Detection of micro-RNA/gene interactions involved in angiogenesis using machine learning techniques

Poster (2007, September)

Motivation: Angiogenesis is the process responsible for the growth of new blood vessels from existing ones. It is also associated with the development of cancer, as tumors need to be irrigated by blood ... [more ▼]

Motivation: Angiogenesis is the process responsible for the growth of new blood vessels from existing ones. It is also associated with the development of cancer, as tumors need to be irrigated by blood vessels for growing. New cancer therapies appear that exploit angiogenesis inhibitors, also called angiostatic agents, to asphyxiate and starve the tumors. Better understanding the regulatory mechanisms that control angiogenesis is thus fundamental. Recently, short non-coding RNA molecules, called micro-RNAs, have been discovered that are involved in post- transcriptional regulation of gene expressions. These molecules bind to RNA messengers following the base pairing rules, preventing them from being translated into proteins and/or tagging them for degradation. The main goal of this work is to use computational approaches to identify micro-RNAs involved in angiogenesis. Method: In order to identify genes involved in angiogenesis, bovine endothelial cells were treated by a known angiogenesis inhibitor [1], prolactin 16K, and their gene expression profile was compared to the profile of untreated cells. The genes were then divided into three classes: up-regulated, down-regulated, and unaffected genes. The 3'UTR regions of these genes were then analysed by machine learning techniques. Different approaches were considered. First, we described each gene by a vector of motif counts in their 3'UTR regions and used machine learning techniques to rank the motifs according to their relevance for separating the genes into the different classes. We considered successively motifs corresponding to the seeds of known micro- RNAs and also all possible motifs of a given length. To rank the motifs, we compared ensemble of decision trees and linear support vector machines. Second, we considered an approach called Segment and Combine that was proposed in [2]. Finally, we also carried out an exhaustive search of all motifs of a given length that satisfy some constraints on specificity and coverage with respect to a given gene category. Results: The ability of the different approaches at identifying relevant motifs was first assessed on genes predicted to be the target of some known miRNAs. In this simple setting, most methods were able to identify the micro-RNA seed. The results obtained on the genes regulated by prolactin 16K are also very encouraging. We were able to identify one micro-RNA already known to play a role in angiogenesis and several motifs are predicted by different approaches as very specific of up- or down-regulation by prolactin 16K. Their relationship with known micro-RNAs is certainly worth exploring. Conclusion: Machine learning approaches are promising techniques for the identification of micro-RNA/gene interactions. Future work will concern the application of the same kind of techniques on promoters for the identification of transcription factor binding sites. [less ▲]

Antiangiogenic peptides

Patent (2007)

The present invention refers to antiangiogenic peptides, especially to tilted peptides having antiangiogenic properties and peptides from the prolactin/growth hormone familiy having antiangiogenic ... [more ▼]

The present invention refers to antiangiogenic peptides, especially to tilted peptides having antiangiogenic properties and peptides from the prolactin/growth hormone familiy having antiangiogenic properties. [less ▲]

Reciprocal endoderm-mesoderm interactions mediated by fgf24 and fgf10 govern pancreas development

in Development (2007), 134(22), 4011-21

In amniotes, the pancreatic mesenchyme plays a crucial role in pancreatic epithelium growth, notably through the secretion of fibroblast growth factors. However, the factors involved in the formation of ... [more ▼]

In amniotes, the pancreatic mesenchyme plays a crucial role in pancreatic epithelium growth, notably through the secretion of fibroblast growth factors. However, the factors involved in the formation of the pancreatic mesenchyme are still largely unknown. In this study, we characterize, in zebrafish embryos, the pancreatic lateral plate mesoderm, which is located adjacent to the ventral pancreatic bud and is essential for its specification and growth. We firstly show that the endoderm, by expressing the fgf24 gene at early stages, triggers the patterning of the pancreatic lateral plate mesoderm. Based on the expression of isl1, fgf10 and meis genes, this tissue is analogous to the murine pancreatic mesenchyme. Secondly, Fgf10 acts redundantly with Fgf24 in the pancreatic lateral plate mesoderm and they are both required to specify the ventral pancreas. Our results unveil sequential signaling between the endoderm and mesoderm that is critical for the specification and growth of the ventral pancreas, and explain why the zebrafish ventral pancreatic bud generates the whole exocrine tissue. [less ▲]

Inhibition of tumor growth and metastasis establishment by adenovirus-mediated gene transfer delivery of the antiangiogenic factor 16K prolactin

Poster (2007)

Protein crystallisation under microgravity conditions: What did we learn on TIM crystallisation from the Soyuz missions?

in Microgravity Science and Technology (2007), XIX(5/6), 90-94

The protein Triose Phosphate Isomerase from the hyperthermophilic organism Thermotoga maritima was crystallised on board of the International Space Station in the framework of the Soyuz missions. In this ... [more ▼]

The protein Triose Phosphate Isomerase from the hyperthermophilic organism Thermotoga maritima was crystallised on board of the International Space Station in the framework of the Soyuz missions. In this paper we report on the scientific results obtained during these flights. Firstly it qas shown that different crystal forms for the same protein in the same crystallisation conditions, what is presumably due to a change in the rate at which supersaturation is achieved. Secondly, the X-ray qualité of the crystals grown in the ISS is superior to their ground control crystals. Mimicking microgravity on ground, by adding a small amourt of gel to avoid convection, also results in an improvement of X-ray quality. Nevertheless our analysis shows that the crystals obtained in this gelled ground environment are of inferior quality as compared to their space homologues. Finally we observed movement of crystals grown in the International Space Station, not only because of g-jitters but also due to residual accelerations. This has an important effect on concentration gradients of precipiants and therefore on the solubility of the protein. [less ▲]

Crystallization of ornithine acetyltransferase from yeast by counter-diffusion and preliminary X-ray study

in Acta Crystallographica Section F-Structural Biology and Crystallization Communications (2006), 62(Part 12), 1294-1297

A study is presented on the crystallization of ornithine acetyltransferase from yeast, which catalyzes the fifth step in microbial arginine synthesis. The use of the counter-diffusion technique removes ... [more ▼]

A study is presented on the crystallization of ornithine acetyltransferase from yeast, which catalyzes the fifth step in microbial arginine synthesis. The use of the counter-diffusion technique removes the disorder present in one dimension in crystals grown by either the batch or hanging-drop techniques. This makes the difference between useless crystals and crystals that allow successful determination of the structure of the protein. The crystals belong to space group P4, with unit-cell parameters a = b = 66.98, c = 427.09 angstrom, and a data set was collected to 2.76 angstrom. [less ▲]

Expression of the somatolactin beta gene during zebrafish embryonic development

in Gene Expression Patterns (2006), 6(2), 156-161

Somatolactin (Sl) is a pituitary hormone closely related to prolactin (Prl) and growth hormone that was until now only found in various fish species. We isolated the cDNA coding for zebrafish Sl beta and ... [more ▼]

Somatolactin (Sl) is a pituitary hormone closely related to prolactin (Prl) and growth hormone that was until now only found in various fish species. We isolated the cDNA coding for zebrafish Sl beta and we identified the gene encoding this hormone. We also obtained a 1 kb genomic fragment corresponding to the sl beta upstream promoter region. Furthermore, the sl beta expression pattern was examined during zebrafish embryogenesis using whole-mount in situ hybridization. Sl beta mRNA is first detected in a single cell at the anterior border of the neural plate starting at 23 h post fertilization (hpf). Sl beta-expressing cells also express the transcription factor pit1 and are located close to prl-expressing cells. Using combined fluorescent in situ hybridization, we show that sl beta- and prl-expressing cells are clearly distinct at 29 hpf. Starting at 30 hpf, the number of sl beta positive cells increases and their location becomes more clearly distinct from lactotrope cells, in a more posterior position. At later stages (48 hpf), sl beta expression was observed posterior to growth hormone expression, again in a distinct cell type. We show that zebrafish mutants aal, as well as mutants in the pit1 gene, are deficient in sl beta expression. In conclusion, sl beta expression defines a new, additional cell type in zebrafish pituitary that depends on pit1 and aal for its differentiation. (C) 2005 Elsevier B.V. All rights reserved. [less ▲]

Tilted peptides of PRL/GH family and their potential role in angiogenesis

Poster (2006)

Prolactin/growth hormone-derived antiangiogenic peptides highlight a potential role of tilted peptides in angiogenesis

in Proceedings of the National Academy of Sciences of the United States of America (2006), 103(39), 14319-14324

Angiogenesis is a crucial step in many pathologies, including tumor growth and metastasis. Here, we show that tilted peptides exert antiangiogenic activity. Tilted (or oblique-oriented) peptides are short ... [more ▼]

Angiogenesis is a crucial step in many pathologies, including tumor growth and metastasis. Here, we show that tilted peptides exert antiangiogenic activity. Tilted (or oblique-oriented) peptides are short peptides known to destabilize membranes and lipid cores and characterized by an asymmetric distribution of hydrophobic residues along the axis when helical. We have previously shown that 16-kDa fragments of the human prolactin/growth hormone (PRL/GH) family members are potent angiogenesis inhibitors. Here, we demonstrate that all these fragments possess a 14-aa sequence having the characteristics of a tilted peptide. The tilted peptides of human prolactin and human growth hormone induce endothelial cell apoptosis, inhibit endothelial cell proliferation, and inhibit capillary formation both in vitro and in vivo. These antiangiogenic effects are abolished when the peptides' hydrophobicity gradient is altered by mutation. We further demonstrate that the well known tilted peptides of simian immunodeficiency virus gp32 and Alzheimer's beta-amyloid peptide are also angiogenesis inhibitors. Taken together, these results point to a potential new role for tilted peptides in regulating angiogenesis. [less ▲]

Expression and functional properties of four slow skeletal troponin T isoforms in rat muscles

in American Journal of Physiology - Cell Physiology (2005), 289(2), 437-443

We investigated the expression and functional properties of slow skeletal troponin T(sTnT) isoforms in rat skeletal muscles. Four sTnT cDNAs were cloned from the slow soleus muscle. Three isoforms were ... [more ▼]

We investigated the expression and functional properties of slow skeletal troponin T(sTnT) isoforms in rat skeletal muscles. Four sTnT cDNAs were cloned from the slow soleus muscle. Three isoforms were found to be similar to sTnT1, sTnT2, and sTnT3 isoforms described in mouse muscles. A new rat isoform, with a molecular weight slightly higher than that of sTnT3, was discovered. This fourth isoform had never been detected previously in any skeletal muscle and was therefore called sTnTx. From both expression pattern and functional measurements, it appears that sTnT isoforms can be separated into two classes, high-molecular-weight ( sTnT1, sTnT2) and low-molecular-weight ( sTnTx, sTnT3) isoforms. By comparison to the apparent migration pattern of the four recombinant sTnT isoforms, the newly described low-molecular-weight sTnTx isoform appeared predominantly and typically expressed in fast skeletal muscles, whereas the higher-molecular-weight isoforms were more abundant in slow soleus muscle. The relative proportion of the sTnT isoforms in the soleus was not modified after exposure to hindlimb unloading (HU), known to induce a functional atrophy and a slow-to-fast isoform transition of several myofibrillar proteins. Functional data gathered from replacement of endogenous troponin complexes in skinned muscle fibers showed that the sTnT isoforms modified the Ca2+ activation characteristics of single skeletal muscle fibers, with sTnT2 and sTnT1 conferring a similar increase in Ca2+ affinity higher than that caused by low-molecular-weight isoforms sTnTx and sTnT3. Thus we show for the first time the presence of sTnT in fast muscle fibers, and our data show that the changes in neuromuscular activity on HU are insufficient to alter the sTnT expression pattern. [less ▲]