@article{GroebnerWorstWeischenfeldtetal.2018, author = {Gr{\"o}bner, Susanne N. and Worst, Barbara C. and Weischenfeldt, Joachim and Buchhalter, Ivo and Kleinheinz, Kortine and Rudneva, Vasilisa A. and Johann, Pascal D. and Balasubramanian, Gnana Prakash and Segura-Wang, Maia and Brabetz, Sebastian and Bender, Sebastian and Hutter, Barbara and Sturm, Dominik and Pfaff, Elke and H{\"u}bschmann, Daniel and Zipprich, Gideon and Heinold, Michael and Eils, J{\"u}rgen and Lawerenz, Christian and Erkek, Serap and Lambo, Sander and Waszak, Sebastian and Blattmann, Claudia and Borkhardt, Arndt and Kuhlen, Michaela and Eggert, Angelika and Fulda, Simone and Gessler, Manfred and Wegert, Jenny and Kappler, Roland and Baumhoer, Daniel and Stefan, Burdach and Kirschner-Schwabe, Renate and Kontny, Udo and Kulozik, Andreas E. and Lohmann, Dietmar and Hettmer, Simone and Eckert, Cornelia and Bielack, Stefan and Nathrath, Michaela and Niemeyer, Charlotte and Richter, G{\"u}nther H. and Schulte, Johannes and Siebert, Reiner and Westermann, Frank and Molenaar, Jan J. and Vassal, Gilles and Witt, Hendrik and Burkhardt, Birgit and Kratz, Christian P. and Witt, Olaf and van Tilburg, Cornelis M. and Kramm, Christof M. and Fleischhack, Gudrun and Dirksen, Uta and Rutkowski, Stefan and Fr{\"u}hwald, Michael and Hoff, Katja von and Wolf, Stephan and Klingebeil, Thomas and Koscielniak, Ewa and Landgraf, Pablo and Koster, Jan and Resnick, Adam C. and Zhang, Jinghui and Liu, Yanling and Zhou, Xin and Waanders, Angela J. and Zwijnenburg, Danny A. and Raman, Pichai and Brors, Benedikt and Weber, Ursula D. and Northcott, Paul A. and Pajtler, Kristian W. and Kool, Marcel and Piro, Rosario M. and Korbel, Jan O. and Schlesner, Matthias and Eils, Roland and Jones, David T. W. and Lichter, Peter and Chavez, Lukas and Zapatka, Marc and Pfister, Stefan M.}, title = {The landscape of genomic alterations across childhood cancers}, series = {Nature}, volume = {555}, journal = {Nature}, organization = {ICGC PedBrain-Seq Project, ICGC MMML-Seq Project,}, doi = {10.1038/nature25480}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229579}, pages = {321-327}, year = {2018}, abstract = {Pan-cancer analyses that examine commonalities and differences among various cancer types have emerged as a powerful way to obtain novel insights into cancer biology. Here we present a comprehensive analysis of genetic alterations in a pan-cancer cohort including 961 tumours from children, adolescents, and young adults, comprising 24 distinct molecular types of cancer. Using a standardized workflow, we identified marked differences in terms of mutation frequency and significantly mutated genes in comparison to previously analysed adult cancers. Genetic alterations in 149 putative cancer driver genes separate the tumours into two classes: small mutation and structural/copy-number variant (correlating with germline variants). Structural variants, hyperdiploidy, and chromothripsis are linked to TP53 mutation status and mutational signatures. Our data suggest that 7-8\% of the children in this cohort carry an unambiguous predisposing germline variant and that nearly 50\% of paediatric neoplasms harbour a potentially druggable event, which is highly relevant for the design of future clinical trials.}, language = {en} } @article{DrubeWeberLoschinskietal.2015, author = {Drube, Sebastian and Weber, Franziska and Loschinski, Romy and Beyer, Mandy and Rothe, Mandy and Rabenhorst, Anja and G{\"o}pfert, Christiane and Meininger, Isabel and Diamanti, Michaela A. and Stegner, David and H{\"a}fner, Norman and B{\"o}ttcher, Martin and Reinecke, Kirstin and Herdegen, Thomas and Greten, Florian R. and Nieswandt, Bernhard and Hartmann, Karin and Kr{\"a}mer, Oliver H. and Kamradt, Thomas}, title = {Subthreshold IKK activation modulates the effector functions of primary mast cells and allows specific targeting of transformed mast cells}, series = {Oncotarget}, volume = {6}, journal = {Oncotarget}, number = {7}, doi = {10.18632/oncotarget.3022}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143681}, pages = {5354-5368}, year = {2015}, abstract = {Mast cell differentiation and proliferation depends on IL-3. IL-3 induces the activation of MAP-kinases and STATs and consequently induces proliferation and survival. Dysregulation of IL-3 signaling pathways also contribute to inflammation and tumorigenesis. We show here that IL-3 induces a SFK- and Ca2\(^{+}\)-dependent activation of the inhibitor of κB kinases 2 (IKK2) which results in mast cell proliferation and survival but does not induce IκBα-degradation and NFκB activation. Therefore we propose the term "subthreshold IKK activation". This subthreshold IKK activation also primes mast cells for enhanced responsiveness to IL-33R signaling. Consequently, co-stimulation with IL-3 and IL-33 increases IKK activation and massively enhances cytokine production induced by IL-33. We further reveal that in neoplastic mast cells expressing constitutively active Ras, subthreshold IKK activation is associated with uncontrolled proliferation. Consequently, pharmacological IKK inhibition reduces tumor growth selectively by inducing apoptosis in vivo. Together, subthreshold IKK activation is crucial to mediate the full IL-33-induced effector functions in primary mast cells and to mediate uncontrolled proliferation of neoplastic mast cells. Thus, IKK2 is a new molecularly defined target structure.}, language = {en} } @phdthesis{Weber2008, author = {Weber, Sebastian}, title = {Simulation of self-assembled nanopatterns in binary alloys on the fcc(111) surface}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-27914}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2008}, abstract = {In this PhD thesis, we study the heteroepitaxial crystal growth by means of Monte Carlo simulations. Of particular interest in this work is the influence of the lattice mismatch of the adsorbates relative to the substrate on surface structures. In the framework of an off-lattice model, we consider one monolayer of adsorbate and investigate the emerging nanopatterns in equilibrium and their formation during growth. In chapter 1, a brief introduction is given, which describes the role of computer simulations in the field of the physics of condensed matter. Chapter 2 is devoted to some technical basics of experimental methods of molecular beam epitaxy and the theoretical description. Before a model for the simulation can be designed, it is necessary to make some considerations of the single processes which occur during epitaxial growth. For that purpose we look at an experimental setup and extract the main microscopic processes. Afterwards a brief overview of different theoretical concepts describing that physical procedures is given. In chapter 3, the model used in the simulations is presented. The aim is to investigate the growth of an fcc crystal in the [111] direction. In order to keep the simulation times within a feasible limit a simple pair potential, the Lennard-Jones potential, with continuous particle positions is used, which are necessary to describe effects resulting from the atomic mismatch in the crystal. Furthermore the detailed algorithm is introduced which is based on the idea to calculate the barrier of each diffusion event and to use the barriers in a rejection-free method. Chapter 4 is attended to the simulation of equilibrium. The influence of different parameters on the emerging structures in the first monolayer upon the surface, which is completely covered with two adsorbate materials, is studied. Especially the competition between binding energy and strain leads to very interesting pattern formations like islands or stripes. In chapter 5 the results of growth simulations are presented. At first, we introduce a model in order to realize off-lattice Kinetic Monte Carlo simulations. Since the costs in simulation time are enormous, some simplifications in the calculation of diffusion barriers are necessary and therefore the previous model is supplemented with some elements from the so-called ball and spring model. The next point is devoted to the calculation of energy barriers followed by the presentation of the growth simulations. Binary systems with only one sort of adsorbate are investigated as well as ternary systems with two different adsorbates. Finally, a comparison to the equilibrium simulations is drawn. Chapter 6 contains some concluding remarks and gives an outlook to possible further investigations.}, subject = {Kristallwachstum}, language = {en} }