Structural basis for inhibition of the epidermal growth factor receptor by cetuximab

SummaryRecent structural studies of epidermal growth factor receptor (EGFR) family extracellular regions have identified an unexpected mechanism for ligand-induced receptor dimerization that has important implications for activation and inhibition of these receptors. Here we describe the 2.8 Å resolution X-ray crystal structure of the antigen binding (Fab) fragment from cetuximab (Erbitux), an inhibitory anti-EGFR antibody, in complex with the soluble extracellular region of EGFR (sEGFR). The sEGFR is in the characteristic “autoinhibited” or “tethered” inactive configuration. Cetuximab interacts exclusively with domain III of sEGFR, partially occluding the ligand binding region on this domain and sterically preventing the receptor from adopting the extended conformation required for dimerization. We suggest that both these effects contribute to potent inhibition of EGFR activation

Differential hormone-dependent transcriptional activation and -repression by naturally occurring human glucocorticoid receptor variants

The molecular mechanisms underlying primary glucocorticoid resistance or hypersensitivity are not well understood. Using transfected COS-1 cells as a model system, we studied gene regulation by naturally occurring mutants of the glucocorticoid receptor (GR) with single-point mutations in the regions encoding the ligand-binding domain or the N-terminal domain reflecting different phenotypic expression. We analyzed the capacity of these GR variants to regulate transcription from different promoters, either by binding directly to positive or negative glucocorticoid-response elements on the DNA or by interfering with protein-protein interactions. Decreased dexamethasone (DEX) binding to GR variants carrying mutations in the ligand-binding domain correlated well with decreased capacity to activate transcription from the mouse mammary tumor virus (MMTV) promoter. One variant, D641V, which suboptimally activated MMTV promoter-mediated transcription, repressed a PRL promoter element containing a negative glucocorticoid-response element with wild type activity. DEX-induced repression of transcription from elements of the intercellular adhesion molecule-1 promoter via nuclear factor-kappaB by the D641V variant was even more efficient compared with the wild type GR. We observed a general DEX-responsive AP-1-mediated transcriptional repression of the collagenase-1 promoter, even when receptor variants did not activate transcription from the MMTV promoter. Our findings indicate that different point mutations in the GR can affect separate pathways of gene regulation in a differential fashion, which can explain the various phenotypes observed

Logarithmic Corrections in Dynamic Isotropic Percolation

Based on the field theoretic formulation of the general epidemic process we study logarithmic corrections to scaling in dynamic isotropic percolation at the upper critical dimension d=6. Employing renormalization group methods we determine these corrections for some of the most interesting time dependent observables in dynamic percolation at the critical point up to and including the next to leading correction. For clusters emanating from a local seed at the origin we calculate the number of active sites, the survival probability as well as the radius of gyration.Comment: 9 pages, 3 figures, version to appear in Phys. Rev.

Induced Parity Nonconserving Interaction and Enhancement of Two-Nucleon Parity Nonconserving Forces

Two-nucleon parity nonconserving (PNC) interaction induced by the single-particle PNC weak potential and the two-nucleon residual strong interaction is considered. An approximate analytical formula for this Induced PNC Interaction (IPNCI) between proton and neutron is derived ($Q({\bf r} {\bf \sigma}_{p} \times {\bf \sigma}_{n}) \delta({\bf r}_{p}-{\bf r}_{n})$), and the interaction constant is estimated. As a result of coherent contributions from the nucleons to the PNC potential, IPNCI is an order of magnitude stronger ($\sim A^{1/3}$) than the residual weak two-nucleon interaction and has a different coordinate and isotopic structure (e.g., the strongest part of IPNCI does not contribute to the PNC mean field). IPNCI plays an important role in the formation of PNC effects, e.g., in neutron-nucleus reactions. In that case, it is a technical way to take into account the contribution of the distant (small) components of a compound state which dominates the result. The absence of such enhancement ($\sim A^{1/3}$) in the case of T- and P-odd interaction completes the picture.Comment: Phys. Rev. C, to appear; 17 pages, revtex 3, no figure

Nuclear Level Density and the Determination of Thermonuclear Rates for Astrophysics

The prediction of cross sections for nuclei far off stability is crucial in the field of nuclear astrophysics. We discuss the model mostly employed for such calculations: the statistical model (Hauser-Feshbach). Special emphasis is put on the uncertainties arising from nuclear level density descriptions and an improved global description is presented. Furthermore, criteria for the applicability of the statistical model are investigated and a "map" for the applicability of the model to reactions of stable and unstable nuclei with neutral and charged particles is given.Comment: REVTeX paper + 7 B/W figures + 2 color figures; PRC, in press. Also available at http://quasar.physik.unibas.ch/preps.htm

Histological assessment of paxgene tissue fixation and stabilization reagents

Within SPIDIA, an EC FP7 project aimed to improve pre analytic procedures, the PAXgene Tissue System (PAXgene), was designed to improve tissue quality for parallel molecular and morphological analysis. Within the SPIDIA project promising results were found in both genomic and proteomic experiments with PAXgene-fixed and paraffin embedded tissue derived biomolecules. But, for this technology to be accepted for use in both clinical and basic research, it is essential that its adequacy for preserving morphology and antigenicity is validated relative to formalin fixation. It is our aim to assess the suitability of PAXgene tissue fixation for (immuno)histological methods. Normal human tissue specimens (n = 70) were collected and divided into equal parts for fixation either with formalin or PAXgene. Sections of the obtained paraffin-embedded tissue were cut and stained. Morphological aspects of PAXgene-fixed tissue were described and also scored relative to formalin-fixed tissue. Performance of PAXgene-fixed tissue in immunohistochemical and in situ hybridization assays was also assessed relative to the corresponding formalin-fixed tissues. Morphology of PAXgene-fixed paraffin embedded tissue was well preserved and deemed adequate for diagnostics in most cases. Some antigens in PAXgene-fixed and paraffin embedded sections were detectable without the need for antigen retrieval, while others were detected using standard, formalin fixation based, immunohistochemistry protocols. Comparable results were obtained with in situ hybridization and histochemical stains. Basically all assessed histological techniques were found to be applicable to PAXgene-fixed and paraffin embedded tissue. In general results obtained with PAXgene-fixed tissue are comparable to those of formalin-fixed tissue. Compromises made in morphology can be called minor compared to the advantages in the molecular pathology possibilities

Search for a strongly decaying neutral charmed pentaquark

We present a search for a charmed pentaquark decaying strongly to $D^{(*)-}p$. Finding no evidence for such a state, we set limits on the cross section times branching ratio relative to $D^{*-}$ and $D^-$ under particular assumptions about the production mechanism.Comment: To be published in Physics Letters

Evaluation of a short RNA within Prostate Cancer Gene 3 in the predictive role for future cancer using non-malignant prostate biopsies.

BACKGROUND: Prostate Cancer 3 (PCA3) is a long non-coding RNA (ncRNA) upregulated in prostate cancer (PCa). We recently identified a short ncRNA expressed from intron 1 of PCA3. Here we test the ability of this ncRNA to predict the presence of cancer in men with a biopsy without PCa. METHODS: We selected men whose initial biopsy did not identify PCa and selected matched cohorts whose subsequent biopsies revealed PCa or benign tissue. We extracted RNA from the initial biopsy and measured PCA3-shRNA2, PCA3 and PSA (qRT-PCR). RESULTS: We identified 116 men with and 94 men without an eventual diagnosis of PCa in 2-5 biopsies (mean 26 months), collected from 2002-2008. The cohorts were similar for age, PSA and surveillance period. We detected PSA and PCA3-shRNA2 RNA in all samples, and PCA3 RNA in 90% of biopsies. The expression of PCA3 and PCA3-shRNA2 were correlated (Pearson's r = 0.37, p<0.01). There was upregulation of PCA3 (2.1-fold, t-test p = 0.02) and PCA3-shRNA2 (1.5-fold) in men with PCa on subsequent biopsy, although this was not significant for the latter RNA (p = 0.2). PCA3 was associated with the future detection of PCa (C-index 0.61, p = 0.01). This was not the case for PCA3-shRNA2 (C-index 0.55, p = 0.2). CONCLUSIONS: PCA3 and PCA3-shRNA2 expression are detectable in historic biopsies and their expression is correlated suggesting co-expression. PCA3 expression was upregulated in men with PCa diagnosed at a future date, the same did not hold for PCA3-shRNA2. Futures studies should explore expression in urine and look at a time course between biopsy and PCa detection

Observation of the decay \psip\rar\kstark

Using 14 million $\psi(2S)$ events collected with the BESII detector, branching fractions of \psip\rar\kstarkpm and \kstarknn are determined to be: \calB(\psip\rar\kstarkpm)=(2.9^{+1.3}_{-1.7}\pm0.4)\times 10^{-5} and \calB(\psip\rar\kstarknn)=(13.3^{+2.4}_{-2.7}\pm1.9)\times 10^{-5}. The results confirm the violation of the "12%" rule for these two decay channels with higher precision. A large isospin violation between the charged and neutral modes is observed.Comment: 5 pages, 3 figure