Walter Luyten

A comprehensive summary of LL-37, the factotum human cathelicidin peptide

Cathelicidins are a group of antimicrobial peptides. Since their discovery, it has become clear that they are an exceptional class of peptides, with some members having pleiotropic effects. Not only do they possess an antibacterial, antifungal and antiviral function, they also show a chemotactic and immunostimulatory/-modulatory effect. Moreover, they are capable of inducing wound healing, angiogenesis and modulating apoptosis. Recent insights even indicate for a role of these peptides in cancer. This review provides a comprehensive summary of the most recent and relevant insights concerning the human cathelicidin LL-37.

Genomic profiling of the response of Candida albicans to itraconazole treatment using a DNA microarray

ABSTRACT The application of genome-wide expression profiling to determine how drugs achieve their therapeutic effect has provided the pharmaceutical industry with an exciting new tool for drug mode-of-action studies. We used DNA chip technology to study cellular responses to perturbations of ergosterol biosynthesis caused by the broad-spectrum antifungal agent itraconazole. Simultaneous examination of over 6,600 Candida albicans gene transcript levels, representing the entire genome, upon treatment of cells with 10 μM itraconazole revealed that 296 genes were responsive. For 116 genes transcript levels were decreased at least 2.5-fold, while for 180 transcript levels were similarly increased. A global upregulation ofERG genes in response to azole treatment was observed.ERG11 and ERG5 were found to be upregulated approximately 12-fold. In addition, a significant upregulation was observed for ERG6, ERG1, ERG3, ERG4, ERG10, ERG9, ERG26, ERG25, ERG2, IDII, HMGS, NCP1, and FEN2, all of which are genes known to be involved in ergosterol biosynthesis. The effects of itraconazole on a wide variety of known metabolic processes are discussed. As over 140 proteins with unknown function were responsive to itraconazole, our analysis might provide—in combination with phenotypic data—first hints of their potential function. The present report is the first to describe the application of DNA chip technology to study the response of a major human fungal pathogen to drug treatment.

p53-Independent Regulation of p21Waf1/Cip1 Expression and Senescence by Chk2

The Chk2 kinase is a tumor suppressor and key component of the DNA damage checkpoint response that encompasses cell cycle arrest, apoptosis, and DNA repair. It has also been shown to have a role in replicative senescence resulting from dysfunctional telomeres. Some of these functions are at least partially exerted through activation of the p53 transcription factor. High-level expression of virally transduced Chk2 in A549 human lung carcinoma cells led to arrested proliferation, apoptosis, and senescence. These were accompanied by various molecular events, including p21Waf1/Cip1 (p21) transcriptional induction, consistent with p53 activation. However, Chk2-dependent senescence and p21 transcriptional induction also occurred in p53-defective SK-BR-3 (breast carcinoma) and HaCaT (immortalized keratinocyte) cells. Small interfering RNA–mediated knockdown of p21 in p53-defective cells expressing Chk2 resulted in a decrease in senescent cells. These results revealed a p53-independent role for Chk2 in p21 induction and senescence that may contribute to tumor suppression and genotoxic treatment outcome.

Characterization of an orphan G protein-coupled receptor localized in the dorsal root ganglia reveals adenine as a signaling molecule

The cloning of novel G protein-coupled receptors and the search for their natural ligands, a process called reverse pharmacology, is an excellent opportunity to discover novel hormones and neurotransmitters. Based on a degenerate primer approach we have cloned a G protein-coupled receptor whose mRNA expression profile indicates highest expression in the dorsal root ganglia, specifically in the subset of small neurons, suggesting a role in nociception. In addition, moderate expression was found in lung, hypothalamus, peripheral blood leukocytes, and ovaries. Guided by a receptor-activation bioassay, we identified adenine as the endogenous ligand, which activated the receptor potently and with high structural stringency. Therefore, we propose to name this receptor as the adenine receptor. Hormonal functions have already been demonstrated for adenine derivatives like 6-benzylaminopurine in plants and 1-methyladenine in lower animals. Here, we demonstrate that adenine functions as a signaling molecule in mammals. This finding adds a third family besides P1 and P2 receptors to the class of purinergic receptors.

Peptidomics Coming of Age: A Review of Contributions from a Bioinformatics Angle

The term peptidomics for a new promising omics field was not introduced until the beginning of 2000. The approach has been proven successful in several domains such as neuroendocrine research and biomarker or drug discovery. This review reports on bioinformatics tools and methodologies within the peptidomics field and the application thereof. Obviously, a plethora of proteomics data analysis tools lends themselves to direct use in peptidomics because the latter is a subfield of the former, at least to a certain extent. Nevertheless, peptidomics-specific tool extensions, inventions, and validation procedures have emerged, and certain tools are more suitable for this subfield than others due to small but important differences in peptidomics sample analysis. This paper focuses on these topics. Furthermore, it gives a comprehensive overview of available online tools tailored to the peptidomics field. To conclude, an ideal pipeline for bioactive peptide identification is presented.

Cloning and expression of a human serotonin 5-HT4 receptor cDNA

Abstract: Using a combination of library screening and nested PCR based on a partial human serotonin 5‐HT4 receptor sequence, we have cloned the complete coding region for a human 5‐HT4 receptor. The sequence shows extensive similarity to the published porcine 5‐HT4A and rat 5‐HT4L receptor cDNA; however, in comparison with the latter, we find an open reading frame corresponding to only 388 amino acids instead of 406 amino acids. This difference is due to a frame shift caused by an additional cytosine found in the human sequence after position 1,154. Moreover, we also found the same additional cytosine in the rat 5‐HT4 sequence. We confirmed the occurrence of the sequence by examining this part of the sequence in genomic DNA of 10 human volunteers and in rat genomic DNA. Based on a part of the genomic 5‐HT4 receptor sequence that was identified in the cloning process, there seem to be at least two possible splice sites in the coding region of the gene. The human 5‐HT4 receptor, transiently expressed in COS‐7 cells, showed radioligand binding properties similar to 5‐HT4 receptors in guinea pig striatal tissue. [3H]GR 113808 revealed KD values of 0.15 ± 0.01 nM for the human receptor and 0.3 ± 0.1 nM in the guinea pig tissue. Binding constants were determined for four investigated 5‐HT4 antagonists and three agonists, and appropriate binding inhibition constants were found in each case. Stimulation of transfected COS‐7 cells with 5‐HT4‐specific agonists caused an increase in cyclic AMP levels.

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs

BackgroundIt was long assumed that proteins are at least 100 amino acids (AAs) long. Moreover, the detection of short translation products (e.g. coded from small Open Reading Frames, sORFs) is very difficult as the short length makes it hard to distinguish true coding ORFs from ORFs occurring by chance. Nevertheless, over the past few years many such non-canonical genes (with ORFs < 100 AAs) have been discovered in different organisms like Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster. Thanks to advances in sequencing, bioinformatics and computing power, it is now possible to scan the genome in unprecedented scrutiny, for example in a search of this type of small ORFs.ResultsUsing bioinformatics methods, we performed a systematic search for putatively functional sORFs in the Mus musculus genome. A genome-wide scan detected all sORFs which were subsequently analyzed for their coding potential, based on evolutionary conservation at the AA level, and ranked using a Support Vector Machine (SVM) learning model. The ranked sORFs are finally overlapped with ribosome profiling data, hinting to sORF translation. All candidates are visually inspected using an in-house developed genome browser. In this way dozens of highly conserved sORFs, targeted by ribosomes were identified in the mouse genome, putatively encoding micropeptides.ConclusionOur combined genome-wide approach leads to the prediction of a comprehensive but manageable set of putatively coding sORFs, a very important first step towards the identification of a new class of bioactive peptides, called micropeptides.

Functional characterization of the putative orphan neuropeptide G-protein coupled receptor C26F1.6 in Caenorhabditis elegans.

In this study, we describe the cloning and the characterization of the third FMRFamide‐related peptide (FaRP) receptor in Caenorhabditis elegans, the VRFa receptor 1. Numerous structurally different FaRPs were synthesized and used to screen the orphan C26F1.6 receptor for activation. Two peptides ending in M(orL)VRFamide elicited a calcium response in receptor expressing mammalian cells. The response is dose‐dependent and appeared to be very specific, since very closely related FaRPs were less active, even the other peptides ending in M(orL)VRFamide. Pharmacological profiling of the most active peptide suggests that SMVRFa is the most active binding core. N‐terminal extension decreases peptide activity.

A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome.

Peptidomics is the identification and study of the in vivo biologically active peptide profile. A combination of high performance liquid chromatography, mass spectrometry, and bioinformatics tools such as database search engines are commonly used to perform the analysis. We report a methodology based on a database system holding the completed translated genome, whereby de novo sequencing and genome-wide database searching are combined. The methodology was applied to the sea urchin neuropeptidome resulting in a 30% increase in identification rate.

Thymosin beta 4 mRNA and peptide expression in phagocytic cells of different mouse tissues

Thymosin beta 4 (Tbeta4) is a peptide of 43 amino acids, mainly recognized as a regulator of actin polymerization by sequestering G-actin. Meanwhile, the peptide has been implicated in lymphocyte maturation, carcinogenesis, apoptosis, angiogenesis, blood coagulation and wound healing. The peptide is also involved in lesion-induced neuroplasticity through microglia upregulation and it participates in the growth of neuronal processes. However, its precise cellular localization throughout the entire body of the mouse has not been documented. We therefore initiated a detailed investigation of the tissue distribution and cellular expression of the Tbeta4 peptide and its precursor mRNA by immunocytochemistry and in situ hybridization, respectively. In the brain, Tbeta4 was clearly present in neurons of the olfactory bulb, neocortex, hippocampus, striatum, amygdala, piriform cortex and cerebellum, and in microglia across the entire brain. We further localized Tbeta4 in cells, typically with many processes, inside thymus, spleen, lung, kidney, liver, adrenal gland, stomach and intestine. Remarkably, Tbeta4 was thus associated with microglia and macrophages, the differentiated phagocytic cells residing in every tissue. Motility and phagocytosis, two important activities of macrophages, depend on actin, which can explain the presence of Tbeta4 in these cells.