Signalling Pathways Involved in Adult Heart Formation Revealed by Gene Expression Profiling in Drosophila

Drosophila provides a powerful system for defining the complex genetic programs that drive organogenesis. Under control of the steroid hormone ecdysone, the adult heart in Drosophila forms during metamorphosis by a remodelling of the larval cardiac organ. Here, we evaluated the extent to which transcriptional signatures revealed by genomic approaches can provide new insights into the molecular pathways that underlie heart organogenesis. Whole-genome expression profiling at eight successive time-points covering adult heart formation revealed a highly dynamic temporal map of gene expression through 13 transcript clusters with distinct expression kinetics. A functional atlas of the transcriptome profile strikingly points to the genomic transcriptional response of the ecdysone cascade, and a sharp regulation of key components belonging to a few evolutionarily conserved signalling pathways. A reverse genetic analysis provided evidence that these specific signalling pathways are involved in discrete steps of adult heart formation. In particular, the Wnt signalling pathway is shown to participate in inflow tract and cardiomyocyte differentiation, while activation of the PDGF-VEGF pathway is required for cardiac valve formation. Thus, a detailed temporal map of gene expression can reveal signalling pathways responsible for specific developmental programs and provides here substantial grasp into heart formation

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

Summary: We present SVDetect, a program designed to identify genomic structural variations from paired-end and mate-pair next-generation sequencing data produced by the Illumina GA and ABI SOLiD platforms. Applying both sliding-window and clustering strategies, we use anomalously mapped read pairs provided by current short read aligners to localize genomic rearrangements and classify them according to their type, e.g. large insertions–deletions, inversions, duplications and balanced or unbalanced inter-chromosomal translocations. SVDetect outputs predicted structural variants in various file formats for appropriate graphical visualization

Bioinformatics for precision medicine in oncology: principles and application to the SHIVA clinical trial

Precision medicine (PM) requires the delivery of individually adapted medical care based on the genetic characteristics of each patient and his/her tumor. The last decade witnessed the development of high-throughput technologies such as microarrays and next-generation sequencing which paved the way to PM in the field of oncology. While the cost of these technologies decreases, we are facing an exponential increase in the amount of data produced. Our ability to use this information in daily practice relies strongly on the availability of an efficient bioinformatics system that assists in the translation of knowledge from the bench towards molecular targeting and diagnosis. Clinical trials and routine diagnoses constitute different approaches, both requiring a strong bioinformatics environment capable of (i) warranting the integration and the traceability of data, (ii) ensuring the correct processing and analyses of genomic data, and (iii) applying well-defined and reproducible procedures for workflow management and decision-making. To address the issues, a seamless information system was developed at Institut Curie which facilitates the data integration and tracks in real-time the processing of individual samples. Moreover, computational pipelines were developed to identify reliably genomic alterations and mutations from the molecular profiles of each patient. After a rigorous quality control, a meaningful report is delivered to the clinicians and biologists for the therapeutic decision. The complete bioinformatics environment and the key points of its implementation are presented in the context of the SHIVA clinical trial, a multicentric randomized phase II trial comparing targeted therapy based on tumor molecular profiling versus conventional therapy in patients with refractory cancer. The numerous challenges faced in practice during the setting up and the conduct of this trial are discussed as an illustration of PM application

Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

Background: We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15–20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases. Methods: We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded. Results: No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5–528.7, P = 1.1 × 10−4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3–8.2], P = 2.1 × 10−4). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1–2635.4], P = 3.4 × 10−3), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3–8.4], P = 7.7 × 10−8). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; P = 1.68 × 10−5). Conclusions: Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old

Contribution à l'étude de la cardiogenèse chez drosophila melanogaster (génomique fonctionnelle et analyse des éléments régulateurs)

Un grand nombre de cardiomyopathies affectent l'organogenèse du muscle cardiaque soulignant l importance d'approfondir nos connaissances de la cardiogenèse. Mon projet de thèse a consisté, par l analyse de l expression des gènes à grande échelle et l identification in silico de séquences régulatrices putatives, en la caractérisation des mécanismes moléculaires contrôlant l organogenèse du coeur chez la drosophile. J ai, dans un premier temps, analyser la dynamique du transcriptome à 8 temps successifs au cours du remodelage du tube cardiaque larvaire en coeur adulte. L analyse fonctionnelle des données de puces à ADN m a permis de dresser une véritable cinétique transcriptionnelle et de mettre en évidence précisément les voies de signalisation potentiellement impliquées dans ce processus. Par une étude génétique de ces voies de signalisation identifiées, je montre d une part que la voie de signalisation Wnt est nécessaire à la reprogrammation des myocytes cardiaques, et d autre part que l activation de la voie EGF-PDGF est requise pour la formation des valves cardiaques adultes. Dans un second temps, j ai analysé l expression différentielle des gènes entre l aorte larvaire et le coeur larvaire, et identifié une quinzaine de gènes partageant spécifiquement le domaine d expression du gène homéotique abd-A dans le coeur. Sous l hypothèse que ces gènes soient régulés directement par abd-A et d autres facteurs de transcription en commun, j ai utilisé à la fois la technique de l empreinte phylogénétique et une méthode de recherche de regroupement de motifs pour identifier les modules cis-régulateurs putatifs responsables de leur co-expression. Trois enhancers se sont révélés être positifs pour récapituler une expression spécifique dans le coeur, et une analyse plus approfondie de ces séquences devrait nous aider à déterminer si les gènes correspondants sont des cibles directes d abd-A.A number of inherited cardiomyopathies affect cardiac muscle organogenesis emphasizing the need to improve our knowledge of heart formation. My thesis project concerned, by whole genome analysis and in silico identification of putative cis-regulatory sequences, the characterization of molecular mechanisms controlling heart organogenesis in drosophila. I have first drawn a molecular portrait of adult heart morphogenesis by whole-genome expression profiling at 8 successive time-points. This transcriptional map pointed out specific signalling pathways as potential players in the process. Phenotypic analysis confirmed they are involved in discrete steps of the remodelling. In particular, the Wnt signalling pathway is involved in cardiac myocyte trans-differentiation, while activation of the VEGF-PDGF pathway is required for adult cardiac valve formation. In a second work, I analyzed the differential expression between the aorta and the heart regions in larvae, and identified a dozen of genes that share the same expression pattern of the homeotic gene abd-A in the heart. As these genes are likely to be regulated by abd-A and other common transcription factors, I used a bioinformatic approach based both on the phylogenetic footprinting method and the research of motif clusters to identify the putative cis-regulatory modules responsible of their co-expression. Three enhancers have been found as positive to drive a specific expression in the heart part, and a more detailed analysis of these sequences should help us determine if the corresponding genes are direct targets of abd-A.AIX-MARSEILLE2-BU Sci.Luminy (130552106) / SudocSudocFranceF

Micro-simulation and visualization of individual space-time paths within a GI

International audienc

Comparison Between Manual and Semiautomated Volumetric Measurements of Pituitary Adenomas

Linear measurements have many limitations. The aim of this study is to compare manual and semiautomated volumetric measurements of pituitary adenomas. Magnetic resonance imaging (MRI) scans of 38 patients with pituitary adenomas were analyzed. Preoperative MRI was acquired on a 1.5 T. MRI volumes of the pituitary adenomas were obtained by two methods: manual (MA) and semiautomated (SA). The concurrent validity for SA and MA methods on 38 patients in the form of correlation coefficient was 0.97 (p < 0.0001). The intraobserver and the interobserver correlation coefficients for SA volumes were both 0.98, as for the intraobserver MA volumes were 0.98. Although the results of both methods are comparable, analysis of volumetric measurements by SA method is more time-efficient than MA segmentation. Precision in volumetric measurement techniques is likely to increase reliability of posttherapeutic monitoring of pituitary adenomas