Macrophage expression of tartrate-resistant acid phosphatase as a prognostic indicator in colon cancer

Recent research has indicated that separate populations of macrophages are associated with differing outcomes in cancer survival. In our study, we examine macrophage expression of tartrate-resistant acid phosphatase (TRAP) and its effect on survival in colon cancer. Immunohistochemical analysis on colorectal adenocarcinomas confirmed macrophage expression of TRAP. Co-localization of TRAP with CD68, a pan-macrophage marker, revealed that TRAP is present in some but not all sub-populations of macrophages. Further co-localization of TRAP with CD163, an M2 marker, revealed that TRAP is expressed by both M2 and non-M2 macrophages. TRAP expression was then measured using the AQUA method of quantitative immunofluorescence in a tissue microarray consisting of 233 colorectal cancer patients seen at Yale-New Haven Hospital. Survival analysis revealed that patients with high TRAP expression have a 22 % increase in 5-year survival (uncorrected log-rank p = 0.025) and a 47 % risk reduction in disease-specific death (p = 0.02). This finding was validated in a second cohort of older cases consisting of 505 colorectal cancer patients. Patients with high TRAP expression in the validation set had a 19 % increase in 5-year survival (log-rank p = 0.0041) and a 52 % risk reduction in death (p = 0.0019). These results provide evidence that macrophage expression of TRAP is associated with improved outcome and implicates TRAP as a potential biomarker in colon cancer.     

Effects of a synthetic antitumoral catechin and its tyrosinase-processed product on the structural properties of phosphatidylcholine membranes

Catechin flavonoids are the main components of green tea extracts which present broad potential physiological activities. Several of their biological activities seem to affect membrane-dependent cellular processes and it is known that some catechins interact with phospholipid membranes. In this study we examine the interactions of a 3-O-(3,4,5-trimethoxybenzoyl)-(−)-catechin (TMCG), and its quinone methide (QM) activated product with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membranes by means of differential scanning calorimetry, X-ray diffraction, Fourier-Transform infrared spectroscopy and molecular dynamics simulation. We report that there are extensive interactions between TMCG and DPPC involving the perturbation of the thermotropic gel to liquid crystalline phase transition of the phospholipid, the decrease of bilayer thickness and the promotion of interdigitated gel phase, together with an increase of the hydrogen bonding pattern of the interfacial region of the bilayer. In contrast, QM shows a weak interaction with the phospholipid bilayer. Molecular dynamics simulation indicates that TMCG locates in the interior of the bilayer, while QM is found interacting with the surface of the membrane. The observations are interpreted in terms of the mechanism of membrane prodrug activation and the underlying membrane perturbations of the biological actions of natural catechins.     

Synthesis and biological evaluation of ((4-keto)-phenoxy)methyl biphenyl-4-sulfonamides: A class of potent aggrecanase-1 inhibitors

The prevention of aggrecan (a key component of cartilage) cleavage via the inhibition of aggrecanase-1 may provide a unique opportunity to stop the progression of cartilage degradation in osteoarthritis. The evaluation of a series of biphenylsulfonamides resulted in the identification of the ((4-keto)-phenoxy)methyl biphenyl-4-sulfonamides analogs (19–21 and 24) with improved Agg-1 inhibition and MMP-2, MMP-13 activity.     

Functional analysis of <Emphasis Type="Italic">SlEZ1</Emphasis> a tomato <Emphasis Type="Italic">Enhancer of zeste</Emphasis> (<Emphasis Type="Italic">E(z))</Emphasis> gene demonstrates a role in flower development

The Enhancer of Zeste (E(z)) Polycomb group (PcG) proteins, which are encoded by a small gene family in Arabidopsis thaliana, have been shown to participate to the control of flowering and seed development. For the time being, little is known about the function of these proteins in other plants. In tomato E(z) proteins are encoded by at least two genes namely SlEZ1 and SlEZ2 while a third gene, SlEZ3, is likely to encode a truncated non-functional protein. The analysis of the corresponding mRNA demonstrates that these two genes are differentially regulated during plant and fruit development. We also show that SlEZ1 and SlEZ2 are targeted to the nuclei. These results together with protein sequence analysis makes it likely that both proteins are functional E(z) proteins. The characterisation of SlEZ1 RNAi lines suggests that although there might be some functional redundancy between SlEZ1 and SlEZ2 in most plant organs, the former protein is likely to play specific function in flower development.     

Characterisation of vortex shedding in vascular anastomosis models using pulsed Doppler ultrasound.

Vortex shedding at vascular anastomoses were investigated in vitro using a 20 MHz pulsed-wave Doppler velocimeter. Centreline velocity measurements were made at various axial distances in simplified polyurethane models of proximal and distal end-to-side anastomoses of angles 15, 30, 45, 60 and 80 degrees using pulsatile flow waveforms similar to those in femoropopliteal bypass grafts. The in-phase and quadrature Doppler signals were recorded and the maximum frequency waveform, averaged over 64 cycles, was obtained using short-time Fourier transform. A fourth-order Butterworth low-pass filter was employed to separate the vortex velocity signal from the convective velocity. The vortex signal envelope was calculated using a Hilbert transform method and the vortex amplitude was taken as the maximum of this envelope. The results show that higher vortex amplitude were found in the proximal anastomoses and under resting flow conditions. Although the vortex amplitudes generally increased with angles of anastomosis, they were found to be higher in the 60 degrees than in the 80 degrees proximal anastomosis. The vortex structures were investigated using spectrograms and these show prominent features at 40-50 Hz indicative of the short-duration oscillatory signals during the decelerative phase of systole expected from the passage of vortices. The study indicates that flow disturbances due to vortex shedding may be a common feature in femoropopliteal bypass grafts.     

Intracellular localization of human cytidine deaminase. Identification of a functional nuclear localization signal.

The cytidine deaminases belong to the family of multisubunit enzymes that catalyze the hydrolytic deamination of their substrate to a corresponding uracil product. They play a major role in pyrimidine nucleoside and nucleotide salvage. The intracellular distribution of cytidine deaminase and related enzymes has previously been considered to be cytosolic. Here we show that human cytidine deaminase (HCDA) is present in the nucleus. A highly specific, affinity purified polyclonal antibody against HCDA was used to analyze the intracellular localization of native HCDA in a variety of mammalian cells by in situ immunochemistry. Native HCDA was found to be present in the nucleus as well as the cytoplasm in several cell types. Indirect immunofluorescence microscopy indicated a predominantly nuclear localization of FLAG-tagged HCDA overexpressed in these cells. We have identified an amino-terminal bipartite nuclear localization signal that is both necessary and sufficient to direct HCDA and a non-nuclear reporter protein to the nucleus. We also show HCDA binding to the nuclear import receptor, importin alpha. Similar putative bipartite nuclear localization sequences are found in other cytidine/deoxycytidylate deaminases. The results presented here suggest that the pyrimidine nucleotide salvage pathway may operate in the nucleus. This localization may have implications in the regulation of nucleoside and nucleotide metabolism and nucleic acid biosynthesis.     

Ensuring the quality and specificity of preregistrations

Researchers face many, often seemingly arbitrary, choices in formulating hypotheses, designing protocols, collecting data, analyzing data, and reporting results. Opportunistic use of “researcher degrees of freedom” aimed at obtaining statistical significance increases the likelihood of obtaining and publishing false-positive results and overestimated effect sizes. Preregistration is a mechanism for reducing such degrees of freedom by specifying designs and analysis plans before observing the research outcomes. The effectiveness of preregistration may depend, in part, on whether the process facilitates sufficiently specific articulation of such plans. In this preregistered study, we compared 2 formats of preregistration available on the OSF: Standard Pre-Data Collection Registration and Prereg Challenge Registration (now called “OSF Preregistration,” http://osf.io/prereg/). The Prereg Challenge format was a “structured” workflow with detailed instructions and an independent review to confirm completeness; the “Standard” format was “unstructured” with minimal direct guidance to give researchers flexibility for what to prespecify. Results of comparing random samples of 53 preregistrations from each format indicate that the “structured” format restricted the opportunistic use of researcher degrees of freedom better (Cliff’s Delta = 0.49) than the “unstructured” format, but neither eliminated all researcher degrees of freedom. We also observed very low concordance among coders about the number of hypotheses (14%), indicating that they are often not clearly stated. We conclude that effective preregistration is challenging, and registration formats that provide effective guidance may improve the quality of research.

Researchers face many, often seemingly arbitrary choices in formulating hypotheses, designing protocols, collecting data, analyzing data, and reporting results. A study of two formats of preregistration available on the OSF reveals that the opportunistic use of researcher degrees of freedom aimed at obtaining statistical significance is restricted by using more extensive preregistration guidelines; however, these guidelines should be further improved.     

Role of TGF-β receptor III localization in polarity and breast cancer progression

The majority of breast cancers originate from the highly polarized luminal epithelial cells lining the breast ducts. However, cell polarity is often lost during breast cancer progression. The type III transforming growth factor-β cell surface receptor (TβRIII) functions as a suppressor of breast cancer progression and also regulates the process of epithelial-to-mesenchymal transition (EMT), a consequence of which is the loss of cell polarity. Many cell surface proteins exhibit polarized expression, being targeted specifically to the apical or basolateral domains. Here we demonstrate that TβRIII is basolaterally localized in polarized breast epithelial cells and that disruption of the basolateral targeting of TβRIII through a single amino acid mutation of proline 826 in the cytosolic domain results in global loss of cell polarity through enhanced EMT. In addition, the mistargeting of TβRIII results in enhanced proliferation, migration, and invasion in vitro and enhanced tumor formation and invasion in an in vivo mouse model of breast carcinoma. These results suggest that proper localization of TβRIII is critical for maintenance of epithelial cell polarity and phenotype and expand the mechanisms by which TβRIII prevents breast cancer initiation and progression.