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Stefan Koch

Publications and source records attributed to Stefan Koch.

7 recordsLinked to original sources
PubMed2026

Comprehensive proximity proteomics expand the known interactome of the oncoprotein β-catenin.

The oncoprotein β-catenin has critical roles in cell adhesion and cell signalling. β-catenin affects human physiology and pathology through numerous interaction partners, of which many have been discovered by standard affinity purification-based proteomics. However, the interaction landscape of β-catenin remains incompletely understood, highlighting a need for new experimental approaches for the exploration of β-catenin biology. Proximity proteomics, which facilitate the discovery of molecules vicinal to proteins-of-interest by mass spectrometry, have recently emerged as a powerful complementary tool for the study of protein-protein interactions, but have not been applied to β-catenin so far. We investigated the interactome of β-catenin in model cell lines by proximity proteomics using expression constructs with the biotin ligases BioID and TurboID. Mass spectrometry analyses following biotin labelling identified numerous candidate interactors of β-catenin, including many that had not been observed in earlier studies using standard proteomics. Enrichment analyses suggested that proximity proteomics capture proteins associated with the known biological functions of β-catenin, including cell adhesion, Wnt/β-catenin signalling, and transcription regulation. The molecular tools and data generated in this study provide new insights into β-catenin biology and highlight potential new regulators of β-catenin function that warrant further exploration.

beta Catenin↗
PubMed2006

Comparative study of the intestinal mucus barrier in normal and inflamed colon.

AIM: To study the role of mucus in the spatial separation of intestinal bacteria from mucosa. PATIENTS AND METHODS: Mucus barrier characteristics were evaluated using histological material obtained by biopsy from purged colon, colon prepared with enema and material from untreated appendices fixed with non-aqueous Carnoy solution. Bacteria were evaluated using fluorescence in situ hybridization, with bacterial 16S RNA probes and related to the periodic acid Schiff alcian blue stain. Biopsies from controls (n = 20), patients with self-limiting colitis (SLC; n = 20), ulcerative colitis (n = 20) and 60 randomly selected appendices were investigated. RESULTS: The mucosal surface beneath the mucus layer was free of bacteria in > or =80% of the normal appendices and biopsies from controls. The thickness of the mucus layer and its spread decreased with increasing severity of the inflammation; the epithelial surface showed bacterial adherence, epithelial tissue defects and deep mucosal infiltration with bacteria and leucocytes. Bacteria and leucocytes were found within mucus in all biopsy specimens from patients with ulcerative colitis, SLC, and acute appendicitis. The concentration of bacteria within mucus was inversely correlated to the numbers of leucocytes. CONCLUSIONS: The large bowel mucus layer effectively prevents contact between the highly concentrated luminal bacteria and the epithelial cells in all parts of the normal colon. Colonic inflammation is always accompanied by breaks in the mucus barrier. Although the inflammatory response gradually reduces the number of bacteria in mucus and faeces, the inflammation itself is not capable of preventing bacterial migration, adherence to and invasion of the mucosa.

Acute Disease↗
PubMed2006

Apoptosis as a therapeutic tool in IBD?

Defective apoptosis of mucosal cell populations seems to be a relevant pathogenetic mechanism in inflammatory bowel disease (IBD). It has been suggested that the induction of apoptosis in various effector cells may be a relevant therapeutic mechanism in IBD. Indeed, it was shown that different drugs used for treatment of IBD have the capacity to induce apoptosis in T cells or monocytes in vitro and in vivo. However, it remains unclear whether these observations are related to clinical efficacy of these agents. TNF-alpha is one of the most relevant proinflammatory mediators in IBD and anti-TNF treatment has been shown to be of particular benefit for patients with IBD. It could subsequently be shown that various anti-TNF-alpha agents, such as infliximab and adalimumab, can induce apoptosis in activated monocytes and lymphocytes in vitro and in vivo. This mechanism requires reverse signaling via transmembranous TNF, thereby eliciting a signal transduction cascade that results in programmed cell death. Although other mechanisms might also contribute to the clinical effect of anti-TNF-alpha, current data suggest that apoptosis is a relevant mechanism that is associated with clinical efficacy of anti-TNF agents. Induction of apoptosis in activated monocytes or T cells may be regarded as therapeutic tool not only for anti-TNF agents, but also for other drugs used in IBD. Future strategies should focus on identification of mechanisms that prevent apoptosis in the mucosa of patients with IBD and in targeting apoptotic pathways as a therapeutic strategy in IBD.

Apoptosis↗
PubMed2006

Chemotherapy with gemcitabine, paclitaxel, and cisplatin in the treatment of patients with advanced transitional cell carcinoma of the urothelium.

Chemotherapeutic agents are active in advanced bladder cancer, and various combinations have shown promising results. The objective of this study was to evaluate the efficacy of combination chemotherapy with gemcitabine, paclitaxel, and cisplatin in patients with advanced urothelial carcinoma. Fifty-nine patients with metastatic or locally advanced transitional cell carcinoma of the urothelium were treated between 2000 and 2005. No patient had received any previous systemic chemotherapy. All patients received chemotherapy intravenously with gemcitabine at a dose of 1000 mg/m(2) on days 1 and 8, paclitaxel at a dose of 80 mg/m(2) on days 1 and 8, and cisplatin at a dose of 50 mg/m(2) on day 2. Treatment courses were repeated every 21 days. After completion of four to six courses in this regimen an intravenous application of gemcitabine was repeated every 28 days at a dose of 1000 mg/m(2). Fifty-nine patients were treated between 2000 and 2005. Nine patients (15%) had >or=1 visceral site of metastases, and no patient had received any previous systemic chemotherapy. Forty-eight patients (81%) achieved objective responses to treatment (56% complete responses). The median actuarial survival was 22 months, and the actuarial 1-year and 2-year survival rates were 68% and 39%, respectively. After a median follow-up of 17.5 months, 29 patients remained alive and 25 were free of disease progression. The median progression-free survival for the entire group was 10 months. The median survival time for patients with an Eastern Cooperative Oncology Group (ECOG) status of 0, 1, and 2 was 37.5, 17, and 12 months, respectively. Grade 3-4 neutropenia occurred in 39% of the patients. The combination of gemcitabine, paclitaxel, and cisplatin is a highly effective and tolerable regimen for patients with advanced urothelial carcinoma. This treatment should be considered as a suitable option that deserves further prospective evaluation. The ECOG performance status is an important predictive factor for survival.

Aged↗
PubMed2005

Crystal structures of active SRC kinase domain complexes.

c-Src was the first proto-oncoprotein to be identified, and has become the focus of many drug discovery programs. Src structures of a major inactive form have shown how the protein kinase is rigidified by several interdomain interactions; active configurations of Src are generated by release from this "assembled" or "bundled" form. Despite the importance of Src as a drug target, there is relatively little structural information available regarding the presumably more flexible active forms. Here we report three crystal structures of a dimeric active c-Src kinase domain, in an apo and two ligand complexed forms, with resolutions ranging from 2.9A to 1.95A. The structures show how the kinase domain, in the absence of the rigidifying interdomain interactions of the inactivation state, adopts a more open and flexible conformation. The ATP site inhibitor CGP77675 binds to the protein kinase with canonical hinge hydrogen bonds and also to the c-Src specific threonine 340. In contrast to purvalanol B binding in CDK2, purvalanol A binds in c-Src with a conformational change in a more open ATP pocket.

Animals↗
PubMed2005

Association of Csk to VE-cadherin and inhibition of cell proliferation.

Vascular endothelial cadherin (VE-cadherin) mediates contact inhibition of cell growth in quiescent endothelial cell layers. Searching for proteins that could be involved in VE-cadherin signaling, we found the cytosolic C-terminal Src kinase (Csk), a negative regulator of Src family kinases. We show that Csk binds via its SH2 domain to the phosphorylated tyrosine 685 of VE-cadherin. VE-cadherin recruits Csk to cell contacts and both proteins can be co-precipitated from cell lysates of transfected cells and endothelial cells. Association of VE-cadherin and Csk in endothelial cells increased with increasing cell density. CHO cells expressing the tyrosine replacement mutant VE-cadherin-Y685F grow to higher cell densities than cells expressing wild-type VE-cadherin. Overexpression of Csk in these cells under an inducible promoter inhibits cell proliferation in the presence and absence of VE-cadherin, but not in the presence of VE-cadherin-Y685F. Reduction of Csk expression by RNA interference enhances endothelial cell proliferation. Our results suggest that the phosphorylated tyrosine residue 685 of VE-cadherin and probably the binding of Csk to this site are involved in inhibition of cell growth triggered by cell density.

Animals↗
PubMed2005

Differential stripping: determination of the amount of topically applied substances penetrated into the hair follicles.

The determination of penetration pathways of topically applied substances into the skin is the subject of several investigations. Recently, follicular penetration has become a major focus of interest. To date, a direct, non-invasive quantification of the amount of topically applied substance penetrated into the follicles had not been possible. The development of such a method was the aim of this study. Therefore, the advantages of both stripping techniques, tape stripping and cyanoacrylate skin surface biopsy, were combined and evaluated. Tape stripping was used to remove the part of the stratum corneum that contained the topically applied dye. Subsequently, the follicular contents were ripped off by cyanoacrylate skin surface biopsy. The combined method termed "differential stripping" was evaluated in vitro and in vivo, and the amount of topically applied fluorescent dye penetrated into the hair follicles was quantified after different penetration times. After 30 min, 5% of the recovered concentration of sodium fluorescein was found in the follicular infundibula, where it was still detectable after 48 h. Altogether, the results of this investigation revealed that differential stripping is a new method that can be used to study the penetration of topically applied substances into the follicular infundibula non-invasively and selectively.

Administration, Topical↗