Comparative modular analysis of gene expression in vertebrate development

The focus of my PhD research was the concept of modularity. In the last 15 years, modularity has become a classic term in different fields of biology. On the conceptual level, a module is a set of interacting elements that remain mostly independent from the elements outside of the module. I used modular analysis techniques to study gene expression evolution in vertebrates. In particular, I identified ``natural'' modules of gene expression in mouse and human, and I showed that expression of organ-specific and system-specific genes tends to be conserved between such distance vertebrates as mammals and fishes. Also with a modular approach, I studied patterns of developmental constraints on transcriptome evolution. I showed that none of the two commonly accepted models of the evolution of embryonic development (``evo-devo'') are exclusively valid. In particular, I found that the conservation of the sequences of regulatory regions is highest during mid-development of zebrafish, and thus it supports the ``hourglass model''. In contrast, events of gene duplication and new gene introduction are most rare in early development, which supports the ``early conservation model''. In addition to the biological insights on transcriptome evolution, I have also discussed in detail the advantages of modular approaches in large-scale data analysis. Moreover, I re-analyzed several studies (published in high-ranking journals), and showed that their conclusions do not hold out under a detailed analysis. This demonstrates that complex analysis of high-throughput data requires a co-operation between biologists, bioinformaticians, and statisticians.

Biomedical and biological applications of scanning electron microscopy

This article summarizes the basic principles of scanning electron microscopy and the capabilities of the technique with different examples ofapplications in biomedical and biological research.

Characterization of the effect of mammary gland irridiation on experimental brest cancer progression and analysis of the implicated mechanisms

SUMMARY Radiotherapy is commonly and efficiently used to treat solid cancer in the clinic. Experimental evidence however suggests that radiation can promote tumor progression by inducing chronic modifications of the tumor microenvironment. Clinically, these observations are highly relevant to aggressive tumoral lesions relapsing after radiation therapy, a leading cause of patients' death. The investigation and understanding of the biological mechanisms implicated in the malignant progression of post-radiation relapses are therefore of major importance. Here we used a syngeneic (immunocompetent) breast cancer orthotopic xenograft model, to show that local irradiation of the mammary gland promotes the appearance of an invasive and metastatic tumor phenotype. Previous studies in our laboratory revealed that inhibition of tumor-induced angiogenesis and consequent increase in tumor hypoxia promotes metastasis formation through the activation of pro-invasive programs in the tumor cells. Our results extend these observations suggesting that mammary gland irradiation induces the recruitment of CD11b+ cells to both the primary tumor and the lungs at pre-metastatic stages through the hypoxia-dependent induction of Kit-ligand (KITL) expression in primary tumors. Abrogation of KITL expression in tumor cells prevented CD11 b+ cells accumulation in both the primary tumor and lungs and significantly reduced metastases of tumors growing in irradiated mammary gland. Importantly, irradiated mammary gland enhanced tumor-induced mobilization of circulating CD11b+cKit+ myelomonocytic cells through a HIF1- and KITL-dependent process. By cell transfer experiments, mobilized circulating CD11b+cKit+ cells were shown to supply both tumor- and lungs infiltrating CD11b+ cells. Using a blocking antibody against cKit (the KITL receptor), the mobilization of CD11b+cKit+ ceils was prevented as well as lung metastases derived from tumors growing in irradiated mammary gland. Taken together, these results indicate that tumors growing in a pre-irradiated mammary gland partially promote their malignant progression through the distant mobilization of circulating myelomonocytic precursor cells. They identify KITL inhibition and/or cKit receptor neutralization as potentially promising therapeutic approaches for post-radiation relapses. RESUME La radiothérapie est largement utilisée comme traitement de choix de nombreux types de cancers. L'agressivité des récidives tumorales observée en clinique après radiothérapie suggère cependant que le recours à l'irradiation pourrait dans certains cas accélérer la progression tumorale. De récents travaux expérimentaux ont en effet permis d'appuyer cette hypothèse, en montrant notamment l'effet néfaste des modifications chroniques de l'environnement induites par l'irradiation sur la progression tumorale. A l'aide d'un modèle murin syngénique orthotopique de cancer de sein, nous avons pu montrer que l'irradiation locale de la glande mammaire facilite l'invasion et la dissémination métastatique des cellules tumorales en favorisant le recrutement de cellules myéloïdes CD11 b+ vers la tumeur primaire et les poumons à un stade pré-métastatique. Comme mécanisme impliqué dans le recrutement des cellules CD11b+, nous avons pu observer après irradiation locale de la glande mammaire une expression augmentée de Kit-ligand (KITL) dans la tumeur (induite par l'hypoxie) ainsi que la mobilisation de cellules myéloïdes circulantes exprimant le récepteur cKit et précurseurs des cellules CD11b+ infiltrant la tumeur et les poumons. En empêchant la mobilisation par la tumeur de cellules circulantes cKit+ par des approches à la fois génétique et pharmacologique nous avons pu prévenir l'accumulation de cellules myéloïdes CD11 b+ dans la tumeur primaire et les poumons ainsi que la dissémination métastatique induites par' l'irradiation de la glande mammaire. De façon générale, ces résultats montrent que la progression agressive des tumeurs qui se développent dans un environnement irradié repose à la fois sur l'expression tumorale de KITL et la mobilisation de cellules myéloïdes précurseurs cKit*. Ils auront permis d'identifier KITL et/ou cKit comme des cibles thérapeutiques potentielles intéressantes pour le traitement des récidives tumorales après radiothérapie.

Une méta-analyse GWA de la glycémie après 2h d'HGPO révèle que GIPR est associé avec la sécrétion de l'insuline en réponse au glucose et que l'ADCY5 est un nouveau gène de suseptibilité au diabète de type 2. [A meta-analysis of GWA blood glucose after 2 h of OGTT revealed that GIPR is associated with the secretion of insulin based on glucose and ADCY5 is a new susceptibility gene for type 2 diabetes.]

Introduction: Les études GVvA (Genome-wide association ,-studies) ont identifié et confirmé plus de 20 gènes de susceptibilité au DT2 et ont contribué à mieux comprendre sa physiopathologie. L'hyperglycémie à jeun (GJ), et 2 heures après une HGPO (G2h) sont les deux mesures cliniques du diagnostic du DT2. Nous avons identifié récemment la G6P du pancréas (G6PC2) comme déterminant de la variabilité physiologique de la GJ puis Ie récepteur à la mélatonine (MTNRIB) qui de plus lie la régulation du rythme circadien au DT2. Dans ce travail nous avons étudié la génétique de la G2h à l'aide de l'approche GWA. Résultats: Nous avons réalisé une méta-analyse GWA dans le cadre de MAGIC (Meta-Analysis of Glucose and Insulin related traits Consortium) qui a inclus 9 études GWA (N=15'234). La réplication de 29 loci (N=6958-30 121, P < 10-5 ) a confirmé 5 nouveaux loci; 2 étant connus comme associés avec Ie DT2 (TCF7L2, P = 1,6 X 10-10 ) et la GJ (GCKR, p = 5,6 X 10-10 ); alors que GIPR (p= 5,2 X 10-12), VSP13C (p= 3,9 X 10-8) et ADCY5 (p = 1,11 X 10-15 ) sont inédits. GIPR code Ie récepteur au GIP (gastric inhibitory polypeptide) qui est sécrété par les ceIlules intestinales pour stimuler la sécrétion de l'insuline en réponse au glucose (l'effet incrétine). Les porteurs du variant GIPR qui augmente la G2h ont également un indice insulinogénique plus bas, (p= 1,0 X 10-17) mais ils ne présentent aucune modification de leur glycémie suite à une hyperglycémie provoquée par voie veineuse (p= 0,21). Ces résultats soutiennent un effet incrétine du locus GIPR qui expliquerait ~9,6 % de la variance total de ce trait. La biologie de ADCY5 et VPS13C et son lien avec l'homéostasie du glucose restent à élucider. GIPR n'est pas associé avec le risque de DT2 indiquant qu'il influence la variabilité physiologique de la G2h alors que le locus ADCY5 est associé avec le DT2 (OR = 1,11, P = 1,5 X 10-15). Conclusion: Notre étude démontre que l'étude de la G2h est une approche efficace d'une part pour la compréhension de la base génétique de la physiologie de ce trait clinique important et d'autre part pour identifier de nouveaux gènes de susceptibilité au DT2.

A system-level, molecular evolutionary analysis of mammalian phototransduction

Visual perception is initiated in the photoreceptor cells of the retina via the phototransduction system.This system has shown marked evolution during mammalian divergence in such complex attributes as activation time and recovery time. We have performed a molecular evolutionary analysis of proteins involved in mammalianphototransduction in order to unravel how the action of natural selection has been distributed throughout thesystem to evolve such traits. We found selective pressures to be non-randomly distributed according to both a simple protein classification scheme and a protein-interaction network representation of the signaling pathway. Proteins which are topologically central in the signaling pathway, such as the G proteins, as well as retinoid cycle chaperones and proteins involved in photoreceptor cell-type determination, were found to be more constrained in their evolution. Proteins peripheral to the pathway, such as ion channels and exchangers, as well as the retinoid cycle enzymes, have experienced a relaxation of selective pressures. Furthermore, signals of positive selection were detected in two genes: the short-wave (blue) opsin (OPN1SW) in hominids and the rod-specific Na+/Ca2+,K+ ion exchanger (SLC24A1) in rodents. The functions of the proteins involved in phototransduction and the topology of the interactions between them have imposed non-random constraints on their evolution. Thus, in shaping or conserving system-level phototransduction traits, natural selection has targeted the underlying proteins in a concerted manner.

Heterogeneity and event dependence in the analysis of sickness absence

Sickness absence (SA) is an important social, economic and public health issue. Identifying and understanding the determinants, whether biological, regulatory or, health services-related, of variability in SA duration is essential for better management of SA. The conditional frailty model (CFM) is useful when repeated SA events occur within the same individual, as it allows simultaneous analysis of event dependence and heterogeneity due to unknown, unmeasured, or unmeasurable factors. However, its use may encounter computational limitations when applied to very large data sets, as may frequently occur in the analysis of SA duration. To overcome the computational issue, we propose a Poisson-based conditional frailty model (CFPM) for repeated SA events that accounts for both event dependence and heterogeneity. To demonstrate the usefulness of the model proposed in the SA duration context, we used data from all non-work-related SA episodes that occurred in Catalonia (Spain) in 2007, initiated by either a diagnosis of neoplasm or mental and behavioral disorders. As expected, the CFPM results were very similar to those of the CFM for both diagnosis groups. The CPU time for the CFPM was substantially shorter than the CFM. The CFPM is an suitable alternative to the CFM in survival analysis with recurrent events,especially with large databases.

Predicting current and future spatial community patterns of plant functional traits

Community-level patterns of functional traits relate to community assembly and ecosystem functioning. By modelling the changes of different indices describing such patterns - trait means, extremes and diversity in communities - as a function of abiotic gradients, we could understand their drivers and build projections of the impact of global change on the functional components of biodiversity. We used five plant functional traits (vegetative height, specific leaf area, leaf dry matter content, leaf nitrogen content and seed mass) and non-woody vegetation plots to model several indices depicting community-level patterns of functional traits from a set of abiotic environmental variables (topographic, climatic and edaphic) over contrasting environmental conditions in a mountainous landscape. We performed a variation partitioning analysis to assess the relative importance of these variables for predicting patterns of functional traits in communities, and projected the best models under several climate change scenarios to examine future potential changes in vegetation functional properties. Not all indices of trait patterns within communities could be modelled with the same level of accuracy: the models for mean and extreme values of functional traits provided substantially better predictive accuracy than the models calibrated for diversity indices. Topographic and climatic factors were more important predictors of functional trait patterns within communities than edaphic predictors. Overall, model projections forecast an increase in mean vegetation height and in mean specific leaf area following climate warming. This trend was important at mid elevation particularly between 1000 and 2000 m asl. With this study we showed that topographic, climatic and edaphic variables can successfully model descriptors of community-level patterns of plant functional traits such as mean and extreme trait values. However, which factors determine the diversity of functional traits in plant communities remains unclear and requires more investigations.

Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases

AbstractBACKGROUND: Scientists have been trying to understand the molecular mechanisms of diseases to design preventive and therapeutic strategies for a long time. For some diseases, it has become evident that it is not enough to obtain a catalogue of the disease-related genes but to uncover how disruptions of molecular networks in the cell give rise to disease phenotypes. Moreover, with the unprecedented wealth of information available, even obtaining such catalogue is extremely difficult.PRINCIPAL FINDINGS: We developed a comprehensive gene-disease association database by integrating associations from several sources that cover different biomedical aspects of diseases. In particular, we focus on the current knowledge of human genetic diseases including mendelian, complex and environmental diseases. To assess the concept of modularity of human diseases, we performed a systematic study of the emergent properties of human gene-disease networks by means of network topology and functional annotation analysis. The results indicate a highly shared genetic origin of human diseases and show that for most diseases, including mendelian, complex and environmental diseases, functional modules exist. Moreover, a core set of biological pathways is found to be associated with most human diseases. We obtained similar results when studying clusters of diseases, suggesting that related diseases might arise due to dysfunction of common biological processes in the cell.CONCLUSIONS: For the first time, we include mendelian, complex and environmental diseases in an integrated gene-disease association database and show that the concept of modularity applies for all of them. We furthermore provide a functional analysis of disease-related modules providing important new biological insights, which might not be discovered when considering each of the gene-disease association repositories independently. Hence, we present a suitable framework for the study of how genetic and environmental factors, such as drugs, contribute to diseases.AVAILABILITY: The gene-disease networks used in this study and part of the analysis are available at http://ibi.imim.es/DisGeNET/DisGeNETweb.html#Download

Neutralizing antibodies in Multiple Sclerosis a model-based analysis of Interferon beta signaling pathway in macrophages

Multiple Sclerosis is the most common non-traumatic cause of neurologicaldisability in young people. There is no cure yet, and until recently, few long-termtherapies existed. Interferon beta (IFNβ) was the first treatment, and remains the mostcommonly prescribed. One of the most significant problems of IFNβ therapy is theproduction of drug specific antibodies. Up to 45% of patients develop neutralizingantibodies (NAbs) to IFNβ products. The neutralizing antibody binds to the biologicalagent preventing its interaction with its receptor, inhibiting the biological action of theprotein, which abrogates the clinical efficacy of IFNβ treatment. Interferon-betamediates its response by binding to its high affinity cell surface receptor and initiatingthe JAK/STAT signalling cascade. In this project we have analyzed the IFNβ signalingpathway in macrophages when neutralizing antibodies are present. The response tothis pathway after IFNβ stimulation shows a transient oscillatory rhythm of STAT1phosphorylation, which varies as NAbs concentration increases. To improve ourunderstanding of that behavior, we extended an existing mathematical model based onnonlinear ordinary differential equations of JAK/STAT pathway by including IFN-NAbassociation and IFN-activation receptor. Combining our theoretical model withexperimental data we could study the role of neutralizing antibodies on the molecularresponse and determine its lifetime after cytokine stimulation.

GSVA: gene set variation analysis for microarray and RNA-seq data

Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise and dimension reduction, as well as greater biological interpretability. As molecular profiling experiments move beyond simple case-control studies, robust and flexible GSE methodologies are needed that can model pathway activity within highly heterogeneous data sets. To address this challenge, we introduce Gene Set Variation Analysis (GSVA), a GSE method that estimates variation of pathway activity over a sample population in an unsupervised manner. We demonstrate the robustness of GSVA in a comparison with current state of the art sample-wise enrichment methods. Further, we provide examples of its utility in differential pathway activity and survival analysis. Lastly, we show how GSVA works analogously with data from both microarray and RNA-seq experiments. GSVA provides increased power to detect subtle pathway activity changes over a sample population in comparison to corresponding methods. While GSE methods are generally regarded as end points of a bioinformatic analysis, GSVA constitutes a starting point to build pathway-centric models of biology. Moreover, GSVA contributes to the current need of GSE methods for RNA-seq data. GSVA is an open source software package for R which forms part of the Bioconductor project and can be downloaded at http://www.bioconductor.org.

Analysis of raw hams using SELDI-TOF-MS to predict the final quality of dry-cured hams

The relationship between protein profiles of Gluteus medius (GM) muscles of raw hams obtained from 4 pure breed pigs (Duroc, Large White, Landrace, and Piétrain) with the final quality of the Semimembranosus and Biceps femoris muscles of dry-cured hams was investigated. As expected, Duroc hams showed higher levels of marbling and intramuscular fat content than the other breeds. Piétrain hams were the leanest and most conformed, and presented the lowest salt content in dry-cured hams. Even if differences in the quality traits (colour, water activity, texture, composition, intramuscular fat, and marbling) of dry-cured hams were observed among the studied breeds, only small differences in the sensory attributes were detected. Surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF-MS) was used to obtain the soluble protein profiles of GM muscles. Some associations between protein peaks obtained with SELDI-TOF-MS and quality traits, mainly colour (b*) and texture (F0, Y2, Y90) were observed. Candidate protein markers for the quality of processed dry-cured hams were identified

2011 lAAF World Championships in Daegu: blood tests for all athletes in the framework of the Athlete Biological Passport.

The 2011 International Association of Athletics Federation (IAAF) World Championships took place in Daegu, Korea. For the first time, all athletes were blood tested prior to the competition in order to give a clear signal to the world athletic community of the wish to enter into the era of the Athlete Biological Passport and fight against doping in their sport. The hematological parameters were measured on site. Thus, a mobile-accredited laboratory for blood testing was created in Daegu. Two serum tubes were collected for clinical chemistry and hormonal analyses in order to build the bases of the endocrine and the androgen (steroid) modules of the Athlete Biological Passport in blood. This paper describes some of the main challenges the project faced with regard to the large number of athletes, competing in different disciplines, and the logistic problems that had to be solved for smart implementation of one of the most complex operations organized in the last decade in the fight against doping.

Fate of Hydrophilic Nanoparticles in Biological Environments

The nanoparticles developed are based on chitosan, a biocompatible and biodegradable polysaccharide. The chitosan nanoparticles are formed in an entirely water-based process by electrostatic interactions with other biocompatible molecules. As a prerequisite to understand the fate of such nanoparticles in cells, comprehensive characterization and stability studies serve to identify quantitatively the impact of the raw material characteristics and preparation conditions on the nanoparticle characteristics. Methods included H-1 NMR spectroscopy, dilution viscometry, particle size analysis and electron microscopy. Cytotoxicity and cell uptake experiments on RAW 264.7 murine macrophages and p23 murine endothelial cells were performed to investigate the correlation with nanoparticle characteristics and effect of surface decoration with alginate. Cytotoxicity was assessed by the MTT survival test; cell uptake was monitored by fluorescent microscopy using labeled polymers.

An evolutionary analysis of the relationship between spite and altruism.

We investigate the selective pressures on a social trait when evolution occurs in a population of constant size. We show that any social trait that is spiteful simultaneously qualifies as altruistic. In other words, any trait that reduces the fitness of less related individuals necessarily increases that of related ones. Our analysis demonstrates that the distinction between "Hamiltonian spite" and "Wilsonian spite" is not justified on the basis of fitness effects. We illustrate this general result with an explicit model for the evolution of a social act that reduces the recipient's survival ("harming trait"). This model shows that the evolution of harming is favoured if local demes are of small size and migration is low (philopatry). Further, deme size and migration rate determine whether harming evolves as a selfish strategy by increasing the fitness of the actor, or as a spiteful/altruistic strategy through its positive effect on the fitness of close kin.