TY - JOUR A1 - Palladino, Viola Stella A1 - Chiocchetti, Andreas G. A1 - Frank, Lukas A1 - Haslinger, Denise A1 - McNeill, Rhiannon A1 - Radtke, Franziska A1 - Till, Andreas A1 - Haupt, Simone A1 - Brüstle, Oliver A1 - Günther, Katharina A1 - Edenhofer, Frank A1 - Hoffmann, Per A1 - Reif, Andreas A1 - Kittel-Schneider, Sarah T1 - Energy metabolism disturbances in cell models of PARK2 CNV carriers with ADHD JF - Journal of Clinical Medicine N2 - The main goal of the present study was the identification of cellular phenotypes in attention-deficit-/hyperactivity disorder (ADHD) patient-derived cellular models from carriers of rare copy number variants (CNVs) in the PARK2 locus that have been previously associated with ADHD. Human-derived fibroblasts (HDF) were cultured and human-induced pluripotent stem cells (hiPSC) were reprogrammed and differentiated into dopaminergic neuronal cells (mDANs). A series of assays in baseline condition and in different stress paradigms (nutrient deprivation, carbonyl cyanide m-chlorophenyl hydrazine (CCCP)) focusing on mitochondrial function and energy metabolism (ATP production, basal oxygen consumption rates, reactive oxygen species (ROS) abundance) were performed and changes in mitochondrial network morphology evaluated. We found changes in PARK2 CNV deletion and duplication carriers with ADHD in PARK2 gene and protein expression, ATP production and basal oxygen consumption rates compared to healthy and ADHD wildtype control cell lines, partly differing between HDF and mDANs and to some extent enhanced in stress paradigms. The generation of ROS was not influenced by the genotype. Our preliminary work suggests an energy impairment in HDF and mDAN cells of PARK2 CNV deletion and duplication carriers with ADHD. The energy impairment could be associated with the role of PARK2 dysregulation in mitochondrial dynamics. KW - ADHD KW - hiPSC KW - PARK2 KW - mitochondria KW - disease modelling Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-220074 SN - 2077-0383 VL - 9 IS - 12 ER - TY - CHAP A1 - Jannidis, Fotis A1 - Reger, Isabella A1 - Weimer, Lukas A1 - Krug, Markus A1 - Puppe, Frank T1 - Automatische Erkennung von Figuren in deutschsprachigen Romanen N2 - Eine wichtige Grundlage für die quantitative Analyse von Erzähltexten, etwa eine Netzwerkanalyse der Figurenkonstellation, ist die automatische Erkennung von Referenzen auf Figuren in Erzähltexten, ein Sonderfall des generischen NLP-Problems der Named Entity Recognition. Bestehende, auf Zeitungstexten trainierte Modelle sind für literarische Texte nur eingeschränkt brauchbar, da die Einbeziehung von Appellativen in die Named Entity-Definition und deren häufige Verwendung in Romantexten zu einem schlechten Ergebnis führt. Dieses Paper stellt eine anhand eines manuell annotierten Korpus auf deutschsprachige Romane des 19. Jahrhunderts angepasste NER-Komponente vor. KW - Digital Humanities KW - Figurenerkennung KW - Named-Entity-Recognition KW - Domänenadaption KW - Literatur Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-143332 UR - https://dhd2015.uni-graz.at/ ER - TY - JOUR A1 - Harreither, Eva A1 - Rydberg, Hanna A. A1 - Åmand, Helene L. A1 - Jadhav, Vaibhav A1 - Fliedl, Lukas A1 - Benda, Christina A1 - Esteban, Miguel A. A1 - Pei, Duanqing A1 - Borth, Nicole A1 - Grillari-Voglauer, Regina A1 - Hommerding, Oliver A1 - Edenhofer, Frank A1 - Nordén, Bengt A1 - Grillari, Johanne T1 - Characterization of a novel cell penetrating peptide derived from human Oct4 JF - Cell Regeneration N2 - BACKGROUND: Oct4 is a transcription factor that plays a major role for the preservation of the pluripotent state in embryonic stem cells as well as for efficient reprogramming of somatic cells to induced pluripotent stem cells (iPSC) or other progenitors. Protein-based reprogramming methods mainly rely on the addition of a fused cell penetrating peptide. This study describes that Oct4 inherently carries a protein transduction domain, which can translocate into human and mouse cells. RESULTS: A 16 amino acid peptide representing the third helix of the human Oct4 homeodomain, referred to as Oct4 protein transduction domain (Oct4-PTD), can internalize in mammalian cells upon conjugation to a fluorescence moiety thereby acting as a cell penetrating peptide (CPP). The cellular distribution of Oct4-PTD shows diffuse cytosolic and nuclear staining, whereas penetratin is strictly localized to a punctuate pattern in the cytoplasm. By using a Cre/loxP-based reporter system, we show that this peptide also drives translocation of a functionally active Oct4-PTD-Cre-fusion protein. We further provide evidence for translocation of full length Oct4 into human and mouse cell lines without the addition of any kind of cationic fusion tag. Finally, physico-chemical properties of the novel CPP are characterized, showing that in contrast to penetratin a helical structure of Oct4-PTD is only observed if the FITC label is present on the N-terminus of the peptide. CONCLUSIONS: Oct4 is a key transcription factor in stem cell research and cellular reprogramming. Since it has been shown that recombinant Oct4 fused to a cationic fusion tag can drive generation of iPSCs, our finding might contribute to further development of protein-based methods to generate iPSCs. Moreover, our data support the idea that transcription factors might be part of an alternative paracrine signalling pathway, where the proteins are transferred to neighbouring cells thereby actively changing the behaviour of the recipient cell. KW - penetratin KW - reprogramming KW - cell penetrating peptides KW - cellular internalization KW - homeodomain transcription factors KW - Oct4 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-120999 SN - 2045-9769 VL - 3 IS - 2 ER - TY - JOUR A1 - Lauruschkat, Chris D. A1 - Etter, Sonja A1 - Schnack, Elisabeth A1 - Ebel, Frank A1 - Schäuble, Sascha A1 - Page, Lukas A1 - Rümens, Dana A1 - Dragan, Mariola A1 - Schlegel, Nicolas A1 - Panagiotou, Gianni A1 - Kniemeyer, Olaf A1 - Brakhage, Axel A. A1 - Einsele, Hermann A1 - Wurster, Sebastian A1 - Loeffler, Juergen T1 - Chronic occupational mold exposure drives expansion of Aspergillus-reactive type 1 and type 2 T-helper cell responses JF - Journal of Fungi N2 - Occupational mold exposure can lead to Aspergillus-associated allergic diseases including asthma and hypersensitivity pneumonitis. Elevated IL-17 levels or disbalanced T-helper (Th) cell expansion were previously linked to Aspergillus-associated allergic diseases, whereas alterations to the Th cell repertoire in healthy occupationally exposed subjects are scarcely studied. Therefore, we employed functional immunoassays to compare Th cell responses to A. fumigatus antigens in organic farmers, a cohort frequently exposed to environmental molds, and non-occupationally exposed controls. Organic farmers harbored significantly higher A. fumigatus-specific Th-cell frequencies than controls, with comparable expansion of Th1- and Th2-cell frequencies but only slightly elevated Th17-cell frequencies. Accordingly, Aspergillus antigen-induced Th1 and Th2 cytokine levels were strongly elevated, whereas induction of IL-17A was minimal. Additionally, increased levels of some innate immune cell-derived cytokines were found in samples from organic farmers. Antigen-induced cytokine release combined with Aspergillus-specific Th-cell frequencies resulted in high classification accuracy between organic farmers and controls. Aspf22, CatB, and CipC elicited the strongest differences in Th1 and Th2 responses between the two cohorts, suggesting these antigens as potential candidates for future bio-effect monitoring approaches. Overall, we found that occupationally exposed agricultural workers display a largely balanced co-expansion of Th1 and Th2 immunity with only minor changes in Th17 responses. KW - mold exposure KW - immunoassay KW - biomarker KW - Aspergillus KW - cytokines KW - inflammation KW - adaptive immunity KW - hypersensitivity Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-245202 SN - 2309-608X VL - 7 IS - 9 ER - TY - JOUR A1 - Lauruschkat, Chris D. A1 - Page, Lukas A1 - White, P. Lewis A1 - Etter, Sonja A1 - Davies, Helen E. A1 - Duckers, Jamie A1 - Ebel, Frank A1 - Schnack, Elisabeth A1 - Backx, Matthijs A1 - Dragan, Mariola A1 - Schlegel, Nicolas A1 - Kniemeyer, Olaf A1 - Brakhage, Axel A. A1 - Einsele, Hermann A1 - Loeffler, Juergen A1 - Wurster, Sebastian T1 - Development of a simple and robust whole blood assay with dual co-stimulation to quantify the release of T-cellular signature cytokines in response to Aspergillus fumigatus antigens JF - Journal of Fungi N2 - Deeper understanding of mold-induced cytokine signatures could promote advances in the diagnosis and treatment of invasive mycoses and mold-associated hypersensitivity syndromes. Currently, most T-cellular immunoassays in medical mycology require the isolation of mononuclear cells and have limited robustness and practicability, hampering their broader applicability in clinical practice. Therefore, we developed a simple, cost-efficient whole blood (WB) assay with dual α-CD28 and α-CD49d co-stimulation to quantify cytokine secretion in response to Aspergillus fumigatus antigens. Dual co-stimulation strongly enhanced A. fumigatus-induced release of T-cellular signature cytokines detectable by enzyme-linked immunosorbent assay (ELISA) or a multiplex cytokine assay. Furthermore, T-cell-dependent activation and cytokine response of innate immune cells was captured by the assay. The protocol consistently showed little technical variation and high robustness to pre-analytic delays of up to 8 h. Stimulation with an A. fumigatus lysate elicited at least 7-fold greater median concentrations of key T-helper cell signature cytokines, including IL-17 and the type 2 T-helper cell cytokines IL-4 and IL-5 in WB samples from patients with Aspergillus-associated lung pathologies versus patients with non-mold-related lung diseases, suggesting high discriminatory power of the assay. These results position WB-ELISA with dual co-stimulation as a simple, accurate, and robust immunoassay for translational applications, encouraging further evaluation as a platform to monitor host immunity to opportunistic pathogens. KW - immunoassay KW - biomarker KW - Aspergillus KW - cytokines KW - inflammation KW - adaptive immunity Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-241025 SN - 2309-608X VL - 7 IS - 6 ER - TY - JOUR A1 - Meder, Lydia A1 - König, Katharina A1 - Ozretić, Luka A1 - Schultheis, Anne M. A1 - Ueckeroth, Frank A1 - Ade, Carsten P. A1 - Albus, Kerstin A1 - Boehm, Diana A1 - Rommerscheidt-Fuss, Ursula A1 - Florin, Alexandra A1 - Buhl, Theresa A1 - Hartmann, Wolfgang A1 - Wolf, Jürgen A1 - Merkelbach-Bruse, Sabine A1 - Eilers, Martin A1 - Perner, Sven A1 - Heukamp, Lukas C. A1 - Buettner, Reinhard T1 - NOTCH, ASCL1, p53 and RB alterations define an alternative pathway driving neuroendocrine and small cell lung carcinomas JF - International Journal of Cancer N2 - Small cell lung cancers (SCLCs) and extrapulmonary small cell cancers (SCCs) are very aggressive tumors arising de novo as primary small cell cancer with characteristic genetic lesions in RB1 and TP53. Based on murine models, neuroendocrine stem cells of the terminal bronchioli have been postulated as the cellular origin of primary SCLC. However, both in lung and many other organs, combined small cell/non-small cell tumors and secondary transitions from non-small cell carcinomas upon cancer therapy to neuroendocrine and small cell tumors occur. We define features of "small cell-ness" based on neuroendocrine markers, characteristic RB1 and TP53 mutations and small cell morphology. Furthermore, here we identify a pathway driving the pathogenesis of secondary SCLC involving inactivating NOTCH mutations, activation of the NOTCH target ASCL1 and canonical WNT-signaling in the context of mutual bi-allelic RB1 and TP53 lesions. Additionaly, we explored ASCL1 dependent RB inactivation by phosphorylation, which is reversible by CDK5 inhibition. We experimentally verify the NOTCH-ASCL1-RB-p53 signaling axis in vitro and validate its activation by genetic alterations in vivo. We analyzed clinical tumor samples including SCLC, SCC and pulmonary large cell neuroendocrine carcinomas and adenocarcinomas using amplicon-based Next Generation Sequencing, immunohistochemistry and fluorescence in situ hybridization. In conclusion, we identified a novel pathway underlying rare secondary SCLC which may drive small cell carcinomas in organs other than lung, as well. KW - lung cancer KW - small cell lung cancer KW - achaete-scute homolog 1 KW - neurogenic locus notch homolog KW - retinoblastoma protein Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-190853 VL - 138 IS - 4 ER - TY - JOUR A1 - Pennig, Lenhard A1 - Hoyer, Ulrike Cornelia Isabel A1 - Krauskopf, Alexandra A1 - Shahzad, Rahil A1 - Jünger, Stephanie T. A1 - Thiele, Frank A1 - Laukamp, Kai Roman A1 - Grunz, Jan-Peter A1 - Perkuhn, Michael A1 - Schlamann, Marc A1 - Kabbasch, Christoph A1 - Borggrefe, Jan A1 - Goertz, Lukas T1 - Deep learning assistance increases the detection sensitivity of radiologists for secondary intracranial aneurysms in subarachnoid hemorrhage JF - Neuroradiology N2 - Purpose To evaluate whether a deep learning model (DLM) could increase the detection sensitivity of radiologists for intracranial aneurysms on CT angiography (CTA) in aneurysmal subarachnoid hemorrhage (aSAH). Methods Three different DLMs were trained on CTA datasets of 68 aSAH patients with 79 aneurysms with their outputs being combined applying ensemble learning (DLM-Ens). The DLM-Ens was evaluated on an independent test set of 104 aSAH patients with 126 aneuryms (mean volume 129.2 ± 185.4 mm3, 13.0% at the posterior circulation), which were determined by two radiologists and one neurosurgeon in consensus using CTA and digital subtraction angiography scans. CTA scans of the test set were then presented to three blinded radiologists (reader 1: 13, reader 2: 4, and reader 3: 3 years of experience in diagnostic neuroradiology), who assessed them individually for aneurysms. Detection sensitivities for aneurysms of the readers with and without the assistance of the DLM were compared. Results In the test set, the detection sensitivity of the DLM-Ens (85.7%) was comparable to the radiologists (reader 1: 91.2%, reader 2: 86.5%, and reader 3: 86.5%; Fleiss κ of 0.502). DLM-assistance significantly increased the detection sensitivity (reader 1: 97.6%, reader 2: 97.6%,and reader 3: 96.0%; overall P=.024; Fleiss κ of 0.878), especially for secondary aneurysms (88.2% of the additional aneurysms provided by the DLM). Conclusion Deep learning significantly improved the detection sensitivity of radiologists for aneurysms in aSAH, especially for secondary aneurysms. It therefore represents a valuable adjunct for physicians to establish an accurate diagnosis in order to optimize patient treatment. KW - aneurysms KW - aneurysmal subarachnoid hemorrhage KW - CT angiography KW - deep learning KW - convolutional neural networks Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-308117 SN - 0028-3940 SN - 1432-1920 VL - 63 IS - 12 ER -