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Baur, Florentin ; Nietzer, Sarah ; Kunz, Meik ; Saal, Fabian ; Jeromin, Julian ; Matschos, Stephanie ; Linnebacher, Michael ; Walles, Heike ; Dandekar, Thomas ; Dandekar, Gudrun
To improve and focus preclinical testing, we combine tumor models based on a decellularized tissue matrix with bioinformatics to stratify tumors according to stage-specific mutations that are linked to central cancer pathways. We generated tissue models with BRAF-mutant colorectal cancer (CRC) cells (HROC24 and HROC87) and compared treatment responses to two-dimensional (2D) cultures and xenografts. As the BRAF inhibitor vemurafenib is—in contrast to melanoma—not effective in CRC, we combined it with the EGFR inhibitor gefitinib. In general, our 3D models showed higher chemoresistance and in contrast to 2D a more active HGFR after gefitinib and combination-therapy. In xenograft models murine HGF could not activate the human HGFR, stressing the importance of the human microenvironment. In order to stratify patient groups for targeted treatment options in CRC, an in silico topology with different stages including mutations and changes in common signaling pathways was developed. We applied the established topology for in silico simulations to predict new therapeutic options for BRAF-mutated CRC patients in advanced stages. Our in silico tool connects genome information with a deeper understanding of tumor engines in clinically relevant signaling networks which goes beyond the consideration of single drivers to improve CRC patient stratification.
Hummel, Eric ; Guttmann, Peter ; Werner, Stephan ; Tarek, Basel ; Schneider, Gerd ; Kunz, Michael ; Frangakis, Achilleas S. ; Westermann, Benedikt
The complex architecture of their structural elements and compartments is a hallmark of eukaryotic cells. The creation of high resolution models of whole cells has been limited by the relatively low resolution of conventional light microscopes and the requirement for ultrathin sections in transmission electron microscopy. We used soft x-ray tomography to study the 3D ultrastructural organization of whole cells of the unicellular green alga Chlamydomonas reinhardtii at unprecedented spatial resolution. Intact frozen hydrated cells were imaged using the natural x-ray absorption contrast of the sample without any staining. We applied different fiducial-based and fiducial-less alignment procedures for the 3D reconstructions. The reconstructed 3D volumes of the cells show features down to 30 nm in size. The whole cell tomograms reveal ultrastructural details such as nuclear envelope membranes, thylakoids, basal apparatus, and flagellar microtubule doublets. In addition, the x-ray tomograms provide quantitative data from the cell architecture. Therefore, nanoscale soft x-ray tomography is a new valuable tool for numerous qualitative and quantitative applications in plant cell biology.
The asymmetric unit of the title compound, [K(C3H3N2)(C12H24O6)], is composed of a potassium cation bonded to the six O atoms of a crown ether molecule and the two N atoms of a pyrazolate anion. The K...O distances range from 2.8416 (8) to 3.0025 (8) Å, and the two K...N distances are 2.7441 (11) and 2.7654 (11) Å. The K cation is displaced by 0.8437 (4) Å from the best plane through the six O atoms. The latter plane is almost perpendicular to the plane of the pyrazolate ring [dihedral angle 83.93 (3)°]. Key indicators: single-crystal X-ray study; T = 173 K; mean σ(C–C) = 0.002 A°; R factor = 0.026; wR factor = 0.066; data-to-parameter ratio = 16.5.
Auburger, Georg ; Klinkenberg, Michael ; Drost, Jessica ; Marcus, Katrin ; Morales-Gordo, Blas ; Kunz, Wolfram S. ; Brandt, Ulrich ; Broccoli, Vania ; Reichmann, Heinz ; Gispert, Suzana ; Jendrach, Marina
Parkinson's disease is the second most frequent neurodegenerative disorder. While most cases occur sporadic mutations in a growing number of genes including Parkin (PARK2) and PINK1 (PARK6) have been associated with the disease. Different animal models and cell models like patient skin fibroblasts and recombinant cell lines can be used as model systems for Parkinson's disease. Skin fibroblasts present a system with defined mutations and the cumulative cellular damage of the patients. PINK1 and Parkin genes show relevant expression levels in human fibroblasts and since both genes participate in stress response pathways, we believe fibroblasts advantageous in order to assess, e.g. the effect of stressors. Furthermore, since a bioenergetic deficit underlies early stage Parkinson's disease, while atrophy underlies later stages, the use of primary cells seems preferable over the use of tumor cell lines. The new option to use fibroblast-derived induced pluripotent stem cells redifferentiated into dopaminergic neurons is an additional benefit. However, the use of fibroblast has also some drawbacks. We have investigated PARK6 fibroblasts and they mirror closely the respiratory alterations, the expression profiles, the mitochondrial dynamics pathology and the vulnerability to proteasomal stress that has been documented in other model systems. Fibroblasts from patients with PARK2, PARK6, idiopathic Parkinson's disease, Alzheimer's disease, and spinocerebellar ataxia type 2 demonstrated a distinct and unique mRNA expression pattern of key genes in neurodegeneration. Thus, primary skin fibroblasts are a useful Parkinson's disease model, able to serve as a complement to animal mutants, transformed cell lines and patient tissues.
Wolking, Stefan ; Schulz, Herbert ; Nies, Anne T ; McCormack, Mark ; Schäffeler, Elke ; Auce, Pauls ; Avbersek, Andreja ; Becker, Felicitas ; Klein, Karl Martin ; Krenn, Martin ; Møller, Rikke S. ; Nikanorova, Marina ; Weckhuysen, Sarah ; Cavalleri, Gianpiero L. ; Delanty, Norman ; Depondt, Chantal ; Johnson, Michael R. ; Koeleman, Bobby P. C. ; Kunz, Wolfram S. ; Marson, Anthony G. ; Sander, Josemir W. ; Sills, Graeme J. ; Striano, Pasquale ; Zara, Federico J. ; Zimprich, Fritz ; Weber, Yvonne G. ; Krause, Roland ; Sisodiya, Sanjay M. ; Schwab, Matthias ; Sander, Thomas ; Lerche, Holger
Aim: Pharmacoresistance is a major burden in epilepsy treatment. We aimed to identify genetic biomarkers in response to specific antiepileptic drugs (AEDs) in genetic generalized epilepsies (GGE). Materials & methods: We conducted a genome-wide association study (GWAS) of 3.3 million autosomal SNPs in 893 European subjects with GGE – responsive or nonresponsive to lamotrigine, levetiracetam and valproic acid. Results: Our GWAS of AED response revealed suggestive evidence for association at 29 genomic loci (p <10-5) but no significant association reflecting its limited power. The suggestive associations highlight candidate genes that are implicated in epileptogenesis and neurodevelopment. Conclusion: This first GWAS of AED response in GGE provides a comprehensive reference of SNP associations for hypothesis-driven candidate gene analyses in upcoming pharmacogenetic studies.
Perkovic, Mario ; Kunz, Michael ; Endesfelder, Ulrike ; Bunse, Stefanie ; Wigge, Christoph ; Yu, Zhou ; Hodirnau, Victor-Valentin ; Scheffer, Margot ; Seybert, Anja ; Malkusch, Sebastian ; Schuman, Erin ; Heilemann, Mike ; Frangakis, Achilleas S.
Correlative microscopy incorporates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Several approaches exist for correlative microscopy, most of which have used the green fluorescent protein (GFP) as the label for light microscopy. Here we use chemical tagging and synthetic fluorophores instead, in order to achieve protein-specific labeling, and to perform multicolor imaging. We show that synthetic fluorophores preserve their post-embedding fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is of such quality that the specimen can be prepared with identical protocols for scanning electron microscopy (SEM) and transmission electron microscopy (TEM); this is particularly valuable when singular or otherwise difficult samples are examined. We show that synthetic fluorophores give bright, well-resolved signals in super-resolution light microscopy, enabling us to superimpose light microscopic images with a precision of up to 25 nm in the x-y plane on electron micrographs. To exemplify the preservation quality of our new method we visualize the molecular arrangement of cadherins in adherens junctions of mouse epithelial cells.
Adler, Clemens ; Ahammed, Zubayer ; Allgower, C. ; Amonett, J. ; Anderson, B.D. ; Anderson, M. ; Averichev, Georgy S. ; Balewski, J. ; Barannikova, O. ; Barnby, L.S. ; Baudot, J. ; Bekele, S. ; Belaga, V.V. ; Bellwied, Rene ; Berger, J. ; Bichsel, H. ; Billmeier, A. ; Bland, L.C. ; Blyth, C.O. ; Bonner, B.E. ; Boucham, A. ; Brandin, A. ; Bravar, A. ; Cadman, R.V. ; Caines, Helen Louise ; Calderón de la Barca Sánchez, Manuel ; Cardenas, A. ; Carroll, J. ; Castillo Castellanos, Javier Ernesto ; Castro, M. ; Cebra, D. ; Chaloupka, Petr ; Chattopadhyay, S. ; Chen, Y. ; Chernenko, S.P. ; Cherney, M. ; Chikanian, A. ; Choi, B. ; Christie, William ; Coffin, J.P. ; Cormier, T.M. ; Cramer, J.G. ; Crawford, H.J. ; Deng, W.S. ; Derevschikov, A.A. ; Didenko, L. ; Dietel, Thomas ; Draper, J.E. ; Dunin, V.B. ; Dunlop, J.C. ; Eckardt, V. ; Efimov, L.G. ; Emelianov, V. ; Engelage, J. ; Eppley, G. ; Erazmus, B. ; Fachini, P. ; Faine, V. ; Filimonov, K. ; Finch, E. ; Fisyak, Y. ; Flierl, D. ; Foley, K.J. ; Fu, J. ; Gagliardi, Carl A. ; Gagunashvili, N. ; Gans, J. ; Gaudichet, L. ; Germain, M. ; Geurts, F. ; Ghazikhanian, V. ; Grachov, O. ; Grigoriev, Vladislav A. ; Guedon, M. ; Gushin, E. ; Hallman, T.J. ; Hardtke, D. ; Harris, J.W. ; Henry, T.W. ; Heppelmann, S. ; Herston, T. ; Hippolyte, Boris ; Hirsch, A. ; Hjort, E. ; Hoffmann, Gerald W. ; Horsley, M. ; Huang, H.Z. ; Humanic, Thomas J. ; Igo, G. ; Ishihara, A. ; Ivanshin, Yu.I. ; Jacobs, P. ; Jacobs, W.W. ; Janik, M. ; Johnson, I. ; Jones, Peter Graham ; Judd, Eleanor G. ; Kaneta, M. ; Kaplan, M. ; Keane, Declan ; Kiryluk, J. ; Kisiel, A. ; Klay, J. ; Klein, S.R. ; Klyachko, A. ; Konstantinov, A.S. ; Kopytine, M. ; Kotchenda, L. ; Kovalenko, A.D. ; Kramer, M. ; Kravtsov, P. ; Krueger, Keith William ; Kuhn, C. ; Kulikov, A.I. ; Kunde, G.J. ; Kunz, C.L. ; Kutuev, R.Kh. ; Kuznetsov, A.A. ; Lakehal-Ayat, L. ; Lamont, Matthew A. C. ; Landgraf, J.M. ; Lange, S. ; Lansdell, C.P. ; Lasiuk, B. ; Laue, F. ; Lebedev, A. ; Lednický, R. ; Leontiev, V.M. ; LeVine, M.J. ; Li, Q. ; Lindenbaum, S.J. ; Lisa, Michael A. ; Liu, F. ; Liu, L. ; Liu, Z. ; Liu, Q.J. ; Ljubicic, T. ; Llope, W.J. ; LoCurto, G. ; Long, H. ; Longacre, R.S. ; Lopez-Noriega, M. ; Love, W.A. ; Ludlam, T. ; Lynn, D. ; Ma, J. ; Majka, R. ; Margetis, Spyridon ; Markert, Christina ; Martin, L. ; Marx, J. ; Matis, Howard S. ; Matulenko, Yu.A. ; McShane, T.S. ; Meissner, F. ; Melnick, Yu. ; Meschanin, A. ; Messer, M. ; Miller, M.L. ; Milosevich, Z. ; Minaev, N.G. ; Mitchell, J. ; Moiseenko, V.A. ; Moore, C.F. ; Morozov, V. ; de Moura, M.M. ; Munhoz, M.G. ; Nelson, J.M. ; Nevski, P. ; Nikitin, V.A. ; Nogach, L.V. ; Norman, B. ; Nurushev, S.B. ; Odyniec, G. ; Ogawa, A. ; Okorokov, Vitaly A. ; Oldenburg, M. ; Olson, D. ; Paic, Guy ; Pandey, S.U. ; Panebratsev, Y. ; Panitkin, S.Y. ; Pavlinov, A.I. ; Pawlak, T. ; Perevoztchikov, V. ; Peryt, W. ; Petrov, V.A. ; Planinic, M. ; Pluta, J. ; Porile, N. ; Porter, J. ; Poskanzer, A.M. ; Potrebenikova, E. ; Prindle, D. ; Pruneau, C. ; Putschke, Jörn H. ; Rai, G. ; Rakness, G. ; Ravel, O. ; Ray, R.L. ; Razin, S.V. ; Reichhold, D. ; Reid, Jeffrey G. ; Retiere, F. ; Ridiger, A. ; Ritter, H.G. ; Roberts, J.B. ; Rogachevski, O.V. ; Romero, J.L. ; Rose, A. ; Roy, C. ; Rykov, V. ; Sakrejda, I. ; Salur, Sevil ; Sandweiss, J. ; Saulys, A.C. ; Savin, I. ; Schambach, Joachim ; Scharenberg, R.P. ; Schmitz, N. ; Schroeder, L.S. ; Schüttauf, A. ; Schweda, Kai ; Seger, J. ; Seliverstov, D. ; Seyboth, P. ; Shahaliev, E. ; Shestermanov, K.E. ; Shimanskii, S.S. ; Shvetcov, V.S. ; Skoro, G. ; Smirnov, Nikolai ; Snellings, Raimond ; Sorensen, P. ; Sowinski, J. ; Spinka, Harold. M. ; Srivastava, B. ; Stephenson, E.J. ; Stock, Reinhard ; Stolpovsky, A. ; Strikhanov, M. ; Stringfellow, B. ; Struck, C. ; Suaide, Alexandre Alarcon do Passo ; Sugarbaker, E. ; Suire, Christophe Pierre ; Šumbera, Michal ; Surrow, Bernd ; Symons, T.J.M. ; Szanto de Toledo, A. ; Szarwas, P. ; Tai, A. ; Takahashi, Jun ; Tang, A.H. ; Thomas, James H. ; Thompson, M. ; Tikhomirov, V. ; Tokarev, M. ; Tonjes, M.B. ; Trainor, T.A. ; Trentalange, Stephen ; Tribble, Robert E. ; Trofimov, V. ; Tsai, Oleg D. ; Ullrich, Thomas ; Underwood, D.G. ; Van Buren, G. ; VanderMolen, A.M. ; Vasilevski, I.M. ; Vasiliev, A.N. ; Vigdor, S.E. ; Voloshin, S.A. ; Wang, Fuqiang ; Ward, H. ; Watson, J.W. ; Wells, R. ; Westfall, Gary D. ; Whitten, C. ; Wieman, H. ; Willson, R. ; Wissink, S.W. ; Witt, Richard ; Wood, J. ; Xu, N. ; Xu, Z. ; Yakutin, A.E. ; Yamamoto, E. ; Yang, J. ; Yepes, P. ; Yurevich, V.I. ; Zanevski, Y.V. ; Zborovský, I. ; Zhang, H. ; Zhang, W.M. ; Zoulkarneev, R. ; Zubarev, A.N.
Mid-rapidity transverse mass spectra and multiplicity densities of charged and neutral kaons are reported for Au + Au collisions at √sNN = 130 GeV at RHIC. The spectra are exponential in transverse mass, with an inverse slope of about 280 MeV in central collisions. The multiplicity densities for these particles scale with the negative hadron pseudo-rapidity density. The charged kaon to pion ratios are K+/π− = 0.161± 0.002(stat) ± 0.024(syst) and K−/π− = 0.146± 0.002(stat) ± 0.022(syst) for the most central collisions. The K+/π− ratio is lower than the same ratio observed at the SPS while the K−/π− is higher than the SPS result. The ratios are enhanced by about 50% relative to p + p and p¯ + p collision data at similar energies.
Bender, Jennifer ; Haller, Sebastian ; Pfeifer, Yvonne ; Hogardt, Michael ; Hunfeld, Klaus-Peter ; Thürmer, Andrea ; Zanuzdana, Arina ; Werner, Markus ; Kunz, Bernd ; Eisenberger, David ; Pfennigwerth, Niels Ernst ; Kempf, Volkhard A. J. ; Werner, Guido ; Eckmanns, Tim
Background: In September 2018, Burkholderia cepacia complex (BCC) infections in 3 patients associated with exposure to a mouthwash solution (MWS) were reported to the Robert Koch Institute (RKI). As the product was still on the market and the scale of the outbreak was unclear, a nation-wide investigation was initiated.
Methods: We aimed to investigate BCC infections/colonizations associated with MWS. Hospitals, laboratories, and public health services were informed that BCC isolates should be sent to the RKI. These isolates were typed by pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS) including development of an ad hoc core genome MLST (cgMLST) scheme.
Results: In total, 36 patients from 6 hospitals met the case definition, the last patient in November 2018. Twenty-nine isolates from 26 of these patients were available for typing. WGS analysis revealed 2 distinct cgMLST clusters. Cluster 1 (Burkholderia arboris) contained isolates from patients and MWS obtained from 4 hospitals and isolates provided by the manufacturer. Patient and MWS isolates from another hospital were assigned to cluster 2 (B. cepacia).
Conclusions: The combined clinical, epidemiological, and microbiological investigation, including whole-genome analysis, allowed for uncovering a supraregional BCC outbreak in health care settings. Strains of B. arboris and B. cepacia were identified as contaminating species of MWS bottles and subsequent colonization and putative infection of patients in several hospitals. Despite a recall of the product by the manufacturer in August 2018, the outbreak lasted until December 2018. Reporting of contaminated medical products and recalls should be optimized to protect patients.
Müller, Lukas ; Mähringer-Kunz, Aline ; Auer, Timo Alexander ; Fehrenbach, Uli ; Gebauer, Bernhard ; Haubold, Johannes ; Schaarschmidt, Benedikt Michael Sebastian ; Kim, Moon-Sung ; Hosch, René ; Nensa, Felix ; Kleesiek, Jens Philipp ; Diallo, Thierno Diawo ; Eisenblätter, Michel ; Kuzior, Hanna ; Röhlen, Natascha ; Bettinger, Dominik ; Steinle, Verena Maria ; Mayer, Philipp ; Zopfs, David ; Pinto dos Santos, Daniel ; Klöckner, Roman Trutz
Highlights:
• Assessment of body composition parameters in a large cohort of patients with HCC undergoing TACE.
• Fully automated artificial intelligence-based quantitative 3D volumetry of abdominal cavity tissue composition.
• Skeletal muscle volume and related parameters were independent prognostic factors in patients with HCC undergoing TACE.
Background & Aims: Body composition assessment (BCA) parameters have recently been identified as relevant prognostic factors for patients with hepatocellular carcinoma (HCC). Herein, we aimed to investigate the role of BCA parameters for prognosis prediction in patients with HCC undergoing transarterial chemoembolization (TACE).
Methods: This retrospective multicenter study included a total of 754 treatment-naïve patients with HCC who underwent TACE at six tertiary care centers between 2010–2020. Fully automated artificial intelligence-based quantitative 3D volumetry of abdominal cavity tissue composition was performed to assess skeletal muscle volume (SM), total adipose tissue (TAT), intra- and intermuscular adipose tissue, visceral adipose tissue, and subcutaneous adipose tissue (SAT) on pre-intervention computed tomography scans. BCA parameters were normalized to the slice number of the abdominal cavity. We assessed the influence of BCA parameters on median overall survival and performed multivariate analysis including established estimates of survival.
Results: Univariate survival analysis revealed that impaired median overall survival was predicted by low SM (p <0.001), high TAT volume (p = 0.013), and high SAT volume (p = 0.006). In multivariate survival analysis, SM remained an independent prognostic factor (p = 0.039), while TAT and SAT volumes no longer showed predictive ability. This predictive role of SM was confirmed in a subgroup analysis of patients with BCLC stage B.
Conclusions: SM is an independent prognostic factor for survival prediction. Thus, the integration of SM into novel scoring systems could potentially improve survival prediction and clinical decision-making. Fully automated approaches are needed to foster the implementation of this imaging biomarker into daily routine.
Impact and implications: Body composition assessment parameters, especially skeletal muscle volume, have been identified as relevant prognostic factors for many diseases and treatments. In this study, skeletal muscle volume has been identified as an independent prognostic factor for patients with hepatocellular carcinoma undergoing transarterial chemoembolization. Therefore, skeletal muscle volume as a metaparameter could play a role as an opportunistic biomarker in holistic patient assessment and be integrated into decision support systems. Workflow integration with artificial intelligence is essential for automated, quantitative body composition assessment, enabling broad availability in multidisciplinary case discussions.