605 research outputs found
Elevated expression of VEGFR-3 in lymphatic endothelial cells from lymphangiomas
<p>Abstract</p> <p>Background</p> <p>Lymphangiomas are neoplasias of childhood. Their etiology is unknown and a causal therapy does not exist. The recent discovery of highly specific markers for lymphatic endothelial cells (LECs) has permitted their isolation and characterization, but expression levels and stability of molecular markers on LECs from healthy and lymphangioma tissues have not been studied yet. We addressed this problem by profiling LECs from normal dermis and two children suffering from lymphangioma, and also compared them with blood endothelial cells (BECs) from umbilical vein, aorta and myometrial microvessels.</p> <p>Methods</p> <p>Lymphangioma tissue samples were obtained from two young patients suffering from lymphangioma in the axillary and upper arm region. Initially isolated with anti-CD31 (PECAM-1) antibodies, the cells were separated by FACS sorting and magnetic beads using anti-podoplanin and/or LYVE-1 antibodies. Characterization was performed by FACS analysis, immunofluorescence staining, ELISA and micro-array gene analysis.</p> <p>Results</p> <p>LECs from foreskin and lymphangioma had an almost identical pattern of lymphendothelial markers such as podoplanin, Prox1, reelin, cMaf and integrin-α1 and -α9. However, LYVE-1 was down-regulated and VEGFR-2 and R-3 were up-regulated in lymphangiomas. Prox1 was constantly expressed in LECs but not in any of the BECs.</p> <p>Conclusion</p> <p>LECs from different sources express slightly variable molecular markers, but can always be distinguished from BECs by their Prox1 expression. High levels of VEGFR-3 and -2 seem to contribute to the etiology of lymphangiomas.</p
Clouded leopard phylogeny revisited: support for species recognition and population division between Borneo and Sumatra
This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens
Better prediction by use of co-data: Adaptive group-regularized ridge regression
For many high-dimensional studies, additional information on the variables,
like (genomic) annotation or external p-values, is available. In the context of
binary and continuous prediction, we develop a method for adaptive
group-regularized (logistic) ridge regression, which makes structural use of
such 'co-data'. Here, 'groups' refer to a partition of the variables according
to the co-data. We derive empirical Bayes estimates of group-specific
penalties, which possess several nice properties: i) they are analytical; ii)
they adapt to the informativeness of the co-data for the data at hand; iii)
only one global penalty parameter requires tuning by cross-validation. In
addition, the method allows use of multiple types of co-data at little extra
computational effort.
We show that the group-specific penalties may lead to a larger distinction
between `near-zero' and relatively large regression parameters, which
facilitates post-hoc variable selection. The method, termed GRridge, is
implemented in an easy-to-use R-package. It is demonstrated on two cancer
genomics studies, which both concern the discrimination of precancerous
cervical lesions from normal cervix tissues using methylation microarray data.
For both examples, GRridge clearly improves the predictive performances of
ordinary logistic ridge regression and the group lasso. In addition, we show
that for the second study the relatively good predictive performance is
maintained when selecting only 42 variables.Comment: 15 pages, 2 figures. Supplementary Information available on first
author's web sit
An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies
BACKGROUND: The use of environmental DNA for species detection via metabarcoding is growing rapidly. We present a co-designed lab workflow and bioinformatic pipeline to mitigate the 2 most important risks of environmental DNA use: sample contamination and taxonomic misassignment. These risks arise from the need for polymerase chain reaction (PCR) amplification to detect the trace amounts of DNA combined with the necessity of using short target regions due to DNA degradation. FINDINGS: Our high-throughput workflow minimizes these risks via a 4-step strategy: (i) technical replication with 2 PCR replicates and 2 extraction replicates; (ii) using multi-markers (12S,16S,CytB); (iii) a "twin-tagging," 2-step PCR protocol; and (iv) use of the probabilistic taxonomic assignment method PROTAX, which can account for incomplete reference databases. Because annotation errors in the reference sequences can result in taxonomic misassignment, we supply a protocol for curating sequence datasets. For some taxonomic groups and some markers, curation resulted in >50% of sequences being deleted from public reference databases, owing to (i) limited overlap between our target amplicon and reference sequences, (ii) mislabelling of reference sequences, and (iii) redundancy. Finally, we provide a bioinformatic pipeline to process amplicons and conduct PROTAX assignment and tested it on an invertebrate-derived DNA dataset from 1,532 leeches from Sabah, Malaysia. Twin-tagging allowed us to detect and exclude sequences with non-matching tags. The smallest DNA fragment (16S) amplified most frequently for all samples but was less powerful for discriminating at species rank. Using a stringent and lax acceptance criterion we found 162 (stringent) and 190 (lax) vertebrate detections of 95 (stringent) and 109 (lax) leech samples. CONCLUSIONS: Our metabarcoding workflow should help research groups increase the robustness of their results and therefore facilitate wider use of environmental and invertebrate-derived DNA, which is turning into a valuable source of ecological and conservation information on tetrapods
miR-9-5p Exerts a Dual Role in Cervical Cancer and Targets Transcription Factor TWIST1
Squamous cell carcinoma (SCC) and adenocarcinoma (AC) represent the major cervical cancer histotypes. Both histotypes are caused by infection with high-risk HPV (hrHPV) and are associated with deregulated microRNA expression. Histotype-dependent expression has been observed for miR-9-5p, showing increased expression in SCC and low expression in AC. Here, we studied the regulation and functionality of miR-9-5p in cervical SCCs and ACs using cervical tissue samples and hrHPV-containing cell lines. Expression and methylation analysis of cervical tissues revealed that low levels of miR-9-5p in ACs are linked to methylation of its precursor genes, particularly miR-9-1. Stratification of tissue samples and hrHPV-containing cell lines suggested that miR-9-5p depends on both histotype and hrHPV type, with higher expression in SCCs and HPV16-positive cells. MiR-9-5p promoted cell viability and anchorage independence in cervical cancer cell lines SiHa (SCC, HPV16) and CaSki (metastasized SCC, HPV16), while it played a tumor suppressive role in HeLa (AC, HPV18). TWIST1, a transcription factor involved in epithelial-to-mesenchymal transition (EMT), was established as a novel miR-9-5p target. Our results show that miR-9-5p plays a dual role in cervical cancer in a histotype- and hrHPV type-dependent manner. MiR-9-5p mediated silencing of TWIST1 suggests two distinct mechanisms towards EMT in cervical cancer
The antiarrhythmic compound efsevin directly modulates voltageâdependent anion channel 2 by binding to its inner wall and enhancing mitochondrial Ca2+ uptake
Background and Purpose
The synthetic compound efsevin was recently identified to suppress arrhythmogenesis in models of cardiac arrhythmia, making it a promising candidate for antiarrhythmic therapy. Its activity was shown to be dependent on the voltageâdependent anion channel 2 (VDAC2) in the outer mitochondrial membrane. Here, we investigated the molecular mechanism of the efsevinâVDAC2 interaction.
Experimental Approach
To evaluate the functional interaction of efsevin and VDAC2, we measured currents through recombinant VDAC2 in planar lipid bilayers. Using molecular ligandâprotein docking and mutational analysis, we identified the efsevin binding site on VDAC2. Finally, physiological consequences of the efsevinâinduced modulation of VDAC2 were analysed in HLâ1 cardiomyocytes.
Key Results
In lipid bilayers, efsevin reduced VDAC2 conductance and shifted the channel's open probability towards less anionâselective closed states. Efsevin binds to a binding pocket formed by the inner channel wall and the poreâlining Nâterminal αâhelix. Exchange of amino acids N207, K236 and N238 within this pocket for alanines abolished the channel's efsevinâresponsiveness. Upon heterologous expression in HLâ1 cardiomyocytes, both channels, wildâtype VDAC2 and the efsevinâinsensitive VDAC2AAA restored mitochondrial Ca2+ uptake, but only wildâtype VDAC2 was sensitive to efsevin.
Conclusion and Implications
In summary, our data indicate a direct interaction of efsevin with VDAC2 inside the channel pore that leads to modified gating and results in enhanced SRâmitochondria Ca2+ transfer. This study sheds new light on the function of VDAC2 and provides a basis for structureâaided chemical optimization of efsevin
VEGF and VEGF-C: Specific Induction of Angiogenesis and Lymphangiogenesis in the Differentiated Avian Chorioallantoic Membrane
AbstractThe lymphangiogenic potency of endothelial growth factors has not been studied to date. This is partially due to the lack ofin vivolymphangiogenesis assays. We have studied the lymphatics of differentiated avian chorioallantoic membrane (CAM) using microinjection of Mercox resin, semi- and ultrathin sectioning, immunohistochemical detection of fibronectin and α-smooth muscle actin, andin situhybridization with VEGFR-2 and VEGFR-3 probes. CAM is drained by lymphatic vessels which are arranged in a regular pattern. Arterioles and arteries are accompanied by a pair of interconnected lymphatics and form a plexus around bigger arteries. Veins are also associated with lymphatics, particularly larger veins, which are surrounded by a lymphatic plexus. The lymphatics are characterized by an extremely thin endothelial lining, pores, and the absence of a basal lamina. Patches of the extracellular matrix can be stained with an antibody against fibronectin. Lymphatic endothelial cells of differentiated CAM show ultrastructural features of this cell type. CAM lymphatics do not possess mediae. In contrast, the lymphatic trunks of the umbilical stalk are invested by a single but discontinuous layer of smooth muscle cells. CAM lymphatics express VEGFR-2 and VEGFR-3. Both the regular pattern and the typical structure of these lymphatics suggest that CAM is a suitable site to study thein vivoeffects of potential lymphangiogenic factors. We have studied the effects of VEGF homo- and heterodimers, VEGF/PlGF heterodimers, and PlGF and VEGF-C homodimers on Day 13 CAM. All the growth factors containing at least one VEGF chain are angiogenic but do not induce lymphangiogenesis. PlGF-1 and PlGF-2 are neither angiogenic nor lymphangiogenic. VEGF-C is the first lymphangiogenic factor and seems to be highly chemoattractive for lymphatic endothelial cells. It induces proliferation of lymphatic endothelial cells and development of new lymphatic sinuses which are directed immediately beneath the chorionic epithelium. Our studies show that VEGF and VEGF-C are specific angiogenic and lymphangiogenic growth factors, respectively
Mouse lung contains endothelial progenitors with high capacity to form blood and lymphatic vessels
<p>Abstract</p> <p>Background</p> <p>Postnatal endothelial progenitor cells (EPCs) have been successfully isolated from whole bone marrow, blood and the walls of conduit vessels. They can, therefore, be classified into circulating and resident progenitor cells. The differentiation capacity of resident lung endothelial progenitor cells from mouse has not been evaluated.</p> <p>Results</p> <p>In an attempt to isolate differentiated mature endothelial cells from mouse lung we found that the lung contains EPCs with a high vasculogenic capacity and capability of <it>de novo </it>vasculogenesis for blood and lymph vessels.</p> <p>Mouse lung microvascular endothelial cells (MLMVECs) were isolated by selection of CD31<sup>+ </sup>cells. Whereas the majority of the CD31<sup>+ </sup>cells did not divide, some scattered cells started to proliferate giving rise to large colonies (> 3000 cells/colony). These highly dividing cells possess the capacity to integrate into various types of vessels including blood and lymph vessels unveiling the existence of local microvascular endothelial progenitor cells (LMEPCs) in adult mouse lung. EPCs could be amplified > passage 30 and still expressed panendothelial markers as well as the progenitor cell antigens, but not antigens for immune cells and hematopoietic stem cells. A high percentage of these cells are also positive for Lyve1, Prox1, podoplanin and VEGFR-3 indicating that a considerabe fraction of the cells are committed to develop lymphatic endothelium. Clonogenic highly proliferating cells from limiting dilution assays were also bipotent. Combined <it>in vitro </it>and <it>in vivo </it>spheroid and matrigel assays revealed that these EPCs exhibit vasculogenic capacity by forming functional blood and lymph vessels.</p> <p>Conclusion</p> <p>The lung contains large numbers of EPCs that display commitment for both types of vessels, suggesting that lung blood and lymphatic endothelial cells are derived from a single progenitor cell.</p
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