Reverse engineering and analysis of genome-wide gene regulatory networks from gene expression profiles using high-performance computing

Regulation of gene expression is a carefully regulated phenomenon in the cell. “Reverse-engineering” algorithms try to reconstruct the regulatory interactions among genes from genome-scale measurements of gene expression profiles (microarrays). Mammalian cells express tens of thousands of genes; hence, hundreds of gene expression profiles are necessary in order to have acceptable statistical evidence of interactions between genes. As the number of profiles to be analyzed increases, so do computational costs and memory requirements. In this work, we designed and developed a parallel computing algorithm to reverse-engineer genome-scale gene regulatory networks from thousands of gene expression profiles. The algorithm is based on computing pairwise Mutual Information between each gene-pair. We successfully tested it to reverse engineer the Mus Musculus (mouse) gene regulatory network in liver from gene expression profiles collected from a public repository. A parallel hierarchical clustering algorithm was implemented to discover “communities” within the gene network. Network communities are enriched for genes involved in the same biological functions. The inferred network was used to identify two mitochondrial proteins.     

Mutagenesis of human DNA polymerase lambda: essential roles of Tyr505 and Phe506 for both DNA polymerase and terminal transferase activities

DNA polymerase (pol) λ is homologous to pol β and has intrinsic polymerase and terminal transferase activities. However, nothing is known about the amino acid residues involved in these activites. In order to precisely define the nucleotide-binding site of human pol λ, we have mutagenised two amino acids, Tyr505 and the neighbouring Phe506, which were predicted by structural homology modelling to correspond to the Tyr271 and Phe272 residues of pol β, which are involved in nucleotide binding. Our analysis demonstrated that pol λ Phe506Arg/Gly mutants possess very low polymerase and terminal transferase activities as well as greatly reduced abilities for processive DNA synthesis and for carrying on translesion synthesis past an abasic site. The Tyr505Ala mutant, on the other hand, showed an altered nucleotide binding selectivity to perform the terminal transferase activity. Our results suggest the existence of a common nucleotide-binding site for the polymerase and terminal transferase activities of pol λ, as well as distinct roles of the amino acids Tyr505 and Phe506 in these two catalytic functions.     

Inhibition of Leishmania infantum trypanothione reductase by diaryl sulfide derivatives

The study presented here aimed at identifying a new class of compounds acting against Leishmania parasites, the causative agent of Leishmaniasis. For this purpose, the thioether derivatives of our in-house library have been evaluated in whole-cell screening assays in order to determine their in vitro activity against Leishmania protozoan. Among them, promising results have been achieved with compound RDS 777 (6-(sec-butoxy)-2-((3-chlorophenyl)thio)pyrimidin-4-amine) (IC_50?=_?29.43?µM), which is able to impair the mechanism of the parasite defence against the reactive oxygen species by inhibiting the trypanothione reductase (TR) with high efficiency (K_i 0.25?±?0.18?µM). The X-ray structure of L. infantum TR in complex with RDS 777 disclosed the mechanism of action of this compound that binds to the catalytic site and engages in hydrogen bonds the residues more involved in the catalysis, namely Glu466', Cys57 and Cys52, thereby inhibiting the trypanothione binding and avoiding its reduction.     

Spacing behaviour and habitat use of rock ptarmigan (Lagopus mutus) at low density in the Italian Alps

Studies of rock ptarmigan Lagopus mutus in northern latitudes have shown that, in the breeding season, the majority of cocks pair monogamously and defend small territories, whilst in most populations, a small proportion of cocks are polygynous or remain unmated. Little is known, however, on spacing behaviour and habitat use of alpine rock ptarmigan populations occurring at low densities at the southern edge of the species’ range. From 1995 to 1997, we trapped, radio-tracked and observed birds in the Central Italian Alps (elevation 2,000–3,000 m) in order to investigate spacing behaviour and habitat use in alpine landscapes where habitats offering rich food and cover are patchy. Both sexes were selective in their habitat use, and cocks did not establish territories on bare ground, artificial or nutrient rich grasslands or bogs. In the breeding season, cocks had larger home ranges than hens (cocks 99 ± 57 ha, hens 50 ± 25 ha) that overlapped with the ranges of neighbouring cocks and hens. Cocks were monogamous and defended relatively large territories (core areas of home ranges: cocks 37 ± 26 ha, hens 24 ± 12 ha), which corresponded with low spring densities (0.47–2.29 cocks km⁻² and 0.35–1.60 pairs km⁻²). Territory size of individual cocks was negatively correlated with the amount of high quality habitat in the core-area. Our results suggest increased home ranges and large breeding territories in low density alpine rock ptarmigan populations, compared to populations occurring at higher densities in the central and northern alps, and on subarctic and arctic grounds at northern latitudes, confirming the predictions of models on food-based territoriality.     

Research resource: New and diverse substrates for the insulin receptor isoform A revealed by quantitative proteomics after stimulation with IGF-II or insulin

The isoform A of the insulin receptor (IR) (IR-A) is a bifunctional receptor, because it binds both insulin and IGF-II. IR-A activation by IGF-II plays a role in development, but its physiological role in adults is unknown. IGF-II signaling through IR-A is deregulated in cancer and favors tumor progression. We hypothesized that IGF-II binding to the IR-A elicits a unique signaling pathway. In order to obtain an unbiased evaluation of IR-A substrates differentially involved after IGF-II and insulin stimulation, we performed quantitative proteomics of IR-A substrates recruited to tyrosine-phosphorylated protein complexes using stable isotope labeling with amino acids in cell culture in combination with antiphosphotyrosine antibody pull down and mass spectrometry. Using cells expressing only the human IR-A and lacking the IGF-I receptor, we identified 38 IR-A substrates. Only 10 were known IR mediators, whereas 28 substrates were not previously related to IR signaling. Eleven substrates were recruited by stimulation with both ligands: two equally recruited by IGF-II and insulin, three more strongly recruited by IGF-II, and six more strongly recruited by insulin. Moreover, 14 substrates were recruited solely by IGF-II and 13 solely by insulin stimulation. Interestingly, discoidin domain receptors, involved in cell migration and tumor metastasis, and ephrin receptor B4, involved in bidirectional signaling upon cell-cell contact, were predominantly activated by IGF-II. These findings indicate that IR-A activation by IGF-II elicits a unique signaling pathway that may play a distinct role in physiology and in disease.     

The Sound and the Fury—Bees Hiss when Expecting Danger

Honey bees are important model systems for the investigation of learning and memory and for a better understanding of the neuronal basics of brain function. Honey bees also possess a rich repertoire of tones and sounds, from queen piping and quacking to worker hissing and buzzing. In this study, we tested whether the worker bees’ sounds can be used as a measure of learning. We therefore conditioned honey bees aversively to odours in a walking arena and recorded both their sound production and their movement. Bees were presented with two odours, one of which was paired with an electric shock. Initially, the bees did not produce any sound upon odour presentation, but responded to the electric shock with a strong hissing response. After learning, many bees hissed at the presentation of the learned odour, while fewer bees hissed upon presentation of another odour. We also found that hissing and movement away from the conditioned odour are independent behaviours that can co-occur but do not necessarily do so. Our data suggest that hissing can be used as a readout for learning after olfactory conditioning, but that there are large individual differences between bees concerning their hissing reaction. The basis for this variability and the possible ecological relevance of the bees’ hissing remain to be investigated.     

A RAB5/RAB4 recycling circuitry induces a proteolytic invasive program and promotes tumor dissemination

The mechanisms by which tumor cells metastasize and the role of endocytic proteins in this process are not well understood. We report that overexpression of the GTPase RAB5A, a master regulator of endocytosis, is predictive of aggressive behavior and metastatic ability in human breast cancers. RAB5A is necessary and sufficient to promote local invasion and distant dissemination of various mammary and nonmammary tumor cell lines, and this prometastatic behavior is associated with increased intratumoral cell motility. Specifically, RAB5A is necessary for the formation of invadosomes, membrane protrusions specialized in extracellular matrix (ECM) degradation. RAB5A promotes RAB4- and RABENOSYN-5–dependent endo/exocytic cycles (EECs) of critical cargos (membrane-type 1 matrix metalloprotease [MT1-MMP] and β3 integrin) required for invadosome formation in response to motogenic stimuli. This trafficking circuitry is necessary for spatially localized hepatocyte growth factor (HGF)/MET signaling that drives invasive, proteolysis-dependent chemotaxis in vitro and for conversion of ductal carcinoma in situ to invasive ductal carcinoma in vivo. Thus, RAB5A/RAB4 EECs promote tumor dissemination by controlling a proteolytic, mesenchymal invasive program.