Human pre-valvular endocardial cells derived from pluripotent stem cells recapitulate cardiac pathophysiological valvulogenesis

Genetically modified mice have advanced our understanding of valve development and disease. Yet, human pathophysiological valvulogenesis remains poorly understood. Here we report that, by combining single cell sequencing and in vivo approaches, a population of human pre-valvular endocardial cells (HPVCs) can be derived from pluripotent stem cells. HPVCs express gene patterns conforming to the E9.0 mouse atrio-ventricular canal (AVC) endocardium signature. HPVCs treated with BMP2, cultured on mouse AVC cushions, or transplanted into the AVC of embryonic mouse hearts, undergo endothelial-to-mesenchymal transition and express markers of valve interstitial cells of different valvular layers, demonstrating cell specificity. Extending this model to patient-specific induced pluripotent stem cells recapitulates features of mitral valve prolapse and identified dysregulation of the SHH pathway. Concurrently increased ECM secretion can be rescued by SHH inhibition, thus providing a putative therapeutic target. In summary, we report a human cell model of valvulogenesis that faithfully recapitulates valve disease in a dish.We thank the Leducq Fondation for supporting Tui Neri, and funding this research under the framework of the MITRAL network and for generously awarding us for the equipment of our cell imaging facility in the frame of their program “Equipement de Recherche et Plateformes Technologiques” (ERPT to M.P.), the Genopole at Evry and the Fondation de la recherche Medicale (grant DEQ20100318280) for supporting the laboratory of Michel Puceat. Part of this work in South Carolina University was conducted in a facility constructed with support from the National Institutes of Health, Grant Number C06 RR018823 from the Extramural Research Facilities Program of the National Center for Research Resources. Other funding sources: National Heart Lung and Blood Institute: RO1-HL33756 (R.R.M.), COBRE P20RR016434–07 (R.R.M., R.A. N.), P20RR016434–09S1 (R.R.M. and R.A.N.); American Heart Association: 11SDG5270006 (R.A.N.); National Science Foundation: EPS-0902795 (R.R.M. and R.A. N.); American Heart Association: 10SDG2630130 (A.C.Z.), NIH: P01HD032573 (A.C. Z.), NIH: U54 HL108460 (A.C.Z), NCATS: UL1TR000100 (A.C.Z.); EH was supported by a fellowship of the Ministere de la recherche et de l’éducation in France.TM-M was supported by a fellowship from the Fondation Foulon Delalande and the Leducq Foundation. P.v.V. was sponsored by a UC San Diego Cardiovascular Scholarship Award and a Postdoctoral Fellowship from the California Institute for Regenerative Medicine (CIRM) Interdisciplinary Stem Cell Training Program II. S.M.E. was funded by a grant from the National Heart, Lung, and Blood Institute (HL-117649). A.T. is supported by the National Heart, Lung, and Blood Institute (R01-HL134664).S

Death and the Societies of Late Antiquity

Ce volume bilingue, comprenant un ensemble de 28 contributions disponibles en français et en anglais (dans leur version longue ou abrégée), propose d’établir un état des lieux des réflexions, recherches et études conduites sur le fait funéraire à l’époque tardo-antique au sein des provinces de l’Empire romain et sur leurs régions limitrophes, afin d’ouvrir de nouvelles perspectives sur ses évolutions possibles. Au cours des trois dernières décennies, les transformations considérables des méthodologies déployées sur le terrain et en laboratoire ont permis un renouveau des questionnements sur les populations et les pratiques funéraires de l’Antiquité tardive, période marquée par de multiples changements politiques, sociaux, démographiques et culturels. L’apparition de ce qui a été initialement désigné comme une « Anthropologie de terrain », qui fut le début de la démarche archéothanatologique, puis le récent développement d’approches collaboratives entre des domaines scientifiques divers (archéothanatologie, biochimie et géochimie, génétique, histoire, épigraphie par exemple) ont été décisives pour le renouvellement des problématiques d’étude : révision d’anciens concepts comme apparition d’axes d’analyse inédits. Les recherches rassemblées dans cet ouvrage sont articulées autour de quatre grands thèmes : l’évolution des pratiques funéraires dans le temps, l’identité sociale dans la mort, les ensembles funéraires en transformation (organisation et topographie) et les territoires de l’empire (du cœur aux marges). Ces études proposent un réexamen et une révision des données, tant anthropologiques qu’archéologiques ou historiques sur l’Antiquité tardive, et révèlent, à cet égard, une mosaïque de paysages politiques, sociaux et culturels singulièrement riches et complexes. Elles accroissent nos connaissances sur le traitement des défunts, l’emplacement des aires funéraires ou encore la structure des sépultures, en révélant une diversité de pratiques, et permettent au final de relancer la réflexion sur la manière dont les sociétés tardo-antiques envisagent la mort et sur les éléments permettant d’identifier et de définir la diversité des groupes qui les composent. Elles démontrent ce faisant que nous pouvons véritablement appréhender les structures culturelles et sociales des communautés anciennes et leurs potentielles transformations, à partir de l’étude des pratiques funéraires.This bilingual volume proposes to draw up an assessment of the recent research conducted on funerary behavior during Late Antiquity in the provinces of the Roman Empire and on their borders, in order to open new perspectives on its possible developments. The considerable transformations of the methodologies have raised the need for a renewal of the questions on the funerary practices during Late Antiquity, a period marked by multiple political, social, demographic and cultural changes. The emergence field anthropology, which was the beginning of archaeothanatology, and then the recent development of collaborative approaches between various scientific fields (archaeothanatology, biochemistry and geochemistry, genetics, history, epigraphy, for example), have been decisive. The research collected in this book is structured around four main themes: Evolution of funerary practices over time; Social identity through death; Changing burial grounds (organisation and topography); Territories of the Empire (from the heart to the margins). These studies propose a review and a revision of the data, both anthropological and archaeological or historical on Late Antiquity, and reveal a mosaic of political, social, and cultural landscapes singularly rich and complex. In doing so, they demonstrate that we can truly understand the cultural and social structures of ancient communities and their potential transformations, based on the study of funerary practices

EXOME SEQUENCING AS A SECOND-TIER DIAGNOSTIC APPROACH FOR CLINICALLY SUSPECTED DYSFERLINOPATHY PATIENTS

International audienceIntroduction: Autosomal recessive muscular dystrophies are heterogeneous genetic disorders, with 39 genes currently implicated. Genetic diagnosis using targeted single-gene analysis by Sanger sequencing yields negative results in 10-20% of samples, warranting clinical re-evaluation and time-consuming testing of additional genes. This applies to dysferlinopathies caused by mutations in the gene encoding dysferlin (DYSF), which presents mainly as limb-girdle muscular dystrophy (LGMD) or distal myopathy. Methods: We evaluated exome sequencing associated with data filtering for selected genes as a second-tier approach for genetic diagnosis in a cohort of 37 patients with an initial negative result on targeted DYSF analysis. Results: Exome sequencing allowed for establishing (16%) or suggesting (8%) the molecular diagnosis by implicating other known LGMD or distal myopathy genes or by revealing DYSF mutations previously missed using mutation-screening techniques with incomplete detection yields. Conclusions: Exome sequencing associated with data filtering constitutes an efficient second-tier analysis for genes implicated in LGMD or distal myopathies

How to Identify Pathogenic Mutations among All Those Variations: Variant Annotation and Filtration in the Genome Sequencing Era

International audienceHigh-throughput sequencing technologies have become fundamental for the identification of disease-causing mutations in human genetic diseases both in research and clinical testing contexts. The cumulative number of genes linked to rare diseases is now close to 3,500 with more than 1,000 genes identified between 2010 and 2014 because of the early adoption of Exome Sequencing technologies. However, despite these encouraging figures, the success rate of clinical exome diagnosis remains low due to several factors including wrong variant annotation and nonoptimal filtration practices, which may lead to misinterpretation of disease-causing mutations. In this review, we describe the critical steps of variant annotation and filtration processes to highlight a handful of potential disease-causing mutations for downstream analysis. We report the key annotation elements to gather at multiple levels for each mutation, and which systems are designed to help in collecting this mandatory information. We describe the filtration options, their efficiency, and limits and provide a generic filtration workflow and highlight potential pitfalls through a use case. (C) 2016 Wiley Periodicals, Inc

VarAFT: a variant annotation and filtration system for human next generation sequencing data

International audienceWith the rapidly developing high-throughput sequencing technologies known as next generation sequencing or NGS, our approach to gene hunting and diagnosis has drastically changed. In <10 years, these technologies have moved from gene panel to whole genome sequencing and from an exclusively research context to clinical practice. Today, the limit is not the sequencing of one, many or all genes but rather the data analysis. Consequently, the challenge is to rapidly and efficiently identify disease-causing mutations within millions of variants. To do so, we developed the VarAFT software to annotate and pinpoint human disease-causing mutations through access to multiple layers of information. VarAFT was designed both for research and clinical contexts and is accessible to all scientists, regardless of bioinformatics training. Data from multiple samples may be combined to address all Mendelian inheritance modes, cancers or population genetics. Optimized filtration parameters can be stored and re-applied to large datasets. In addition to classical annotations from dbNSFP, VarAFT contains unique features at the disease (OMIM), phenotypic (HPO), gene (Gene Ontology, pathways) and variation levels (predictions from UMD-Predictor and Human Splicing Finder) that can be combined to optimally select candidate pathogenic mutations. VarAFT is freely available at: http://varaft.eu

Tectonic and climatic controls on coastal sedimentation: The Late Pliocene–Middle Pleistocene of northeastern Rhodes, Greece

International audienceThe Late Pliocene to Middle Pleistocene coastal sediments of northeastern Rhodes (Greece) were deposited in an active tectonic setting. They provide an excellent opportunity to investigate the relative roles played by climate and tectonics in sedimentary processes. The tectono-sedimentary organization of these deposits is revised in the light of an integrated study combining data from field investigations, sedimentology, bio- and magnetostratigraphy, radiometric dating, palaeoecology, and palynology. Three lithostratigraphic units are recognised: the Rhodes Formation, the newly defined Ladiko–Tsampika Formation, and the Lindos Acropolis Formation. A major erosional surface separates the Rhodes Formation from the Ladiko–Tsampika Formation, which was deposited in deep and narrow palaeovalleys. The Rhodes Formation (Late Pliocene to 1.4–1.3 Ma) comprises three Members: the Kritika, the Lindos Bay clay and the Cape Arkhangelos calcarenite. The shallow-water clastic sediments of the Ladiko–Tsampika Formation (1.3 to 0.3 Ma) are subdivided into two Members: the Ladiko (mostly sandy) and the Tsampika (predominantly clayey). The Lindos Acropolis Formation is Late Pleistocene in age. Two major transgression–regression cycles occurred prior to the Lindos Acropolis cycle. The deposition of the first cycle (Rhodes Formation) is tectonically controlled, with very high rates of vertical movements (2.6–5.2 mm/year). The second cycle (Ladiko–Tsampika Formation) records sea-level changes controlled by slow vertical motions (around 0.16 mm/year) and glacioeustatic events with 40-kyr and 100-kyr periods. Finally, the tectonic and sedimentary evolution of Rhodes is integrated into the geodynamic context of the eastern Aegean fore-arc

Alleins (13) - Jardinets de Pierrefeu, avenue du 14 juillet 1789, Rapport de fouille archéologique préventive

Cette fouille a permis d'attester la présence d'une occupation néolithique, bien que de façon lâche : onze fosses, silo et foyers ont été identifiés. Leur fouille a livré des mobiliers céramiques et lithiques qui permettent de rattacher cette occupation au néolithique final, de façon identique aux sites fouillés à proximité (« Sainte-Anne » et « avenue du 14 juillet »).Pour la période antique, de nombreux murs ont pu être dégagés, mais leur piètre état de conservation, l’absence de niveaux de sols attenants et plus généralement leur déconnexion de toute stratigraphie, interdit de restituer un plan des bâtiment et d’affiner leur chronologie au sein du haut-empire. Il est cependant très probable qu’ils constituent l’extension vers le nord de l’établissement agricole identifié plus au sud lors du diagnostic. En dépit du caractère lacunaire de ces vestiges, des maçonneries plus puissantes, situées en bordure méridionale de la fouille pourraient être rattachées à un chai.Sur les deux tiers orientaux du chantier, plusieurs réseaux de traces agraires se succèdent, témoignant de la longévité de l’occupation agricole. La culture de la vigne est attestée par des fosses de plantations alignées et par des défoncements linéaires avec des logettes latérales de provignage ou des surcreusements axiaux, selon une technique inhabituelle. Des creusements quadrangulaires largement espacés peuvent correspondre à la mise en placed’une oliveraie.Le site est encore occupé aux IVe-Ve s. de notre ère, sans qu’il soit possible de déterminer si il y a continuité de cette occupation entre le Ier et le Ve s ou s’il existe un hiatus au IIIe s. pour lequel aucun vestige n’a été identifié. Cette ultime phase d’occupation du site est très partiellement conservée, mais il est vraisemblable que la vocation agricole du lieu soit maintenue