Comparative transcriptomic analyses reveal activation of the epithelial-mesenchymal transition program in non-metastasizing low grade pseudomyxoma peritonei.

Epithelial-mesenchymal transition (EMT), angiogenesis, cell adhesion and extracellular matrix (ECM) interaction are essential for colorectal cancer (CRC) metastasis. Low grade mucinous neoplasia of the appendix (LAMN) and its advanced state low grade pseudomyxoma peritonei (lgPMP) show local aggressiveness with very limited metastatic potential as opposed to CRC. To better understand the underlying processes that foster or impede metastatic spread, we compared LAMN, lgPMP, and CRC with respect to their molecular profile with subsequent pathway analysis. LAMN, lgPMP and (mucinous) CRC cases were subjected to transcriptomic analysis utilizing Poly(A) RNA sequencing. Successfully sequenced cases (LAMN n = 10, 77%, lgPMP n = 13, 100% and CRC n = 8, 100%) were investigated using bioinformatic and statistical tests (differential expression analysis, hierarchical clustering, principal component analysis and gene set enrichment analysis). We identified a gene signature of 28 genes distinguishing LAMN, lgPMP and CRC neoplasias. Ontology analyses revealed that multiple pathways including EMT, ECM interaction and angiogenesis are differentially regulated. Fifty-three significantly differentially regulated gene sets were identified between lgPMP and CRC followed by CRC vs. LAMN (n = 21) and lgPMP vs. LAMN (n = 16). Unexpectedly, a substantial enrichment of the EMT gene set was observed in lgPMP vs. LAMN (FDR=0.011) and CRC (FDR=0.004). Typical EMT markers were significantly upregulated (Vimentin, TWIST1, N-Cadherin) or downregulated (E-Cadherin) in lgPMP. However, MMP1 and MMP3 levels, associated with EMT, ECM and metastasis, were considerably higher in CRC. We show that the different tumor biological behaviour and metastatic spread pattern of midgut malignancies is reflected in a different gene expression profile. We revealed a strong activation of the EMT program in non-metastasizing lgPMP vs. CRC. Hence, although EMT is considered a key step in hematogenous spread, successful EMT does not necessarily lead to hematogenous dissemination. This emphasizes the need for further pathway analyses and forms the basis for mechanistic and therapy-targeting research.

In-vitro model to mimic T cell subset change in human PDAC organoid co-culture.

PURPOSE: Immunotherapies have largely failed as treatment options for pancreatic ductal adenocarcinoma (PDAC). In this field, clinical translational studies into personalized treatment are of fundamental importance. In our study, we model tumor-cell immune-cell interactions in a co-culture of primary human PDAC organoids and matched peripheral blood mononuclear cells (PBMCs). METHODS: Using flow cytometry, we evaluated changes in T cell subtypes upon co-culture of patient-derived PDAC organoids and matched PBMCs. RESULTS: After co-culturing PDAC organoids with PBMCs, we observed changes in CD4+, CD8+ and Treg cell populations. We observed favorable clinical outcome in patients whose PBMCs reacted to the co-culture with organoids. CONCLUSION: This experimental model allows to investigate interactions between patient derived PDAC organoids and their PBMCs. This co-culture system could serve as a preclinical platform to guide personalized therapeutic strategies in the future.

Computation of Burgers vectors from elastic strain and lattice rotation data.

A theoretical framework for computation of Burgers vectors from strain and lattice rotation data in materials with low dislocation density is presented, as well as implementation into a computer program to automate the process. The efficacy of the method is verified using simulated data of dislocations with known results. A three-dimensional dataset retrieved from Bragg coherent diffraction imaging (BCDI) and a two-dimensional dataset from high-resolution transmission Kikuchi diffraction (HR-TKD) are used as inputs to demonstrate the reliable identification of dislocation positions and accurate determination of Burgers vectors from experimental data. For BCDI data, the results found using our approach show very close agreement to those expected from empirical methods. For the HR-TKD data, the predicted dislocation position and the computed Burgers vector showed fair agreement with the expected result, which is promising considering the substantial experimental uncertainties in this dataset. The method reported in this paper provides a general and robust framework for determining dislocation position and associated Burgers vector, and can be readily applied to data from different experimental techniques.

An X-ray chimney extending hundreds of parsecs above and below the Galactic Centre.

Evidence has mounted in recent decades that outflows of matter and energy from the central few parsecs of our Galaxy have shaped the observed structure of the Milky Way on a variety of larger scales1. On scales of 15 parsecs, the Galactic Centre has bipolar lobes that can be seen in both the X-ray and radio parts of the spectrum2,3, indicating broadly collimated outflows from the centre, directed perpendicular to the Galactic plane. On larger scales, approaching the size of the Galaxy itself, γ-ray observations have revealed the so-called 'Fermi bubble' features4, implying that our Galactic Centre has had a period of active energy release leading to the production of relativistic particles that now populate huge cavities on both sides of the Galactic plane. The X-ray maps from the ROSAT all-sky survey show that the edges of these cavities close to the Galactic plane are bright in X-rays4-6. At intermediate scales (about 150 parsecs), radio astronomers have observed the Galactic Centre lobe, an apparent bubble of emission seen only at positive Galactic latitudes7,8, but again indicative of energy injection from near the Galactic Centre. Here we report prominent X-ray structures on these intermediate scales (hundreds of parsecs) above and below the plane, which appear to connect the Galactic Centre region to the Fermi bubbles. We propose that these structures, which we term the Galactic Centre 'chimneys', constitute exhaust channels through which energy and mass, injected by a quasi-continuous train of episodic events at the Galactic Centre, are transported from the central few parsecs to the base of the Fermi bubbles4.

Type 2 diabetes patients have accelerated cartilage matrix degeneration compared to diabetes free controls: data from the Osteoarthritis Initiative.

PURPOSE: Osteoarthritis (OA) and diabetes mellitus (DM) share common risk factors with a potential underlying relationship between both diseases. The purpose of this study was to investigate the longitudinal effects of DM on cartilage deterioration over 24-months with MR-based T2 relaxation time measurements. METHODS: From the Osteoarthritis Initiative (OAI) cohort 196 diabetics were matched in small sets for age, sex, BMI and Kellgren-Lawrence score with 196 non-diabetic controls. Knee cartilage semi-automatic segmentation was performed on 2D multi-slice multi-echo spin-echo sequences. Texture of cartilage T2 maps was obtained via grey level co-occurrence matrix analysis. Linear regression analysis was used to compare cross-sectional and changes in T2 and texture parameters between the groups. RESULTS: Both study groups were similar in age (63.3 vs 63.0 years, P = 0.70), BMI (30.9 vs 31.2 kg/m2, P = 0.52), sex (female 53.6% vs 54.1%, P = 0.92) and KL score distribution (P = 0.97). In diabetics, except for the patella, all compartments showed a significantly higher increase in mean T2 values when compared to non-diabetic controls. Global T2 values increased almost twice as much; 1.77ms vs 0.98ms (0.79ms [CI: 0.39,1.19]) (P < 0.001). Additionally, global T2 values showed a significantly higher increase in the bone layer (P = 0.006), and in a separate analysis of the texture parameters, diabetics also showed consistently higher texture values (P < 0.05), indicating a more disordered cartilage composition. CONCLUSION: Cartilage T2 values in diabetics show a faster increase with a consistently more heterogeneous cartilage texture composition. DM seems to be a risk factor for developing early OA with an accelerated degeneration of the articular cartilage in the knee.

Cross-disorder risk gene CACNA1C differentially modulates susceptibility to psychiatric disorders during development and adulthood.

Single-nucleotide polymorphisms (SNPs) in CACNA1C, the α1C subunit of the voltage-gated L-type calcium channel Cav1.2, rank among the most consistent and replicable genetics findings in psychiatry and have been associated with schizophrenia, bipolar disorder and major depression. However, genetic variants of complex diseases often only confer a marginal increase in disease risk, which is additionally influenced by the environment. Here we show that embryonic deletion of Cacna1c in forebrain glutamatergic neurons promotes the manifestation of endophenotypes related to psychiatric disorders including cognitive decline, impaired synaptic plasticity, reduced sociability, hyperactivity and increased anxiety. Additional analyses revealed that depletion of Cacna1c during embryonic development also increases the susceptibility to chronic stress, which suggest that Cav1.2 interacts with the environment to shape disease vulnerability. Remarkably, this was not observed when Cacna1c was deleted in glutamatergic neurons during adulthood, where the later deletion even improved cognitive flexibility, strengthened synaptic plasticity and induced stress resilience. In a parallel gene × environment design in humans, we additionally demonstrate that SNPs in CACNA1C significantly interact with adverse life events to alter the risk to develop symptoms of psychiatric disorders. Overall, our results further validate Cacna1c as a cross-disorder risk gene in mice and humans, and additionally suggest a differential role for Cav1.2 during development and adulthood in shaping cognition, sociability, emotional behavior and stress susceptibility. This may prompt the consideration for pharmacological manipulation of Cav1.2 in neuropsychiatric disorders with developmental and/or stress-related origins.

Observation of crack growth in a polycrystalline ferroelectric by synchrotron X-ray diffraction.

Pre-cracked samples of unpoled, polycrystalline, soft ferroelectric lead zirconate titanate were subjected to electrical and mechanical loading whilst using synchrotron X-ray diffraction to map strain-fields. Clear evidence is found of switching around the crack tip and development of a crack-wake. A J-integral estimate based on strain-field data provided a sensitive measure of strain changes during loading. Electrical loading did not cause crack advance or crack-tip switching; this provides evidence for electrically permeable crack models. There was also enhancement of electrically-driven switching in the crack-wake region. The results provide improved understanding and a resource for testing fracture models in ferroelectrics.

Complementary activities of DOT1L and Menin inhibitors in MLL-rearranged leukemia.

Chromosomal rearrangements of the mixed lineage leukemia (MLL/KMT2A) gene leading to oncogenic MLL-fusion proteins occur in ~10% of acute leukemias and are associated with poor clinical outcomes, emphasizing the need for new treatment modalities. Inhibition of the DOT1-like histone H3K79 methyltransferase (DOT1L) is a specific therapeutic approach for such leukemias that is currently being tested in clinical trials. However, in most MLL-rearranged leukemia models responses to DOT1L inhibitors are limited. Here, we performed deep-coverage short hairpin RNA sensitizer screens in DOT1L inhibitor-treated MLL-rearranged leukemia cell lines and discovered that targeting additional nodes of MLL complexes concomitantly with DOT1L inhibition bears great potential for superior therapeutic results. Most notably, combination of a DOT1L inhibitor with an inhibitor of the MLL-Menin interaction markedly enhanced induction of differentiation and cell killing in various MLL disease models including primary leukemia cells, while sparing normal hematopoiesis and leukemias without MLL rearrangements. Gene expression analysis on human and murine leukemic cells revealed that target genes of MLL-fusion proteins and MYC were suppressed more profoundly upon combination treatment. Our findings provide a strong rationale for a novel targeted combination therapy that is expected to improve therapeutic outcomes in patients with MLL-rearranged leukemia.

Bragg coherent diffraction imaging and metrics for radiation damage in protein micro-crystallography.

The proliferation of extremely intense synchrotron sources has enabled ever higher-resolution structures to be obtained using data collected from smaller and often more imperfect biological crystals (Helliwell, 1984). Synchrotron beamlines now exist that are capable of measuring data from single crystals that are just a few micrometres in size. This provides renewed motivation to study and understand the radiation damage behaviour of small protein crystals. Reciprocal-space mapping and Bragg coherent diffractive imaging experiments have been performed on cryo-cooled microcrystals of hen egg-white lysozyme as they undergo radiation damage. Several well established metrics, such as intensity-loss and lattice expansion, are applied to the diffraction data and the results are compared with several new metrics that can be extracted from the coherent imaging experiments. Individually some of these metrics are inconclusive. However, combining metrics, the results suggest that radiation damage behaviour in protein micro-crystals differs from that of larger protein crystals and may allow them to continue to diffract for longer. A possible mechanism to account for these observations is proposed.

Non-Contact Measurement of Thermal Diffusivity in Ion-Implanted Nuclear Materials.

Knowledge of mechanical and physical property evolution due to irradiation damage is essential for the development of future fission and fusion reactors. Ion-irradiation provides an excellent proxy for studying irradiation damage, allowing high damage doses without sample activation. Limited ion-penetration-depth means that only few-micron-thick damaged layers are produced. Substantial effort has been devoted to probing the mechanical properties of these thin implanted layers. Yet, whilst key to reactor design, their thermal transport properties remain largely unexplored due to a lack of suitable measurement techniques. Here we demonstrate non-contact thermal diffusivity measurements in ion-implanted tungsten for nuclear fusion armour. Alloying with transmutation elements and the interaction of retained gas with implantation-induced defects both lead to dramatic reductions in thermal diffusivity. These changes are well captured by our modelling approaches. Our observations have important implications for the design of future fusion power plants.

Laue-DIC: a new method for improved stress field measurements at the micrometer scale.

A better understanding of the effective mechanical behavior of polycrystalline materials requires an accurate knowledge of the behavior at a scale smaller than the grain size. The X-ray Laue microdiffraction technique available at beamline BM32 at the European Synchrotron Radiation Facility is ideally suited for probing elastic strains (and associated stresses) in deformed polycrystalline materials with a spatial resolution smaller than a micrometer. However, the standard technique used to evaluate local stresses from the distortion of Laue patterns lacks accuracy for many micromechanical applications, mostly due to (i) the fitting of Laue spots by analytical functions, and (ii) the necessary comparison of the measured pattern with the theoretical one from an unstrained reference specimen. In the present paper, a new method for the analysis of Laue images is presented. A Digital Image Correlation (DIC) technique, which is essentially insensitive to the shape of Laue spots, is applied to measure the relative distortion of Laue patterns acquired at two different positions on the specimen. The new method is tested on an in situ deformed Si single-crystal, for which the prescribed stress distribution has been calculated by finite-element analysis. It is shown that the new Laue-DIC method allows determination of local stresses with a strain resolution of the order of 10(-5).

Lifetime of high-order thickness resonances of thin silicon membranes.

Femtosecond laser pulses are used to excite and probe high-order longitudinal thickness resonances at a frequency of ∼270 GHz in suspended Si membranes with thickness ranging from 0.4 to 15 µm. The measured acoustic lifetime scales linearly with the membrane thickness and is shown to be controlled by the surface specularity which correlates with roughness characterized by atomic force microscopy. Observed Q-factor values up to 2400 at room temperature result from the existence of a local maximum of the material Q in the sub-THz range. However, surface specularity would need to be improved over measured values of ∼0.5 in order to achieve high Q values in nanoscale devices. The results support the validity of the diffuse boundary scattering model in analyzing thermal transport in thin Si membranes.

Radiation damage in a micron-sized protein crystal studied via reciprocal space mapping and Bragg coherent diffractive imaging.

For laboratory and synchrotron based X-ray sources, radiation damage has posed a significant barrier to obtaining high-resolution structural data from biological macromolecules. The problem is particularly acute for micron-sized crystals where the weaker signal often necessitates the use of higher intensity beams to obtain the relevant data. Here, we employ a combination of techniques, including Bragg coherent diffractive imaging to characterise the radiation induced damage in a micron-sized protein crystal over time. The approach we adopt here could help screen for potential protein crystal candidates for measurement at X-ray free election laser sources.

Type 2 cGMP-dependent protein kinase regulates homeostasis by blocking c-Jun N-terminal kinase in the colon epithelium.

Analysis of knockout animals indicates that 3',5'cyclic guanosine monophosphate (cGMP) has an important role in gut homeostasis but the signaling mechanism is not known. The goals of this study were to test whether increasing cGMP could affect colon homeostasis and determine the mechanism. We increased cGMP in the gut of Prkg2(+/+) and Prkg2(-/-) mice by treating with the PDE5 inhibitor Vardenafil (IP). Proliferation, differentiation and apoptosis in the colon mucosa were then quantitated. Vardenafil (Vard) treatment increased cGMP in colon mucosa of all mice, but reduced proliferation and apoptosis, and increased differentiation only in Prkg2(+/+) mice. Vard and cGMP treatment also increased dual specificity protein phosphatase 10 (DUSP10) expression and reduced phospho-c-Jun N-terminal kinase (JNK) levels in the colon mucosa of Prkg2(+/+) but not Prkg2(-/-) mice. Treatment of Prkg2(-/-) mice with the JNK inhibitor SP600125 reversed the defective homeostasis observed in these animals. Activation of protein kinase G2 (PKG2) in goblet-like LS174T cells increased DUSP10 expression and reduced JNK activity. PKG2 also increased goblet cell-specific MUC2 expression in LS174T cells, and this process was blocked by DUSP10-specific siRNA. The ability of cGMP signaling to inhibit JNK-induced apoptosis in vivo was demonstrated using dextran sodium sulfate (DSS) to stress the colon epithelium. Vard was a potent inhibitor of DSS-induced epithelial apoptosis, and significantly blocked pathological endpoints in this model of experimental colitis. In conclusion, Vard treatment activates cGMP signaling in the colon epithelium. Increased PKG2 activity alters homeostasis by suppressing proliferation and apoptosis while promoting differentiation. The PKG2-dependent mechanism was shown to involve increased DUSP10 and subsequent inhibition of JNK activity.

Intrinsic to extrinsic phonon lifetime transition in a GaAs-AlAs superlattice.

We have measured the lifetimes of two zone-center longitudinal acoustic phonon modes, at 320 and 640 GHz, in a 14 nm GaAs/2 nm AlAs superlattice structure. By comparing measurements at 296 and 79 K we separate the intrinsic contribution to phonon lifetime determined by phonon-phonon scattering from the extrinsic contribution due to defects and interface roughness. At 296 K, the 320 GHz phonon lifetime has approximately equal contributions from intrinsic and extrinsic scattering, whilst at 640 GHz it is dominated by extrinsic effects. These measurements are compared with intrinsic and extrinsic scattering rates in the superlattice obtained from first-principles lattice dynamics calculations. The calculated room-temperature intrinsic lifetime of longitudinal phonons at 320 GHz is in agreement with the experimentally measured value of 0.9 ns. The model correctly predicts the transition from predominantly intrinsic to predominantly extrinsic scattering; however the predicted transition occurs at higher frequencies. Our analysis indicates that the 'interfacial atomic disorder' model is not entirely adequate and that the observed frequency dependence of the extrinsic scattering rate is likely to be determined by a finite correlation length of interface roughness.

[Cancer through the handling of biological agents]. / Krebsdurch den Umgang mit Biostoffen.

In March 2012, the International Agency for Research on Cancer (IARC), an agency of the World Health Organization (WHO) issued a list. It lists 108 agents for which there is sufficient evidence of a carcinogenic effect in humans, depending on the cancer site. The vast majority of these actions can take place in the workplace. What is new in the list, in addition to the long-known cancer-causing chemical and physical agents now biomaterials have been added, such as hepatitis B virus, hepatitis C virus, Human papilloma virus, Helicobacter pylori. This paper gives an overview on the basis of identifying carcinogenic agents and can be displayed in certain cancer site and occupational exposure occupational diseases according to the occupational disease regulation.

Diagnóstico de enfermedades gastroenterológicas en provincia / Diagnosis of gastroenterological diseases in provincial setting

The “diagnosis of gastroenterological diseases in province setting” does not differ from the diagnosis made in the Metropolitan Region (MR). However, in the MR, there are more complex centers with greater numbers of gastroenterologists. The specialists are more concentrated in the private health sector, leaving the public health sector lacking medical hours, at the MR and province. Digestive pathologies expressed by mortality and hospital discharge rates, vary in the different regions of the country, particularly in the case of gastric cancer, which is more frequent in the less developed areas in the central and southern regions of the country. Regions are well equipped in terms of imaging and laboratory for gastroenterological purposes, in both public and private sectors, however, the private sector has achieved more development in the last years.

El “diagnóstico de enfermedades gastroenterológicas en provincia” no difiere mayormente con el que se hace en la Región Metropolitana (RM), no obstante existen centros con implementación más compleja y mayor número de especialistas en gastroenterología a nivel central. La distribución de gastroenterólogos es mayor en el área privada de salud, con gran carencia de horas médicas en el sistema público, tanto en la RM como en provincia. Las patologías digestivas expresadas por tasas de mortalidad y egresos hospitalarios difieren en las distintas zonas del país, especialmente el cáncer gástrico, en áreas más pobres, preferentemente zona centro sur del país. Las regiones cuentan con implementación en gastroenterología, imágenes y laboratorio tanto en el sector público, como privado, no obstante este último ha logrado mayor desarrollo en los últimos años.

Microbial diagnostics in patients with presumed severe infection in the emergency department.

INTRODUCTION: Sepsis in the early stage is a common disease in emergency medicine, and rapid diagnosis is essential. Our aim was to compare pathogen diagnosis using blood cultures (BC) and the multiplex polymerase chain reaction (PCR) test.Methods. At total of 211 patients admitted to the multidisciplinary emergency department of our university hospital between 2006 and 2009 with suspected severe infection from any origin were studied. Blood samples for BC (aerobic and anaerobic) and multiplex PCR were taken for identification of infectious microorganisms immediately after hospital admission. Results of the BC and PCR correlated with procalcitonin concentration (PCT) and clinical diagnosis of sepsis (≥2 positive SIRS criteria) as well as with severity of disease at admission and with clinical outcome measures. RESULTS: Results of the BC were available in 200 patients (94.8%) and PCR were available in 119 patients (56.3%), respectively. In total, 87 BC (43.5%) were positive and identified 94 pathogens. In 45 positive PCRs, 47 pathogens (37.8%) were found. Identical results were obtained in 81.4%. In addition, BC identified 9 Gram-positive and 3 Gram-negative bacteria, while PCR added 5 Gram-negative pathogens. Coagulase-negative staphylococci were detected in blood cultures only (n=20, 21.3%), whereas PCR identified significantly more Gram-negative bacteria than BC. In patients with positive PCR results, the PCT level was significantly higher than in patients with negative PCR (15.0±23.3 vs. 8.8±32.8 ng/ml, p<0.001). This difference was not observed for BC (10.6±25.7 vs. 11.6±44.9 ng/ml, p=0.075). The APACHE II score correlated with PCR (19.2±9.1 vs. 15.8±8.9, p<0.05) and was also higher in positive BC (18.7±8.7 vs. 14.4±8.0, p<0.01). Positive PCR and BC were correlated with negative clinical outcomes (e.g., transfer to ICU, mechanical ventilation, renal replacement therapy, death). CONCLUSION: In patients admitted with suspected severe infection, a high percentage of positive BC and PCR were observed. Positive findings in the PCR correlate with elevated levels of PCT and high APACHE II scores.