Genomes and Genes
Affiliation: University of Freiburg
- Nilse L, Avci D, Heisterkamp P, Serang O, Lemberg M, Schilling O. Yeast membrane proteomics using leucine metabolic labelling: Bioinformatic data processing and exemplary application to the ER-intramembrane protease Ypf1. Biochim Biophys Acta. 2016;1864:1363-71 pubmed publisher..As an exemplary application, we show the identification of the copper transporter Ctr1 as a putative substrate of the ER-intramembrane protease Ypf1 by yeast membrane proteomics using d3-leucine isotopic labelling. ..
- Petrera A, Gassenhuber J, Ruf S, Gunasekaran D, Esser J, Shahinian J, et al. Cathepsin A inhibition attenuates myocardial infarction-induced heart failure on the functional and proteomic levels. J Transl Med. 2016;14:153 pubmed publisher..Our proteomic and functional data suggest that cathepsin A inhibition has cardioprotective properties and support a beneficial effect of cathepsin A inhibition in the treatment of heart failure after myocardial infarction. ..
- Biniossek M, Niemer M, Maksimchuk K, Mayer B, Fuchs J, Huesgen P, et al. Identification of Protease Specificity by Combining Proteome-Derived Peptide Libraries and Quantitative Proteomics. Mol Cell Proteomics. 2016;15:2515-24 pubmed publisher..Our protocol is fast, avoids enrichment or synthesis steps, and enables probing for lysine selectivity as well as subsite cooperativity. Due to its simplicity, we anticipate usability by most proteomic laboratories. ..
- Gomez Auli A, Hillebrand L, Biniossek M, Peters C, Reinheckel T, Schilling O. Impact of cathepsin B on the interstitial fluid proteome of murine breast cancers. Biochimie. 2016;122:88-98 pubmed publisher..Our study establishes tumor IF as a rich source for the investigation of secreted proteins in tumor biology and sheds light on complex proteolytic networks in the breast cancer secretome. ..
- Lai Z, Weisser J, Nilse L, Costa F, Keller E, Tholen M, et al. Formalin-Fixed, Paraffin-Embedded Tissues (FFPE) as a Robust Source for the Profiling of Native and Protease-Generated Protein Amino Termini. Mol Cell Proteomics. 2016;15:2203-13 pubmed publisher..Our study establishes FFPE specimens as a valuable alternative to cryopreserved tissues for degradomic studies. ..
- Lai Z, Bolm L, Fuellgraf H, Biniossek M, Makowiec F, Hopt U, et al. Characterization of various cell lines from different ampullary cancer subtypes and cancer associated fibroblast-mediated responses. BMC Cancer. 2016;16:195 pubmed publisher..We suggest that the most appropriate cell line model for intestinal-like AMPAC is the SNU869, while others seem to reflect aggressive AMPAC subtypes. ..
- Lai Z, Schilling O. Identification of Protease Cleavage Sites by Charge-Based Enrichment of Protein N-Termini. Methods Mol Biol. 2017;1579:199-207 pubmed publisher..In addition, this straightforward method can be used in combination with gel-based pre-separation of proteins to allow better estimation of the molecular weight of the identified cleavage product of a given bioactive substrate. ..
- Lai Z, Schilling O. System-Wide Profiling of Protein Amino Termini from Formalin-Fixed, Paraffin-Embedded Tissue Specimens for the Identification of Novel Substrates. Methods Mol Biol. 2017;1574:105-114 pubmed publisher..As a result, protein amino termini are analyzed using mass spectrometers to elucidate the biological regulation of protease-substrate interactions in healthy and diseased tissues. ..
- Chen C, Mayer B, Schilling O. Profiling of Protease Cleavage Sites by Proteome-Derived Peptide Libraries and Quantitative Proteomics. Methods Mol Biol. 2017;1574:197-204 pubmed publisher..The method is fast, cost-effective, and suited for proteases with narrow or loose specificity. ..
- Koczorowska M, Friedemann C, Geiger K, Follo M, Biniossek M, Schilling O. Differential effect of TGF? on the proteome of cancer associated fibroblasts and cancer epithelial cells in a co-culture approach - a short report. Cell Oncol (Dordr). 2017;40:639-650 pubmed publisher..In addition, we found that the TGF? treated CAFs exhibited increased N-cadherin levels. From our data we conclude that CAFs respond to TGF? treatment by changing their proteome composition, while ETCs appear to be rather resilient. ..
- Föll M, Fahrner M, Gretzmeier C, Thoma K, Biniossek M, Kiritsi D, et al. Identification of tissue damage, extracellular matrix remodeling and bacterial challenge as common mechanisms associated with high-risk cutaneous squamous cell carcinomas. Matrix Biol. 2018;66:1-21 pubmed publisher..The proteins identified here could serve as potential diagnostic markers and therapeutic targets in high-risk cSCCs. ..
- Müller A, Föll M, Heckelmann B, Kiefer S, Werner M, Schilling O, et al. Proteomic Characterization of Prostate Cancer to Distinguish Nonmetastasizing and Metastasizing Primary Tumors and Lymph Node Metastases. Neoplasia. 2018;20:140-151 pubmed publisher..This study highlights the usefulness of a combined proteomic-IHC approach to explore novel aspects in tumor biology. Our initial results open novel opportunities for follow-up studies. ..
- WeiÃŸer J, Lai Z, Bronsert P, Kuehs M, Drendel V, Timme S, et al. Quantitative proteomic analysis of formalin-fixed, paraffin-embedded clear cell renal cell carcinoma tissue using stable isotopic dimethylation of primary amines. BMC Genomics. 2015;16:559 pubmed publisher..Our study establishes isotopic amine dimethylation as a versatile tool for quantitative proteomic analysis of FFPE specimens and underlines proteome alterations in ccRCC. ..
- Knopf J, Tholen S, Koczorowska M, De Wever O, Biniossek M, Schilling O. The stromal cell-surface protease fibroblast activation protein-Î± localizes to lipid rafts and is recruited to invadopodia. Biochim Biophys Acta. 2015;1853:2515-25 pubmed publisher..In essence, we provide one of the first interactome analyses of a cell surface protease and translate these results into novel biological aspects of a marker protein for cancer-associated fibroblasts. ..
- Videm P, Gunasekaran D, Schröder B, Mayer B, Biniossek M, Schilling O. Automated peptide mapping and protein-topographical annotation of proteomics data. BMC Bioinformatics. 2014;15:207 pubmed publisher..As an exemplary application, we show its usage in the proteomic analysis of regulated intramembrane proteolysis. ImproViser is the first tool to enable automated peptide mapping of the widely-used protXML format. ..