Genetic model of colorectal cancer and B-Raf(V600E) dependent cancer traits

Für ein genetisches Modell B-Raf(V600E)-mutierter Darmkrebszellen und korrespondierender Wildtyp-Zellen wurde erstmalig in Deutschland das Somatic Cell Gene Targeting eingesetzt. Dabei konnte demonstriert werden, dass RKO eine Oncogene Addiction bezüglich der BRAF-Mutation aufweist. Als weitere B-Raf(V600E)-abhängige Effekte wurden die Selbstversorgung mit Wachstumssignalen (Self-Sufficiency of Growth Signals) und die Resistenz gegen Apoptose in dem Modell festgestellt. Darüber hinaus war die proliferative Kontaktinhibition in V600E-mutierten Klonen durch eine verstärkte Akt-Phosphorylierung aufgehoben und wurde nach Knockout der mutierten Allele im Wildtyp-Zellklon RBW-1 wieder hergestellt. Somit konnten vier zentrale Merkmale der Onkogenität dem mutierten B-Raf(V600E) zugeordnet werden. Andere onkogene Mechanismen waren dagegen vermutlich aufgrund einer Mutation der PI3-Kinase auch in BRAF-Wildtyp-Zellen noch intakt. So waren das Wachstum unter guten Kulturbedingungen und eine verstärkte Expression des EGF-Rezeptors unter Mangelbedingungen nicht vom BRAF-Mutationsstatus abhängig. Außerdem behielten Wildtyp-Zellen ihre Immortalisierung bei und zeigten weiterhin kein relevantes Auftreten von Seneszenz. Es wurden neue Spleißvarianten des BRAF-Gens gefunden und basal charakterisiert. Die alternativen Transkripte zeigten keine Kinase-Aktivität und waren in einem Ausmaß nachweisbar, das eine physiologische Bedeutung vermuten lässt. Hinsichtlich der Herkunft-Allele alternativer Isoformen und den Ursachen für das Auftreten alternativen Spleißens wurden neue Erkenntnisse gewonnen, die zudem die Interpretation publizierter Daten erleichtern. Es wurde gezeigt, dass die durch E-Cadherin vermittelten Zellkontakte essentiell für die epitheliale Komponente der intestinalen Barriere sind. Darüber hinaus wurde der Einfluss von E-Cadherin auf die Ausreifung sekretierender Zellen im Darm ermittelt und damit ein weiterer entscheidender Mechanismus der Abwehr bakterieller Invasionen aufgeklärt.In order to establish a genetic model of B-Raf V600E mutated colorectal cancer cells and corresponding wild-type tumor cells, the method of somatic cell gene targeting was successfully applied for the first time in Germany. Using this approach it was demonstrated that RKO cells show an oncogene addiction for B-Raf(V600E). Furthermore, self-sufficiency of growth signals and resistance against apoptosis were found to be B-Raf(V600E) dependent effects. Moreover, contact inhibition of proliferation was found in RBW-1 wild-type cells while it was abrogated in V600E mutated cell clones by an increased phosphorylation of Akt kinase. Therefore, four crucial hallmarks of cancer were dependent on the B-Raf(V600E) mutation. Presumably due to a mutation of PI3 kinase in RKO cells other cogenic mechanisms were still intact in RBW-1 wild-type cells. Namely the high proliferation rates under optimal conditions and the increase of EGFR expression under serum deprivation were independent from BRAF mutation status. Additionally, BRAF wild-type cells kept their immortality and still showed no relevant amount of cellular senescence. New splicing variants of the BRAF gene were found and characterized. The correspondent gene products showed no kinase activity and were detectable in amounts that indicate a physiological role. New insights into the allelic origin of alternative isoforms have been gained facilitating the interpretation of published data. It has been shown that E-Cadherin mediated cell-cell contacts are essential for the epithelial contribution of the intestinal barrier. Moreover, the role of E-Cadherin in the maturation of secreting cells in the intestine was determined, elucidating a crucial role in the defense against bacterial invasion

Genetic targeting of B-Raf(V600E) affects survival and proliferation and identifies selective agents against BRAF-mutant colorectal cancer cells

Background: Colorectal cancers carrying the B-Raf V600E-mutation are associated with a poor prognosis. The purpose of this study was to identify B-Raf(V600E)-mediated traits of cancer cells in a genetic in vitro model and to assess the selective sensitization of B-Raf(V600E)-mutant cancer cells towards therapeutic agents. Methods: Somatic cell gene targeting was used to generate subclones of the colorectal cancer cell line RKO containing either wild-type or V600E-mutant B-Raf kinase. Cell-biologic analyses were performed in order to link cancer cell traits to the BRAF-mutant genotype. Subsequently, the corresponding tumor cell clones were characterized pharmacogenetically to identify therapeutic agents exhibiting selective sensitivity in B-Raf(V600E)-mutant cells. Results: Genetic targeting of mutant BRAF resulted in restoration of sensitivity to serum starvation-induced apoptosis and efficiently inhibited cell proliferation in the absence of growth factors. Among tested agents, the B-Raf inhibitor dabrafenib was found to induce a strong V600E-dependent shift in cell viability. In contrast, no differential sensitizing effect was observed for conventional chemotherapeutic agents (mitomycin C, oxaliplatin, paclitaxel, etoposide, 5-fluorouracil), nor for the targeted agents cetuximab, sorafenib, vemurafenib, RAF265, or for inhibition of PI3 kinase. Treatment with dabrafenib efficiently inhibited phosphorylation of the B-Raf downstream targets Mek 1/2 and Erk 1/2. Conclusion: Mutant BRAF alleles mediate self-sufficiency of growth signals and serum starvation-induced resistance to apoptosis. Targeting of the BRAF mutation leads to a loss of these hallmarks of cancer. Dabrafenib selectively inhibits cell viability in B-Raf(V600E) mutant cancer cells

A quantitative study of particle size effects in the magnetorelaxometry of magnetic nanoparticles using atomic magnetometry

The discrimination of immobilised superparamagnetic iron oxide nanoparticles (SPIONs) against SPIONs in fluid environments via their magnetic relaxation behaviour is a powerful tool for bio-medical imaging. Here we demonstrate that a gradiometer of laser-pumped atomic magnetometers can be used to record accurate time series of the relaxing magnetic field produced by pre-polarised SPIONs. We have investigated dry in vitro maghemite nanoparticle samples with different size distributions (average radii ranging from 14 to 21 nm) and analysed their relaxation using the Néel–Brown formalism. Fitting our model function to the magnetorelaxation (MRX) data allows us to extract the anisotropy constant K and the saturation magnetisation MS of each sample. While the latter was found not to depend on the particle size, we observe that K is inversely proportional to the (time- and size-) averaged volume of the magnetised particle fraction. We have identified the range of SPION sizes that are best suited for MRX detection considering our specific experimental conditions and sample preparation technique

Lack of Pericytes Leads to Endothelial Hyperplasia and Abnormal Vascular Morphogenesis

The association of pericytes (PCs) to newly formed blood vessels has been suggested to regulate endothelial cell (EC) proliferation, survival, migration, differentiation, and vascular branching. Here, we addressed these issues using PDGF-B– and PDGF receptor-β (PDGFR-β)–deficient mice as in vivo models of brain angiogenesis in the absence of PCs. Quantitative morphological analysis showed that these mutants have normal microvessel density, length, and number of branch points. However, absence of PCs correlates with endothelial hyperplasia, increased capillary diameter, abnormal EC shape and ultrastructure, changed cellular distribution of certain junctional proteins, and morphological signs of increased transendothelial permeability. Brain endothelial hyperplasia was observed already at embryonic day (E) 11.5 and persisted throughout development. From E 13.5, vascular endothelial growth factor-A (VEGF-A) and other genes responsive to metabolic stress became upregulated, suggesting that the abnormal microvessel architecture has systemic metabolic consequences. VEGF-A upregulation correlated temporally with the occurrence of vascular abnormalities in the placenta and dilation of the heart. Thus, although PC deficiency appears to have direct effects on EC number before E 13.5, the subsequent increased VEGF-A levels may further abrogate microvessel architecture, promote vascular permeability, and contribute to formation of the edematous phenotype observed in late gestation PDGF-B and PDGFR-β knock out embryos

UFO 2.0: the ‘Universal Feynman Output’ format

We present an update of the Universal FeynRules Output model format, commonly known as the UFO format, that is used by several automated matrix-element generators and high-energy physics software. We detail different features that have been proposed as extensions of the initial format during the last ten years, and collect them in the current second version of the model format that we coin the Universal Feynman Output format. Following the initial philosophy of the UFO, they consist of flexible and modular additions to address particle decays, custom propagators, form factors, the renormalisation group running of parameters and masses, and higher-order quantum corrections

Tracing the Reionization-Epoch Intergalactic Medium with Metal Absorption Lines

IGM metal absorption lines observed in z>6 spectra offer the opportunity to probe early feedback processes, the nature of enriching sources, and the topology of reionization. We run high-resolution cosmological simulations including galactic outflows to study the observability and physical properties of 5 ions (C II, C IV, O I, Si II, Si IV) in absorption between z=8->5. We apply three cases for ionization conditions: Fully neutral, fully reionized, and a patchy model based on the flux from the nearest galaxy. We find that our simulations broadly fit available z~5-6 IGM metal-line data, although all observations cannot be accommodated with a single ionization condition. Variations in O I absorbers among sight lines seen by Becker et al. (2006) suggest significant neutral IGM patches down to z~6. Strong C IV absorbers at z~6 may be the result of ionization by their parent galaxy. Our outflows have typical speeds of ~200 km/s and mass loading factors of ~6. Such high mass loading is critical for enriching the IGM to the observed levels while curtailing star formation to match the observed z~6 rest-frame UV luminosity function. The volume filling factor of metals increases during this epoch, but only reaches ~1% for Z>10^(-3) Zsolar by z=5. C IV is an ideal tracer of IGM metals at z~5-6, with dropping global ionization fractions to either higher or lower redshifts. This results in a strongly increasing global Omega(C IV) from z=8->5, in contrast to its relative constancy from z=5->2. Our simulations do not support widespread early IGM enrichment from e.g. Pop III stars. High-z absorbers arise from metals on their first outward journey from galaxies, at distances less than 50 kpc. The galaxies responsible for early IGM enrichment have typical M*=10^(7.0-8.5) Msolar.Comment: Accepted to MNRAS, 34 pages, 24 figures, 1 table (Sections 5.5, 6.3.1, & 6.3.2 added as well as 5 figures and 1 table

The Bern Birth Cohort (BeBiCo) to study the development of the infant intestinal microbiota in a high-resource setting in Switzerland: rationale, design, and methods.

BACKGROUND Microbiota composition is fundamental to human health with the intestinal microbiota undergoing critical changes within the first two years of life. The developing intestinal microbiota is shaped by maternal seeding, breast milk and its complex constituents, other nutrients, and the environment. Understanding microbiota-dependent pathologies requires a profound understanding of the early development of the healthy infant microbiota. METHODS Two hundred and fifty healthy pregnant women (≥20 weeks of gestation) from the greater Bern area will be enrolled at Bern University hospital's maternity department. Participants will be followed as mother-baby pairs at delivery, week(s) 1, 2, 6, 10, 14, 24, 36, 48, 96, and at years 5 and 10 after birth. Clinical parameters describing infant growth and development, morbidity, and allergic conditions as well as socio-economic, nutritional, and epidemiological data will be documented. Neuro-developmental outcomes and behavior will be assessed by child behavior checklists at and beyond 2 years of age. Maternal stool, milk, skin and vaginal swabs, infant stool, and skin swabs will be collected at enrolment and at follow-up visits. For the primary outcome, the trajectory of the infant intestinal microbiota will be characterized by 16S and metagenomic sequencing regarding composition, metabolic potential, and stability during the first 2 years of life. Secondary outcomes will assess the cellular and chemical composition of maternal milk, the impact of nutrition and environment on microbiota development, the maternal microbiome transfer at vaginal or caesarean birth and thereafter on the infant, and correlate parameters of microbiota and maternal milk on infant growth, development, health, and mental well-being. DISCUSSION The Bern birth cohort study will provide a detailed description and normal ranges of the trajectory of microbiota maturation in a high-resource setting. These data will be compared to data from low-resource settings such as from the Zimbabwe-College of Health-Sciences-Birth-Cohort study. Prospective bio-sampling and data collection will allow studying the association of the microbiota with common childhood conditions concerning allergies, obesity, neuro-developmental outcomes , and behaviour. Trial registration The trial has been registered at www. CLINICALTRIALS gov , Identifier: NCT04447742

The basidiomycetous yeast Trichosporon may cause severe lung exacerbation in cystic fibrosis patients - clinical analysis of Trichosporon positive patients in a Munich cohort

Background: The relevance of Trichosporon species for cystic fibrosis (CF) patients has not yet been extensively investigated. Methods: The clinical course of CF patients with Trichosporon spp. in their respiratory secretions was analysed between 2003 and 2010 in the Munich CF center. All respiratory samples of 360 CF patients (0 - 52.4 years; mean FEV1 2010 81.4% pred) were investigated. Results: In 8 patients (2.2%, 3 male, mean age 21.8 years) Trichosporon was detected at least once. One patient carried T. asahii. One patient carried T. mycotoxinivorans and one patient T. inkin as determined by DNA sequencing. As potential risk factors for Trichosporon colonization steroid treatment, allergic bronchopulmonary aspergillosis (ABPA) and CF associated diabetes were identified in 6, 5, and 2 patients respectively. For one patient, the observation period was not long enough to determine the clinical course. One patient had only a single positive specimen and exhibited a stable clinical course determined by change in forced expiratory volume in one second (FEV1), body-mass-index (BMI), C-reactive protein (CRP) and immunoglobulin G (IgG). Of 6 patients with repeatedly positive specimen (mean detection period 4.5 years), 4 patients had a greater decline in FEV1 than expected, 2 of these a decline in BMI and 1 an increase in IgG above the reference range. 2 patients received antimycotic treatment: one patient with a tormenting dry cough subjectively improved under Amphotericin B inhalation; one patient with a severe exacerbation due to T. inkin was treated with i.v. Amphotericin B, oral Voriconazole and Posaconazole which stabilized the clinical condition. Conclusions: This study demonstrates the potential association of Trichosporon spp. with severe exacerbations in CF patients