The "extreme phenotype approach" applied to male breast cancer allows the identification of rare variants of ATR as potential breast cancer susceptibility alleles

In oncogenetics, some patients could be considered as "extreme phenotypes", such as those with very early onset presentation or multiple primary malignancies, unusually high numbers of cancers of the same spectrum or rare cancer types in the same parental branch. For these cases, a genetic predisposition is very likely, but classical candidate gene panel analyses often and frustratingly remains negative. In the framework of the EX2TRICAN project, exploring unresolved extreme cancer phenotypes, we applied exome sequencing on rare familial cases with male breast cancer, identifying a novel pathogenic variant of ATR (p.Leu1808*). ATR has already been suspected as being a predisposing gene to breast cancer in women. We next identified 3 additional ATR variants in a cohort of both male and female with early onset and familial breast cancers (c.7762-2A>C; c.2078+1G>A; c.1A>G). Further molecular and cellular investigations showed impacts on transcripts for variants affecting splicing sites and reduction of ATR expression and phosphorylation of the ATR substrate CHEK1. This work further demonstrates the interest of an extended genetic analysis such as exome sequencing to identify very rare variants that can play a role in cancer predisposition in extreme phenotype cancer cases unexplained by classical cancer gene panels testing

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

A first update on mapping the human genetic architecture of COVID-19

peer reviewe

Blue mussel (Mytilus edulis) bouchot culture in Mont-St Michel Bay: potential mitigation effects on climate change and eutrophication

International audienceBivalve production is an important aquaculture activity worldwide, but few environmental assessments have focused on it. In particular, bivalves' ability to extract nutrients from the environment by intensely filtering water and producing a shell must be considered in the environmental assessment. LCA of blue mussel bouchot culture (grown out on wood pilings) in Mont Saint-Michel Bay (France) was performed to identify its impact hotspots. The chemical composition of mussel flesh and shell was analyzed to accurately identify potential positive effects on eutrophication and climate change. The fate of mussel shells after consumption was also considered. Its potential as a carbon-sink is influenced by assumptions made about the carbon sequestration in wooden bouchots and in the mussel shell. The fate of the shells which depends on management of discarded mussels and household waste plays also an important role. Its carbon-sink potential barely compensates the climate change impact induced by the use of fuel used for on-site transportation. The export of N and P in mussel flesh slightly decreases potential eutrophication. Environmental impacts of blue mussel culture are determined by the location of production and mussel yields, which are influenced by marine currents and the distance to on-shore technical base. Bouchot mussel culture has low environmental impacts compared to livestock systems, but the overall environmental performances depend on farming practices and the amount of fuel used. Changes to the surrounding ecosystem induced by high mussel density must be considered in future LCA studies

Influence of OSHV-1 oyster mortality episode on dissolved inorganic fluxes: An ex situ experiment at the individual scale

Ostreid herpesvirus 1 (OsHV-1 μvar) infection has caused significant mortalities in juvenile oysters (Crassostrea gigas). In contrast to the practices of other animal production industries, sick and dead oysters are not separated from live ones and are left to decay in the surrounding environment, with unknown consequences on fluxes of dissolved materials. A laboratory approach was used in this study to test the influence of oyster mortality episode on dissolved inorganic fluxes at the oyster interface, dissociating (i) the effect of viral infection on metabolism of juvenile oysters and (ii) the effect of flesh decomposition on oxygen consumption and nutrient releases at the individual scale. Nine batches of juvenile oysters (Individual Total wet weight 1 g) were infected via injection of OsHV-1 enriched inoculums at different viral loads (108 and 109 OsHV-1 DNA copies per oyster) to explore infection thresholds. Oysters injected with filtered seawater were used as controls (C). Oysters were maintained under standard conditions to avoid stress linked to hypoxia, starvation, or ammonia excess. Before, after the injection and during the mortality episode, i.e. at days 1, 3, 7, 10 and 14, nine oysters per treatment were incubated in individual metabolic chambers to quantify oxygen, ammonium and phosphate fluxes at the seawater-oyster interface. Nine empty chambers served as a reference. Injections of the two viral loads of OsHV-1 induced similar mortality rates (38%), beginning at day 3 and lasting until day 14. The observed mortality kinetics were slower than those reported in previous experimental pathology studies, but comparable to those observed in the field (Thau lagoon, France). This study highlights that oxygen and nutrient fluxes significantly varied during mortality episode. Indeed (i) OsHV-1 infection firstly modifies oyster metabolism, with significant decreases in oxygen consumption and ammonium excretion, and (ii) dead oysters lead to a strong increase of ammonium (6 fold) and phosphate (41 fold) fluxes and a decrease in the N/P ratio due to mineralisation of their flesh. The latter may modify the structure of the planktonic community in the field during mortality episode. This study is a first step of the MORTAFLUX program. The second step was to in situ confirm this abnormal nutrient loading during a mortality episode and show its impact on bacterio-, phyto- and protozoo-plankton

Next Generation Mapping a novel approach that enables the detection of unbalanced as well as balanced structural variants

International audienceStructural variants (SVs) include large unbalanced (CNVs) and balanced variants (insertions, inversions and translocations). Whereas the detection of unbalanced SVs has been significantly improved by technological breakthrough such as Chromosomal Microarray Analysis (CMA), the detection of balanced SVs still relies on karyotype despite its very low resolution. Massively parallel sequencing enables the detection of some SVs but its use in clinical setting is yet limited by technical and computational challenges, among which the read length. Next Generation Mapping using the Bionano system is a novel non-sequencing based technology. Long high molecular weight DNA fragments are labelled at specific sites and then stretched out into a nano-channel system for fluorescence reading. The labelling pattern is then compared to a reference genome pattern allowing for the identification of SVs without complex bioinformatic analyses. We sought to evaluate the performance of this technology and its ease of use in a routine cytogenetic laboratory. Our study includes 29 patients bearing balanced (11 translocations and 4 inversions) or unbalanced SVs (1 unbalanced translocation, 7 CNVs ranging from 500kb to 4Mb), complex chromosomal rearrangements (n=4), isochromosomes (n=2) and one case of aneuploidy, all previously identified by karyotype or CMA. The results are analysed blindly and then compared to karyotype or CMA results. Preliminary data on four samples show reliable detection of the expected SVs. This approach has the potential to improve the resolution of the pangenome detection of different sorts of SVs, and could hence complement or even replace karyotype and CMA as a unique, simple and comprehensive test. This would have a significant clinical impact for diseases in which balanced SVs are mainly involved, such as reproductive diseases and recurrent miscarriages

Bagatelles pour l’éternité

Bagatelles pour l’éternité (littéraire). On se souvient du jugement de Pline sur Martial : « il a écrit ses bagatelles en vue de la postérité ». Jeux, mais jeux sérieux de moraliste, suggérait de son côté Martial. Le paradoxe de l’épigramme achemine vers quelques questions. Comment le texte bref peut-il faire œuvre ? À ce qui n’a pas d’étendue, quelle place donner dans le champ de la littérature ? Et quel poids quand la ténuité de la forme se double de la frivolité ou de la contingence radicale du sujet ? Le choix de la brièveté relève souvent d’une démarche ambiguë : modestie affichée, mais biais pour échapper aux contraintes des grands genres et contestation des valeurs, stylistiques et mentales, qu’ils véhiculent. Les dix-sept études ici rassemblées permettent d’envisager, à partir d’exemples typiques, depuis l’antiquité jusqu’à nos jours, des fables d’Ésope aux nouvelles de Borges, des lais de Marie de France à un roman éclaté de R. Pinget, de Gaspard de la Nuit d’Aloysius Bertrand aux Phrases pour éventail de Claudel, certaines des stratégies et des significations de la brièveté. Là, comme dans les prologues de théâtre, les pièces en un acte, et aussi, pour une part, la fable, le miracle (Gautier de Coincy), ou le conte, dominent la considération pratique de la réception, le souci de s’accorder à l’impatience ou la fantaisie du public. Mais le bref ne se conçoit guère sans une esthétique. Malgré la diversité des postulations et des projets, on repère des méthodes similaires : l’ellipse, présente dans le récit lacunaire du poème en prose, et, déjà, dans les silences d’histoires folkloriques du xvie siècle ; la discontinuité, qu’imposent l’impressionnisme de la notation dans le Journal des Goncourt, et plus encore les souvenirs inorganisés de l’autobiographie contemporaine ; l’art du démembrement, qu’il s’agisse du discours, pour l’ostentation spectaculaire d’un aphorisme, ou de la structure syntaxique, pour la sourde résonance des mots du poème. Quelques approches complètent ces analyses en dégageant tel modèle épistémologique sous-jacent à l’écriture des moralistes classiques, ou en étudiant des textes réflexifs, arts poétiques, théorie romantique du fragment

An Improved Method to Extract DNA from 1 ml of Uncultured Amniotic Fluid from Patients at Less than 16 Weeks’ Gestation

<div><p>The aim of this study was to develop an improved technique for DNA extraction from 1 ml of uncultured AF from patients with a gestational age less than 16 weeks and to allow the use of array-CGH without DNA amplification. The DNA extraction protocol was tested in a series of 90 samples including 41 of uncultured AF at less than 16 weeks of gestation. Statistical analyses were performed using linear regression. To evaluate the sensitivity and the specificity of array-CGH on 1 ml of uncultured AF, five samples with an abnormal karyotype (three with aneuploidy, two with structural abnormalities) and five with a normal karyotype were studied. This protocol was reproducible and we were able to show a great improvement with higher yield of DNA obtained from all patients, including those with a gestational age less than 16 weeks (p = 0.003). All chromosomal abnormalities were detected and characterized by array-CGH and normal samples showed normal profiles. This new DNA extraction protocol associated with array-CGH analysis could be used in prenatal testing even when gestational age is less than 16 weeks, especially in cases with abnormal ultrasound findings.</p> </div

EPHA7 haploinsufficiency is associated with a neurodevelopmental disorder

International audienceEphrin receptor and their ligands, the ephrins, are widely expressed in the developing brain. They are implicated in several developmental processes that are crucial for brain development. Deletions in genes encoding for members of the Eph/ephrin receptor family were reported in several neurodevelopmental disorders. The ephrin receptor A7 gene (EPHA7) encodes a member of ephrin receptor subfamily of the protein-tyrosine kinase family. EPHA7 plays a role in corticogenesis processes, determines brain size and shape, and is involved in development of the central nervous system. One patient only was reported so far with a de novo deletion encompassing EPHA7 in 6q16.1. We report 12 additional patients from nine unrelated pedigrees with similar deletions. The deletions were inherited in nine out of 12 patients, suggesting variable expressivity and incomplete penetrance. Four patients had tiny deletions involving only EPHA7, suggesting a critical role of EPHA7 in a neurodevelopmental disability phenotype. We provide further evidence for EPHA7 deletion as a risk factor for neurodevelopmental disorder and delineate its clinical phenotype

Genome views of five number and structural abnormalities characterized by array-CGH, extracted from 1 ml of uncultured amniotic fluid from patients at less than 16 weeks of gestation.

<p>(cases 1 to 5).</p