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Ferderer, Anna ; Krüger, Sina ; Rogowska, Dagmara ; Frey, Lisa ; Weber, Nadine ; Clauss, Charlotte ; Majcherová, Diana ; Dreiling, Lisa ; Drusche, Janine ; Hetzelt, Nora-Marie ; Noto Siswo, Jennifer ; Klaus, Natalia ; Hepp, Lisa ; Glock, Valerie ; Wegner, Viola ; Polster, Lena ; Eikelschulte, Nadine ; Kohler, Martin ; Puije, Nina van der
Murat, Claude ; Payen, Thibaut ; Noel, Benjamin ; Kuo, Alan ; Morin, Emmanuelle ; Chen, Juan ; Kohler, Annegret ; Krizsán, Krisztina ; Balestrini, Raffaella ; Da Silva, Corinne ; Montanini, Barbara ; Hainaut, Mathieu ; Levati, Elisabetta ; Barry, Kerrie W. ; Belfiori, Beatrice ; Cichocki, Nicolas ; Clum, Alicia ; Dockter, Rhyan B. ; Fauchery, Laure ; Guy, Julie ; Iotti, Mirco ; Le Tacon, François ; Lindquist, Erika A. ; Lipzen, Anna ; Malagnac, Fabienne ; Mello, Antonietta ; Molinier, Virginie ; Miyauchi, Shingo ; Poulain, Julie ; Riccioni, Claudia ; Rubini, Andrea ; Sitrit, Yaron ; Splivallo, Richard ; Traeger, Stefanie ; Wang, Mei ; Žifčáková, Lucia ; Wipf, Daniel ; Zambonelli, Alessandra ; Paolocci, Francesco ; Nowrousian, Minou ; Ottonello, Simone ; Baldrian, Petr ; Spatafora, Joseph W. ; Henrissat, Bernard ; Nagy, László ; Aury, Jean-Marc ; Wincker, Patrick ; Grigoriev, Igor V. ; Bonfante, Paola ; Martin, Francis
Tuberaceae is one of the most diverse lineages of symbiotic truffle-forming fungi. To understand the molecular underpinning of the ectomycorrhizal truffle lifestyle, we compared the genomes of Piedmont white truffle (Tuber magnatum), Périgord black truffle (Tuber melanosporum), Burgundy truffle (Tuber aestivum), pig truffle (Choiromyces venosus) and desert truffle (Terfezia boudieri) to saprotrophic Pezizomycetes. Reconstructed gene duplication/loss histories along a time-calibrated phylogeny of Ascomycetes revealed that Tuberaceae-specific traits may be related to a higher gene diversification rate. Genomic features in Tuber species appear to be very similar, with high transposon content, few genes coding lignocellulose-degrading enzymes, a substantial set of lineage-specific fruiting-body-upregulated genes and high expression of genes involved in volatile organic compound metabolism. Developmental and metabolic pathways expressed in ectomycorrhizae and fruiting bodies of T. magnatum and T. melanosporum are unexpectedly very similar, owing to the fact that they diverged ~100 Ma. Volatile organic compounds from pungent truffle odours are not the products of Tuber-specific gene innovations, but rely on the differential expression of an existing gene repertoire. These genomic resources will help to address fundamental questions in the evolution of the truffle lifestyle and the ecology of fungi that have been praised as food delicacies for centuries.
Adam, Pia ; Kircher, Stefan Josef ; Sbiera, Iuliu ; Köhler, Viktoria Florentine ; Berg, Elke ; Knösel, Thomas ; Sandner, Benjamin ; Fenske, Wiebke Kristin ; Bläker, Hendrik ; Smaxwil, Constantin ; Zielke, Andreas ; Sipos, Bence ; Allelein, Stephanie ; Schott, Matthias ; Dierks, Christine ; Spitzweg, Christine ; Faßnacht, Martin ; Kroiß, Matthias
Background: Treatment options for poorly differentiated (PDTC) and anaplastic (ATC) thyroid carcinoma are unsatisfactory and prognosis is generally poor. Lenvatinib (LEN), a multi-tyrosine kinase inhibitor targeting fibroblast growth factor receptors (FGFR) 1-4 is approved for advanced radioiodine refractory thyroid carcinoma, but response to single agent is poor in ATC. Recent reports of combining LEN with PD-1 inhibitor pembrolizumab (PEM) are promising. Materials and Methods: Primary ATC (n=93) and PDTC (n=47) tissue samples diagnosed 1997-2019 at five German tertiary care centers were assessed for PD-L1 expression by immunohistochemistry using Tumor Proportion Score (TPS). FGFR 1-4 mRNA was quantified in 31 ATC and 14 PDTC with RNAscope in-situ hybridization. Normal thyroid tissue (NT) and papillary thyroid carcinoma (PTC) served as controls. Disease specific survival (DSS) was the primary outcome variable. Results: PD-L1 TPS≥50% was observed in 42% of ATC and 26% of PDTC specimens. Mean PD-L1 expression was significantly higher in ATC (TPS 30%) than in PDTC (5%; p<0.01) and NT (0%, p<0.001). 53% of PDTC samples had PD-L1 expression ≤5%. FGFR mRNA expression was generally low in all samples but combined FGFR1-4 expression was significantly higher in PDTC and ATC compared to NT (each p<0.001). No impact of PD-L1 and FGFR 1-4 expression was observed on DSS. Conclusion: High tumoral expression of PD-L1 in a large proportion of ATCs and a subgroup of PDTCs provides a rationale for immune checkpoint inhibition. FGFR expression is low thyroid tumor cells. The clinically observed synergism of PEM with LEN may be caused by immune modulation.
Jemaà, Mohamed ; Sime, Wondossen ; Abassi, Yasmin ; Lasorsa, Vito Alessandro ; Køhler, Julie Bonne ; Michaelis, Martin ; Cinatl, Jindrich ; Capasso, Mario ; Massoumi, Ramin
Drug resistance of childhood cancer neuroblastoma is a serious clinical problem. Patients with relapsed disease have a poor prognosis despite intense treatment. In the present study, we aimed to identify chemoresistance gene expression signatures in vincristine resistant neuroblastoma cells. We found that vincristine-resistant neuroblastoma cells formed larger clones and survived under reduced serum conditions as compared with non-resistant parental cells. To identify the possible mechanisms underlying vincristine resistance in neuroblastoma cells, we investigated the expression profiles of genes known to be involved in cancer drug resistance. This specific gene expression patterns could predict the behavior of a tumor in response to chemotherapy and for predicting the prognosis of high-risk neuroblastoma patients. Our signature could help chemoresistant neuroblastoma patients in avoiding useless and harmful chemotherapy cycles.
COMP and TSP-4 interact specifically with the novel GXKGHR motif only found in fibrillar collagens
(2018)
Gebauer, Jan Martin Ulrich ; Köhler, Anna ; Dietmar, Helen ; Gompert, Monika ; Neundorf, Ines ; Zaucke, Frank ; Koch, Manuel ; Baumann, Ulrich
COMP (cartilage oligomeric matrix protein) is a member of the thrombospondin family and forms homopentamers as well as mixed heterooligomers with its closely related family member TSP-4. COMP is long known to bind to collagens and to influence collagen fibril formation. Recent work indicates that already intracellular interaction with collagen is important for collagen secretion. However, the exact binding site of COMP on the collagen triple helix has not been described up to now. In this study we have identified a GXKGHR motif on the collagen II helix to bind to COMP, using a recombinantly expressed collagen II peptide library. This binding sequence is conserved throughout evolution and we demonstrate that TSP-4 binds to the same sequence. The identified binding motif overlaps with the recognition sites of many other collagen-binding partners (e.g. PEDF, Heparin) and also spans the lysine residues, which form collagen cross-links. COMP might thereby protect collagen helices from premature modification and cross-linking. Interestingly, this motif is only found in classical fibrillar collagens, although COMP is known to also bind other types. This might indicate that COMP has a unique interface for fibrillar collagens, thus making it an interesting target for the development of antifibrotic drugs.
Gehara, Marcelo ; Crawford, Andrew J. ; Orrico, Victor G. D. ; Rodríguez, Ariel ; Lötters, Stefan ; Fouquet, Antoine ; Barrientos, Lucas S. ; Brusquetti, Francisco ; De la Riva, Ignacio ; Ernst, Raffael ; Gagliardi Urrutia, Giuseppe ; Glaw, Frank ; Guayasamin, Juan M. ; Hölting, Monique ; Jansen, Martin ; Kok, Philippe Jacques Robert ; Kwet, Axel ; Lingnau, Rodrigo ; Lyra, Mariana ; Moravec, Jiří ; Pombal Jr, José P. ; J. M. Rojas-Runjaic, Fernando ; Schulze, Arne ; Señaris, J. Celsa ; Solé, Mirco ; Trefaut Rodrigues, Miguel ; Twomey, Evan ; Haddad, Célio Fernando Baptista ; Vences, Miguel ; Köhler, Jörn
Species distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and closely related species distributed across eleven countries, effectively comprising the entire range of the group. We performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of eight mtDNA lineages have ranges >100,000 km2. One of them occupies an area of almost one million km2 encompassing multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered.
The ICON single-column mode
(2021)
Bašták Ďurán, Ivan ; Köhler, Martin ; Eichhorn-Müller, Astrid ; Maurer, Vera ; Schmidli, Jürg ; Schomburg, Annika ; Klocke, Daniel ; Göcke, Tobias ; Schäfer, Sophia ; Schlemmer, Linda ; Dewani, Noviana
The single-column mode (SCM) of the ICON (ICOsahedral Nonhydrostatic) modeling framework is presented. The primary purpose of the ICON SCM is to use it as a tool for research, model evaluation and development. Thanks to the simplified geometry of the ICON SCM, various aspects of the ICON model, in particular the model physics, can be studied in a well-controlled environment. Additionally, the ICON SCM has a reduced computational cost and a low data storage demand. The ICON SCM can be utilized for idealized cases—several well-established cases are already included—or for semi-realistic cases based on analyses or model forecasts. As the case setup is defined by a single NetCDF file, new cases can be prepared easily by the modification of this file. We demonstrate the usage of the ICON SCM for different idealized cases such as shallow convection, stratocumulus clouds, and radiative transfer. Additionally, the ICON SCM is tested for a semi-realistic case together with an equivalent three-dimensional setup and the large eddy simulation mode of ICON. Such consistent comparisons across the hierarchy of ICON configurations are very helpful for model development. The ICON SCM will be implemented into the operational ICON model and will serve as an additional tool for advancing the development of the ICON model.