, University of York [York, UK], Biologie des Semences (LBS), Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G), Sichuan University [Chengdu] (SCU), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Systems Biology, Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Nottingham, UK (UON), Institute of Bioinformatics and System Biology (IBIS), Helmholtz Zentrum München = German Research Center for Environmental Health, Saint Mary's University [Halifax], Max Planck Institute for Plant Breeding Research (MPIPZ), National Institute of Genetics (NIG), University of Copenhagen = Københavns Universitet (UCPH), Division of Biology [La Jolla], University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Earlham Institute [Norwich], Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, University of Missouri [Columbia] (Mizzou), University of Missouri System, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Biology, Carnegie Institution for Science, Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Plateforme de Spectrométrie de Masse Protéomique - Mass Spectrometry Proteomics Platform (MSPP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Systems Biology, Institute of Physiology and Biotechnology of plants, RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Unité de recherche Génétique et amélioration des plantes (GAP), Institut National de la Recherche Agronomique (INRA), Department of Biology, Duke University, Genetics and Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland [Galway] (NUI Galway), Universidade Federal de São Paulo, RIKEN Plant Science Center and RIKEN Bioinformatics and Systems Engineering Division, Cold Spring Harbor Laboratory (CSHL), University of Vienna [Vienna], University of California [Los Angeles] (UCLA), Department of Plant Molecular Biology, Université de Lausanne = University of Lausanne (UNIL), UKRI-BBSRC grant BB/M004376/1, HHMI Faculty Scholar Fellowship, Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) 118Z137, UK Research & Innovation (UKRI) Biotechnology and Biological Sciences Research Council (BBSRC) BB/M004376/1, Sainsbury Lab, Norwich Research Park, Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Helmholtz-Zentrum München (HZM), University of Copenhagen = Københavns Universitet (KU), University of California-University of California, Carnegie Institution for Science [Washington], Université de Lausanne (UNIL), Ege Üniversitesi, Organismal and Evolutionary Biology Research Programme, Plant Biology, Viikki Plant Science Centre (ViPS), Receptor-Ligand Signaling Group, University of Zurich, Parry, Geraint, Provart, Nicholas J, and Brady, Siobhan M

Subjects
0106 biological sciences, Arabidopsis thaliana, [SDV]Life Sciences [q-bio], White Paper, Genetics and Molecular Biology (miscellaneous), Plant Science, Biochemistry, 01 natural sciences, Dewey Decimal Classification::500 | Naturwissenschaften::580 | Pflanzen (Botanik), Research community, Arabidopsis, 1110 Plant Science, 0303 health sciences, Ecology, biology, 1184 Genetics, developmental biology, physiology, ddc:580, Multinational corporation, MAP, 590 Animals (Zoology), Life Sciences & Biomedicine, Arabidopsis research community, Evolution, Steering committee, Multinational Arabidopsis Steering Committee, Library science, 1301 Biochemistry, Genetics and Molecular Biology (miscellaneous), Biochemistry, Genetics and Molecular Biology (miscellaneous), Business and Economics, 10127 Institute of Evolutionary Biology and Environmental Studies, 03 medical and health sciences, Behavior and Systematics, Political science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MASC, roadmap, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Plant Sciences, Botany, 15. Life on land, 11831 Plant biology, biology.organism_classification, White Papers, collaboration, 1105 Ecology, Evolution, Behavior and Systematics, QK1-989, Arabidopsis Thaliana, Collaboration, Research Network, Roadmap, 570 Life sciences, 1182 Biochemistry, cell and molecular biology, 2303 Ecology, 010606 plant biology & botany
Abstract

The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plantArabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the "fourth decadal roadmap," which will advise and coordinate the global activities of the Arabidopsis research community., UKRI-BBSRC grant [BB/M004376/1]; HHMI Faculty Scholar Fellowship; Scientific and Technological Research Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [118Z137], UKRI-BBSRC grant, Grant/Award Number: BB/M004376/1; HHMI Faculty Scholar Fellowship; the Scientific and Technological Research Council of Turkey, Grant/Award Number: 118Z137

Published
2020
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23. Diffuse glioneuronal tumour with oligodendroglioma-like features and nuclear clusters (DGONC) - a molecularly defined glioneuronal CNS tumour class displaying recurrent monosomy 14

Author

Deng, M. Y., Sill, M., Sturm, D., Stichel, D., Witt, H., Ecker, J., Wittmann, A., Schittenhelm, J., Ebinger, M., Schuhmann, M. U., Figarella-Branger, D., Aronica, E., Staszewski, O., Preusser, M., Haberler, C., Lauten, M., Schueller, U., Hartmann, C., Snuderl, M., Dunham, C., Jabado, N., Wesseling, P., Deckert, M., Keyvani, K., Gottardo, N., Giangaspero, F., von Hoff, K., Ellison, D. W., Pietsch, T., Herold-Mende, C., Milde, T., Witt, O., Kool, M., Korshunov, A., Wick, W., von Deimling, A., Pfister, S. M., Jones, D. T. W., Sahm, F., Deng, M. Y., Sill, M., Sturm, D., Stichel, D., Witt, H., Ecker, J., Wittmann, A., Schittenhelm, J., Ebinger, M., Schuhmann, M. U., Figarella-Branger, D., Aronica, E., Staszewski, O., Preusser, M., Haberler, C., Lauten, M., Schueller, U., Hartmann, C., Snuderl, M., Dunham, C., Jabado, N., Wesseling, P., Deckert, M., Keyvani, K., Gottardo, N., Giangaspero, F., von Hoff, K., Ellison, D. W., Pietsch, T., Herold-Mende, C., Milde, T., Witt, O., Kool, M., Korshunov, A., Wick, W., von Deimling, A., Pfister, S. M., Jones, D. T. W., and Sahm, F.

Abstract

Aims DNA methylation-based central nervous system (CNS) tumour classification has identified numerous molecularly distinct tumour types, and clinically relevant subgroups among known CNS tumour entities that were previously thought to represent homogeneous diseases. Our study aimed at characterizing a novel, molecularly defined variant of glioneuronal CNS tumour. Patients and methods DNA methylation profiling was performed using the Infinium MethylationEPIC or 450 k BeadChip arrays (Illumina) and analysed using the 'conumee' package in R computing environment. Additional gene panel sequencing was also performed. Tumour samples were collected at the German Cancer Research Centre (DKFZ) and provided by multinational collaborators. Histological sections were also collected and independently reviewed. Results Genome-wide DNA methylation data from >25 000 CNS tumours were screened for clusters separated from established DNA methylation classes, revealing a novel group comprising 31 tumours, mainly found in paediatric patients. This DNA methylation-defined variant of low-grade CNS tumours with glioneuronal differentiation displays recurrent monosomy 14, nuclear clusters within a morphology that is otherwise reminiscent of oligodendroglioma and other established entities with clear cell histology, and a lack of genetic alterations commonly observed in other (paediatric) glioneuronal entities. Conclusions DNA methylation-based tumour classification is an objective method of assessing tumour origins, which may aid in diagnosis, especially for atypical cases. With increasing sample size, methylation analysis allows for the identification of rare, putative new tumour entities, which are currently not recognized by the WHO classification. Our study revealed the existence of a DNA methylation-defined class of low-grade glioneuronal tumours with recurrent monosomy 14, oligodendroglioma-like features and nuclear clusters.

Published
2020

25. Diffuse glioneuronal tumour with oligodendroglioma‐like features and nuclear clusters (DGONC) – a molecularly defined glioneuronal CNS tumour class displaying recurrent monosomy 14

Author

Deng, M. Y., primary, Sill, M., additional, Sturm, D., additional, Stichel, D., additional, Witt, H., additional, Ecker, J., additional, Wittmann, A., additional, Schittenhelm, J., additional, Ebinger, M., additional, Schuhmann, M. U., additional, Figarella‐Branger, D., additional, Aronica, E., additional, Staszewski, O., additional, Preusser, M., additional, Haberler, C., additional, Lauten, M., additional, Schüller, U., additional, Hartmann, C., additional, Snuderl, M., additional, Dunham, C., additional, Jabado, N., additional, Wesseling, P., additional, Deckert, M., additional, Keyvani, K., additional, Gottardo, N., additional, Giangaspero, F., additional, Hoff, K., additional, Ellison, D. W., additional, Pietsch, T., additional, Herold-Mende, C., additional, Milde, T., additional, Witt, O., additional, Kool, M., additional, Korshunov, A., additional, Wick, W., additional, Deimling, A., additional, Pfister, S. M., additional, Jones, D. T. W., additional, and Sahm, F., additional

Published
2020
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33. Grand Challenges for Biological and Environmental Research: A Long-Term Vision

Author

Arkin, A., primary, Baliga, N., additional, Braam, J., additional, Church, G., additional, Collins, J, additional, Cottingham, R., additional, Ecker, J., additional, Gerstein, M., additional, Gilna, P., additional, Greenberg, J., additional, Handelsman, J., additional, Hubbard, S., additional, Joachimiak, A., additional, Liao, J., additional, Looger, L., additional, Meyerowitz, E., additional, Mjolness, E., additional, Petsko, G., additional, Sayler, G., additional, Simpson, M., additional, Stacey, G., additional, Sussman, M., additional, Tiedje, J., additional, Bader, D., additional, Cessi, P., additional, Collins, W., additional, Denning, S., additional, Dickinson, R., additional, Easterling, D., additional, Edmonds, J., additional, Feddema, J., additional, Field, C., additional, Fridlind, A., additional, Fung, I., additional, Held, I., additional, Jackson, R., additional, Janetos, A., additional, Large, W., additional, Leinen, M., additional, Leung, R., additional, Long, S., additional, Mace, G., additional, Masiello, C., additional, Meehl, G., additional, Ort, D., additional, Otto-Bliesner, B., additional, Penner, J., additional, Prather, M., additional, Randall, D., additional, Rasch, P., additional, Schneider, E., additional, Shugart, H., additional, Thornton, P., additional, Washington, W., additional, Wildung, R., additional, Wiscombe, W., additional, Zak, D., additional, Zhang, M., additional, Bielicki, J., additional, Buford, M., additional, Cleland, E., additional, Dale, V., additional, Duke, C., additional, Ehleringer, J., additional, Hecht, A., additional, Kammen, D., additional, Marland, G., additional, Pataki, D., additional, and Riley, M. Robertson, P., additional

Published
2010
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37. A note on solution of nonlinear programming problems with imprecise function and gradient values

Author

Kupferschmid, Michael, Ecker, J. G., Balinski, M. L., editor, Cottle, R. W., editor, Todd, M. J., editor, Dennis, J. E., Jr., editor, Korte, B., editor, Rinnooy Kan, A. H. G., editor, Allgower, E. L., editor, Birge, J. R., editor, Bixby, R. E., editor, Conn, A., editor, Cunningham, W. H., editor, Dixon, L. C. W., editor, Eaves, B. C., editor, Fletcher, R., editor, Goldfarb, D., editor, Grötschel, M., editor, Iri, M., editor, Johnson, D. S., editor, Lemarechal, C., editor, Lovasz, L., editor, McLinden, L., editor, Megiddo, N., editor, Powell, M. J. D., editor, Pulleyblank, W. R., editor, Robinson, S. M., editor, Shanno, D. F., editor, Toint, Ph., editor, Trotter, L. E., Jr., editor, Wolsey, L., editor, Wright, M. H., editor, Dantzig, G. B., editor, Tucker, A. W., editor, Wolfe, P., editor, Hoffman, K. L., editor, Jackson, R. H. F., editor, and Telgen, J., editor

Published
1987
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38. Using deep cuts in an ellipsoid algorithm for nonlinear programming

Author

Dziuban, Stephen T., Ecker, J. G., Kupferschmid, Michael, Cottle, R. W., editor, Dixon, L. C. W., editor, Korte, B., editor, Todd, M. J., editor, Allgower, E. L., editor, Cunningham, W. H., editor, Dennis, J. E., Jr., editor, Eaves, B. C., editor, Fletcher, R., editor, Goldfarb, D., editor, Hiriart-Urruty, J.- B., editor, Iri, M., editor, Jeroslow, R. G., editor, Johnson, D. S., editor, Lemarechal, C., editor, Lovasz, L., editor, McLinden, L., editor, Powell, M. J. D., editor, Pulleyblank, W. R., editor, Rinnooy Kan, A. H. G., editor, Ritter, K., editor, Sargent, R. W. H., editor, Shanno, D. F., editor, Trotter, L. E., Jr., editor, Tuy, H., editor, Wets, R. J. B., editor, Beale, E. M. L., editor, Dantzig, G. B., editor, Kantorovich, L. V., editor, Koopmans, T. C., editor, Tucker, A. W., editor, Wolfe, P., editor, and Cottle, Richard W., editor

Published
1985
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43. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis

Author

Chang, K, Zhong, S, Weirauch, M, Hon, G, Pelizzola, M, Li, H, Carol Huang, S, Schmitz, R, Urich, M, Kuo, D, Nery, J, Qiao, H, Yang, A, Jamali, A, Chen, H, Ideker, T, Ren, B, Bar-Joseph, Z, Hughes, T, Ecker, J, Chang K. N., Zhong S., Weirauch M. T., Hon G., Pelizzola M., Li H., Carol Huang S-S., Schmitz R. J., Urich M. A., Kuo D., Nery J. R., Qiao H., Yang A., Jamali A., Chen H., Ideker T., Ren B., Bar-Joseph Z., Hughes T. R., Ecker J. R., Chang, K, Zhong, S, Weirauch, M, Hon, G, Pelizzola, M, Li, H, Carol Huang, S, Schmitz, R, Urich, M, Kuo, D, Nery, J, Qiao, H, Yang, A, Jamali, A, Chen, H, Ideker, T, Ren, B, Bar-Joseph, Z, Hughes, T, Ecker, J, Chang K. N., Zhong S., Weirauch M. T., Hon G., Pelizzola M., Li H., Carol Huang S-S., Schmitz R. J., Urich M. A., Kuo D., Nery J. R., Qiao H., Yang A., Jamali A., Chen H., Ideker T., Ren B., Bar-Joseph Z., Hughes T. R., and Ecker J. R.

Abstract

The gaseous plant hormone ethylene regulates a multitude of growth and developmental processes. How the numerous growth control pathways are coordinated by the ethylene transcriptional response remains elusive. We characterized the dynamic ethylene transcriptional response by identifying targets of the master regulator of the ethylene signaling pathway, ETHYLENE INSENSITIVE3 (EIN3), using chromatin immunoprecipitation sequencing and transcript sequencing during a timecourse of ethylene treatment. Ethylene-induced transcription occurs in temporal waves regulated by EIN3, suggesting distinct layers of transcriptional control. EIN3 binding was found to modulate a multitude of downstream transcriptional cascades, including a major feedback regulatory circuitry of the ethylene signaling pathway, as well as integrating numerous connections between most of the hormone mediated growth response pathways. These findings provide direct evidence linking each of the major plant growth and development networks in novel ways.

Published
2013

44. Neuropathische Gelenksveränderungen bei Syringomyelie

Author

Ecker J

Subjects
musculoskeletal diseases, medicine.medical_specialty, animal structures, business.industry, Arthrodesis, medicine.medical_treatment, Elbow, Ulna, musculoskeletal system, medicine.disease, Surgery, body regions, Sepsis, medicine.anatomical_structure, Fracture fixation, medicine, Orthopedics and Sports Medicine, Humerus, business, Ulna Fractures, Syringomyelia
Abstract

This is a report of a patient with syringomyelia and septic Charcot joint of the left elbow. In cause of the inflammatory condition we performed an arthrodesis of the elbow. In spite of postoperative complications with fracture of the humerus and ulna we obtained a satisfactory result of treatment with weight-bearing arthrodesis and stop of the joint sepsis.

Published
2008
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46. Characterization of oncogene-induced senescence and the role of the senescence-associated secretory phenotype in pilocytic astrocytoma

Author

Hohloch, J, additional, Selt, F, additional, Hielscher, T, additional, Sahm, F, additional, Capper, D, additional, Usta, D, additional, Ecker, J, additional, Oehme, I, additional, van Tilburg, CM, additional, Deimling, A, additional, Schuhmann, MU, additional, Korshunov, A, additional, Jones, DTW, additional, Brummer, T, additional, Pfister, SM, additional, Witt, O, additional, and Milde, T, additional

Published
2017
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47. Interference with the function of MYC – novel insights into the consequences of class I HDAC inhibition in Group 3 Medulloblastoma

Author

Ecker, J, additional, Oehme, I, additional, Selt, F, additional, Kool, M, additional, Chavez, L, additional, Hohloch, J, additional, Valinciute, G, additional, van Tilburg, CM, additional, Thatikonda, V, additional, Schnölzer, M, additional, Warnken, U, additional, Wechsler-Reya, R, additional, Pfister, SM, additional, Witt, O, additional, and Milde, T, additional

Published
2017
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48. Oncogene-induced senescence and the senescence-associated secretory phenotype in pilocytic astrocytoma

Author

Hohloch, J, additional, Selt, F, additional, Hielscher, T, additional, Sahm, F, additional, Capper, D, additional, Usta, D, additional, Ecker, J, additional, Oehme, I, additional, van Tilburg, CM, additional, Deimling, A, additional, Schuhmann, MU, additional, Korshunov, A, additional, Jones, DTW, additional, Brummer, T, additional, Pfister, SM, additional, Witt, O, additional, and Milde, T, additional

Published
2017
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49. Human DNA methylomes at base resolution show widespread epigenomic differences

Author

Lister, R, Pelizzola, M, Dowen, R, Hawkins, R, Hon, G, Tonti-Filippini, J, Nery, J, Lee, L, Ye, Z, Ngo, Q, Edsall, L, Antosiewicz-Bourget, J, Stewart, R, Ruotti, V, Millar, A, Thomson, J, Ren, B, Ecker, J, Lister R., Pelizzola M., Dowen R. H., Hawkins R. D., Hon G., Tonti-Filippini J., Nery J. R., Lee L., Ye Z., Ngo Q. -M., Edsall L., Antosiewicz-Bourget J., Stewart R., Ruotti V., Millar A. H., Thomson J. A., Ren B., Ecker J. R., Lister, R, Pelizzola, M, Dowen, R, Hawkins, R, Hon, G, Tonti-Filippini, J, Nery, J, Lee, L, Ye, Z, Ngo, Q, Edsall, L, Antosiewicz-Bourget, J, Stewart, R, Ruotti, V, Millar, A, Thomson, J, Ren, B, Ecker, J, Lister R., Pelizzola M., Dowen R. H., Hawkins R. D., Hon G., Tonti-Filippini J., Nery J. R., Lee L., Ye Z., Ngo Q. -M., Edsall L., Antosiewicz-Bourget J., Stewart R., Ruotti V., Millar A. H., Thomson J. A., Ren B., and Ecker J. R.

Abstract

DNA cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease. Here we present the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of DNAĝ€"protein interaction for several key regulatory factors. Widespread differences were identified in the composition and patterning of cytosine methylation between the two genomes. Nearly one-quarter of all methylation identified in embryonic stem cells was in a non-CG context, suggesting that embryonic stem cells may use different methylation mechanisms to affect gene regulation. Methylation in non-CG contexts showed enrichment in gene bodies and depletion in protein binding sites and enhancers. Non-CG methylation disappeared upon induced differentiation of the embryonic stem cells, and was restored in induced pluripotent stem cells. We identified hundreds of differentially methylated regions proximal to genes involved in pluripotency and differentiation, and widespread reduced methylation levels in fibroblasts associated with lower transcriptional activity. These reference epigenomes provide a foundation for future studies exploring this key epigenetic modification in human disease and development.

Published
2009

50. Antibiotikaprophylaxe in der Orthopädie unter besonderer Berücksichtigung von Wirbelsäuleneingriffen

Author

Ecker J and Erschbaumer H

Subjects
medicine.medical_specialty, medicine.drug_class, business.industry, Orthopedic surgery, Antibiotics, medicine, Orthopedics and Sports Medicine, Surgery, Perioperative, Antibiotic prophylaxis, business, Intensive care medicine, Spinal column
Abstract

We report about our experience was the perioperative prophylaxis with antibiotics. We use a prophylaxis only in operations of the spinal column. In our opinion the prevention with antibiotics in other orthopaedic operations is not necessary. As an example we show our hip arthroplasties with a rate of infection under 0,5 percent.

Published
2008
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