Caractérisation du complexe NuA4/TIP60 et ses liens avec le variant d'histone H2A.Z

L'organisation des génomes eucaryotes sous forme de chromatine constitue un élément de régulation essentiel de tous les processus cellulaires dépendants de l'ADN. Les facteurs intervenant sur cette organisation jouent donc un rôle crucial dans le bon fonctionnement et le maintien de l'identité des cellules et l'intégrité du matériel génomique. Le complexe NuA4/TIP60 est capable d'agir sur l'organisation de la chromatine de deux façons distinctes : premièrement en acétylant les histones H2A et H4 via sa sous-unité KAT5/Tip60, conduisant à une structure chromatinienne plus relâchée et accessible; deuxièmement en incorporant le variant d'histone H2A.Z dans la chromatine, conférant des propriétés particulières aux régions du génome concernées. NuA4/TIP60 joue ainsi un rôle central dans la régulation de nombreux processus cellulaires, en particulier l'expression des gènes et la réparation des dommages à l'ADN. Le complexe est composé d'au moins 17 sous-unités chez l'humain; les propriétés et fonctions de certaines de ces sous-unités restent à préciser dans le but de mieux comprendre comment NuA4/TIP60 régule l'organisation de la chromatine. Dans la première partie de mes travaux de doctorat présentés ici, nous avons cherché à clarifier la fonction du chromodomaine de KAT5/Tip60, la sous-unité catalytique du complexe. En effet des observations contradictoires avaient été rapportées dans la littérature, en particulier en ce qui concerne la capacité du chromodomaine à reconnaître des marques d'histones spécifiques. Nos résultats suggèrent que ce domaine régule plutôt l'activité acétyltransférase du complexe indépendamment des marques d'histones. Nous avons également caractérisé des mutations de KAT5/Tip60, dont l'une dans le chromodomaine, liées à un syndrome neurodéveloppemental chez plusieurs patients. Dans une deuxième partie, nous nous sommes intéressés à l'incorporation du variant d'histone H2A.Z au sein de la chromatine par NuA4/TIP60 et par un autre complexe, SRCAP. Nos résultats suggèrent que NuA4/TIP60 favorise l'un des paralogues de H2A.Z, H2A.Z.2, par rapport à H2A.Z.1, contrairement à SRCAP. Nous avons également identifié des partenaires spécifiques pour chaque paralogue de H2A.Z qui permettent d'expliquer une partie des rôles différents joués par ces paralogues dans la régulation de la transcription. Dans leur ensemble ces travaux contribuent à améliorer notre compréhension de la façon dont le complexe NuA4/TIP60 affecte l'organisation chromatinienne, et comment des perturbations de cette fonction peuvent entraîner des conséquences pathologiques sérieuses.Eucaryotic genomes take the shape of chromatin, the organization of which affects all DNA-based cellular processes. Hence, factors involved in this organization are critical for maintaining proper cell function, identity, and genome integrity. The NuA4/TIP60 complex affects chromatin organization through two different mechanisms: first by acetylating histones H2A and H4 in chromatin, increasing its relaxation and accessibility; second by incorporating the histone variant H2A.Z into chromatin, assigning distinct properties to given genomic regions. NuA4/TIP60 therefore acts as a central regulator of many cellular processes, in particular gene expression and DNA damage repair. NuA4/TIP60 comprises at least 17 subunits, the functions and properties of many of which still need elucidating in order to better understand how the complex regulates chromatin structure. In the first part of my PhD project presented hereby, we aimed to clarify the function of KAT5/Tip60, the catalytical subunit of NuA4/Tip60. Contradictory results had been previously reported regarding the chromodomain ability to bind specific histone marks. Our results suggest that this domain instead regulates the acetyltransferase activity of NuA4/Tip60 independently of histone marks. We have also characterized mutations in KAT5/Tip60, one of them inside the chromodomain, linked to a rare neurodevelopmental syndrome. In the second part, we were interested in the incorporation of the histone variant H2A.Z in chromatin by NuA4/TIP60 as well as another complex, SRCAP. Our results suggest that NuA4/TIP60 favors one of the two H2A.Z paralogs, H2A.Z.2, over H2A.Z.1, as opposed to SRCAP which binds both equally. We also identified specific interactors for each paralog, which could explain in part how H2A.Z.1 and H2A.Z.2 regulate gene expression differently. Overall this work contributes to a better understanding of how NuA4/TIP60 regulates chromatin organization, and how disruption of these functions can lead to serious pathological outcomes

Effect of fixed-dose subcutaneous reslizumab on asthma exacerbations in patients with severe uncontrolled asthma and corticosteroid sparing in patients with oral corticosteroid-dependent asthma : results from two phase 3, randomised, double-blind, placebo-controlled trials

BACKGROUND: Reslizumab 3 mg/kg administered intravenously is approved for the treatment of severe eosinophilic asthma. We assessed the safety and efficacy of subcutaneous reslizumab 110 mg in two trials in patients with uncontrolled severe asthma and increased blood eosinophils. The aim was to establish whether subcutaneous reslizumab 110 mg can reduce exacerbation rates in these patients (study 1) or reduce maintenance oral corticosteroid dose in patients with corticosteroid-dependent asthma (study 2). METHODS: Both studies were randomised, double-blind, placebo-controlled, phase 3 studies. Entry criteria for study 1 were uncontrolled severe asthma, two or more asthma exacerbations in the previous year, a blood eosinophil count of 300 cells per μL or more (including no more than 30% patients with an eosinophil count <400 cells/μL), and at least a medium dose of inhaled corticosteroids with one or more additional asthma controllers. Patients in study 2 had severe asthma, a blood eosinophil count of 300 cells per μL or more, daily maintenance oral corticosteroid (prednisone 5-40 mg, or equivalent), and high-dose inhaled corticosteroids plus another controller. Patients were randomly assigned (1:1) to subcutaneous reslizumab (110 mg) or placebo once every 4 weeks for 52 weeks in study 1 and 24 weeks in study 2. Patients and investigators were masked to treatment assignment. Primary efficacy outcomes were frequency of exacerbations during 52 weeks in study 1 and categorised percentage reduction in daily oral corticosteroid dose from baseline to weeks 20-24 in study 2. Primary efficacy analyses were by intention to treat, and safety analyses included all patients who received at least one dose of study treatment. These studies are registered with ClinicalTrials.gov, NCT02452190 (study 1) and NCT02501629 (study 2). FINDINGS: Between Aug 12, 2015, and Jan 31, 2018, 468 patients in study 1 were randomly assigned to placebo (n=232) or subcutaneous reslizumab (n=236), and 177 in study 2 to placebo (n=89) or subcutaneous reslizumab (n=88). In study 1, we found no significant difference in the exacerbation rate between reslizumab and placebo in the intention-to-treat population (rate ratio 0·79, 95% CI 0·56-1·12; p=0·19). Subcutaneous reslizumab reduced exacerbation frequency compared with placebo in the subgroup of patients with blood eosinophil counts of 400 cells per μL or more (0·64, 95% CI 0·43-0·95). Greater reductions in annual exacerbation risk (p=0·0035) and longer time to first exacerbation were observed for patients with higher trough serum reslizumab concentrations. In study 2, we found no difference between placebo and fixed-dose subcutaneous reslizumab in categorised percentage reduction in daily oral corticosteroid dose (odds ratio for a lower category of oral corticosteroid use in the reslizumab group vs the placebo group, 1·23, 95% CI 0·70-2·16; p=0·47). The frequency of adverse events and serious adverse events with reslizumab were similar to those with placebo in both studies. INTERPRETATION: Fixed-dose (110 mg) subcutaneous reslizumab was not effective in reducing exacerbation frequency in patients with uncontrolled asthma and increased blood eosinophils (≥300 cells/μL), or in reducing the daily maintenance oral corticosteroid dose in patients with oral corticosteroid-dependent severe eosinophilic asthma. Higher exposures than those observed with 110 mg subcutaneous reslizumab are required to achieve maximal efficacy. FUNDING: Teva Branded Pharmaceutical Products R&D

Clinical and molecular genetic features of pulmonary hypertension in patients with hereditary hemorrhagic telangiectasia

BACKGROUND: Most patients with familial primary pulmonary hypertension have defects in the gene for bone morphogenetic protein receptor II (BMPR2), a member of the transforming growth factor beta (TGF-beta) superfamily of receptors. Because patients with hereditary hemorrhagic telangiectasia may have lung disease that is indistinguishable from primary pulmonary hypertension, we investigated the genetic basis of lung disease in these patients. METHODS: We evaluated members of five kindreds plus one individual patient with hereditary hemorrhagic telangiectasia and identified 10 cases of pulmonary hypertension. In the two largest families, we used microsatellite markers to test for linkage to genes encoding TGF-beta-receptor proteins, including endoglin and activin-receptor-like kinase 1 (ALK1), and BMPR2. In subjects with hereditary hemorrhagic telangiectasia and pulmonary hypertension, we also scanned ALK1 and BMPR2 for mutations. RESULTS: We identified suggestive linkage of pulmonary hypertension with hereditary hemorrhagic telangiectasia on chromosome 12q13, a region that includes ALK1. We identified amino acid changes in activin-receptor-like kinase 1 that were inherited in subjects who had a disorder with clinical and histologic features indistinguishable from those of primary pulmonary hypertension. Immunohistochemical analysis in four subjects and one control showed pulmonary vascular endothelial expression of activin-receptor-like kinase 1 in normal and diseased pulmonary arteries. CONCLUSIONS: Pulmonary hypertension in association with hereditary hemorrhagic telangiectasia can involve mutations in ALK1. These mutations are associated with diverse effects, including the vascular dilatation characteristic of hereditary hemorrhagic telangiectasia and the occlusion of small pulmonary arteries that is typical of primary pulmonary hypertension

Greenland Mass Trends From Airborne and Satellite Altimetry During 2011–2020

We use satellite and airborne altimetry to estimate annual mass changes of the Greenland Ice Sheet. We estimate ice loss corresponding to a sea-level rise of 6.9 ± 0.4 mm from April 2011 to April 2020, with a highest annual ice loss rate of 1.4 mm/yr sea-level equivalent from April 2019 to April 2020. On a regional scale, our annual mass loss timeseries reveals 10–15 m/yr dynamic thickening at the terminus of Jakobshavn Isbræ from April 2016 to April 2018, followed by a return to dynamic thinning. We observe contrasting patterns of mass loss acceleration in different basins across the ice sheet and suggest that these spatiotemporal trends could be useful for calibrating and validating prognostic ice sheet models. In addition to resolving the spatial and temporal fingerprint of Greenland's recent ice loss, these mass loss grids are key for partitioning contemporary elastic vertical land motion from longer-term glacial isostatic adjustment (GIA) trends at GPS stations around the ice sheet. Our ice-loss product results in a significantly different GIA interpretation from a previous ice-loss product

An Anti-HIV-1 V3 Loop Antibody Fully Protects Cross-Clade and Elicits T-Cell Immunity in Macaques Mucosally Challenged with an R5 Clade C SHIV

Neutralizing antibodies have been shown to protect macaques against SHIV challenge. However, genetically diverse HIV-1 clades have evolved, and a key question left unanswered is whether neutralizing antibodies can confer cross-clade protection in vivo. The novel human monoclonal antibody HGN194 was isolated from an individual infected with an HIV-1 clade AG recombinant circulating recombinant form (CRF). HGN194 targets an epitope in the third hypervariable loop (V3) of HIV-1 gp120 and neutralizes a range of relatively neutralization-sensitive and resistant viruses. We evaluated the potential of HGN194 to protect infant rhesus monkeys against a SHIV encoding a primary CCR5-tropic HIV-1 clade C envelope. After high-dose mucosal challenge, all untreated controls became highly viremic while all HGN194-treated animals (50 mg/kg) were completely protected. When HGN194 was given at 1 mg/kg, one out of two monkeys remained aviremic, whereas the other had delayed, lower peak viremia. Interestingly, all protected monkeys given high-dose HGN194 developed Gag-specific proliferative responses of both CD4+ and CD8+ T cells. To test whether generation of the latter involved cryptic infection, we ablated CD8+ cells after HGN194 clearance. No viremia was detected in any protected monkeys, thus ruling out virus reservoirs. Thus, induction of CD8 T-cell immunity may have resulted from transient “Hit and Run” infection or cross priming via Ag-Ab-mediated cross-presentation. Together, our data identified the HGN194 epitope as protective and provide proof-of-concept that this anti-V3 loop mAb can prevent infection with sterilizing immunity after challenge with virus of a different clade, implying that V3 is a potential vaccine target

A global database for metacommunity ecology, integrating species, traits, environment and space

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology

"Monkey see, monkey do" : peers’ behaviors predict preschoolers’ physical activity and dietary intake in childcare centers

Abstract : Preschoolers observe and imitate the behaviors of those who are similar to them. Therefore, peers may be important role models for preschoolers’ dietary intake and physical activity in childcare centers. This study examined whether peers’ behaviors predict change in preschoolers’ dietary intake and physical activity in childcare centers over 9 months. A total of 238 preschoolers (3 to 5 years old) from 23 childcare centers in two Canadian provinces provided data at the beginning (October 2013 and 2014) and the end (June 2014 and 2015) of a 9-month period for this longitudinal study. Dietary intake was collected at lunch using weighed plate waste and digital photography on two consecutive weekdays. Physical activity was assessed using accelerometers over five days. Multilevel linear regressions were used to estimate the influence of peers’ behaviors on preschoolers’ change in dietary intake and physical activity over 9 months. Results showed that preschoolers whose dietary intake or physical activity level deviated the most from those of their peers at the beginning of the year demonstrated greater change in their intakes and activity levels over 9 months (all p values<0.05), which enabled them to become more similar to their peers. This study suggests that preschoolers’ dietary intake and physical activity may be influenced by the behaviors of their peers in childcare centers. Since peers could play an important role in promoting healthy eating behaviors and physical activity in childcare centers, future studies should test interventions based on positive role modeling by children

Design and results of the ice sheet model initialisation experiments initMIP-Greenland: an ISMIP6 intercomparison

Earlier large-scale Greenland ice sheet sea-level projections (e.g. those run during the ice2sea and SeaRISE initiatives) have shown that ice sheet initial conditions have a large effect on the projections and give rise to important uncertainties. The goal of this initMIP-Greenland intercomparison exercise is to compare, evaluate, and improve the initialisation techniques used in the ice sheet modelling community and to estimate the associated uncertainties in modelled mass changes. initMIP-Greenland is the first in a series of ice sheet model intercomparison activities within ISMIP6 (the Ice Sheet Model Intercomparison Project for CMIP6), which is the primary activity within the Coupled Model Intercomparison Project Phase 6 (CMIP6) focusing on the ice sheets. Two experiments for the large-scale Greenland ice sheet have been designed to allow intercomparison between participating models of (1) the initial present-day state of the ice sheet and (2) the response in two idealised forward experiments. The forward experiments serve to evaluate the initialisation in terms of model drift (forward run without additional forcing) and in response to a large perturbation (prescribed surface mass balance anomaly); they should not be interpreted as sea-level projections. We present and discuss results that highlight the diversity of data sets, boundary conditions, and initialisation techniques used in the community to generate initial states of the Greenland ice sheet. We find good agreement across the ensemble for the dynamic response to surface mass balance changes in areas where the simulated ice sheets overlap but differences arising from the initial size of the ice sheet. The model drift in the control experiment is reduced for models that participated in earlier intercomparison exercises

initMIP-Antarctica: an ice sheet model initialization experiment of ISMIP6

Ice sheet numerical modeling is an important tool to estimate the dynamic contribution of the Antarctic ice sheet to sea level rise over the coming centuries. The influence of initial conditions on ice sheet model simulations, however, is still unclear. To better understand this influence, an initial state intercomparison exercise (initMIP) has been developed to compare, evaluate, and improve initialization procedures and estimate their impact on century-scale simulations. initMIP is the first set of experiments of the Ice Sheet Model Intercomparison Project for CMIP6 (ISMIP6), which is the primary Coupled Model Intercomparison Project Phase 6 (CMIP6) activity focusing on the Greenland and Antarctic ice sheets. Following initMIP-Greenland, initMIP-Antarctica has been designed to explore uncertainties associated with model initialization and spin-up and to evaluate the impact of changes in external forcings. Starting from the state of the Antarctic ice sheet at the end of the initialization procedure, three forward experiments are each run for 100 years: a control run, a run with a surface mass balance anomaly, and a run with a basal melting anomaly beneath floating ice. This study presents the results of initMIP-Antarctica from 25 simulations performed by 16 international modeling groups. The submitted results use different initial conditions and initialization methods, as well as ice flow model parameters and reference external forcings. We find a good agreement among model responses to the surface mass balance anomaly but large variations in responses to the basal melting anomaly. These variations can be attributed to differences in the extent of ice shelves and their upstream tributaries, the numerical treatment of grounding line, and the initial ocean conditions applied, suggesting that ongoing efforts to better represent ice shelves in continental-scale models should continue